Science.gov

Sample records for acid analysis shows

  1. Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly.

    PubMed Central

    Ramli, Umi S; Baker, Darren S; Quant, Patti A; Harwood, John L

    2002-01-01

    Top-Down (Metabolic) Control Analysis (TDCA) was used to examine, quantitatively, lipid biosynthesis in tissue cultures from two commercially important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). A conceptually simplified system was defined comprising two blocks of reactions: fatty acid synthesis (Block A) and lipid assembly (Block B), which produced and consumed, respectively, a common and unique system intermediate, cytosolic acyl-CoA. We manipulated the steady-state levels of the system intermediate by adding exogenous oleic acid and, using two independent assays, measured the effect of the addition on the system fluxes (J(A) and J(B)). These were the rate of incorporation of radioactivity: (i) through Block A from [1-(14)C]acetate into fatty acids and (ii) via Block B from [U-(14)C]glycerol into complex lipids respectively. The data showed that fatty acid formation (Block A) exerted higher control than lipid assembly (Block B) in both tissues with the following group flux control coefficients (C):(i) Oil palm: *C(J(TL))(BlkA)=0.64+/-0.05 and *C(J(TL))(BlkB)=0.36+/-0.05(ii) Olive: *C(J(TL))(BlkA)=0.57+/-0.10 and *C(J(TL))(BlkB)=0.43+/-0.10where *C indicates the group flux control coefficient over the lipid biosynthesis flux (J(TL)) and the subscripts BlkA and BlkB refer to defined blocks of the system, Block A and Block B. Nevertheless, because both parts of the lipid biosynthetic pathway exert significant flux control, we suggest strongly that manipulation of single enzyme steps will not affect product yield appreciably. The present study represents the first use of TDCA to examine the overall lipid biosynthetic pathway in any tissue, and its findings are of immediate academic and economic relevance to the yield and nutritional quality of oil crops. PMID:12023882

  2. Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly.

    PubMed

    Ramli, Umi S; Baker, Darren S; Quant, Patti A; Harwood, John L

    2002-06-01

    Top-Down (Metabolic) Control Analysis (TDCA) was used to examine, quantitatively, lipid biosynthesis in tissue cultures from two commercially important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). A conceptually simplified system was defined comprising two blocks of reactions: fatty acid synthesis (Block A) and lipid assembly (Block B), which produced and consumed, respectively, a common and unique system intermediate, cytosolic acyl-CoA. We manipulated the steady-state levels of the system intermediate by adding exogenous oleic acid and, using two independent assays, measured the effect of the addition on the system fluxes (J(A) and J(B)). These were the rate of incorporation of radioactivity: (i) through Block A from [1-(14)C]acetate into fatty acids and (ii) via Block B from [U-(14)C]glycerol into complex lipids respectively. The data showed that fatty acid formation (Block A) exerted higher control than lipid assembly (Block B) in both tissues with the following group flux control coefficients (C):(i) Oil palm: *C(J(TL))(BlkA)=0.64+/-0.05 and *C(J(TL))(BlkB)=0.36+/-0.05(ii) Olive: *C(J(TL))(BlkA)=0.57+/-0.10 and *C(J(TL))(BlkB)=0.43+/-0.10where *C indicates the group flux control coefficient over the lipid biosynthesis flux (J(TL)) and the subscripts BlkA and BlkB refer to defined blocks of the system, Block A and Block B. Nevertheless, because both parts of the lipid biosynthetic pathway exert significant flux control, we suggest strongly that manipulation of single enzyme steps will not affect product yield appreciably. The present study represents the first use of TDCA to examine the overall lipid biosynthetic pathway in any tissue, and its findings are of immediate academic and economic relevance to the yield and nutritional quality of oil crops.

  3. Showing Enantiomorphous Crystals of Tartaric Acid

    ERIC Educational Resources Information Center

    Andrade-Gamboa, Julio

    2007-01-01

    Most of the articles and textbooks that show drawings of enantiomorphous crystals use an inadequate view to appreciate the fact that they are non-superimposable mirror images of one another. If a graphical presentation of crystal chirality is not evident, the main attribute of crystal enantiomorphism can not be recognized by students. The classic…

  4. A novel nucleic acid analogue shows strong angiogenic activity

    SciTech Connect

    Tsukamoto, Ikuko; Sakakibara, Norikazu; Maruyama, Tokumi; Igarashi, Junsuke; Kosaka, Hiroaki; Kubota, Yasuo; Tokuda, Masaaki; Ashino, Hiromi; Hattori, Kenichi; Tanaka, Shinji; Kawata, Mitsuhiro; Konishi, Ryoji

    2010-09-03

    Research highlights: {yields} A novel nucleic acid analogue (2Cl-C.OXT-A, m.w. 284) showed angiogenic potency. {yields} It stimulated the tube formation, proliferation and migration of HUVEC in vitro. {yields} 2Cl-C.OXT-A induced the activation of ERK1/2 and MEK in HUVEC. {yields} Angiogenic potency in vivo was confirmed in CAM assay and rabbit cornea assay. {yields} A synthesized small angiogenic agent would have great clinical therapeutic value. -- Abstract: A novel nucleic acid analogue (2Cl-C.OXT-A) significantly stimulated tube formation of human umbilical endothelial cells (HUVEC). Its maximum potency at 100 {mu}M was stronger than that of vascular endothelial growth factor (VEGF), a positive control. At this concentration, 2Cl-C.OXT-A moderately stimulated proliferation as well as migration of HUVEC. To gain mechanistic insights how 2Cl-C.OXT-A promotes angiogenic responses in HUVEC, we performed immunoblot analyses using phospho-specific antibodies as probes. 2Cl-C.OXT-A induced robust phosphorylation/activation of MAP kinase ERK1/2 and an upstream MAP kinase kinase MEK. Conversely, a MEK inhibitor PD98059 abolished ERK1/2 activation and tube formation both enhanced by 2Cl-C.OXT-A. In contrast, MAP kinase responses elicited by 2Cl-C.OXT-A were not inhibited by SU5416, a specific inhibitor of VEGF receptor tyrosine kinase. Collectively these results suggest that 2Cl-C.OXT-A-induces angiogenic responses in HUVEC mediated by a MAP kinase cascade comprising MEK and ERK1/2, but independently of VEGF receptor tyrosine kinase. In vivo assay using chicken chorioallantoic membrane (CAM) and rabbit cornea also suggested the angiogenic potency of 2Cl-C.OXT-A.

  5. Amino acid analysis

    NASA Technical Reports Server (NTRS)

    Winitz, M.; Graff, J. (Inventor)

    1974-01-01

    The process and apparatus for qualitative and quantitative analysis of the amino acid content of a biological sample are presented. The sample is deposited on a cation exchange resin and then is washed with suitable solvents. The amino acids and various cations and organic material with a basic function remain on the resin. The resin is eluted with an acid eluant, and the eluate containing the amino acids is transferred to a reaction vessel where the eluant is removed. Final analysis of the purified acylated amino acid esters is accomplished by gas-liquid chromatographic techniques.

  6. Isolation of Lactic Acid Bacteria Showing Antioxidative and Probiotic Activities from Kimchi and Infant Feces.

    PubMed

    Ji, Keunho; Jang, Na Young; Kim, Young Tae

    2015-09-01

    The purpose of this study was to investigate lactic acid bacteria with antioxidative and probiotic activities isolated from Korean healthy infant feces and kimchi. Isolates A1, A2, S1, S2, and S3 were assigned to Lactobacillus sp. and isolates A3, A4, E1, E2, E3, and E4 were assigned to Leuconostoc sp. on the basis of their physiological properties and 16S ribosomal DNA sequence analysis. Most strains were confirmed as safe bioresources through nonhemolytic activities and non-production of harmful enzymes such as β-glucosidase, β- glucuronidase and tryptophanase. The 11 isolates showed different resistance to acid and bile acids. In addition, they exhibited antibacterial activity against foodborne bacteria, especially Bacillus cereus, Listeria monocytogenes, and Escherichia coli. Furthermore, all strains showed significantly high levels of hydrophobicity. The antioxidant effects of culture filtrates of the 11 strains included 2,2-diphenyl-1-picryl-hydrazyl (DPPH) radical scavenging capacity, 2.2'- azino-bis (2-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical cation scavenging activity, and superoxide dismutase activity. The results revealed that most of the culture filtrates have effective scavenging activity for DPPH and ABTS radicals. All strains appeared to have effective superoxide dismutase activity. In conclusion, the isolated strains A1, A3, S1, and S3 have significant probiotic activities applicable to the development of functional foods and health-related products. These strains might also contribute to preventing and controlling several diseases associated with oxidative stress, when used as probiotics.

  7. Tranexamic acid-induced ligneous conjunctivitis with renal failure showed reversible hypoplasminogenaemia.

    PubMed

    Song, Youngseok; Izumi, Naohiro; Potts, Luke Benjamin; Yoshida, Akitoshi

    2014-05-19

    Ligneous conjunctivitis is a rare severe conjunctivitis characterised by fibrin-rich, 'woody', pseudomembranes on the tarsal conjunctiva complicated by congenital hypoplasminogenaemia. A previous report suggested that ligneous conjunctivitis may result from tranexamic acid (TA)-induced 'secondary' hypoplasminogenaemia. However, the serum plasminogen level has not been confirmed in that scenario. We report for the first time a case of TA-induced ligneous conjunctivitis with reversible hypoplasminogenaemia. A 70-year-old woman developed a gastric ulcer that was treated with oral TA. After 5 weeks of treatment, the patient presented with bilateral pale yellow pseudomembranes on the palpebral conjunctivae. Haematological analysis showed hypoplasminogenaemia. We diagnosed ligneous conjunctivitis. TA was discontinued after 14 weeks after the gastric ulcer symptoms resolved. Six weeks after discontinuation of therapy, the pseudomembranes regressed and the serum plasminogen level returned to the normal range. TA should be considered a possible aetiology in the setting of unresolving ligneous conjunctivitis.

  8. Detail, Face C (rear), showing Interference Analysis System Linear Test ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail, Face C (rear), showing Interference Analysis System Linear Test Array mounted at Level 4A - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

  9. Snacking on Television: A Content Analysis of Adolescents’ Favorite Shows

    PubMed Central

    Larson, Nicole I.; Gollust, Sarah E.; Neumark-Sztainer, Dianne

    2016-01-01

    Introduction Snacking is a complex behavior that may be influenced by entertainment media. Research suggests that snacking and unhealthy foods are commonly shown in programming that targets young audiences, but shows selected for study have been limited. We conducted a content analysis on shows that were named as favorites by adolescents to characterize portrayals of snacking on popular television. Methods A diverse sample of 2,130 adolescents (mean age, 14.3 y) listed 3 favorite television shows in a 2010 school-based survey. Three episodes each of the 25 most popular shows were coded for food-related content, including healthfulness, portion size, screen time use, setting, and social context. We also analyzed the characteristics of characters involved in eating incidents, the show type, and the show rating. We used χ2 tests, binomial tests, and multilevel regression models to compare incidence of snacks versus meals, the characteristics of those involved, and snacking across show characteristics. Results Almost half of food incidents on television shows were snacks. Snacks were significantly more likely than meals to be “mostly unhealthy” (69.3% vs 22.6%, P < .001) and were more likely to include screen time use (25.0% of snacking incidents vs 4.0% of meals, P < .001). Young characters and those coded as being of low socioeconomic status or overweight were overrepresented in snacking incidents. Sitcoms and shows rated for a youth audience were significantly more likely to portray snacking than were shows for adult audiences. Conclusion Media awareness and literacy programs should include foods and snacking behaviors among the issues they address. More healthful portrayals of food and dietary intake in entertainment shows’ content would create a healthier media environment for youth. PMID:27197079

  10. Glial fibrillary acidic protein (GFAP) shows circadian oscillations in crayfish Procambarus clarkii putative pacemakers.

    PubMed

    Rodríguez-Muñoz, María de la Paz; Escamilla-Chimal, Elsa G

    2015-01-01

    Although several studies of glia have examined glial fibrillary acid protein (GFAP) and its relationship to the circadian rhythms of different organisms, they have not explored the daily GFAP oscillations in the putative pacemakers of the crayfish Procambarus clarkii or in other crustaceans. In this study we investigated the daily variations in GFAP concentrations in the eyestalk and brain, which are considered to be putative pacemakers in adult P. clarkii. In both structures, the glial GFAP was quantified using the indirect enzyme-linked immunosorbent assay (ELISA), and double labeling immunofluorescence was used to detect it and its co-localization with protein Period (PER), an important component of the circadian clock, in various regions of both structures. The ELISA results were analyzed using Cosinor and one-way ANOVA with Bonferroni and Scheffé's post hoc tests. The results of this analysis showed that the GFAP levels present circadian oscillations in both structures. Moreover, GFAP was localized in different structures of the eyestalk and brain; however, co-localization with PER occurred only in the lamina ganglionaris, specifically in the cartridges of the eyestalk and in some of the cluster 9 brain cells. These results suggest that as in other invertebrates and vertebrates, glial cells could be involved in the circadian system of P. clarkii; however, thus far we cannot know whether the glial cells are only effectors, participate in afferent pathways, or are part of the circadian clock.

  11. An acid phosphatase in the plasma membranes of human astrocytoma showing marked specificity toward phosphotyrosine protein.

    PubMed

    Leis, J F; Kaplan, N O

    1982-11-01

    The plasma membrane from the human tumor astrocytoma contains an active acid phosphatase activity based on hydrolysis of p-nitrophenyl phosphate. Other acid phosphatase substrates--beta-glycerophosphate, O-phosphorylcholine, and 5'-AMP--are not hydrolyzed significantly. The phosphatase activity is tartrate insensitive and is stimulated by Triton X-100 and EDTA. Of the three known phosphoamino acids, only free O-phosphotyrosine is hydrolyzed by the membrane phosphatase activity. Other acid phosphatases tested from potato, wheat germ, milk, and bovine prostate did not show this degree of specificity. The plasma membrane activity also dephosphorylated phosphotyrosine histone at a much greater rate than did the other acid phosphatases. pH profiles for free O-phosphotyrosine and phosphotyrosine histone showed a shift toward physiological pH, indicating possible physiological significance. Phosphotyrosine histone dephosphorylation activity was nearly 10 times greater than that seen for phosphoserine histone dephosphorylation, and Km values were much lower for phosphotyrosine histone dephosphorylation (0.5 microM vs. 10 microM). Fluoride and zinc significantly inhibited phosphoserine histone dephosphorylation. Vanadate, on the other hand, was a potent inhibitor of phosphotyrosine histone dephosphorylation (50% inhibition at 0.5 microM) but not of phosphoserine histone. ATP stimulated phosphotyrosine histone dephosphorylation (160-250%) but inhibited phosphoserine histone dephosphorylation (95%). These results suggest the existence of a highly specific phosphotyrosine protein phosphatase activity associated with the plasma membrane of human astrocytoma.

  12. Tannic acid modified silver nanoparticles show antiviral activity in herpes simplex virus type 2 infection.

    PubMed

    Orlowski, Piotr; Tomaszewska, Emilia; Gniadek, Marianna; Baska, Piotr; Nowakowska, Julita; Sokolowska, Justyna; Nowak, Zuzanna; Donten, Mikolaj; Celichowski, Grzegorz; Grobelny, Jaroslaw; Krzyzowska, Malgorzata

    2014-01-01

    The interaction between silver nanoparticles and herpesviruses is attracting great interest due to their antiviral activity and possibility to use as microbicides for oral and anogenital herpes. In this work, we demonstrate that tannic acid modified silver nanoparticles sized 13 nm, 33 nm and 46 nm are capable of reducing HSV-2 infectivity both in vitro and in vivo. The antiviral activity of tannic acid modified silver nanoparticles was size-related, required direct interaction and blocked virus attachment, penetration and further spread. All tested tannic acid modified silver nanoparticles reduced both infection and inflammatory reaction in the mouse model of HSV-2 infection when used at infection or for a post-infection treatment. Smaller-sized nanoparticles induced production of cytokines and chemokines important for anti-viral response. The corresponding control buffers with tannic acid showed inferior antiviral effects in vitro and were ineffective in blocking in vivo infection. Our results show that tannic acid modified silver nanoparticles are good candidates for microbicides used in treatment of herpesvirus infections.

  13. Tannic Acid Modified Silver Nanoparticles Show Antiviral Activity in Herpes Simplex Virus Type 2 Infection

    PubMed Central

    Orlowski, Piotr; Tomaszewska, Emilia; Gniadek, Marianna; Baska, Piotr; Nowakowska, Julita; Sokolowska, Justyna; Nowak, Zuzanna; Donten, Mikolaj; Celichowski, Grzegorz; Grobelny, Jaroslaw; Krzyzowska, Malgorzata

    2014-01-01

    The interaction between silver nanoparticles and herpesviruses is attracting great interest due to their antiviral activity and possibility to use as microbicides for oral and anogenital herpes. In this work, we demonstrate that tannic acid modified silver nanoparticles sized 13 nm, 33 nm and 46 nm are capable of reducing HSV-2 infectivity both in vitro and in vivo. The antiviral activity of tannic acid modified silver nanoparticles was size-related, required direct interaction and blocked virus attachment, penetration and further spread. All tested tannic acid modified silver nanoparticles reduced both infection and inflammatory reaction in the mouse model of HSV-2 infection when used at infection or for a post-infection treatment. Smaller-sized nanoparticles induced production of cytokines and chemokines important for anti-viral response. The corresponding control buffers with tannic acid showed inferior antiviral effects in vitro and were ineffective in blocking in vivo infection. Our results show that tannic acid modified silver nanoparticles are good candidates for microbicides used in treatment of herpesvirus infections. PMID:25117537

  14. Analysis of Organic Acids.

    ERIC Educational Resources Information Center

    Griswold, John R.; Rauner, Richard A.

    1990-01-01

    Presented are the procedures and a discussion of the results for an experiment in which students select unknown carboxylic acids, determine their melting points, and investigate their solubility behavior in water and ethanol. A table of selected carboxylic acids is included. (CW)

  15. Trajectory Hunting: Analysis of UARS Measurements showing Rapid Chlorine Activation

    NASA Technical Reports Server (NTRS)

    Danilin, M.Y.; Santee, M. L.; Rodriquez, J. M.; Ko, M. K. W.; Mergenthaler, J. M.; Kumer, J. B.; Tabazadeh, A.

    1998-01-01

    Trajectory hunting (i.e., a technique to find air parcels sampled at least twice over the course of a few days) is applied to analyze Upper Atmosphere Research Satellite (UARS) measurements in conjunction with the AER photochemical box model. In this study, we investigate rapid chlorine activation in the Arctic lower stratosphere on 29 Dec 1992 associated with a polar stratospheric cloud (PSC) event. Six air parcels that have been sampled twice were followed along 5-day trajectories at the 465 K (approximately 46 mb) and 585 K (approximately 22 mb) levels. A detailed sensitivity study with the AER. photochemical box model along these trajectories leads to the following conclusions for the episode considered: (1) model results are in better agreement with UARS measurements at these levels if the UKMO temperature is decreased by at least 1-2 K; (2) the NAT (nitric acid trihydrate) PSC formation scheme produces results in better agreement with observations than the STS (supercooled ternary solution) scheme; (3) the model can explain the UARS measurements at 585 K, but under-estimates the ClO abundance at 465 K, suggesting some inconsistency between the UARS measurements at this level.

  16. Trajectory Hunting: Analysis of UARS Measurements Showing Rapid Chlorine Activation

    NASA Technical Reports Server (NTRS)

    Danilin, M. Y.; Santee, M. L.; Rodriquez, J. M.; Ko, M. K. W.; Mergenthaler, J. M.; Kumer, J. B.; Tabazadeh, A.

    1998-01-01

    Trajectory hunting (i.e., a technique to find air parcels sampled at least twice over the course of a few days) is applied to analyze Upper Atmosphere Research Satellite (UARS) measurements in conjunction with the AER photochemical box model. In this study, we investigate rapid chlorine activation in the Arctic lower stratosphere on 29 Dec. 1992 associated with a polar stratospheric cloud (PSC) event. Six air parcels that have been sampled twice were followed along 5-day trajectories at the 465 K (approx. 46 mb) and 585 K (approxi. 22 mb) levels. A detailed sensitivity study with the AER photochemical box model along these trajectories leads to the following conclusions for the episode considered: 1) model results are in better agreement with UARS measurements at these levels if the U.K. Meteorological Office (UKMO) temperature is decreased by at least 1-2 K; 2) the NAT (nitric acid trihydrate) PSC formation scheme produces results in better agreement with observations than the STS (supercooled ternary solution) scheme; 3) the model can explain the UARS measurements at 585 K, but under-estimates the ClO abundance at 465 K, suggesting some inconsistency between the UARS measurements at this level.

  17. Valproic Acid Increases CD133 Positive Cells that Show Low Sensitivity to Cytostatics in Neuroblastoma

    PubMed Central

    Khalil, Mohamed Ashraf; Hraběta, Jan; Groh, Tomáš; Procházka, Pavel; Doktorová, Helena; Eckschlager, Tomáš

    2016-01-01

    Valproic acid (VPA) is a well-known antiepileptic drug that exhibits antitumor activities through its action as a histone deacetylase inhibitor. CD133 is considered to be a cancer stem cell marker in several tumors including neuroblastoma. CD133 transcription is strictly regulated by epigenetic modifications. We evaluated the epigenetic effects of treatment with 1mM VPA and its influence on the expression of CD133 in four human neuroblastoma cell lines. Chemoresistance and cell cycle of CD133+ and CD133− populations were examined by flow cytometry. We performed bisulfite conversion followed by methylation-sensitive high resolution melting analysis to assess the methylation status of CD133 promoters P1 and P3. Our results revealed that VPA induced CD133 expression that was associated with increased acetylation of histones H3 and H4. On treatment with VPA and cytostatics, CD133+ cells were mainly detected in the S and G2/M phases of the cell cycle and they showed less activated caspase-3 compared to CD133− cells. UKF-NB-3 neuroblastoma cells which express CD133 displayed higher colony and neurosphere formation capacities when treated with VPA, unlike IMR-32 which lacks for CD133 protein. Induction of CD133 in UKF-NB-3 was associated with increased expression of phosphorylated Akt and pluripotency transcription factors Nanog, Oct-4 and Sox2. VPA did not induce CD133 expression in cell lines with methylated P1 and P3 promoters, where the CD133 protein was not detected. Applying the demethylating agent 5-aza-2’-deoxycytidine to the cell lines with methylated promoters resulted in CD133 re-expression that was associated with a drop in P1 and P3 methylation level. In conclusion, CD133 expression in neuroblastoma can be regulated by histone acetylation and/or methylation of its CpG promoters. VPA can induce CD133+ cells which display high proliferation potential and low sensitivity to cytostatics in neuroblastoma. These results give new insight into the possible

  18. Folic acid-polydopamine nanofibers show enhanced ordered-stacking via π-π interactions.

    PubMed

    Fan, Hailong; Yu, Xiang; Liu, Yang; Shi, Zujin; Liu, Huihui; Nie, Zongxiu; Wu, Decheng; Jin, Zhaoxia

    2015-06-21

    Recent research has indicated that polydopamine and synthetic eumelanins are optoelectronic biomaterials in which one-dimensional aggregates composed of ordered-stacking oligomers have been proposed as unique organic semiconductors. However, improving the ordered-stacking of oligomers in polydopamine nanostructures is a big challenge. Herein, we first demonstrate how folic acid molecules influence the morphology and nanostructure of polydopamine via tuning the π-π interactions of oligomers. MALDI-TOF mass spectrometry reveals that porphyrin-like tetramers are characteristic of folic acid-polydopamine (FA-PDA) nanofibers. X-ray diffraction combined with simulation studies indicate that these oligomers favour aggregation into graphite-like ordered nanostructures via strong π-π interactions. High-resolution TEM characterization of carbonized FA-PDA hybrids show that in FA-PDA nanofibers the size of the graphite-like domains is over 100 nm. The addition of folic acid in polydopamine enhances the ordered stacking of oligomers in its nanostructure. Our study steps forward to discover the mystery of the structure-property relationship of FA-PDA hybrids. It paves a way to optimize the properties of PDA through the design and selection of oligomer structures.

  19. Performic acid (PFA): tests on an advanced primary effluent show promising disinfection performance.

    PubMed

    Gehr, R; Chen, D; Moreau, M

    2009-01-01

    Performic acid, or PFA (CH(2)O(3)), is a well-known oxidizing agent and disinfectant in the medical field and food industry. It has recently become available on a commercial scale for potential use in wastewater disinfection. This study investigated its application to an advanced primary effluent which is recalcitrant to disinfection by UV and peracetic acid (PAA). Methods were developed for determining PFA concentrations in stock solutions as well as in residual concentrations in the wastewater. Batch and continuous-flow pilot studies showed a correlation between log fecal coliform removals and PFA doses. A PFA dose of approximately 3.4 mg/L and a contact time of 45 minutes could achieve 3-logs removal, and almost total disinfection could be achieved using a dose of 6 mg/L. The by-products of PFA addition are hydrogen peroxide and formic acid (CHOOH), neither of which is considered to be toxic to aquatic fauna at the doses required for disinfection.

  20. Authenticity and TV Shows: A Multidimensional Analysis Perspective

    ERIC Educational Resources Information Center

    Al-Surmi, Mansoor

    2012-01-01

    Television shows, especially soap operas and sitcoms, are usually considered by English as a second language practitioners as a source of authentic spoken conversational materials presumably because they reflect the linguistic features of natural conversation. However, practitioners are faced with the dilemma of how to assess whether such…

  1. Metabolic profiling of plasma amino acids shows that histidine increases following the consumption of pork

    PubMed Central

    Samman, Samir; Crossett, Ben; Somers, Miles; Bell, Kirstine J; Lai, Nicole T; Sullivan, David R; Petocz, Peter

    2014-01-01

    Amino acid (AA) status is determined by factors including nutrition, metabolic rate, and interactions between the metabolism of AA, carbohydrates, and lipids. Analysis of the plasma AA profile, together with markers of glucose and lipid metabolism, will shed light on metabolic regulation. The objectives of this study were to investigate the acute responses to the consumption of meals containing either pork (PM) or chicken (CM), and to identify relationships between plasma AA and markers of glycemic and lipemic control. A secondary aim was to explore AA predictors of plasma zinc concentrations. Ten healthy adults participated in a postprandial study on two separate occasions. In a randomized cross-over design, participants consumed PM or CM. The concentrations of 21 AA, glucose, insulin, triglycerides, nonesterified fatty acids, and zinc were determined over 5 hours postprandially. The meal composition did not influence glucose, insulin, triglyceride, nonesterified fatty acid, or zinc concentrations. Plasma histidine was higher following the consumption of PM (P=0.014), with consistently higher changes observed after 60 minutes (P<0.001). Greater percentage increases were noted at limited time points for valine and leucine + isoleucine in those who consumed CM compared to PM. In linear regression, some AAs emerged as predictors of the metabolic responses, irrespective of the meal that was consumed. The present study demonstrates that a single meal of PM or CM produces a differential profile of AA in the postprandial state. The sustained increase in histidine following the consumption of a PM is consistent with the reported effects of lean pork on cardiometabolic risk factors. PMID:24971025

  2. Metabolic profiling of plasma amino acids shows that histidine increases following the consumption of pork.

    PubMed

    Samman, Samir; Crossett, Ben; Somers, Miles; Bell, Kirstine J; Lai, Nicole T; Sullivan, David R; Petocz, Peter

    2014-01-01

    Amino acid (AA) status is determined by factors including nutrition, metabolic rate, and interactions between the metabolism of AA, carbohydrates, and lipids. Analysis of the plasma AA profile, together with markers of glucose and lipid metabolism, will shed light on metabolic regulation. The objectives of this study were to investigate the acute responses to the consumption of meals containing either pork (PM) or chicken (CM), and to identify relationships between plasma AA and markers of glycemic and lipemic control. A secondary aim was to explore AA predictors of plasma zinc concentrations. Ten healthy adults participated in a postprandial study on two separate occasions. In a randomized cross-over design, participants consumed PM or CM. The concentrations of 21 AA, glucose, insulin, triglycerides, nonesterified fatty acids, and zinc were determined over 5 hours postprandially. The meal composition did not influence glucose, insulin, triglyceride, nonesterified fatty acid, or zinc concentrations. Plasma histidine was higher following the consumption of PM (P=0.014), with consistently higher changes observed after 60 minutes (P<0.001). Greater percentage increases were noted at limited time points for valine and leucine + isoleucine in those who consumed CM compared to PM. In linear regression, some AAs emerged as predictors of the metabolic responses, irrespective of the meal that was consumed. The present study demonstrates that a single meal of PM or CM produces a differential profile of AA in the postprandial state. The sustained increase in histidine following the consumption of a PM is consistent with the reported effects of lean pork on cardiometabolic risk factors.

  3. Pinus pinaster seedlings and their fungal symbionts show high plasticity in phosphorus acquisition in acidic soils.

    PubMed

    Ali, M A; Louche, J; Legname, E; Duchemin, M; Plassard, C

    2009-12-01

    Young seedlings of maritime pine (Pinus pinaster Soland in Aït.) were grown in rhizoboxes using intact spodosol soil samples from the southwest of France, in Landes of Gascogne, presenting a large variation of phosphorus (P) availability. Soils were collected from a 93-year-old unfertilized stand and a 13-year-old P. pinaster stand with regular annual fertilization of either only P or P and nitrogen (N). After 6 months of culture in controlled conditions, different morphotypes of ectomycorrhiza (ECM) were used for the measurements of acid phosphatase activity and molecular identification of fungal species using amplification of the ITS region. Total biomass, N and P contents were measured in roots and shoots of plants. Bicarbonate- and NaOH-available inorganic P (Pi), organic P (Po) and ergosterol concentrations were measured in bulk and rhizosphere soil. The results showed that bulk soil from the 93-year-old forest stand presented the highest Po levels, but relatively higher bicarbonate-extractable Pi levels compared to 13-year-old unfertilized stand. Fertilizers significantly increased the concentrations of inorganic P fractions in bulk soil. Ergosterol contents in rhizosphere soil were increased by fertilizer application. The dominant fungal species was Rhizopogon luteolus forming 66.6% of analysed ECM tips. Acid phosphatase activity was highly variable and varied inversely with bicarbonate-extractable Pi levels in the rhizosphere soil. Total P or total N in plants was linearly correlated with total plant biomass, but the slope was steep only between total P and biomass in fertilized soil samples. In spite of high phosphatase activity in ECM tips, P availability remained a limiting nutrient in soil samples from unfertilized stands. Nevertheless young P. pinaster seedlings showed a high plasticity for biomass production at low P availability in soils.

  4. Salvianolic acid A shows selective cytotoxicity against multidrug-resistant MCF-7 breast cancer cells.

    PubMed

    Wang, Xin; Wang, Chunyan; Zhang, Longjiang; Li, Yanjun; Wang, Shouju; Wang, Jiandong; Yuan, Caiyun; Niu, Jia; Wang, Chengsheng; Lu, Guangming

    2015-02-01

    Multidrug resistance (MDR) is a major cause for incurable breast cancer. Salvianolic acid A (SAA), the hydrophilic polyphenolic derivative of Salvia miltiorrhiza Bunge (Danshen/Red Sage), was examined for cytotoxicities to MDR MCF-7 human breast cancer cells and their parental counterparts. We have shown that SAA inhibited proliferation, caused cell cycle arrest at the S phase, and induced apoptosis dose dependently to the two kinds of cancer cells. However, the resistant cells were significantly susceptible to the inhibition of SAA compared with the parental cells. SAA increased the level of reactive oxygen species (ROS) by 6.2-fold in the resistant cells, whereas the level of SAA-induced ROS changed only by 1.6-fold in their parental counterparts. Thus, the data showed that the selective cytotoxicity resulted from the hypersensitivity of the resistant cells to the strongly elevated ROS by SAA. In addition, SAA-triggered apoptosis was associated with increased caspase-3 activity, disrupted mitochondrial membrane potential, downregulated Bcl-2 expression, and upregulated Bax expression in the resistant cells. Moreover, SAA downregulated the level of P-glycoprotein, which was overexpressed in the resistant cells. This indicated that SAA modulated MDR. Furthermore, SAA showed higher antitumor activity than did doxorubicin in xenografts established from the resistant cells. The present work raised a possibility that SAA might be considered a potential choice to overcome MDR for the selective susceptibility of the resistant breast cancer cells to SAA treatment.

  5. Salvianolic Acid A, as a Novel ETA Receptor Antagonist, Shows Inhibitory Effects on Tumor in Vitro.

    PubMed

    Zhang, Qiao; Wang, Shifeng; Yu, Yangyang; Sun, Shengnan; Zhang, Yuxin; Zhang, Yanling; Yang, Wei; Li, Shiyou; Qiao, Yanjiang

    2016-08-02

    Endothelin-1 (ET-1) autocrine and paracrine signaling modulate cell proliferation of tumor cells by activating its receptors, endothelin A receptor (ETAR) and endothelin B receptor (ETBR). Dysregulation of ETAR activation promotes tumor development and progression. The potential of ETAR antagonists and the dual-ETAR and ETBR antagonists as therapeutic approaches are under preclinical and clinical studies. Salvianolic acid A (Sal A) is a hydrophilic polyphenolic derivative isolated from Salvia miltiorrhiza Bunge (Danshen), which has been reported as an anti-cancer and cardio-protective herbal medicine. In this study, we demonstrate that Sal A inhibits ETAR activation induced by ET-1 in both recombinant and endogenous ETAR expression cell lines. The IC50 values were determined as 5.7 µM in the HEK293/ETAR cell line and 3.14 µM in HeLa cells, respectively. Furthermore, our results showed that Sal A suppressed cell proliferation and extended the doubling times of multiple cancer cells, including HeLa, DU145, H1975, and A549 cell lines. In addition, Sal A inhibited proliferation of DU145 cell lines stimulated by exogenous ET-1 treatment. Moreover, the cytotoxicity and cardio-toxicity of Sal A were assessed in human umbilical vein endothelial cells (HUVEC) and Human-induced pluripotent stem cell-derived cardiomyocytes (hiPS-CMs), which proved that Sal A demonstrates no cytotoxicity or cardiotoxicity. Collectively, our findings indicate that Sal A is a novel anti-cancer candidate through targeting ETAR.

  6. Salvianolic Acid A, as a Novel ETA Receptor Antagonist, Shows Inhibitory Effects on Tumor in Vitro

    PubMed Central

    Zhang, Qiao; Wang, Shifeng; Yu, Yangyang; Sun, Shengnan; Zhang, Yuxin; Zhang, Yanling; Yang, Wei; Li, Shiyou; Qiao, Yanjiang

    2016-01-01

    Endothelin-1 (ET-1) autocrine and paracrine signaling modulate cell proliferation of tumor cells by activating its receptors, endothelin A receptor (ETAR) and endothelin B receptor (ETBR). Dysregulation of ETAR activation promotes tumor development and progression. The potential of ETAR antagonists and the dual-ETAR and ETBR antagonists as therapeutic approaches are under preclinical and clinical studies. Salvianolic acid A (Sal A) is a hydrophilic polyphenolic derivative isolated from Salvia miltiorrhiza Bunge (Danshen), which has been reported as an anti-cancer and cardio-protective herbal medicine. In this study, we demonstrate that Sal A inhibits ETAR activation induced by ET-1 in both recombinant and endogenous ETAR expression cell lines. The IC50 values were determined as 5.7 µM in the HEK293/ETAR cell line and 3.14 µM in HeLa cells, respectively. Furthermore, our results showed that Sal A suppressed cell proliferation and extended the doubling times of multiple cancer cells, including HeLa, DU145, H1975, and A549 cell lines. In addition, Sal A inhibited proliferation of DU145 cell lines stimulated by exogenous ET-1 treatment. Moreover, the cytotoxicity and cardio-toxicity of Sal A were assessed in human umbilical vein endothelial cells (HUVEC) and Human-induced pluripotent stem cell-derived cardiomyocytes (hiPS-CMs), which proved that Sal A demonstrates no cytotoxicity or cardiotoxicity. Collectively, our findings indicate that Sal A is a novel anti-cancer candidate through targeting ETAR. PMID:27490540

  7. Features of “All LNA” Duplexes Showing a New Type of Nucleic Acid Geometry

    PubMed Central

    Förster, Charlotte; Eichert, André; Oberthür, Dominik; Betzel, Christian; Geßner, Reinhard; Nitsche, Andreas; Fürste, Jens P.

    2012-01-01

    “Locked nucleic acids” (LNAs) belong to the backbone-modified nucleic acid family. The 2′-O,4′-C-methylene-β-D-ribofuranose nucleotides are used for single or multiple substitutions in RNA molecules and thereby introduce enhanced bio- and thermostability. This renders LNAs powerful tools for diagnostic and therapeutic applications. RNA molecules maintain the overall canonical A-type conformation upon substitution of single or multiple residues/nucleotides by LNA monomers. The structures of “all” LNA homoduplexes, however, exhibit significant differences in their overall geometry, in particular a decreased twist, roll and propeller twist. This results in a widening of the major groove, a decrease in helical winding, and an enlarged helical pitch. Therefore, the LNA duplex structure can no longer be described as a canonical A-type RNA geometry but can rather be brought into proximity to other backbone-modified nucleic acids, like glycol nucleic acids or peptide nucleic acids. LNA-modified nucleic acids provide thus structural and functional features that may be successfully exploited for future application in biotechnology and drug discovery. PMID:22666550

  8. Isolation of thermophilic L-lactic acid producing bacteria showing homo-fermentative manner under high aeration condition.

    PubMed

    Tongpim, Saowanit; Meidong, Ratchanu; Poudel, Pramod; Yoshino, Satoshi; Okugawa, Yuki; Tashiro, Yukihiro; Taniguchi, Masayuki; Sakai, Kenji

    2014-03-01

    By applying non-sterile open fermentation of food waste, various thermotolerant l-lactic acid-producing bacteria were isolated and identified. The predominant bacterial isolates showing higher accumulation of l-lactic acid belong to 3 groups of Bacillus coagulans, according to their 16S rRNA gene sequence similarities. B. coagulans strains M21 and M36 produced high amounts of l-lactic acid of high optical purity and lactic acid selectivity in model kitchen refuse medium and glucose-yeast extract-peptone medium. Other thermotolerant isolates resembling to Bacillus humi, B. ruris, B. subtilis, B. niacini and B. soli were also identified. These bacteria produced low amounts of l-lactic acid of more than 99% optical purity. All isolated strains showed the highest growth rate at temperatures around 55-60°C. They showed unique responses to various oxygen supply conditions. The majority of isolates produced l-lactic acid at a low overall oxygen transfer coefficient (KLa); however, acetic acid was produced instead of l-lactic acid at a high KLa. B. coagulans M21 was the only strain that produced high, consistent, and reproducible amounts of optically pure l-lactic acid (>99% optical purity) under high and low KLa conditions in a homo-fermentative manner.

  9. A Boronic Acid Conjugate of Angiogenin that Shows ROS-Responsive Neuroprotective Activity.

    PubMed

    Hoang, Trish T; Smith, Thomas P; Raines, Ronald T

    2017-03-01

    Angiogenin (ANG) is a human ribonuclease that is compromised in patients with amyotrophic lateral sclerosis (ALS). ANG also promotes neovascularization, and can induce hemorrhage and encourage tumor growth. The causal neurodegeneration of ALS is associated with reactive oxygen species, which are also known to elicit the oxidative cleavage of carbon-boron bonds. We have developed a synthetic boronic acid mask that restrains the ribonucleolytic activity of ANG. The masked ANG does not stimulate endothelial cell proliferation but protects astrocytes from oxidative stress. By differentiating between the two dichotomous biological activities of ANG, this strategy could provide a viable pharmacological approach for the treatment of ALS.

  10. Lectin staining and Western blot data showing differential sialylation of nutrient-deprived cancer cells to sialic acid supplementation.

    PubMed

    Badr, Haitham A; AlSadek, Dina M M; Mathew, Mohit P; Li, Chen-Zhong; Djansugurova, Leyla B; Yarema, Kevin J; Ahmed, Hafiz

    2015-12-01

    This report provides data that are specifically related to the differential sialylation of nutrient deprived breast cancer cells to sialic acid supplementation in support of the research article entitled, "Nutrient-deprived cancer cells preferentially use sialic acid to maintain cell surface glycosylation" [1]. Particularly, breast cancer cells, when supplemented with sialic acid under nutrient deprivation, display sialylated glycans at the cell surface, but non-malignant mammary cells show sialylated glycans intracellularly. The impact of sialic acid supplementation under nutrient deprivation was demonstrated by measuring levels of expression and sialylation of two markers, EGFR1 and MUC1. This Data in Brief article complements the main manuscript by providing detailed instructions and representative results for cell-level imaging and Western blot analyses of changes in sialylation during nutrient deprivation and sialic acid supplementation. These methods can be readily generalized for the study of many types of glycosylation and various glycoprotein markers through the appropriate selection of fluorescently-labeled lectins.

  11. Size Controlled Heparin Fragment-Deoxycholic Acid Conjugate Showed Anticancer Property by Inhibiting VEGF165.

    PubMed

    Park, Jooho; Jeong, Jee-Heon; Al-Hilal, Taslim A; Kim, Ji-Young; Byun, Youngro

    2015-05-20

    Heparin is a highly sulfated, long, and linear polysaccharide, which can inhibit tumor growth by interacting with growth factors such as bFGF and VEGF. Several researchers have shown the anti-angiogenic effect of heparin and its conjugates in relation to growth factor inhibition. For drug development and inhibition of growth factors using heparin conjugates, the molecular size of heparin may be crucial considering the size of the heparin binding site of growth factors. In this study, we synthesized heparin fragments and deoxycholic acid conjugated heparin fragments (HFD) to search for the optimal size-controlled conjugate that will inhibit the angiogenic effect of VEGF165. We have also shown that the HFDs could have an enhanced therapeutic effect in vitro and in vivo consequent to the molecular size control. HFDs have significant anti-angiogenic effects by blocking the angiogenic activity of VEGF165 depending on its molecular size. Among them, HFD2 was a promising candidate for oral angiogenesis inhibitor. These results suggest that size-controlled synthesis is necessary for heparin-based drug development.

  12. Bisphosphonate-functionalized hyaluronic acid showing selective affinity for osteoclasts as a potential treatment for osteoporosis.

    PubMed

    Kootala, Sujit; Ossipov, Dmitri; van den Beucken, Jeroen J J P; Leeuwenburgh, Sander; Hilborn, Jöns

    2015-08-01

    Current treatments for osteoporosis involve the administration of high doses of bisphosphonates (BPs) over a number of years. However, the efficiency of the absorption of these drugs and specificity towards targeted osteoclastic cells is still suboptimal. In this study, we have exploited the natural affinity of high (H) and low (L) molecular-weight hyaluronic acid (HA) towards a cluster of differentiation 44 (CD44) receptors on osteoclasts to use it as a biodegradable targeting vehicle. We covalently bonded BP to functionalised HA (HA-BP) and found that HA-BP conjugates were highly specific to osteoclastic cells and reduced mature osteoclast numbers significantly more than free BP. To study the uptake of HA-BP, we fluorescently derivatised the polymer-drug with fluorescein B isothiocyanate (FITC) and found that L-HA-BP could seamlessly enter osteoclastic cells. Alternatively, we tested polyvinyl alcohol (PVA) as a synthetic polymer delivery vehicle using similar chemistry to link BP and found that osteoclast numbers did not reduce in the same way. These findings could pave the way for biodegradable polymers to be used as vehicles for targeted delivery of anti-osteoporotic drugs.

  13. Nucleotide sequences of the Pseudomonas savastanoi indoleacetic acid genes show homology with Agrobacterium tumefaciens T-DNA

    PubMed Central

    Yamada, Tetsuji; Palm, Curtis J.; Brooks, Bob; Kosuge, Tsune

    1985-01-01

    We report the nucleotide sequences of iaaM and iaaH, the genetic determinants for, respectively, tryptophan 2-monooxygenase and indoleacetamide hydrolase, the enzymes that catalyze the conversion of L-tryptophan to indoleacetic acid in the tumor-forming bacterium Pseudomonas syringae pv. savastanoi. The sequence analysis indicates that the iaaM locus contains an open reading frame encoding 557 amino acids that would comprise a protein with a molecular weight of 61,783; the iaaH locus contains an open reading frame of 455 amino acids that would comprise a protein with a molecular weight of 48,515. Significant amino acid sequence homology was found between the predicted sequence of the tryptophan monooxygenase of P. savastanoi and the deduced product of the T-DNA tms-1 gene of the octopine-type plasmid pTiA6NC from Agrobacterium tumefaciens. Strong homology was found in the 25 amino acid sequence in the putative FAD-binding region of tryptophan monooxygenase. Homology was also found in the amino acid sequences representing the central regions of the putative products of iaaH and tms-2 T-DNA. The results suggest a strong similarity in the pathways for indoleacetic acid synthesis encoded by genes in P. savastanoi and in A. tumefaciens T-DNA. Images PMID:16593610

  14. Lactobacillus kefiri shows inter-strain variations in the amino acid sequence of the S-layer proteins.

    PubMed

    Malamud, Mariano; Carasi, Paula; Bronsoms, Sílvia; Trejo, Sebastián A; Serradell, María de Los Angeles

    2017-04-01

    The S-layer is a proteinaceous envelope constituted by subunits that self-assemble to form a two-dimensional lattice that covers the surface of different species of Bacteria and Archaea, and it could be involved in cell recognition of microbes among other several distinct functions. In this work, both proteomic and genomic approaches were used to gain knowledge about the sequences of the S-layer protein (SLPs) encoding genes expressed by six aggregative and sixteen non-aggregative strains of potentially probiotic Lactobacillus kefiri. Peptide mass fingerprint (PMF) analysis confirmed the identity of SLPs extracted from L. kefiri, and based on the homology with phylogenetically related species, primers located outside and inside the SLP-genes were employed to amplify genomic DNA. The O-glycosylation site SASSAS was found in all L. kefiri SLPs. Ten strains were selected for sequencing of the complete genes. The total length of the mature proteins varies from 492 to 576 amino acids, and all SLPs have a calculated pI between 9.37 and 9.60. The N-terminal region is relatively conserved and shows a high percentage of positively charged amino acids. Major differences among strains are found in the C-terminal region. Different groups could be distinguished regarding the mature SLPs and the similarities observed in the PMF spectra. Interestingly, SLPs of the aggregative strains are 100% homologous, although these strains were isolated from different kefir grains. This knowledge provides relevant data for better understanding of the mechanisms involved in SLPs functionality and could contribute to the development of products of biotechnological interest from potentially probiotic bacteria.

  15. Mefenamic acid in combination with ribavirin shows significant effects in reducing chikungunya virus infection in vitro and in vivo.

    PubMed

    Rothan, Hussin A; Bahrani, Hirbod; Abdulrahman, Ammar Y; Mohamed, Zulqarnain; Teoh, Teow Chong; Othman, Shatrah; Rashid, Nurshamimi Nor; Rahman, Noorsaadah A; Yusof, Rohana

    2016-03-01

    Chikungunya virus (CHIKV) infection is a persistent problem worldwide due to efficient adaptation of the viral vectors, Aedes aegypti and Aedes albopictus mosquitoes. Therefore, the absence of effective anti-CHIKV drugs to combat chikungunya outbreaks often leads to a significant impact on public health care. In this study, we investigated the antiviral activity of drugs that are used to alleviate infection symptoms, namely, the non-steroidal anti-inflammatory drugs (NSAIDs), on the premise that active compounds with potential antiviral and anti-inflammatory activities could be directly subjected for human use to treat CHIKV infections. Amongst the various NSAID compounds, Mefenamic acid (MEFE) and Meclofenamic acid (MECLO) showed considerable antiviral activity against viral replication individually or in combination with the common antiviral drug, Ribavirin (RIBA). The 50% effective concentration (EC50) was estimated to be 13 μM for MEFE, 18 μM for MECLO and 10 μM for RIBA, while MEFE + RIBA (1:1) exhibited an EC50 of 3 μM, and MECLO + RIBA (1:1) was 5 μM. Because MEFE is commercially available and its synthesis is easier compared with MECLO, MEFE was selected for further in vivo antiviral activity analysis. Treatment with MEFE + RIBA resulted in a significant reduction of hypertrophic effects by CHIKV on the mouse liver and spleen. Viral titre quantification in the blood of CHIKV-infected mice through the plaque formation assay revealed that treatment with MEFE + RIBA exhibited a 6.5-fold reduction compared with untreated controls. In conclusion, our study demonstrated that MEFE in combination with RIBA exhibited significant anti-CHIKV activity by impairing viral replication in vitro and in vivo. Indeed, this finding may lead to an even broader application of these combinatorial treatments against other viral infections.

  16. 2,4-D and IAA Amino Acid Conjugates Show Distinct Metabolism in Arabidopsis

    PubMed Central

    Eyer, Luděk; Vain, Thomas; Pařízková, Barbora; Oklestkova, Jana; Barbez, Elke; Kozubíková, Hana; Pospíšil, Tomáš; Wierzbicka, Roksana; Kleine-Vehn, Jürgen; Fránek, Milan; Strnad, Miroslav; Robert, Stéphanie

    2016-01-01

    The herbicide 2,4-D exhibits an auxinic activity and therefore can be used as a synthetic and traceable analog to study auxin-related responses. Here we identified that not only exogenous 2,4-D but also its amide-linked metabolite 2,4-D-Glu displayed an inhibitory effect on plant growth via the TIR1/AFB auxin-mediated signaling pathway. To further investigate 2,4-D metabolite conversion, identity and activity, we have developed a novel purification procedure based on the combination of ion exchange and immuno-specific sorbents combined with a sensitive liquid chromatography-mass spectrometry method. In 2,4-D treated samples, 2,4-D-Glu and 2,4-D-Asp were detected at 100-fold lower concentrations compared to 2,4-D levels, showing that 2,4-D can be metabolized in the plant. Moreover, 2,4-D-Asp and 2,4-D-Glu were identified as reversible forms of 2,4-D homeostasis that can be converted to free 2,4-D. This work paves the way to new studies of auxin action in plant development. PMID:27434212

  17. The Transcriptional Heat Shock Response of Salmonella Typhimurium Shows Hysteresis and Heated Cells Show Increased Resistance to Heat and Acid Stress

    PubMed Central

    Pin, Carmen; Hansen, Trine; Muñoz-Cuevas, Marina; de Jonge, Rob; Rosenkrantz, Jesper T.; Löfström, Charlotta; Aarts, Henk; Olsen, John E.

    2012-01-01

    We investigated if the transcriptional response of Salmonella Typhimurium to temperature and acid variations was hysteretic, i.e. whether the transcriptional regulation caused by environmental stimuli showed memory and remained after the stimuli ceased. The transcriptional activity of non-replicating stationary phase cells of S. Typhimurium caused by the exposure to 45°C and to pH 5 for 30 min was monitored by microarray hybridizations at the end of the treatment period as well as immediately and 30 minutes after conditions were set back to their initial values, 25°C and pH 7. One hundred and two out of 120 up-regulated genes during the heat shock remained up-regulated 30 minutes after the temperature was set back to 25°C, while only 86 out of 293 down regulated genes remained down regulated 30 minutes after the heat shock ceased. Thus, the majority of the induced genes exhibited hysteresis, i.e., they remained up-regulated after the environmental stress ceased. At 25°C the transcriptional regulation of genes encoding for heat shock proteins was determined by the previous environment. Gene networks constructed with up-regulated genes were significantly more modular than those of down-regulated genes, implying that down-regulation was significantly less synchronized than up-regulation. The hysteretic transcriptional response to heat shock was accompanied by higher resistance to inactivation at 50°C as well as cross-resistance to inactivation at pH 3; however, growth rates and lag times at 43°C and at pH 4.5 were not affected. The exposure to pH 5 only caused up-regulation of 12 genes and this response was neither hysteretic nor accompanied of increased resistance to inactivation conditions. Cellular memory at the transcriptional level may represent a mechanism of adaptation to the environment and a deterministic source of variability in gene regulation. PMID:23236453

  18. Comparative Analyses of the Lipooligosaccharides from Nontypeable Haemophilus influenzae and Haemophilus haemolyticus Show Differences in Sialic Acid and Phosphorylcholine Modifications

    PubMed Central

    Post, Deborah M. B.; Ketterer, Margaret R.; Coffin, Jeremy E.; Reinders, Lorri M.; Munson, Robert S.; Bair, Thomas; Murphy, Timothy F.; Foster, Eric D.; Gibson, Bradford W.

    2016-01-01

    Haemophilus haemolyticus and nontypeable Haemophilus influenzae (NTHi) are closely related upper airway commensal bacteria that are difficult to distinguish phenotypically. NTHi causes upper and lower airway tract infections in individuals with compromised airways, while H. haemolyticus rarely causes such infections. The lipooligosaccharide (LOS) is an outer membrane component of both species and plays a role in NTHi pathogenesis. In this study, comparative analyses of the LOS structures and corresponding biosynthesis genes were performed. Mass spectrometric and immunochemical analyses showed that NTHi LOS contained terminal sialic acid more frequently and to a higher extent than H. haemolyticus LOS did. Genomic analyses of 10 strains demonstrated that H. haemolyticus lacked the sialyltransferase genes lic3A and lic3B (9/10) and siaA (10/10), but all strains contained the sialic acid uptake genes siaP and siaT (10/10). However, isothermal titration calorimetry analyses of SiaP from two H. haemolyticus strains showed a 3.4- to 7.3-fold lower affinity for sialic acid compared to that of NTHi SiaP. Additionally, mass spectrometric and immunochemical analyses showed that the LOS from H. haemolyticus contained phosphorylcholine (ChoP) less frequently than the LOS from NTHi strains. These differences observed in the levels of sialic acid and ChoP incorporation in the LOS structures from H. haemolyticus and NTHi may explain some of the differences in their propensities to cause disease. PMID:26729761

  19. Comparative Analyses of the Lipooligosaccharides from Nontypeable Haemophilus influenzae and Haemophilus haemolyticus Show Differences in Sialic Acid and Phosphorylcholine Modifications.

    PubMed

    Post, Deborah M B; Ketterer, Margaret R; Coffin, Jeremy E; Reinders, Lorri M; Munson, Robert S; Bair, Thomas; Murphy, Timothy F; Foster, Eric D; Gibson, Bradford W; Apicella, Michael A

    2016-01-04

    Haemophilus haemolyticus and nontypeable Haemophilus influenzae (NTHi) are closely related upper airway commensal bacteria that are difficult to distinguish phenotypically. NTHi causes upper and lower airway tract infections in individuals with compromised airways, while H. haemolyticus rarely causes such infections. The lipooligosaccharide (LOS) is an outer membrane component of both species and plays a role in NTHi pathogenesis. In this study, comparative analyses of the LOS structures and corresponding biosynthesis genes were performed. Mass spectrometric and immunochemical analyses showed that NTHi LOS contained terminal sialic acid more frequently and to a higher extent than H. haemolyticus LOS did. Genomic analyses of 10 strains demonstrated that H. haemolyticus lacked the sialyltransferase genes lic3A and lic3B (9/10) and siaA (10/10), but all strains contained the sialic acid uptake genes siaP and siaT (10/10). However, isothermal titration calorimetry analyses of SiaP from two H. haemolyticus strains showed a 3.4- to 7.3-fold lower affinity for sialic acid compared to that of NTHi SiaP. Additionally, mass spectrometric and immunochemical analyses showed that the LOS from H. haemolyticus contained phosphorylcholine (ChoP) less frequently than the LOS from NTHi strains. These differences observed in the levels of sialic acid and ChoP incorporation in the LOS structures from H. haemolyticus and NTHi may explain some of the differences in their propensities to cause disease.

  20. Ion-exchange chromatographic analysis of peroxynitric acid.

    PubMed

    Nakashima, Yoichi; Ikawa, Satoshi; Tani, Atsushi; Kitano, Katsuhisa

    2016-01-29

    Ion-exchange chromatographic analysis of peroxynitric acid (O2NOOH) was performed by combining an acidic eluate with an UV-vis detector and immersing the separation column in an ice-water bath. The decomposition behavior of peroxynitric acid in the solution was also studied using this system. The fraction for the peroxynitric acid peak was collected. Ion-exchange chromatographic analysis of this fraction, after standing at room temperature for 24h, showed that the decomposition products were mainly nitrate ions with a very small amount of nitrous acid. The peroxynitric acid peak area correlated perfectly with the total amount of decomposition products. The ion-exchange chromatographic isolation allowed us to evaluate the molar extinction coefficient of peroxynitric acid precisely in a wider wavelength range than previous reports. The value decreases monotonically from 1729±26M(-1)cm(-1) at 200nm to 12.0±0.5M(-1)cm(-1) at 290nm.

  1. Applications of cellular fatty acid analysis.

    PubMed Central

    Welch, D F

    1991-01-01

    More than ever, new technology is having an impact on the tools of clinical microbiologists. The analysis of cellular fatty acids by gas-liquid chromatography (GLC) has become markedly more practical with the advent of the fused-silica capillary column, computer-controlled chromatography and data analysis, simplified sample preparation, and a commercially available GLC system dedicated to microbiological applications. Experience with applications in diagnostic microbiology ranges from substantial success in work with mycobacteria, legionellae, and nonfermentative gram-negative bacilli to minimal involvement with fungi and other nonbacterial agents. GLC is a good alternative to other means for the identification of mycobacteria or legionellae because it is rapid, specific, and independent of other specialized testing, e.g., DNA hybridization. Nonfermenters show features in their cellular fatty acid content that are useful in identifying species and, in some cases, subspecies. Less frequently encountered nonfermenters, including those belonging to unclassified groups, can ideally be characterized by GLC. Information is just beginning to materialize on the usefulness of cellular fatty acids for the identification of gram-positive bacteria and anaerobes, despite the traditional role of GLC in detecting metabolic products as an aid to identification of anaerobes. When species identification of coagulase-negative staphylococci is called for, GLC may offer an alternative to biochemical testing. Methods for direct analysis of clinical material have been developed, but in practical and economic terms they are not yet ready for use in the clinical laboratory. Direct analysis holds promise for detecting markers of infection due to an uncultivable agent or in clinical specimens that presently require cultures and prolonged incubation to yield an etiologic agent. PMID:1747860

  2. Amino acid isotopic analysis in agricultural systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A relatively new approach to stable isotopic analysis—referred to as compound-specific isotopic analysis (CSIA)—has emerged, centering on the measurement of 15N:14N ratios in amino acids (glutamic acid and phenylalanine). CSIA has recently been used to generate trophic position estimates among anima...

  3. Principal component analysis of phenolic acid spectra

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenolic acids are common plant metabolites that exhibit bioactive properties and have applications in functional food and animal feed formulations. The ultraviolet (UV) and infrared (IR) spectra of four closely related phenolic acid structures were evaluated by principal component analysis (PCA) to...

  4. Boric Acid in Kjeldahl Analysis

    ERIC Educational Resources Information Center

    Cruz, Gregorio

    2013-01-01

    The use of boric acid in the Kjeldahl determination of nitrogen is a variant of the original method widely applied in many laboratories all over the world. Its use is recommended by control organizations such as ISO, IDF, and EPA because it yields reliable and accurate results. However, the chemical principles the method is based on are not…

  5. Phytic Acid and Sodium Chloride Show Marked Synergistic Bactericidal Effects against Nonadapted and Acid-Adapted Escherichia coli O157:H7 Strains

    PubMed Central

    Kim, Nam Hee

    2015-01-01

    The synergistic antimicrobial effects of phytic acid (PA), a natural extract from rice bran, plus sodium chloride against Escherichia coli O157:H7 were examined. Exposure to NaCl alone at concentrations up to 36% (wt/wt) for 5 min did not reduce bacterial populations. The bactericidal effects of PA alone were much greater than those of other organic acids (acetic, citric, lactic, and malic acids) under the same experimental conditions (P < 0.05). Combining PA and NaCl under conditions that yielded negligible effects when each was used alone led to marked synergistic effects. For example, whereas 0.4% PA or 3 or 4% NaCl alone had little or no effect on cell viability, combining the two completely inactivated both nonadapted and acid-adapted cells, reducing their numbers to unrecoverable levels (>7-log CFU/ml reduction). Flow cytometry confirmed that PA disrupted the cell membrane to a greater extent than did other organic acids, although the cells remained viable. The combination of PA and NaCl induced complete disintegration of the cell membrane. By comparison, none of the other organic acids acted synergistically with NaCl, and neither did NaCl-HCl solutions at the same pH values as the test solutions of PA plus NaCl. These results suggest that PA has great potential as an effective bacterial membrane-permeabilizing agent, and we show that the combination is a promising alternative to conventional chemical disinfectants. These findings provide new insight into the utility of natural compounds as novel antimicrobial agents and increase our understanding of the mechanisms underlying the antibacterial activity of PA. PMID:26637600

  6. Phytic Acid and Sodium Chloride Show Marked Synergistic Bactericidal Effects against Nonadapted and Acid-Adapted Escherichia coli O157:H7 Strains.

    PubMed

    Kim, Nam Hee; Rhee, Min Suk

    2015-12-04

    The synergistic antimicrobial effects of phytic acid (PA), a natural extract from rice bran, plus sodium chloride against Escherichia coli O157:H7 were examined. Exposure to NaCl alone at concentrations up to 36% (wt/wt) for 5 min did not reduce bacterial populations. The bactericidal effects of PA alone were much greater than those of other organic acids (acetic, citric, lactic, and malic acids) under the same experimental conditions (P < 0.05). Combining PA and NaCl under conditions that yielded negligible effects when each was used alone led to marked synergistic effects. For example, whereas 0.4% PA or 3 or 4% NaCl alone had little or no effect on cell viability, combining the two completely inactivated both nonadapted and acid-adapted cells, reducing their numbers to unrecoverable levels (>7-log CFU/ml reduction). Flow cytometry confirmed that PA disrupted the cell membrane to a greater extent than did other organic acids, although the cells remained viable. The combination of PA and NaCl induced complete disintegration of the cell membrane. By comparison, none of the other organic acids acted synergistically with NaCl, and neither did NaCl-HCl solutions at the same pH values as the test solutions of PA plus NaCl. These results suggest that PA has great potential as an effective bacterial membrane-permeabilizing agent, and we show that the combination is a promising alternative to conventional chemical disinfectants. These findings provide new insight into the utility of natural compounds as novel antimicrobial agents and increase our understanding of the mechanisms underlying the antibacterial activity of PA.

  7. Functional analysis of rat acidic calponin.

    PubMed

    Fujii, Toshihiro; Yabe, Sachiko; Nakamura, Kouta; Koizumi, Youichi

    2002-05-01

    Recombinant acidic calponin, a member of the calponin family, interacted with F-actin, but not with microtubules, desmin filaments, tropomyosin, calmodulin, S100 and phosphatidylserine (PS) vesicles with significant affinity. The bindings of acidic calponin to F-actin occurred in a concentration-dependent manner and were saturated at a molar ratio of about 1 acidic calponin to 1-2 actin molecules. The apparent Kd value of acidic calponin to F-actin was calculated to be 1.6 x 10(5) M(-1). Chemical cross-linking experiments indicated that a 1:1 molar covalent complex of acidic calponin and actin monomer was produced as in the case of basic calponinactin binding. No significant morphologic change of F-actin was observed by the addition of acidic calponin. Acidic calponin had little effect on actomyosin Mg2+-ATPase activity unlike basic calponin. Basic calponin partially competed with acidic calponin for binding to F-actin. Domain mapping with V8 protease revealed that acidic calponin binding site resided within the C-terminal 16 kDa fragment of actin, where the binding of basic calponin also occurs. However, both calponins showed reversal effects on fluorescence intensity of pyrene-labeled F-actin. Fragments of acidic calponin with 30 and 22 kDa, lacking the C-terminal acidic tail, were bound to F-actin. Interestingly, both the fragments became bound to PS vesicles, but not to other components. Circular dichroism studies showed that limited digestion of acidic calponin resulted in about 30% decrease of alpha-helix and beta contents. The present results suggest that acidic calponin is functionally distinct from basic calponin and expresses a novel characteristic after removal of the acidic tail region.

  8. Mice overexpressing 70-kDa heat shock protein show increased resistance to malonate and 3-nitropropionic acid.

    PubMed

    Dedeoglu, Alpaslan; Ferrante, Robert J; Andreassen, Ole A; Dillmann, Wolfgang H; Beal, M Flint

    2002-07-01

    Heat shock proteins (HSPs) are induced in response to oxidative stress, hypoxia-ischemia, and neuronal injury and play a protective role. Malonate and 3-nitropropionic acid (3-NP) are well-characterized animal models of Huntington's Disease (HD). They inhibit succinate dehydrogenase, inducing mitochondrial dysfunction, which triggers the generation of superoxide radicals, secondary excitotoxicity, and apoptosis. In this study, we examined whether the 70-kDa heat shock protein (HSP-70) is protective against neurotoxicity induced by malonate and 3-NP. Homozygous and heterozygous HSP-70 overexpressing mice (HSP-70+/+, HSP-70+/-) and wild-type controls received 3-NP or malonate and striatal lesion sizes were evaluated by stereology. Compared to HSP-70+/+ and HSP-70+/-, wild-type controls showed significantly larger striatal lesions following 3-NP or malonate injections. These findings support the idea that HSP-70 has a neuroprotective role that may be useful in the treatment of neurodegenerative diseases.

  9. Mixed species biofilms of Listeria monocytogenes and Lactobacillus plantarum show enhanced resistance to benzalkonium chloride and peracetic acid.

    PubMed

    van der Veen, Stijn; Abee, Tjakko

    2011-01-05

    We investigated the formation of single and mixed species biofilms of Listeria monocytogenes strains EGD-e and LR-991, with Lactobacillus plantarum WCFS1 as secondary species, and their resistance to the disinfectants benzalkonium chloride and peracetic acid. Modulation of growth, biofilm formation, and biofilm composition was achieved by addition of manganese sulfate and/or glucose to the BHI medium. Composition analyses of the mixed species biofilms using plate counts and fluorescence microscopy with dual fluorophores showed that mixed species biofilms were formed in BHI (total count, 8-9 log₁₀ cfu/well) and that they contained 1-2 log₁₀ cfu/well more L. monocytogenes than L. plantarum cells. Addition of manganese sulfate resulted in equal numbers of both species (total count, 8 log₁₀ cfu/well) in the mixed species biofilm, while manganese sulfate in combination with glucose, resulted in 1-2 log₁₀ more L. plantarum than L. monocytogenes cells (total count, 9 log₁₀ cfu/well). Corresponding single species biofilms of L. monocytogenes and L. plantarum contained up to 9 log₁₀ cfu/well. Subsequent disinfection treatments showed mixed species biofilms to be more resistant to treatments with the selected disinfectants. In BHI with additional manganese sulfate, both L. monocytogenes strains and L. plantarum grown in the mixed species biofilm showed less than 2 log₁₀ cfu/well inactivation after exposure for 15 min to 100 μg/ml benzalkonium chloride, while single species biofilms of both L. monocytogenes strains showed 4.5 log₁₀ cfu/well inactivation and single species biofilms of L. plantarum showed 3.3 log₁₀ cfu/well inactivation. Our results indicate that L. monocytogenes and L. plantarum mixed species biofilms can be more resistant to disinfection treatments than single species biofilms.

  10. Ultrastructural analysis of an enterolith composed of deoxycholic acid.

    PubMed

    Iwamuro, Masaya; Miyashima, Yuichi; Yoshioka, Takahiro; Murata, Toshihiro; Miyabe, Yoshio; Kawai, Yoshinari; Urata, Haruo; Shiraha, Hidenori; Okada, Hiroyuki; Yamamoto, Kazuhide

    2014-12-01

    A 67-year-old Japanese man underwent enterotomy because of enterolith ileus. Component analysis by infrared spectroscopy revealed that the enterolith was composed of a high concentration of deoxycholic acid. We further analyzed and compared the ultrastructure of the enterolith and a commercially available powdered form of deoxycholic acid by means of scanning electron microscopy and energy dispersive X-ray spectroscopy. Energy dispersive X-ray spectroscopy analysis revealed that the ratios of carbon and oxygen in the enterolith were equal to those in the deoxycholic acid powder. Scanning electron microscopy analysis showed rectangular prism-shaped particles on the surface of the enterolith. This structure was similar to that of the deoxycholic acid powder. The surgically removed enterolith had a twisted and coiled appearance. Possible mechanisms underlying the formation of this unique form are discussed.

  11. Analysis of Chiral Carboxylic Acids in Meteorites

    NASA Technical Reports Server (NTRS)

    Burton, A. S.; Elsila, J. E.; Hein, J. E.; Aponte, J. C.; Parker, E. T.; Glavin, D. P.; Dworkin, J. P.

    2015-01-01

    our efforts to develop highly sensitive LC-MS methods for the analysis of chiral carboxylic acids including hydroxy acids.

  12. Amino acid analysis for pharmacopoeial purposes.

    PubMed

    Wahl, Oliver; Holzgrabe, Ulrike

    2016-07-01

    The impurity profile of amino acids depends strongly on the production process. Since there are many different production methods (e.g. fermentation, protein hydrolysis or chemical synthesis) universal, state of the art methods are required to determine the impurity profile of amino acids produced by all relevant competitors. At the moment TLC tests provided by the Ph. Eur. are being replaced by a very specific amino acid analysis procedure possibly missing out on currently unknown process related impurities. Production methods and possible impurities as well as separation and detection methods suitable for said impurities are subject to this review.

  13. Novel biodegradable poly(gamma-glutamic acid)-amphotericin B complexes show promise as improved amphotericin B formulations.

    PubMed

    Dinh, T; Zia, Q; Zubair, S; Stapleton, P; Singh, R; Owais, M; Somavarapu, S

    2017-02-16

    Commercially available amphotericin B (AmB) formulations are limited by cytotoxicities, lower efficacies, shelf-life related issues or high production costs. AmB complexes based on poly(gamma-glutamic acid) (PGGA) have been prepared and evaluated for their efficacies against AmB-deoxycholate (Fungizone®) and liposomal AmB (AmBisome®). Physical characterizations showed that AmB/PGGA complexes are nanoscopic (20-40 nm) with a negative zeta potential (-51.0 mV), water-soluble, stable in solution (up to 4 weeks, at 4 °C and 25 °C), and have a theoretical drug loading (up to 76.9%). In vitro, AmB/PGGA complexes exhibited an improved and comparable cytotoxicity profile as compared with Fungizone® and AmBisome® respectively, with respect to hemolytic activity and up-regulation of cytokine productions (TNF-α and IL-1ß). AmB/PGGA complexes were significantly more efficacious in vivo than both Fungizone® and AmBisome® in experimental murine candidiasis. These results provide strong evidence that AmB/PGGA complexes have a better efficacy and safety profile than the currently approved AmB products.

  14. Spermatozoa bound to solid state hyaluronic acid show chromatin structure with high DNA chain integrity: an acridine orange fluorescence study.

    PubMed

    Yagci, Artay; Murk, William; Stronk, Jill; Huszar, Gabor

    2010-01-01

    During human spermiogenesis, the elongated spermatids undergo a plasma membrane remodeling step that facilitates formation of the zona pellucida and hyaluronic acid (HA) binding sites. Various biochemical sperm markers indicated that human sperm bound to HA exhibit attributes similar to that of zona pellucida-bound sperm, including minimal DNA fragmentation, normal shape, and low frequency of chromosomal aneuploidies. In this work, we tested the hypothesis that HA-bound sperm would be enhanced in sperm of high DNA chain integrity and green acridine orange fluorescence (AOF) compared with the original sperm in semen. Sperm DNA integrity in semen and in their respective HA-bound sperm fractions was studied in 50 men tested for fertility. In the semen samples, the proportions of sperm with green AOF (high DNA integrity) and red AOF (DNA breaks) were 54.9% ± 2.0% and 45.0% ± 1.9%, whereas in the HA-bound sperm fraction, the respective proportions were 99% and 1.0%, respectively. The data indeed demonstrated that HA shows a high degree of selectivity for sperm with high DNA integrity. These findings are important from the points of view of human sperm DNA integrity, sperm function, and the potential efficacy of HA-mediated sperm selection for intracytoplasmic sperm injection.

  15. Analysis of amino acids by miniaturised isotachophoresis.

    PubMed

    Prest, Jeff E; Baldock, Sara J; Fielden, Peter R; Goddard, Nicholas J; Brown, Bernard J Treves

    2004-10-08

    A method allowing the miniaturised isotachophoretic analysis of amino acids has been developed. To overcome the problems of carbonate contamination which occur when performing separations at alkaline pH levels glycolate was used as the leading ion. Addition of magnesium to the leading electrolyte as a counter species was found to improve the separations. The method has been used on a poly(methyl methacrylate) microdevice with integrated on-column conductivity detectors. The behaviour of a range of common amino acids was investigated and successful separations of up to seven amino acids were made. Good linearity was observed with calibration curves for aspartic acid and phenylalanine over the range 0.063-1.0 mM. Limits of detection for these two species were calculated to be 0.060 and 0.018 mM, respectively.

  16. Vibrational analysis of α-cyanohydroxycinnamic acid

    NASA Astrophysics Data System (ADS)

    Mojica, Elmer-Rico E.; Vedad, Jayson; Desamero, Ruel Z. B.

    2015-08-01

    In the present study, a comparative Raman vibrational analysis of alpha-cyano-4-hydroxycinnamic acid (4CHCA) and its derivative, alpha-cyano-3-hydroxycinnamic acid (3CHCA), was performed. The Raman spectra of the 4CHCA and 3CHCA in solid form were obtained and analyzed to determine differences between the two structurally similar derivatives. For comparison, the CHCA derivatives cyanocinnamic acid (CCA) and coumaric acid (CA) were also studied. The plausible vibrational assignments were made and matched with those obtained theoretically using density functional theory (DFT) based method employing a 6-31 g basis set. The computational wavenumbers obtained were in good agreement with the observed experimental results. This was the first reported Raman study of CCA, 3CHCA and 4CHCA.

  17. Novel biochip platform for nucleic acid analysis.

    PubMed

    Pernagallo, Salvatore; Ventimiglia, Giorgio; Cavalluzzo, Claudia; Alessi, Enrico; Ilyine, Hugh; Bradley, Mark; Diaz-Mochon, Juan J

    2012-01-01

    This manuscript describes the use of a novel biochip platform for the rapid analysis/identification of nucleic acids, including DNA and microRNAs, with very high specificity. This approach combines a unique dynamic chemistry approach for nucleic acid testing and analysis developed by DestiNA Genomics with the STMicroelectronics In-Check platform, which comprises two microfluidic optimized and independent PCR reaction chambers, and a sequential microarray area for nucleic acid capture and identification by fluorescence. With its compact bench-top "footprint" requiring only a single technician to operate, the biochip system promises to transform and expand routine clinical diagnostic testing and screening for genetic diseases, cancers, drug toxicology and heart disease, as well as employment in the emerging companion diagnostics market.

  18. AMS 14C analysis of teeth from archaeological sites showing anomalous esr dating results

    NASA Astrophysics Data System (ADS)

    Grün, Rainer; Abeyratne, Mohan; Head, John; Tuniz, Claudio; Hedges, Robert E. M.

    We have carried out AMS radiocarbon analysis on two groups of samples: the first one gave reasonable ESR age estimates and the second one yielded serious age underestinations. All samples were supposedly older than 35 ka, the oldest being around 160 ka. Two pretreatment techniques were used for radiocarbon dating: acid evolution and thermal release. Heating to 600, 750 and 900°C combined with total de-gassing at these temperatures was chosen to obtain age estimates on the organic fraction, secondary carbonates and original carbonate present in the hydroxyapatite mineral phase, respectively. All radiocarbon results present serious age underestimations. The secondary carbonate fraction gives almost modern results indicating an extremely rapid exchange of this component. Owing to this very rapid carbonate exchange it is not likely that the ESR signals used for dating are associated with the secondary carbonates. One tooth from Tabun with independent age estimates of >150 ka was further investigated by the Oxford AMS laboratory, yielding an age estimate of 1930±100 BP on the residual collagen from dentine and 18,000±160 BP on the carbonate component of the enamel bioapatite. We did not, however, find an explanation of why some samples give serious ESR underestimatioils whilst many others provide reasonable results.

  19. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic.

    PubMed

    Storfer, Andrew; Alfaro, Michael E; Ridenhour, Benjamin J; Jancovich, James K; Mech, Stephen G; Parris, Matthew J; Collins, James P

    2007-11-01

    Distinguishing whether pathogens are novel or endemic is critical for controlling emerging infectious diseases, an increasing threat to wildlife and human health. To test the endemic vs. novel pathogen hypothesis, we present a unique analysis of intraspecific host-pathogen phylogenetic concordance of tiger salamanders and an emerging Ranavirus throughout Western North America. There is significant non-concordance of host and virus gene trees, suggesting pathogen novelty. However, non-concordance has likely resulted from virus introductions by human movement of infected salamanders. When human-associated viral introductions are excluded, host and virus gene trees are identical, strongly supporting coevolution and endemism. A laboratory experiment showed an introduced virus strain is significantly more virulent than endemic strains, likely due to artificial selection for high virulence. Thus, our analysis of intraspecific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection.

  20. Analysis of competition performance in dressage and show jumping of Dutch Warmblood horses.

    PubMed

    Rovere, G; Ducro, B J; van Arendonk, J A M; Norberg, E; Madsen, P

    2016-12-01

    Most Warmblood horse studbooks aim to improve the performance in dressage and show jumping. The Dutch Royal Warmblood Studbook (KWPN) includes the highest score achieved in competition by a horse to evaluate its genetic ability of performance. However, the records collected during competition are associated with some aspects that might affect the quality of the genetic evaluation based on these records. These aspects include the influence of rider, censoring and preselection of the data. The aim of this study was to quantify the impact of rider effect, censoring and preselection on the genetic analysis of competition data of dressage and show jumping of KWPN. Different models including rider effect were evaluated. To assess the impact of censoring, genetic parameters were estimated in data sets that differed in the degree of censoring. The effect of preselection on variance components was analysed by defining a binary trait (sport-status) depending on whether the horse has a competition record or not. This trait was included in a bivariate model with the competition trait and used all horses registered by KWPN since 1984. Results showed that performance in competition for dressage and show jumping is a heritable trait (h(2) ~ 0.11-0.13) and that it is important to account for the effect of rider in the genetic analysis. Censoring had a small effect on the genetic parameter for highest performance achieved by the horse. A moderate heritability obtained for sport-status indicates that preselection has a genetic basis, but the effect on genetic parameters was relatively small.

  1. Network Analysis Shows Novel Molecular Mechanisms of Action for Copper-Based Chemotherapy

    PubMed Central

    Espinal-Enríquez, Jesús; Hernández-Lemus, Enrique; Mejía, Carmen; Ruiz-Azuara, Lena

    2016-01-01

    The understanding of the mechanisms associated with the action of chemotherapeutic agents is fundamental to assess and account for possible side-effects of such treatments. Casiopeínas have demonstrated a cytotoxic effect by activation of pro-apoptotic processes in malignant cells. Such processes have been proved to activate the apoptotic intrinsic route, as well as cell cycle arrest. Despite this knowledge, the whole mechanism of action of Casiopeínas is yet to be completely understood. In this work we implement a systems biology approach based on two pathway analysis tools (Over-Representation Analysis and Causal Network Analysis) to observe changes in some hallmarks of cancer, induced by this copper-based chemotherapeutic agent in HeLa cell lines. We find that the metabolism of metal ions is exacerbated, as well as cell division processes being globally diminished. We also show that cellular migration and proliferation events are decreased. Moreover, the molecular mechanisms of liver protection are increased in the cell cultures under the actions of Casiopeínas, unlike the case in many other cytotoxic drugs. We argue that this chemotherapeutic agent may be promising, given its protective hepatic function, concomitant with its cytotoxic participation in the onset of apoptotic processes in malignant cells. PMID:26793116

  2. Imidazopyridine-Based Fatty Acid Synthase Inhibitors That Show Anti-HCV Activity and in Vivo Target Modulation

    PubMed Central

    2012-01-01

    Potent imidazopyridine-based inhibitors of fatty acid synthase (FASN) are described. The compounds are shown to have antiviral (HCV replicon) activities that track with their biochemical activities. The most potent analogue (compound 19) also inhibits rat FASN and inhibits de novo palmitate synthesis in vitro (cell-based) as well as in vivo. PMID:24900571

  3. Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis.

    PubMed

    Dunlap, Christopher A

    2015-10-01

    ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.

  4. Kranz and single-cell forms of C4 plants in the subfamily Suaedoideae show kinetic C4 convergence for PEPC and Rubisco with divergent amino acid substitutions

    PubMed Central

    Rosnow, Josh J.; Evans, Marc A.; Kapralov, Maxim V.; Cousins, Asaph B.; Edwards, Gerald E.; Roalson, Eric H.

    2015-01-01

    The two carboxylation reactions performed by phosphoenolpyruvate carboxylase (PEPC) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are vital in the fixation of inorganic carbon for C4 plants. The abundance of PEPC is substantially elevated in C4 leaves, while the location of Rubisco is restricted to one of two chloroplast types. These differences compared with C3 leaves have been shown to result in convergent enzyme optimization in some C4 species. Investigation into the kinetic properties of PEPC and Rubisco from Kranz C4, single cell C4, and C3 species in Chenopodiaceae s. s. subfamily Suaedoideae showed that these major carboxylases in C4 Suaedoideae species lack the same mutations found in other C4 systems which have been examined; but still have similar convergent kinetic properties. Positive selection analysis on the N-terminus of PEPC identified residues 364 and 368 to be under positive selection with a posterior probability >0.99 using Bayes empirical Bayes. Compared with previous analyses on other C4 species, PEPC from C4 Suaedoideae species have different convergent amino acids that result in a higher K m for PEP and malate tolerance compared with C3 species. Kinetic analysis of Rubisco showed that C4 species have a higher catalytic efficiency of Rubisco (k catc in mol CO2 mol–1 Rubisco active sites s–1), despite lacking convergent substitutions in the rbcL gene. The importance of kinetic changes to the two-carboxylation reactions in C4 leaves related to amino acid selection is discussed. PMID:26417023

  5. HIV-1 Phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues

    PubMed Central

    Lamers, Susanna L.; Gray, Rebecca R.; Salemi, Marco; Huysentruyt, Leanne C.; McGrath, Michael

    2010-01-01

    Brain infection by the human immunodeficiency virus type 1 (HIV-1) has been investigated in many reports with a variety of conclusions concerning the time of entry and degree of viral compartmentalization. To address these diverse findings, we sequenced HIV-1 gp120 clones from a wide range of brain, peripheral and meningeal tissues from five patients who died from several HIV-1 associated disease pathologies. High-resolution phylogenetic analysis confirmed previous studies that showed a significant degree of compartmentalization in brain and peripheral tissue subpopulations. Some intermixing between the HIV-1 subpopulations was evident, especially in patients that died from pathologies other than HIV-associated dementia. Interestingly, the major tissue harboring virus from both the brain and peripheral tissues was the meninges. These results show that 1) HIV-1 is clearly capable of migrating out of the brain, 2) the meninges are the most likely primary transport tissues, and 3) infected brain macrophages comprise an important HIV reservoir during highly active antiretroviral therapy. PMID:21055482

  6. Chemical mutagenesis of Gluconobacter frateurii to construct methanol-resistant mutants showing glyceric acid production from methanol-containing glycerol.

    PubMed

    Sato, Shun; Kitamoto, Dai; Habe, Hiroshi

    2014-02-01

    To produce glyceric acid (GA) from methanol-containing glycerol, resistance to methanol of Gluconobacter frateurii NBRC103465 was improved by chemical mutagenesis using N-methyl-N'-nitro-N-nitrosoguanidine. The obtained mutant Gf398 produced 6.3 g/L GA in 5% (v/v) methanol-containing 17% (w/v) glycerol medium, in which the wild-type strain neither grew nor produced GA.

  7. Rearing conditions affected responses of weaned pigs to organic acids showing a positive effect on digestibility, microflora and immunity.

    PubMed

    Wang, Yu; Kuang, Yiwen; Zhang, Yalin; Song, Yumo; Zhang, Xiaoling; Lin, Yan; Che, Lianqiang; Xu, Shengyu; Wu, De; Xue, Bai; Fang, Zhengfeng

    2016-10-01

    Three experiments were conducted to assess the response of weaned pigs to organic acid SF3, which contains 34% calcium formate, 16% calcium lactate, 7% citric acid and 13% medium chain fatty acids. Dietary treatments had no effect on growth performance of piglets (21-day weaning) fed the commercial prestart diet for 1 week before receiving the experimental diets supplemented with SF3 at 0, 3 or 5 g/kg diet (Exp. 1), whereas diarrhea frequency averaged across a week was decreased by SF3 supplementation (5 g/kg diet) in piglets fed the experimental diets immediately after weaning (Exp. 2). In Exp. 3, piglets (28-day weaning) were fed the control (containing pure colistin sulfate and enramycin, respectively, at 20 mg/kg diet) for 1 week and then were fed the control or SF3-supplemented (5 g/kg diet) diet for 2 weeks. The SF3-fed piglets had greater apparent ileal digestibility of calcium and dry matter, while also demonstrating greater overall gross energy, up-regulated jejunal expression of sodium-glucose cotransporter-1 and transforming growth factor-β, down-regulated jejunal expression of tumor necrosis factor (TNF)-α, higher ileal Lactobacillus, with lower total bacteria content, lower plasma TNF-α but higher IgG levels than the control-fed piglets. Collectively, SF3 consumption improved diarrhea resistance of weaned pigs by improving nutrient digestibility, piglet immunity and intestinal bacteria profile. © 2016 Japanese Society of Animal Science.

  8. Proximate composition, fatty acid analysis and protein digestibility-corrected amino acid score of three Mediterranean cephalopods.

    PubMed

    Zlatanos, Spiros; Laskaridis, Kostas; Feist, Christian; Sagredos, Angelos

    2006-10-01

    Proximate composition, fatty acid analysis and protein digestibility-corrected amino acid score (PDCAAS) in three commercially important cephalopods of the Mediterranean sea (cuttlefish, octopus and squid) were determined. The results of the proximate analysis showed that these species had very high protein:fat ratios similar to lean beef. Docosahexaenoic, palmitic and eicosipentaenoic acid were the most abundant fatty acids among analyzed species. The amount of n-3 fatty acids was higher than that of saturated, monounsaturated and n-6 fatty acids. Despite the fact that cephalopods contain small amounts of fat they were found quite rich in n-3 fatty acids. Finally, PDCAAS indicated that these organisms had a very good protein quality.

  9. Cooperative Genome-Wide Analysis Shows Increased Homozygosity in Early Onset Parkinson's Disease

    PubMed Central

    Nalls, Michael A.; Martinez, Maria; Schulte, Claudia; Holmans, Peter; Gasser, Thomas; Hardy, John; Singleton, Andrew B.; Wood, Nicholas W.; Brice, Alexis; Heutink, Peter; Williams, Nigel; Morris, Huw R.

    2012-01-01

    Parkinson's disease (PD) occurs in both familial and sporadic forms, and both monogenic and complex genetic factors have been identified. Early onset PD (EOPD) is particularly associated with autosomal recessive (AR) mutations, and three genes, PARK2, PARK7 and PINK1, have been found to carry mutations leading to AR disease. Since mutations in these genes account for less than 10% of EOPD patients, we hypothesized that further recessive genetic factors are involved in this disorder, which may appear in extended runs of homozygosity. We carried out genome wide SNP genotyping to look for extended runs of homozygosity (ROHs) in 1,445 EOPD cases and 6,987 controls. Logistic regression analyses showed an increased level of genomic homozygosity in EOPD cases compared to controls. These differences are larger for ROH of 9 Mb and above, where there is a more than three-fold increase in the proportion of cases carrying a ROH. These differences are not explained by occult recessive mutations at existing loci. Controlling for genome wide homozygosity in logistic regression analyses increased the differences between cases and controls, indicating that in EOPD cases ROHs do not simply relate to genome wide measures of inbreeding. Homozygosity at a locus on chromosome19p13.3 was identified as being more common in EOPD cases as compared to controls. Sequencing analysis of genes and predicted transcripts within this locus failed to identify a novel mutation causing EOPD in our cohort. There is an increased rate of genome wide homozygosity in EOPD, as measured by an increase in ROHs. These ROHs are a signature of inbreeding and do not necessarily harbour disease-causing genetic variants. Although there might be other regions of interest apart from chromosome 19p13.3, we lack the power to detect them with this analysis. PMID:22427796

  10. Linkage analysis followed by association show NRG1 associated with cannabis dependence in African-Americans

    PubMed Central

    Han, Shizhong; Yang, Bao-Zhu; Kranzler, Henry R.; Oslin, David; Anton, Raymond; Farrer, Lindsay A.; Gelernter, Joel

    2013-01-01

    Background A genetic contribution to cannabis dependence (CaD) has been established, but susceptibility genes for CaD remain largely unknown. Methods We employed a multi-stage design to identify genetic variants underlying CaD. We first performed a genomewide linkage scan for CaD in 384 African-American (AA) and 354 European-American (EA) families ascertained for genetic studies of cocaine and opioid dependence. We then conducted association analysis under the linkage peak, first using data from a genomewide association study from the Study of Addiction: Genetics and Environment (SAGE), followed by replication studies of prioritized single nucleotide polymorphisms (SNPs) in independent samples. Results We identified the strongest linkage evidence with CaD (lod=2.9) on chromosome 8p21.1 in AAs. In the association analysis of the SAGE sample under the linkage peak, we identified one SNP (rs17664708) associated with CaD in both AAs (minor allele frequency (MAF) = 0.02, OR=2.93, 95% CI=1.47–5.85, P=0.0022) and EAs (MAF=0.096, OR=1.38, 95% CI=1.05–1.81, P=0.02). This SNP, located at NRG1, a susceptibility gene for schizophrenia, was prioritized for further study. We replicated the association of rs17664708 with CaD in an independent sample of AAs (MAF=0.013, OR=2.81, 95% CI=1.23–6.45, P=0.0068). The joint analysis of the two AA samples demonstrated highly significant association between rs17664708 and CaD with adjustment for either global (OR=2.34, 95% CI=1.42–3.85, P=0.00044) or local ancestry (OR=2.33, 95% CI=1.39–3.91, P=0.00075). Conclusions Our study shows that NRG1 is probably a susceptibility gene for CaD, based on convergent evidence of linkage and replicated associations in two independent AA samples. PMID:22520967

  11. Brain regions that show repetition suppression and enhancement: A meta-analysis of 137 neuroimaging experiments.

    PubMed

    Kim, Hongkeun

    2017-04-01

    Repetition suppression and enhancement refer to the reduction and increase in the neural responses for repeated rather than novel stimuli, respectively. This study provides a meta-analysis of the effects of repetition suppression and enhancement, restricting the data used to that involving fMRI/PET, visual stimulus presentation, and healthy participants. The major findings were as follows. First, the global topography of the repetition suppression effects was strikingly similar to that of the "subsequent memory" effects, indicating that the mechanism for repetition suppression is the reduced engagement of an encoding system. The lateral frontal cortex effects involved the frontoparietal control network regions anteriorly and the dorsal attention network regions posteriorly. The left fusiform cortex effects predominantly involved the dorsal attention network regions, whereas the right fusiform cortex effects mainly involved the visual network regions. Second, the category-specific meta-analyses and their comparisons indicated that most parts of the alleged category-specific regions showed repetition suppression for more than one stimulus category. In this regard, these regions may not be "dedicated cortical modules," but are more likely parts of multiple overlapping large-scale maps of simple features. Finally, the global topography of the repetition enhancement effects was similar to that of the "retrieval success" effects, suggesting that the mechanism for repetition enhancement is voluntary or involuntary explicit retrieval during an implicit memory task. Taken together, these results clarify the network affiliations of the regions showing reliable repetition suppression and enhancement effects and contribute to the theoretical interpretations of the local and global topography of these two effects. Hum Brain Mapp 38:1894-1913, 2017. © 2017 Wiley Periodicals, Inc.

  12. Mass cytometry analysis shows that a novel memory phenotype B cell is expanded in multiple myeloma

    PubMed Central

    Hansmann, Leo; Blum, Lisa; Ju, Chia-Hsin; Liedtke, Michaela; Robinson, William H.; Davis, Mark M.

    2015-01-01

    It would be very beneficial if the status of cancers could be determined from a blood specimen. However, peripheral blood leukocytes are very heterogeneous between individuals and thus high resolution technologies are likely required. We used cytometry by time-of-flight (CyTOF) and next generation sequencing to ask whether a plasma cell cancer (multiple myeloma) and related pre-cancerous states had any consistent effect on the peripheral blood mononuclear cell phenotypes of patients. Analysis of peripheral blood samples from 13 cancer patients, 9 pre-cancer patients, and 9 healthy individuals revealed significant differences in the frequencies of the T, B, and natural killer cell compartments. Most strikingly, we identified a novel B-cell population that normally accounts for 4.0±0.7% (mean±SD) of total B cells and is up to 13-fold expanded in multiple myeloma patients with active disease. This population expressed markers previously associated with both memory (CD27+) and naïve (CD24loCD38+) phenotypes. Single-cell immunoglobulin gene sequencing showed polyclonality, indicating that these cells are not precursors to the myeloma, and somatic mutations, a characteristic of memory cells. SYK, ERK, and p38 phosphorylation responses, and the fact that most of these cells expressed isotypes other than IgM or IgD, confirmed the memory character of this population, defining it as a novel type of memory B cells. PMID:25711758

  13. Proteomic analysis of rice leaves shows the different regulations to osmotic stress and stress signals.

    PubMed

    Shu, Lie-Bo; Ding, Wei; Wu, Jin-Hong; Feng, Fang-Jun; Luo, Li-Jun; Mei, Han-Wei

    2010-11-01

    Following the idea of partial root-zone drying (PRD) in crop cultivation, the morphological and physiological responses to partial root osmotic stress (PROS) and whole root osmotic stress (WROS) were investigated in rice. WROS caused stress symptoms like leaf rolling and membrane leakage. PROS stimulated stress signals, but did not cause severe leaf damage. By proteomic analysis, a total of 58 proteins showed differential expression after one or both treatments, and functional classification of these proteins suggests that stress signals regulate photosynthesis, carbohydrate and energy metabolism. Two other proteins (anthranilate synthase and submergence-induced nickel-binding protein) were upregulated only in the PROS plants, indicating their important roles in stress resistance. Additionally, more enzymes were involved in stress defense, redox homeostasis, lignin and ethylene synthesis in WROS leaves, suggesting a more comprehensive regulatory mechanism induced by osmotic stress. This study provides new insights into the complex molecular networks within plant leaves involved in the adaptation to osmotic stress and stress signals.

  14. Immobilized MAS1 lipase showed high esterification activity in the production of triacylglycerols with n-3 polyunsaturated fatty acids.

    PubMed

    Wang, Xiumei; Li, Daoming; Qu, Man; Durrani, Rabia; Yang, Bo; Wang, Yonghua

    2017-02-01

    Immobilization of lipase MAS1 from marine Streptomyces sp. strain W007 and its application in catalyzing esterification of n-3 polyunsaturated fatty acids (PUFA) with glycerol were investigated. The resin XAD1180 was selected as a suitable support for the immobilization of lipase MAS1, and its absorption ability was 75mg/g (lipase/resin ratio) with initial buffer pH value of 8.0. The thermal stability of immobilized MAS1 was improved significantly compared with that of the free lipase. Immobilized MAS1 had no regiospecificity in the hydrolysis of triolein. The highest esterification degree (99.31%) and TAG content (92.26%) by immobilized MAS1-catalyzed esterification were achieved under the optimized conditions, which were significantly better than those (82.16% and 47.26%, respectively) by Novozym 435. More than 92% n-3 PUFA was incorporated into TAG that had similar fatty acids composition to the substrate (n-3 PUFA). The immobilized MAS1 exhibited 50% of its initial activity after being used for five cycles.

  15. Two Theobroma cacao genotypes with contrasting pathogen tolerance show aberrant transcriptional and ROS responses after salicylic acid treatment.

    PubMed

    Fister, Andrew S; O'Neil, Shawn T; Shi, Zi; Zhang, Yufan; Tyler, Brett M; Guiltinan, Mark J; Maximova, Siela N

    2015-10-01

    Understanding the genetic basis of pathogen susceptibility in various crop plants is crucial to increasing the stability of food, feed, and fuel production. Varietal differences in defence responses provide insights into the mechanisms of resistance and are a key resource for plant breeders. To explore the role of salicylic acid in the regulation of defence in cacao, we demonstrated that SA treatment decreased susceptibility to a pod rot pathogen, Phytophthora tropicalis in two genotypes, Scavina 6 and Imperial College Selection 1, which differ in their resistance to several agriculturally important pathogens. Transient overexpression of TcNPR1, a major transcriptional regulator of the SA-dependent plant immune system, also increased pathogen tolerance in cacao leaves. To explore further the genetic basis of resistance in cacao, we used microarrays to measure gene expression profiles after salicylic acid (SA) treatment in these two cacao genotypes. The two genotypes displayed distinct transcriptional responses to SA. Unexpectedly, the expression profile of the susceptible genotype ICS1 included a larger number of pathogenesis-related genes that were induced by SA at 24h after treatment, whereas genes encoding many chloroplast and mitochondrial proteins implicated in reactive oxygen species production were up-regulated in the resistant genotype, Sca6. Sca6 accumulated significantly more superoxide at 24h after treatment of leaves with SA. These experiments revealed critical insights regarding the molecular differences between cacao varieties, which will allow a better understanding of defence mechanisms to help guide breeding programmes.

  16. Two Theobroma cacao genotypes with contrasting pathogen tolerance show aberrant transcriptional and ROS responses after salicylic acid treatment

    PubMed Central

    Fister, Andrew S.; O’Neil, Shawn T.; Shi, Zi; Zhang, Yufan; Tyler, Brett M.; Guiltinan, Mark J.; Maximova, Siela N.

    2015-01-01

    Understanding the genetic basis of pathogen susceptibility in various crop plants is crucial to increasing the stability of food, feed, and fuel production. Varietal differences in defence responses provide insights into the mechanisms of resistance and are a key resource for plant breeders. To explore the role of salicylic acid in the regulation of defence in cacao, we demonstrated that SA treatment decreased susceptibility to a pod rot pathogen, Phytophthora tropicalis in two genotypes, Scavina 6 and Imperial College Selection 1, which differ in their resistance to several agriculturally important pathogens. Transient overexpression of TcNPR1, a major transcriptional regulator of the SA-dependent plant immune system, also increased pathogen tolerance in cacao leaves. To explore further the genetic basis of resistance in cacao, we used microarrays to measure gene expression profiles after salicylic acid (SA) treatment in these two cacao genotypes. The two genotypes displayed distinct transcriptional responses to SA. Unexpectedly, the expression profile of the susceptible genotype ICS1 included a larger number of pathogenesis-related genes that were induced by SA at 24h after treatment, whereas genes encoding many chloroplast and mitochondrial proteins implicated in reactive oxygen species production were up-regulated in the resistant genotype, Sca6. Sca6 accumulated significantly more superoxide at 24h after treatment of leaves with SA. These experiments revealed critical insights regarding the molecular differences between cacao varieties, which will allow a better understanding of defence mechanisms to help guide breeding programmes. PMID:26163705

  17. Influences of acidic reaction and hydrolytic conditions on monosaccharide composition analysis of acidic, neutral and basic polysaccharides.

    PubMed

    Wang, Qing-Chi; Zhao, Xia; Pu, Jiang-Hua; Luan, Xiao-Hong

    2016-06-05

    Monosaccharide composition analysis is important for structural characterization of polysaccharides. To investigate the influences of acidic reaction and hydrolytic conditions on monosaccharide composition analysis of polysaccharides, we chose alginate, starch, chitosan and chondroitin sulfate as representative of acidic, neutral, basic and complex polysaccharides to compare the release degree of monosaccharides under different hydrolytic conditions. The hydrolysis stability of 10 monosaccharide standards was also explored. Results showed that the basic sugars were hard to release but stable, the acidic sugars (uronic acids) were easy to release but unstable, and the release and stability of neutral sugars were in between acidic and basic sugars. In addition, the hydrolysis process was applied to monosaccharide composition analysis of Hippocampus trimaculatus polysaccharide and the appropriate hydrolytic condition was accorded with that of the above four polysaccharides. Thus, different hydrolytic conditions should be used for the monosaccharide composition analysis of polysaccharides based on their structural characteristics.

  18. Arabidopsis AtDjA3 Null Mutant Shows Increased Sensitivity to Abscisic Acid, Salt, and Osmotic Stress in Germination and Post-germination Stages

    PubMed Central

    Salas-Muñoz, Silvia; Rodríguez-Hernández, Aída A.; Ortega-Amaro, Maria A.; Salazar-Badillo, Fatima B.; Jiménez-Bremont, Juan F.

    2016-01-01

    DnaJ proteins are essential co-chaperones involved in abiotic and biotic stress responses. Arabidopsis AtDjA3 gene encodes a molecular co-chaperone of 420 amino acids, which belongs to the J-protein family. In this study, we report the functional characterization of the AtDjA3 gene using the Arabidopsis knockout line designated j3 and the 35S::AtDjA3 overexpression lines. Loss of AtDjA3 function was associated with small seed production. In fact, j3 mutant seeds showed a reduction of 24% in seed weight compared to Col-0 seeds. Expression analysis showed that the AtDjA3 gene was modulated in response to NaCl, glucose, and abscisic acid (ABA). The j3 line had increased sensitivity to NaCl and glucose treatments in the germination and cotyledon development in comparison to parental Col-0. Furthermore, the j3 mutant line exhibited higher ABA sensitivity in comparison to parental Col-0 and 35S::AtDjA3 overexpression lines. In addition, we examined the expression of ABI3 gene, which is a central regulator in ABA signaling, in j3 mutant and 35S::AtDjA3 overexpression lines. Under 5 μM ABA treatment at 24 h, j3 mutant seedlings displayed higher ABI3 expression, whereas in 35S::AtDjA3 overexpression lines, ABI3 gene expression was repressed. Taken together, these results demonstrate that the AtDjA3 gene is involved in seed development and abiotic stress tolerance. PMID:26941772

  19. System A amino acid transporter SNAT2 shows subtype-specific affinity for betaine and hyperosmotic inducibility in placental trophoblasts.

    PubMed

    Nishimura, Tomohiro; Yagi, Risa; Usuda, Mariko; Oda, Kenji; Yamazaki, Mai; Suda, Sayaka; Takahashi, Yu; Okazaki, Fumiyasu; Sai, Yoshimichi; Higuchi, Kei; Maruyama, Tetsuo; Tomi, Masatoshi; Nakashima, Emi

    2014-05-01

    Betaine uptake is induced by hypertonic stress in a placental trophoblast cell line, and involvement of amino acid transport system A was proposed. Here, we aimed to identify the subtype(s) of system A that mediates hypertonicity-induced betaine uptake. Measurement of [(14)C]betaine uptake by HEK293 cells transiently transfected with human or rat sodium-coupled neutral amino acid transporters (SNATs), SNAT1, SNAT2 and SNAT4 revealed that only human and rat SNAT2 have betaine uptake activity. The Michaelis constants (Km) of betaine uptake by human and rat SNAT2 were estimated to be 5.3 mM and 4.6 mM, respectively. Betaine exclusively inhibited the uptake activity of SNAT2 among the rat system A subtypes. We found that rat SNAT1, SNAT2 and SNAT4 were expressed at the mRNA level under isotonic conditions, while expression of SNAT2 and SNAT4 was induced by hypertonicity in TR-TBT 18d-1 cells. Western blot analyses revealed that SNAT2 expression on plasma membrane of TR-TBT 18d-1 cells was more potently induced by hypertonicity than that in total cell lysate. Immunocytochemistry confirmed the induction of SNAT2 expression in TR-TBT 18d-1 cells exposed to hypertonic conditions and indicated that SNAT2 was localized on the plasma membrane in these cells. Our results indicate that SNAT2 transports betaine, and that tonicity-sensitive SNAT2 expression may be involved in regulation of betaine concentration in placental trophoblasts.

  20. [Analysis of citric acid and citrates. Citric acid and urolithiasis].

    PubMed

    Leskovar, P

    1979-08-01

    In the first part the physico-chemical, analytic chemical and physiologic biochemical properties of the citric acid are discussed. In the second part the author enters the role of the citric acid in the formation of uric calculi. In the third part is reported on the individual methods of the determination of citric acid and the method practised in the author's laboratory is described.

  1. Plasma bile acids show a positive correlation with body mass index and are negatively associated with cognitive restraint of eating in obese patients

    PubMed Central

    Prinz, Philip; Hofmann, Tobias; Ahnis, Anne; Elbelt, Ulf; Goebel-Stengel, Miriam; Klapp, Burghard F.; Rose, Matthias; Stengel, Andreas

    2015-01-01

    Bile acids may be involved in the regulation of food intake and energy metabolism. The aim of the study was to investigate the association of plasma bile acids with body mass index (BMI) and the possible involvement of circulating bile acids in the modulation of physical activity and eating behavior. Blood was obtained in a group of hospitalized patients with normal weight (BMI 18.5–25 kg/m2), underweight (anorexia nervosa, BMI < 17.5 kg/m2) and overweight (obesity with BMI 30–40, 40–50 and >50 kg/m2, n = 14–15/group) and plasma bile acid concentrations assessed. Physical activity and plasma bile acids were measured in a group of patients with anorexia nervosa (BMI 14.6 ± 0.3 kg/m2, n = 43). Lastly, in a population of obese patients (BMI 48.5 ± 0.9 kg/m2, n = 85), psychometric parameters related to disordered eating and plasma bile acids were assessed. Plasma bile acids showed a positive correlation with BMI (r = 0.26, p = 0.03) in the population of patients with broad range of BMI (9–85 kg/m2, n = 74). No associations were observed between plasma bile acids and different parameters of physical activity in anorexic patients (p > 0.05). Plasma bile acids were negatively correlated with cognitive restraint of eating (r = −0.30, p = 0.008), while no associations were observed with other psychometric eating behavior-related parameters (p > 0.05) in obese patients. In conclusion, these data may point toward a role of bile acids in the regulation of body weight. Since plasma bile acids are negatively correlated with the cognitive restraint of eating in obese patients, this may represent a compensatory adaptation to prevent further overeating. PMID:26089773

  2. Plasma bile acids show a positive correlation with body mass index and are negatively associated with cognitive restraint of eating in obese patients.

    PubMed

    Prinz, Philip; Hofmann, Tobias; Ahnis, Anne; Elbelt, Ulf; Goebel-Stengel, Miriam; Klapp, Burghard F; Rose, Matthias; Stengel, Andreas

    2015-01-01

    Bile acids may be involved in the regulation of food intake and energy metabolism. The aim of the study was to investigate the association of plasma bile acids with body mass index (BMI) and the possible involvement of circulating bile acids in the modulation of physical activity and eating behavior. Blood was obtained in a group of hospitalized patients with normal weight (BMI 18.5-25 kg/m(2)), underweight (anorexia nervosa, BMI < 17.5 kg/m(2)) and overweight (obesity with BMI 30-40, 40-50 and >50 kg/m(2), n = 14-15/group) and plasma bile acid concentrations assessed. Physical activity and plasma bile acids were measured in a group of patients with anorexia nervosa (BMI 14.6 ± 0.3 kg/m(2), n = 43). Lastly, in a population of obese patients (BMI 48.5 ± 0.9 kg/m(2), n = 85), psychometric parameters related to disordered eating and plasma bile acids were assessed. Plasma bile acids showed a positive correlation with BMI (r = 0.26, p = 0.03) in the population of patients with broad range of BMI (9-85 kg/m(2), n = 74). No associations were observed between plasma bile acids and different parameters of physical activity in anorexic patients (p > 0.05). Plasma bile acids were negatively correlated with cognitive restraint of eating (r = -0.30, p = 0.008), while no associations were observed with other psychometric eating behavior-related parameters (p > 0.05) in obese patients. In conclusion, these data may point toward a role of bile acids in the regulation of body weight. Since plasma bile acids are negatively correlated with the cognitive restraint of eating in obese patients, this may represent a compensatory adaptation to prevent further overeating.

  3. An Agrobacterium tumefaciens Strain with Gamma-Aminobutyric Acid Transaminase Activity Shows an Enhanced Genetic Transformation Ability in Plants

    PubMed Central

    Nonaka, Satoko; Someya, Tatsuhiko; Zhou, Sha; Takayama, Mariko; Nakamura, Kouji; Ezura, Hiroshi

    2017-01-01

    Agrobacterium tumefaciens has the unique ability to mediate inter-kingdom DNA transfer, and for this reason, it has been utilized for plant genetic engineering. To increase the transformation frequency in plant genetic engineering, we focused on gamma-aminobutyric acid (GABA), which is a negative factor in the Agrobacterium-plant interaction. Recent studies have shown contradictory results regarding the effects of GABA on vir gene expression, leading to the speculation that GABA inhibits T-DNA transfer. In this study, we examined the effect of GABA on T-DNA transfer using a tomato line with a low GABA content. Compared with the control, the T-DNA transfer frequency was increased in the low-GABA tomato line, indicating that GABA inhibits T-DNA transfer. Therefore, we bred a new A. tumefaciens strain with GABA transaminase activity and the ability to degrade GABA. The A. tumefaciens strain exhibited increased T-DNA transfer in two tomato cultivars and Erianthus arundinacues and an increased frequency of stable transformation in tomato. PMID:28220841

  4. Single nucleotide polymorphisms of PAD1 and FDC1 show a positive relationship with ferulic acid decarboxylation ability among industrial yeasts used in alcoholic beverage production.

    PubMed

    Mukai, Nobuhiko; Masaki, Kazuo; Fujii, Tsutomu; Iefuji, Haruyuki

    2014-07-01

    Among industrial yeasts used for alcoholic beverage production, most wine and weizen beer yeasts decarboxylate ferulic acid to 4-vinylguaiacol, which has a smoke-like flavor, whereas sake, shochu, top-fermenting, and bottom-fermenting yeast strains lack this ability. However, the factors underlying this difference among industrial yeasts are not clear. We previously confirmed that both PAD1 (phenylacrylic acid decarboxylase gene, YDR538W) and FDC1 (ferulic acid decarboxylase gene, YDR539W) are essential for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae. In the present study, single nucleotide polymorphisms (SNPs) of PAD1 and FDC1 in sake, shochu, wine, weizen, top-fermenting, bottom-fermenting, and laboratory yeast strains were examined to clarify the differences in ferulic acid decarboxylation ability between these types of yeast. For PAD1, a nonsense mutation was observed in the gene sequence of standard top-fermenting yeast. Gene sequence analysis of FDC1 revealed that sake, shochu, and standard top-fermenting yeasts contained a nonsense mutation, whereas a frameshift mutation was identified in the FDC1 gene of bottom-fermenting yeast. No nonsense or frameshift mutations were detected in laboratory, wine, or weizen beer yeast strains. When FDC1 was introduced into sake and shochu yeast strains, the transformants exhibited ferulic acid decarboxylation activity. Our findings indicate that a positive relationship exists between SNPs in PAD1 and FDC1 genes and the ferulic acid decarboxylation ability of industrial yeast strains.

  5. Using Willie's Acid-Base Box for Blood Gas Analysis

    ERIC Educational Resources Information Center

    Dietz, John R.

    2011-01-01

    In this article, the author describes a method developed by Dr. William T. Lipscomb for teaching blood gas analysis of acid-base status and provides three examples using Willie's acid-base box. Willie's acid-base box is constructed using three of the parameters of standard arterial blood gas analysis: (1) pH; (2) bicarbonate; and (3) CO[subscript…

  6. Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Bacillus vanillea’ XY18T (=CGMCC 8629 T =NCCB 100507 T) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this type strain was assembled and yielded a length of 3.72 Mbp and a GC content of 46.3%. Comparative genomic analysis with its ...

  7. EPA Analysis Shows Decreased Toxic Chemical Releases in Massachusetts in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Massachusetts, the reporting data show that overall releases of pollutants to the environment decreased since the previous reporting year (2014).

  8. EPA Analysis Shows Increased Toxic Chemical Releases in Vermont in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Vermont, the reporting data show that overall releases of pollutants to the environment increased since the previous reporting year (2014).

  9. EPA Analysis Shows Increased Toxic Chemical Releases in Rhode Island in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Rhode Island, the reporting data show that overall releases of pollutants to the environment increased since the previous reporting year (2014).

  10. EPA Analysis Shows Decreased Toxic Chemical Releases in Connecticut in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Connecticut, the reporting data show that overall releases of pollutants to the environment decreased since the previous reporting year (2014).

  11. EPA Analysis Shows Decreased Toxic Chemical Releases in Maine in 2015

    EPA Pesticide Factsheets

    EPA's most recent Toxic Release Inventory (TRI) data is now available for the reporting year of 2015. In Maine, the reporting data show that overall releases of pollutants to the environment decreased since the previous reporting year (2014).

  12. The Coordination of Verbal and Nonverbal Interaction towards Three Parties: The Analysis of a Talk Show.

    ERIC Educational Resources Information Center

    von Raffler-Engel, Walburga

    A study of randomly selected "Donahue" shows revealed how host Phil Donahue interacts with several parties at one time and how he subordinates various interactions to suit the hierarchy of importance he attributes to each party, with the television viewer being the most important. Donahue organizes his body movement mainly for television…

  13. Molecular analysis of mixed endometrial carcinomas shows clonality in most cases

    PubMed Central

    Hoang, Lien N.; Almadani, Noorah; Li, Xiaodong; Soslow, Robert A; Gilks, C. Blake; Lee, Cheng-Han

    2016-01-01

    Mixed endometrial carcinoma refers to a tumor that is comprised of two or more distinct histotypes. We studied 18 mixed-type endometrial carcinomas - 11 mixed serous and low-grade endometrioid carcinomas (SC/EC), 5 mixed clear cell and low-grade endometrioid carcinomas (CCC/EC), and 2 mixed clear cell and serous carcinoma (CCC/SC), using targeted next generation sequencing and immunohistochemistry to compare the molecular profiles of the different histotypes present in each case. In 16 of 18 cases there was molecular evidence that both components shared a clonal origin. Eight cases (6 EC/SC, 1 EC/CCC and 1 SC/CCC) showed a serous carcinoma molecular profile that was the same in both components. Five cases (3 CCC/EC and 2 SC/EC) showed a shared endometrioid molecular profile and identical mismatch repair protein (MMR) deficiency in both components. A single SC/EC case harbored the same POLE exonuclease domain mutation in both components. One SC/CCC and one EC/CCC case showed both shared and unique molecular features in the two histotype components, suggesting early molecular divergence from a common clonal origin. In two cases, there were no shared molecular features and these appear to be biologically unrelated synchronous tumors. Overall, these results show that the different histologic components in mixed endometrial carcinomas typically share the same molecular aberrations. Mixed endometrial carcinomas most commonly occur through morphological mimicry, whereby tumors with serous-type molecular profile show morphological features of endometrioid or clear cell carcinoma, or through underlying deficiency in DNA nucleotide repair, with resulting rapid accrual of mutations and intratumoral phenotypic heterogeneity. Less commonly, mixed endometrial carcinomas are the result of early molecular divergence from a common progenitor clone or are synchronous biologically unrelated tumors (collision tumors). PMID:26492180

  14. Social Network Analysis Shows Direct Evidence for Social Transmission of Tool Use in Wild Chimpanzees

    PubMed Central

    Hobaiter, Catherine; Poisot, Timothée; Zuberbühler, Klaus; Hoppitt, William; Gruber, Thibaud

    2014-01-01

    Social network analysis methods have made it possible to test whether novel behaviors in animals spread through individual or social learning. To date, however, social network analysis of wild populations has been limited to static models that cannot precisely reflect the dynamics of learning, for instance, the impact of multiple observations across time. Here, we present a novel dynamic version of network analysis that is capable of capturing temporal aspects of acquisition—that is, how successive observations by an individual influence its acquisition of the novel behavior. We apply this model to studying the spread of two novel tool-use variants, “moss-sponging” and “leaf-sponge re-use,” in the Sonso chimpanzee community of Budongo Forest, Uganda. Chimpanzees are widely considered the most “cultural” of all animal species, with 39 behaviors suspected as socially acquired, most of them in the domain of tool-use. The cultural hypothesis is supported by experimental data from captive chimpanzees and a range of observational data. However, for wild groups, there is still no direct experimental evidence for social learning, nor has there been any direct observation of social diffusion of behavioral innovations. Here, we tested both a static and a dynamic network model and found strong evidence that diffusion patterns of moss-sponging, but not leaf-sponge re-use, were significantly better explained by social than individual learning. The most conservative estimate of social transmission accounted for 85% of observed events, with an estimated 15-fold increase in learning rate for each time a novice observed an informed individual moss-sponging. We conclude that group-specific behavioral variants in wild chimpanzees can be socially learned, adding to the evidence that this prerequisite for culture originated in a common ancestor of great apes and humans, long before the advent of modern humans. PMID:25268798

  15. SR-FTIR Coupled with Principal Component Analysis Shows Evidence for the Cellular Bystander Effect.

    PubMed

    Lipiec, E; Bambery, K R; Lekki, J; Tobin, M J; Vogel, C; Whelan, D R; Wood, B R; Kwiatek, W M

    2015-07-01

    Synchrotron radiation-Fourier transform infrared (SR-FTIR) microscopy coupled with multivariate data analysis was used as an independent modality to monitor the cellular bystander effect. Single, living prostate cancer PC-3 cells were irradiated with various numbers of protons, ranging from 50-2,000, with an energy of either 1 or 2 MeV using a proton microprobe. SR-FTIR spectra of cells, fixed after exposure to protons and nonirradiated neighboring cells (bystander cells), were recorded. Spectral differences were observed in both the directly targeted and bystander cells and included changes in the DNA backbone and nucleic bases, along with changes in the protein secondary structure. Principal component analysis (PCA) was used to investigate the variance in the entire data set. The percentage of bystander cells relative to the applied number of protons with two different energies was calculated. Of all the applied quantities, the dose of 400 protons at 2 MeV was found to be the most effective for causing significant macromolecular perturbation in bystander PC-3 cells.

  16. Complete genome sequence analysis of goatpox virus isolated from China shows high variation.

    PubMed

    Zeng, Xiancheng; Chi, Xuelin; Li, Wei; Hao, Wenbo; Li, Ming; Huang, Xiaohong; Huang, Yifan; Rock, Daniel L; Luo, Shuhong; Wang, Shihua

    2014-09-17

    Goatpox virus (GTPV), a member of the Capripoxvirus genus of the Poxviridae family, is the causative agent of variolo caprina (goatpox). GTPV can cause significant economic losses of domestic ruminants in endemic regions and can threaten breeding stocks. In this study, we report on the compilation of the complete genomic sequence of an isolated GTPV field strain FZ (GTPV_FZ). The 150,194bp GTPV genome consists of a central coding region bounded by two identical 2301bp inverted terminal repeats and contains 151 putative genes. Comparative genomic analysis reveals the apparent genetic relationships among Capripoxviruses are close, but sufficient genomic variants in the field isolate strain FZ have been identified to distinguish it from other GTPV strains and other Capripoxvirus species. Phylogenetic analysis based on the p32 and complete GTPV genome can be used to differentiate SPPVs, GTPVs and LSDVs. These data may contribute to the epidemiological study of the Chinese capripoxvirus and help to develop more specific detection methods to distinguish GTPVs, SPPVs and LSDVs.

  17. Integrated single-cell analysis shows Pichia pastoris secretes protein stochastically.

    PubMed

    Love, Kerry Routenberg; Panagiotou, Vasiliki; Jiang, Bo; Stadheim, Terrance A; Love, J Christopher

    2010-06-01

    The production of heterologous proteins by secretion from cellular hosts is an important determinant for the cost of biotherapeutics. A single-cell analytical method called microengraving was used to examine the heterogeneity in secretion by the methylotrophic yeast Pichia pastoris. We show that constitutive secretion of a human Fc fragment by P. pastoris is not cell-cycle dependent, but rather fluctuates between states of high and low productivity in a stochastic manner.

  18. Ultrastructural analysis of Vitis vinifera leaf tissues showing atypical symptoms of Plasmopara viticola.

    PubMed

    Musetti, R; Stringher, L; Borselli, S; Vecchione, A; Zulini, L; Pertot, I

    2005-01-01

    In an abandoned farm in Tuscany a year by year regression of downy mildew disease on grapevines was observed and a decrease in virulence as well as vigor and fertility of the causal fungus, Plasmopara viticola. Anomalous spots of the fungus (i.e. atypical coloration of leaves or mosaic) on leaf tissues of a sensitive Vitis vinifera grapevine were observed. The anomalous symptoms were often associated with the typical 'oil spots' and were present under environmental conditions favourable for a normal development of the disease. An ultrastructural study was carried out on leaf tissues of grapevine plants aimed at clarifying the cause of this phenomenon and detecting whether there were alterations in P. viticola mycelium and endophytes present. ELISA was also performed to check the presence of grapevine viruses in the plants. TEM results demonstrated that characteristic P. viticola was present in leaf samples showing oil spots, while, both the fungus and the host tissues showed cytological alterations in leaves with mosaic symptoms. Finally, hyphae were absent in leaf tissues without downy mildew spots, but showing severe ultrastructural modifications. Several plant virus infections were found in these grapevines. Literature reports that the development and sporulation of some phytopathogenic fungi inside their hosts can be limited by virus infections. Further experimental approaches are required to determine if resistance to P. viticola can be induced by viral infections in grapevines.

  19. Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency

    PubMed Central

    2012-01-01

    Background Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far. Results A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism. Conclusions The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency. PMID:22433273

  20. Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

    PubMed Central

    2011-01-01

    Background In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics backgrounds is essential for their successful use in Marker-assisted Selection. In this study, an attempt was made to locate consistent QTL regions associated with yield increase under drought by applying a genome-wide QTL meta-analysis approach. Results The integration of 15 maps resulted in a consensus map with 531 markers and a total map length of 1821 cM. Fifty-three yield QTL reported in 15 studies were projected on a consensus map and meta-analysis was performed. Fourteen meta-QTL were obtained on seven chromosomes. MQTL1.2, MQTL1.3, MQTL1.4, and MQTL12.1 were around 700 kb and corresponded to a reasonably small genetic distance of 1.8 to 5 cM and they are suitable for use in marker-assisted selection (MAS). The meta-QTL for grain yield under drought coincided with at least one of the meta-QTL identified for root and leaf morphology traits under drought in earlier reports. Validation of major-effect QTL on a panel of random drought-tolerant lines revealed the presence of at least one major QTL in each line. DTY12.1 was present in 85% of the lines, followed by DTY4.1 in 79% and DTY1.1 in 64% of the lines. Comparative genomics of meta-QTL with other cereals revealed that the homologous regions of MQTL1.4 and MQTL3.2 had QTL for grain yield under drought in maize, wheat, and barley respectively. The genes in the meta-QTL regions were analyzed by a comparative genomics approach and candidate genes were deduced for grain yield under drought. Three groups of genes such as stress-inducible genes, growth and development-related genes, and sugar transport-related genes were found in clusters in most of the meta-QTL. Conclusions Meta-QTL with small genetic and physical intervals could be useful in Marker-assisted selection individually and in

  1. PCR-DGGE analysis of the bacterial composition of a kaolin slurry showing altered rheology.

    PubMed

    Papp, Ildikó; Balázs, Margit; Tombácz, Etelka; Babcsán, Norbert; Kesserű, Péter; Kiss, István; Szvetnik, Attila

    2012-04-01

    Kaolin is an important industrial raw material and a basis of a range of different products. Microbial spoilage is a detrimental process observed especially in kaolin slurries, leading to low quality products and economic loss. Although the alteration of kaolin slurries in ceramic industry was observed, the process and the microbial background have not been analyzed in details. This study provides the first data using a cultivation independent molecular biological approach (PCR-DGGE) regarding the bacterial composition of an altered kaolin slurry. The results show that potential exopolymer (EPS) producer bacteria (e.g. Acinetobacter, Pseudomonas) appear in the altered kaolin slurry, which may have an important role in the modification of kaolin slurries.

  2. Retrospective Analysis of Patient Presentations at the Sydney (Australia) Royal Easter Show from 2012 to 2014.

    PubMed

    Crabtree, Nathan; Mo, Shirley; Ong, Leon; Jegathees, Thuvarahan; Wei, Daniel; Fahey, David; Liu, Jia Jenny

    2017-04-01

    Introduction Comprehensive studies on the relationship between patient demographics and subsequent treatment and disposition at a single mass-gathering event are lacking. The Sydney Royal Easter Show (SRES; Sydney Olympic Park, New South Wales, Australia) is an annual, 14-day, agricultural mass-gathering event occurring around the Easter weekend, attracting more than 800,000 patrons per year. In this study, patient records from the SRES were analyzed to examine relationships between weather, crowd size, day of week, and demographics on treatment and disposition. This information would help to predict factors affecting patient treatment and disposition to guide ongoing training of first responders and to evaluate the appropriateness of staffing skills mix at future events. Hypothesis Patient demographics, environmental factors, and attendance would influence the nature and severity of presentations at the SRES, which would influence staffing requirements.

  3. Analysis of Cylinder-pressure-indicator Diagrams Showing Effects of Mixture Strength and Spark Timing

    NASA Technical Reports Server (NTRS)

    Gerrish, Harold C; Voss, Fred

    1940-01-01

    An investigation was made to determine the effect of mixture strength and of normal as well as optimum spark timing on the combustion, on the cylinder temperature, and on the performance characteristics of an engine. A single-cylinder test unit utilizing an air-cooled cylinder and a carburetor and operating with gasoline having an octane rating of 92 was used. The investigation covered a range of fuel-air ratios from 0.053 to 0.118. Indicator diagrams and engine-performance data were taken for each change in engine conditions. Examination of the indicator shows that for fuel-air ratios less than and greater than 0.082 the rate and the amount of effective fuel burned decreased. For a fuel-air ratio of 0.118 the combustion efficiency was only 58 percent. Advancing the spark timing increased the rate of pressure rise. This effect was more pronounced with leaner mixtures.

  4. Retrospective analysis showing the water method increased adenoma detection rate — a hypothesis generating observation

    PubMed Central

    Leung, Joseph W; Do, Lynne D; Siao-Salera, Rodelei M; Ngo, Catherine; Parikh, Dhavan A; Mann, Surinder K

    2011-01-01

    Background A water method developed to attenuate discomfort during colonoscopy enhanced cecal intubation in unsedated patients. Serendipitously a numerically increased adenoma detection rate (ADR) was noted. Objective To explore databases of sedated patients examined by the air and water methods to identify hypothesis-generating findings. Design: Retrospective analysis. Setting: VA endoscopy center. Patients: creening colonoscopy. Interventions: From 1/2000–6/2006 the air method was used - judicious air insufflation to permit visualization of the lumen to aid colonoscope insertion and water spray for washing mucosal surfaces. From 6/2006–11/2009 the water method was adopted - warm water infusion in lieu of air insufflation and suction removal of residual air to aid colonoscope insertion. During colonoscope withdrawal adequate air was insufflated to distend the colonic lumen for inspection, biopsy and polypectomy in a similar fashion in both periods. Main outcome measurements: ADR. Results The air (n=683) vs. water (n=495) method comparisons revealed significant differences in overall ADR 26.8% (183 of 683) vs. 34.9% (173 of 495) and ADR of adenomas >9 mm, 7.2% vs. 13.7%, respectively (both P<0.05, Fisher's exact test). Limitations: Non-randomized data susceptible to bias by unmeasured parameters unrelated to the methods. Conclusion Confirmation of the serendipitous observation of an impact of the water method on ADR provides impetus to call for randomized controlled trials to test hypotheses related to the water method as an approach to improving adenoma detection. Because of recent concerns over missed lesions during colonoscopy, the provocative hypothesis-generating observations warrant presentation. PMID:21686105

  5. Transgenic barley (Hordeum vulgare L.) expressing the wheat aluminium resistance gene (TaALMT1) shows enhanced phosphorus nutrition and grain production when grown on an acid soil.

    PubMed

    Delhaize, Emmanuel; Taylor, Phillip; Hocking, Peter J; Simpson, Richard J; Ryan, Peter R; Richardson, Alan E

    2009-06-01

    Barley (Hordeum vulgare L.), genetically modified with the Al(3+) resistance gene of wheat (TaALMT1), was compared with a non-transformed sibling line when grown on an acidic and highly phosphate-fixing ferrosol supplied with a range of phosphorus concentrations. In short-term pot trials (26 days), transgenic barley expressing TaALMT1 (GP-ALMT1) was more efficient than a non-transformed sibling line (GP) at taking up phosphorus on acid soil, but the genotypes did not differ when the soil was limed. Differences in phosphorus uptake efficiency on acid soil could be attributed not only to the differential effects of aluminium toxicity on root growth between the genotypes, but also to differences in phosphorus uptake per unit root length. Although GP-ALMT1 out-performed GP on acid soil, it was still not as efficient at taking up phosphorus as plants grown on limed soil. GP-ALMT1 plants grown in acid soil possessed substantially smaller rhizosheaths than those grown in limed soil, suggesting that root hairs were shorter. This is a probable reason for the lower phosphorus uptake efficiency. When grown to maturity in large pots, GP-ALMT1 plants produced more than twice the grain as GP plants grown on acid soil and 80% of the grain produced by limed controls. Expression of TaALMT1 in barley was not associated with a penalty in either total shoot or grain production in the absence of Al(3+), with both genotypes showing equivalent yields in limed soil. These findings demonstrate that an important crop species can be genetically engineered to successfully increase grain production on an acid soil.

  6. Recent trends in the advanced analysis of bioactive fatty acids.

    PubMed

    Ruiz-Rodriguez, Alejandro; Reglero, Guillermo; Ibañez, Elena

    2010-01-20

    The consumption of dietary fats have been long associated to chronic diseases such as obesity, diabetes, cancer, arthritis, asthma, and cardiovascular disease; although some controversy still exists in the role of dietary fats in human health, certain fats have demonstrated their positive effect in the modulation of abnormal fatty acid and eicosanoid metabolism, both of them associated to chronic diseases. Among the different fats, some fatty acids can be used as functional ingredients such as alpha-linolenic acid (ALA), arachidonic acid (AA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), gamma-linolenic acid (GLA), stearidonic acid (STA) and conjugated linoleic acid (CLA), among others. The present review is focused on recent developments in FAs analysis, covering sample preparation methods such as extraction, fractionation and derivatization as well as new advances in chromatographic methods such as GC and HPLC. Special attention is paid to trans fatty acids due its increasing interest for the food industry.

  7. GENETIC ANALYSIS OF ABSCISIC ACID BIOSYNTHESIS

    SciTech Connect

    MCCARTY D R

    2012-01-10

    The carotenoid cleavage dioxygenases (CCD) catalyze synthesis of a variety of apo-carotenoid secondary metabolites in plants, animals and bacteria. In plants, the reaction catalyzed by the 11, 12, 9-cis-epoxy carotenoid dioxygenase (NCED) is the first committed and key regulated step in synthesis of the plant hormone, abscisic acid (ABA). ABA is a key regulator of plant stress responses and has critical functions in normal root and seed development. The molecular mechanisms responsible for developmental control of ABA synthesis in plant tissues are poorly understood. Five of the nine CCD genes present in the Arabidopsis genome encode NCED's involved in control of ABA synthesis in the plant. This project is focused on functional analysis of these five AtNCED genes as a key to understanding developmental regulation of ABA synthesis and dissecting the role of ABA in plant development. For this purpose, the project developed a comprehensive set of gene knockouts in the AtNCED genes that facilitate genetic dissection of ABA synthesis. These mutants were used in combination with key molecular tools to address the following specific objectives: (1) the role of ABA synthesis in root development; (2) developmental control of ABA synthesis in seeds; (3) analysis of ATNCED over-expressers; (4) preliminary crystallography of the maize VP14 protein.

  8. Lead-iodide nanowire perovskite with methylviologen showing interfacial charge-transfer absorption: a DFT analysis.

    PubMed

    Fujisawa, Jun-ichi; Giorgi, Giacomo

    2014-09-07

    Methylviologen lead-iodide perovskite (MVPb2I6) is a self-assembled one-dimensional (1-D) material consisting of lead-iodide nanowires and intervening organic electron-accepting molecules, methylviologen (MV(2+)). MVPb2I6 characteristically shows optical interfacial charge-transfer (ICT) transitions from the lead-iodide nanowire to MV(2+) in the visible region and unique ambipolar photoconductivity, in which electrons are transported through the three-dimensional (3-D) organic network and holes along the 1-D lead-iodide nanowire. In this work, we theoretically study the electronic band-structure and photocarrier properties of MVPb2I6 by density functional theory (DFT) calculations. Our results clearly confirm the experimentally reported type-II band alignment, whose valence band mainly consists of 5p (I) orbitals of the lead-iodide nanowires and the conduction band of the lowest unoccupied molecular orbital of MV(2+). The DFT calculation also reveals weak charge-transfer interactions between the lead-iodide nanowires and MV(2+). In addition, the electronic distributions of the valence and conduction bands indicate the 3-D transport of electrons and 1-D transport of holes, supporting the reported experimental result.

  9. Transcriptome analysis of Bifidobacterium longum strains that show a differential response to hydrogen peroxide stress.

    PubMed

    Oberg, Taylor S; Ward, Robert E; Steele, James L; Broadbent, Jeff R

    2015-10-20

    Consumer and commercial interest in foods containing probiotic bifidobacteria is increasing. However, because bifidobacteria are anaerobic, oxidative stress can diminish cell viability during production and storage of bioactive foods. We previously found Bifidobacterium longum strain NCC2705 had significantly greater intrinsic and inducible resistance to hydrogen peroxide (H2O2) than strain D2957. Here, we explored the basis for these differences by examining the transcriptional responses of both strains to sub-lethal H2O2 exposure for 5- or 60-min. Strain NCC2705 had 288 genes that were differentially expressed after the 5-min treatment and 114 differentially expressed genes after the 60-min treatment. In contrast, strain D2957 had only 21 and 90 differentially expressed genes after the 5- and 60-min treatments, respectively. Both strains showed up-regulation of genes coding enzymes implicated in oxidative stress resistance, such as thioredoxin, thioredoxin reductase, peroxiredoxin, ferredoxin, glutaredoxin, and anaerobic ribonucleotide reductase, but induction levels were typically highest in NCC2705. Compared to D2957, NCC2705 also had more up-regulated genes involved in transcriptional regulation and more down-regulated genes involved in sugar transport and metabolism. These results provide a greater understanding of the molecular basis for oxidative stress resistance in B. longum and the factors that contribute to strain-to-strain variability in survival in bioactive food products.

  10. Transcriptome Analysis Showed a Differential Signature between Invasive and Non-invasive Corticotrophinomas

    PubMed Central

    de Araújo, Leonardo Jose Tadeu; Lerario, Antonio Marcondes; de Castro, Margaret; Martins, Clarissa Silva; Bronstein, Marcello Delano; Machado, Marcio Carlos; Trarbach, Ericka Barbosa; Villares Fragoso, Maria Candida Barisson

    2017-01-01

    ACTH-dependent hypercortisolism caused by a pituitary adenoma [Cushing’s disease (CD)] is the most common cause of endogenous Cushing’s syndrome. CD is often associated with several morbidities, including hypertension, diabetes, osteoporosis/bone fractures, secondary infections, and increased cardiovascular mortality. While the majority (≈80%) of the corticotrophinomas visible on pituitary magnetic resonance imaging are microadenomas (MICs, <10 mm of diameter), some tumors are macroadenomas (MACs, ≥10 mm) with increased growth potential and invasiveness, exceptionally exhibiting malignant demeanor. In addition, larger and invasive MACs are associated with a significant increased risk of local complications, such as hypopituitarism and visual defects. Given the clinical and molecular heterogeneity of corticotrophinomas, the aim of this study was to investigate the pattern of genetic differential expression between MIC and MAC, including the invasiveness grade as a criterion for categorizing these tumors. In this study, were included tumor samples from patients with clinical, laboratorial, radiological, and histopathological diagnosis of hypercortisolism due to an ACTH-producing pituitary adenoma. Differential gene expression was studied using an Affymetrix microarray platform in 12 corticotrophinomas, classified as non-invasive MIC (n = 4) and MAC (n = 5), and invasive MAC (n = 3), according to modified Hardy criteria. Somatic mutations in USP8 were also investigated, but none of the patients exhibited USP8 variants. Differential expression analysis demonstrated that non-invasive MIC and MAC have a similar genetic signature, while invasive MACs exhibited a differential expression profile. Among the genes differentially expressed, we highlighted CCND2, ZNF676, DAPK1, and TIMP2, and their differential expression was validated through quantitative real-time PCR in another cohort of 15 non-invasive and 3 invasive cortocotrophinomas. We also

  11. Trophic spectra under the lens of amino acid isotopic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in compound specific isotopic ratio analysis (CSIRA) have allowed researchers to measure trophic fractionation of 15N in specific amino acids, namely glutamic acid and phenylalanine. These amino acids have proven useful in food web studies because of the wide and consistent disparity...

  12. Seizure control by derivatives of medium chain fatty acids associated with the ketogenic diet show novel branching-point structure for enhanced potency.

    PubMed

    Chang, Pishan; Zuckermann, Alexandra M E; Williams, Sophie; Close, Adam J; Cano-Jaimez, Marife; McEvoy, James P; Spencer, John; Walker, Matthew C; Williams, Robin S B

    2015-01-01

    The medium chain triglyceride (MCT) ketogenic diet is a major treatment of drug-resistant epilepsy but is problematic, particularly in adults, because of poor tolerability. Branched derivatives of octanoic acid (OA), a medium chain fat provided in the diet have been suggested as potential new treatments for drug-resistant epilepsy, but the structural basis of this functionality has not been determined. Here we investigate structural variants of branched medium chain fatty acids as new seizure-control treatments. We initially employ a series of methyl-branched OA derivatives, and using the GABAA receptor antagonist pentylenetetrazol to induce seizure-like activity in rat hippocampal slices, we show a strong, branch-point-specific activity that improves upon the related epilepsy treatment valproic acid. Using low magnesium conditions to induce glutamate excitotoxicity in rat primary hippocampal neuronal cultures for the assessment of neuroprotection, we also show a structural dependence identical to that for seizure control, suggesting a related mechanism of action for these compounds in both seizure control and neuroprotection. In contrast, the effect of these compounds on histone deacetylase (HDAC) inhibition, associated with teratogenicity, shows no correlation with therapeutic efficacy. Furthermore, small structural modifications of the starting compounds provide active compounds without HDAC inhibitory effects. Finally, using multiple in vivo seizure models, we identify potent lead candidates for the treatment of epilepsy. This study therefore identifies a novel family of fatty acids, related to the MCT ketogenic diet, that show promise as new treatments for epilepsy control and possibly other MCT ketogenic diet-responding conditions, such as Alzheimer disease.

  13. Analysis of Valproic Acid, Salicylic Acid and Ibuprofen in Whole Blood by GC-MS.

    PubMed

    Stephenson, Jon B; Flater, Melanie L; Bain, Lisa T

    2016-10-01

    The Georgia Bureau of Investigation utilized a silylation method of analysis for low molecular weight carboxylic acids in the past. Due to the negative impact such derivatizations can have on gas chromatography-mass spectrometry (GC-MS) systems an alternative means of analysis was investigated. The described method is a whole blood solid phase extraction of valproic acid, salicylic acid and ibuprofen utilizing butylation for sensitivity and improved chromatography by GC-MS. The method produced a limit of detection and limit of quantitation at 1 mg/L for valproic acid, 2 mg/L for salicylic acid and 0.25 mg/L for ibuprofen. The variability based upon the middle of the calibration curve estimated to be 7% for valproic acid, 8% for salicylic acid and 11% for ibuprofen established upon a 95% confidence interval, with the highest percent coefficient of variation being 5.3% for ibuprofen.

  14. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

    PubMed Central

    Keane, Thomas M; Creevey, Christopher J; Pentony, Melissa M; Naughton, Thomas J; Mclnerney, James O

    2006-01-01

    Background In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner. Results We start by highlighting the potential dangers of arbitrarily choosing protein models by demonstrating an empirical example where a single alignment can produce two topologically different and strongly supported phylogenies using two different arbitrarily-chosen amino acid substitution models. We demonstrate that in simple simulations, statistical methods of model selection are indeed robust and likely to be useful for protein model selection. We have investigated patterns of amino acid substitution among homologous sequences from the three Domains of life and our results show that no single amino acid matrix is optimal for any of the datasets. Perhaps most interestingly, we demonstrate that for two large datasets derived from the proteobacteria and archaea, one of the most favored models in both datasets is a model that was originally derived from retroviral Pol proteins. Conclusion This demonstrates that choosing protein models based on their source or method of construction may not be appropriate. PMID:16563161

  15. Analysis of peroxytrifluoroacetic acid oxidation products from Victorian brown coal

    SciTech Connect

    Verheyen, T.V.; Johns, R.B.

    1983-08-01

    A method is described for the detailed quantitative structural identification of the components present in the oxidation product mixtures of a highly aliphatic brown coal. The results showed them to be predominantly long chain diols, hydroxy acids, dicarboxylic acids and short chain polycarboxylic acids.

  16. GC-MS Analysis of [gamma]-Hydroxybutyric Acid Analogs: A Forensic Chemistry Experiment

    ERIC Educational Resources Information Center

    Henck, Colin; Nally, Luke

    2007-01-01

    An upper-division forensic chemistry experiment is described. It involves using glycolic acid and sodium glycolate as analogs of [gamma]-hydroxybutyric acid and its sodium salt. The experiment shows the use of silylation in GC-MS analysis and gives students the opportunity to work with a commonly used silylating reagent,…

  17. "The Show"

    ERIC Educational Resources Information Center

    Gehring, John

    2004-01-01

    For the past 16 years, the blue-collar city of Huntington, West Virginia, has rolled out the red carpet to welcome young wrestlers and their families as old friends. They have come to town chasing the same dream for a spot in what many of them call "The Show". For three days, under the lights of an arena packed with 5,000 fans, the…

  18. Metabolic control analysis of developing oilseed rape (Brassica napus cv Westar) embryos shows that lipid assembly exerts significant control over oil accumulation.

    PubMed

    Tang, Mingguo; Guschina, Irina A; O'Hara, Paul; Slabas, Antoni R; Quant, Patti A; Fawcett, Tony; Harwood, John L

    2012-10-01

    Metabolic control analysis allows the study of metabolic regulation. We applied both single- and double-manipulation top-down control analysis to examine the control of lipid accumulation in developing oilseed rape (Brassica napus) embryos. The biosynthetic pathway was conceptually divided into two blocks of reactions (fatty acid biosynthesis (Block A), lipid assembly (Block B)) connected by a single system intermediate, the acyl-coenzyme A (acyl-CoA) pool. Single manipulation used exogenous oleate. Triclosan was used to inhibit specifically Block A, whereas diazepam selectively manipulated flux through Block B. Exogenous oleate inhibited the radiolabelling of fatty acids from [1-(14)C]acetate, but stimulated that from [U-14C]glycerol into acyl lipids. The calculation of group flux control coefficients showed that c. 70% of the metabolic control was in the lipid assembly block of reactions. Monte Carlo simulations gave an estimation of the error of the resulting group flux control coefficients as 0.27±0.06 for Block A and 0.73±0.06 for Block B. The two methods of control analysis gave very similar results and showed that Block B reactions were more important under our conditions. This contrasts notably with data from oil palm or olive fruit cultures and is important for efforts to increase oilseed rape lipid yields.

  19. Extraterrestrial material analysis: loss of amino acids during liquid-phase acid hydrolysis

    NASA Astrophysics Data System (ADS)

    Buch, Arnaud; Brault, Amaury; Szopa, Cyril; Freissinet, Caroline

    2015-04-01

    Searching for building blocks of life in extraterrestrial material is a way to learn more about how life could have appeared on Earth. With this aim, liquid-phase acid hydrolysis has been used, since at least 1970 , in order to extract amino acids and other organic molecules from extraterrestrial materials (e.g. meteorites, lunar fines) or Earth analogues (e.g. Atacama desert soil). This procedure involves drastic conditions such as heating samples in 6N HCl for 24 h, either under inert atmosphere/vacuum, or air. Analysis of the hydrolyzed part of the sample should give its total (free plus bound) amino acid content. The present work deals with the influence of the 6N HCl hydrolysis on amino acid degradation. Our experiments have been performed on a standard solution of 17 amino acids. After liquid-phase acid hydrolysis (6N HCl) under argon atmosphere (24 h at 100°C), the liquid phase was evaporated and the dry residue was derivatized with N-Methyl-N-(t-butyldimethylsilyl)trifluoroacetamide (MTBSTFA) and dimethylformamide (DMF), followed by gas chromatography-mass spectrometry analysis. After comparison with derivatized amino acids from the standard solution, a significant reduction of the chromatographic peak areas was observed for most of the amino acids after liquid-phase acid hydrolysis. Furthermore, the same loss pattern was observed when the amino acids were exposed to cold 6N HCl for a short amount of time. The least affected amino acid, i.e. glycine, was found to be 73,93% percent less abundant compared to the non-hydrolyzed standard, while the most affected, i.e. histidine, was not found in the chromatograms after hydrolysis. Our experiments thereby indicate that liquid-phase acid hydrolysis, even under inert atmosphere, leads to a partial or total loss of all of the 17 amino acids present in the standard solution, and that a quick cold contact with 6N HCl is sufficient to lead to a loss of amino acids. Therefore, in the literature, the reported increase

  20. Nanopore Back Titration Analysis of Dipicolinic Acid

    PubMed Central

    Han, Yujing; Zhou, Shuo; Wang, Liang; Guan, Xiyun

    2015-01-01

    Here we report a novel label-free nanopore back titration method for the detection of dipicolinic acid, a marker molecule for bacterial spores. By competitive binding of the target analyte and a large ligand probe to metal ions, dipicolinic acid could be sensitively and selectively detected. This nanopore back titration approach should find useful applications in the detection of other species of medical, biological, or environmental importance if their direct detection is difficult to achieve. PMID:25074707

  1. Thermodynamic origin of the solubility profile of drugs showing one or two maxima against the polarity of aqueous and nonaqueous mixtures: niflumic acid and caffeine.

    PubMed

    Bustamante, Pilar; Navarro, J; Romero, S; Escalera, B

    2002-03-01

    The purpose of this work was to investigate the origin of the different solubility profiles of drugs against the polarity of solvent mixtures with a common cosolvent. Niflumic acid and caffeine where chosen as model drugs. The solubilities were measured at five or six temperatures in aqueous (ethanol-water) and nonaqueous (ethyl acetate-ethanol) mixtures. The enthalpies of solution were obtained at the harmonic mean of the experimental temperature. Solid phase changes were analyzed using differential scanning calorimetry and thermomicroscopy. A single solubility maximum was obtained for niflumic acid against the solubility parameter of both mixtures that is not related to solid phase changes. In contrast, caffeine displays two maxima and anhydrous-hydrate transition occurs at the solubility peak in the amphiprotic mixture. The apparent enthalpies of solution of both drugs show endothermic maxima against solvent composition that are related to hydrophobic hydration. A general explanation for the cosolvent action in aqueous mixtures is proposed. The dominant mechanism shifts from entropy to enthalpy at a certain cosolvent ratio dependent on the hydrophobicity and the solubility parameter of the drug. Niflumic acid and caffeine show enthalpy-entropy compensation in ethanol-water, and this relationship is demonstrated for the first time in nonaqueous mixtures. The results support that enthalpy-entropy compensation is a general effect for the solubility of drugs in solvent mixtures. The shape of the solubility curves is correlated with the compensation plots. The solubility peaks separate different enthalpy-entropy relationships that also differentiate the solubility behavior of the hydrate and the anhydrous forms of caffeine.

  2. Analysis of intact cholesteryl esters of furan fatty acids in cod liver.

    PubMed

    Hammann, Simon; Wendlinger, Christine; Vetter, Walter

    2015-06-01

    Furan fatty acids (F-acids) are a class of natural antioxidants with a furan moiety in the acyl chain. These minor fatty acids have been reported to occur with high proportions in the cholesteryl ester fraction of fish livers. Here we present a method for the direct analysis of intact cholesteryl esters with F-acids and other fatty acids in cod liver lipids. For this purpose, the cholesteryl ester fraction was isolated by solid phase extraction (SPE) and subsequently analyzed by gas chromatography with mass spectrometry (GC/MS) using a cool-on-column inlet. Pentadecanoic acid esterified with cholesterol was used as an internal standard. GC/MS spectra of F-acid cholesteryl esters featured the molecular ion along with characteristic fragment ions for both the cholesterol and the F-acid moiety. All investigated cod liver samples (n = 8) showed cholesteryl esters of F-acids and, to a lower degree, of conventional fatty acids. By means of GC/MS-SIM up to ten F-acid cholesteryl esters could be determined in the samples. The concentrations of cholesteryl esters with conventional fatty acids amounted to 78-140 mg/100 g lipids (mean 97 mg/100 g lipids), while F-acid cholesteryl esters were present at 47-270 mg/100 g lipids (mean 130 mg/100 g lipids).

  3. Evaluation of Meterorite Amono Acid Analysis Data Using Multivariate Techniques

    NASA Technical Reports Server (NTRS)

    McDonald, G.; Storrie-Lombardi, M.; Nealson, K.

    1999-01-01

    The amino acid distributions in the Murchison carbonaceous chondrite, Mars meteorite ALH84001, and ice from the Allan Hills region of Antarctica are shown, using a multivariate technique known as Principal Component Analysis (PCA), to be statistically distinct from the average amino acid compostion of 101 terrestrial protein superfamilies.

  4. Matrix-based three-dimensional culture of buffalo mammary epithelial cells showed higher induction of genes related to milk protein and fatty acid metabolism.

    PubMed

    Shandilya, Umesh K; Sharma, Ankita; Sodhi, Monika; Kapila, Neha; Kishore, Amit; Mohanty, Ashok; Kataria, Ranjit; Malakar, Dhruva; Mukesh, Manishi

    2016-02-01

    Demanding transcriptomic studies in livestock animal species could be replaced by good in vitro models mimicking the function of mammary gland. Mammary epithelial cells (MEC) are the functional unit of the mammary gland. Extracellular matrix is known to be a key factor providing normal homeostasis in three-dimensional (3D) environment as important signals are lost when cells are cultured in two-dimensional (2D) environment. The aims of this study were to establish a buffalo mammary epithelial cells (BMECs) in 3D culture using extracellular matrix and to determine whether such a 3D culture model has different expression pattern than 2D counterpart. The purified MEC generated after several passages were used to establish 3D culture using Geltrex matrix. The expression of milk casein genes viz., alpha S1-casein (CSN1S1), alpha S2-casein (CSN1S2), beta-casein (CSN2), kappa-casein (CSN3); and fatty acid metabolism genes viz., butyrophilin (BTN1A1), glycerol-3-phosphate acyltransferase (GPAM), fatty acid-binding protein 3 (FABP3), and stearoyl-CoA desaturase (SCD) was assessed in 3D culture in comparison to traditional monolayer culture using qRT-PCR. Notable morphological differences were observed for BMECs grown in 3D culture in comparison to 2D culture. Morphologically, epithelial structures grown in Geltrex matrix (3D) environment showed enhanced functional differentiation in comparison to 2D culture. In 3D culture, lumen and dome-like structures were formed by day 5, whereas polarized acinus-like structure were formed within 15 days of culturing. The expression data showed higher mRNA induction of milk casein and fatty acid metabolism genes in 10-day-old 3D BMECs culture in comparison to 2D monolayer culture. The result suggests that 3D organization of epithelial cells has favorable effect on induction of milk and fatty acid metabolism-related genes. Therefore, matrix-based 3D culture of MEC that recapitulate the structural and functional context of normal tissues

  5. Los Alamos sequence analysis package for nucleic acids and proteins.

    PubMed Central

    Kanehisa, M I

    1982-01-01

    An interactive system for computer analysis of nucleic acid and protein sequences has been developed for the Los Alamos DNA Sequence Database. It provides a convenient way to search or verify various sequence features, e.g., restriction enzyme sites, protein coding frames, and properties of coded proteins. Further, the comprehensive analysis package on a large-scale database can be used for comparative studies on sequence and structural homologies in order to find unnoted information stored in nucleic acid sequences. PMID:6174934

  6. NMR metabolomics profiling of blood plasma mimics shows that medium- and long-chain fatty acids differently release metabolites from human serum albumin

    NASA Astrophysics Data System (ADS)

    Jupin, M.; Michiels, P. J.; Girard, F. C.; Spraul, M.; Wijmenga, S. S.

    2014-02-01

    Metabolite profiling by NMR of body fluids is increasingly used to successfully differentiate patients from healthy individuals. Metabolites and their concentrations are direct reporters of body biochemistry. However, in blood plasma the NMR-detected free-metabolite concentrations are also strongly affected by interactions with the abundant plasma proteins, which have as of yet not been considered much in metabolic profiling. We previously reported that many of the common NMR-detected metabolites in blood plasma bind to human serum albumin (HSA) and many are released by fatty acids present in fatted HSA. HSA is the most abundant plasma protein and main transporter of endogenous and exogenous metabolites. Here, we show by NMR how the two most common fatty acids (FAs) in blood plasma - the long-chain FA, stearate (C18:0) and medium-chain FA, myristate (C14:0) - affect metabolite-HSA interaction. Of the set of 18 common NMR-detected metabolites, many are released by stearate and/or myristate, lactate appearing the most strongly affected. Myristate, but not stearate, reduces HSA-binding of phenylalanine and pyruvate. Citrate signals were NMR invisible in the presence of HSA. Only at high myristate-HSA mole ratios 11:1, is citrate sufficiently released to be detected. Finally, we find that limited dilution of blood-plasma mimics releases HSA-bound metabolites, a finding confirmed in real blood plasma samples. Based on these findings, we provide recommendations for NMR experiments for quantitative metabolite profiling.

  7. NMR metabolomics profiling of blood plasma mimics shows that medium- and long-chain fatty acids differently release metabolites from human serum albumin.

    PubMed

    Jupin, M; Michiels, P J; Girard, F C; Spraul, M; Wijmenga, S S

    2014-02-01

    Metabolite profiling by NMR of body fluids is increasingly used to successfully differentiate patients from healthy individuals. Metabolites and their concentrations are direct reporters of body biochemistry. However, in blood plasma the NMR-detected free-metabolite concentrations are also strongly affected by interactions with the abundant plasma proteins, which have as of yet not been considered much in metabolic profiling. We previously reported that many of the common NMR-detected metabolites in blood plasma bind to human serum albumin (HSA) and many are released by fatty acids present in fatted HSA. HSA is the most abundant plasma protein and main transporter of endogenous and exogenous metabolites. Here, we show by NMR how the two most common fatty acids (FAs) in blood plasma - the long-chain FA, stearate (C18:0) and medium-chain FA, myristate (C14:0) - affect metabolite-HSA interaction. Of the set of 18 common NMR-detected metabolites, many are released by stearate and/or myristate, lactate appearing the most strongly affected. Myristate, but not stearate, reduces HSA-binding of phenylalanine and pyruvate. Citrate signals were NMR invisible in the presence of HSA. Only at high myristate-HSA mole ratios 11:1, is citrate sufficiently released to be detected. Finally, we find that limited dilution of blood-plasma mimics releases HSA-bound metabolites, a finding confirmed in real blood plasma samples. Based on these findings, we provide recommendations for NMR experiments for quantitative metabolite profiling.

  8. Dual fatty acid synthase and HER2 signaling blockade shows marked antitumor activity against breast cancer models resistant to anti-HER2 drugs.

    PubMed

    Blancafort, Adriana; Giró-Perafita, Ariadna; Oliveras, Glòria; Palomeras, Sònia; Turrado, Carlos; Campuzano, Òscar; Carrión-Salip, Dolors; Massaguer, Anna; Brugada, Ramon; Palafox, Marta; Gómez-Miragaya, Jorge; González-Suárez, Eva; Puig, Teresa

    2015-01-01

    Blocking the enzyme Fatty Acid Synthase (FASN) leads to apoptosis of HER2-positive breast carcinoma cells. The hypothesis is that blocking FASN, in combination with anti-HER2 signaling agents, would be an effective antitumor strategy in preclinical HER2+ breast cancer models of trastuzumab and lapatinib resistance. We developed and molecularly characterized in vitro HER2+ models of resistance to trastuzumab (SKTR), lapatinib (SKLR) and both (SKLTR). The cellular interactions of combining anti-FASN polyphenolic compounds (EGCG and the synthetic G28UCM) with anti-HER2 signaling drugs (trastuzumab plus pertuzumab and temsirolimus) were analyzed. Tumor growth inhibition after treatment with EGCG, pertuzumab, temsirolimus or the combination was evaluated in two in vivo orthoxenopatients: one derived from a HER2+ patient and another from a patient who relapsed on trastuzumab and lapatinib-based therapy. SKTR, SKLR and SKLTR showed hyperactivation of EGFR and p-ERK1/2 and PI3KCA mutations. Dual-resistant cells (SKLTR) also showed hyperactivation of HER4 and recovered levels of p-AKT compared with mono-resistant cells. mTOR, p-mTOR and FASN expression remained stable in SKTR, SKLR and SKLTR. In vitro, anti-FASN compounds plus pertuzumab showed synergistic interactions in lapatinib- and dual- resistant cells and improved the results of pertuzumab plus trastuzumab co-treatment. FASN inhibitors combined with temsirolimus displayed the strongest synergistic interactions in resistant cells. In vivo, both orthoxenopatients showed strong response to the antitumor activity of the combination of EGCG with pertuzumab or temsirolimus, without signs of toxicity. We showed that the simultaneous blockade of FASN and HER2 pathways is effective in cells and in breast cancer models refractory to anti-HER2 therapies.

  9. Dual Fatty Acid Synthase and HER2 Signaling Blockade Shows Marked Antitumor Activity against Breast Cancer Models Resistant to Anti-HER2 Drugs

    PubMed Central

    Blancafort, Adriana; Giró-Perafita, Ariadna; Oliveras, Glòria; Palomeras, Sònia; Turrado, Carlos; Campuzano, Òscar; Carrión-Salip, Dolors; Massaguer, Anna; Brugada, Ramon; Palafox, Marta; Gómez-Miragaya, Jorge; González-Suárez, Eva; Puig, Teresa

    2015-01-01

    Blocking the enzyme Fatty Acid Synthase (FASN) leads to apoptosis of HER2-positive breast carcinoma cells. The hypothesis is that blocking FASN, in combination with anti-HER2 signaling agents, would be an effective antitumor strategy in preclinical HER2+ breast cancer models of trastuzumab and lapatinib resistance. We developed and molecularly characterized in vitro HER2+ models of resistance to trastuzumab (SKTR), lapatinib (SKLR) and both (SKLTR). The cellular interactions of combining anti-FASN polyphenolic compounds (EGCG and the synthetic G28UCM) with anti-HER2 signaling drugs (trastuzumab plus pertuzumab and temsirolimus) were analyzed. Tumor growth inhibition after treatment with EGCG, pertuzumab, temsirolimus or the combination was evaluated in two in vivo orthoxenopatients: one derived from a HER2+ patient and another from a patient who relapsed on trastuzumab and lapatinib-based therapy. SKTR, SKLR and SKLTR showed hyperactivation of EGFR and p-ERK1/2 and PI3KCA mutations. Dual-resistant cells (SKLTR) also showed hyperactivation of HER4 and recovered levels of p-AKT compared with mono-resistant cells. mTOR, p-mTOR and FASN expression remained stable in SKTR, SKLR and SKLTR. In vitro, anti-FASN compounds plus pertuzumab showed synergistic interactions in lapatinib- and dual- resistant cells and improved the results of pertuzumab plus trastuzumab co-treatment. FASN inhibitors combined with temsirolimus displayed the strongest synergistic interactions in resistant cells. In vivo, both orthoxenopatients showed strong response to the antitumor activity of the combination of EGCG with pertuzumab or temsirolimus, without signs of toxicity. We showed that the simultaneous blockade of FASN and HER2 pathways is effective in cells and in breast cancer models refractory to anti-HER2 therapies. PMID:26107737

  10. Fatty Acid Structure and Degradation Analysis in Fingerprint Residues.

    PubMed

    Pleik, Stefanie; Spengler, Bernhard; Schäfer, Thomas; Urbach, Dieter; Luhn, Steven; Kirsch, Dieter

    2016-09-01

    GC-MS investigations were carried out to elucidate the aging behavior of unsaturated fatty acids in fingerprint residues and to identify their degradation products in aged samples. For this purpose, a new sample preparation technique for fingerprint residues was developed that allows producing N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA) derivatives of the analyzed unsaturated fatty acids and their degradation products. MSTFA derivatization catalyzed by iodotrimethylsilane enables the reliable identification of aldehydes and oxoacids as characteristic MSTFA derivatives in GCMS. The obtained results elucidate the degradation pathway of unsaturated fatty acids. Our study of aged fingerprint residues reveals that decanal is the main degradation product of the observed unsaturated fatty acids. Furthermore, oxoacids with different chain lengths are detected as specific degradation products of the unsaturated fatty acids. The detection of the degradation products and their chain length is a simple and effective method to determine the double bond position in unsaturated compounds. We can show that the hexadecenoic and octadecenoic acids found in fingerprint residues are not the pervasive fatty acids Δ9-hexadecenoic (palmitoleic acid) and Δ9-octadecenoic (oleic acid) acid but Δ6-hexadecenoic acid (sapienic acid) and Δ8-octadecenoic acid. The present study focuses on the structure identification of human sebum-specific unsaturated fatty acids in fingerprint residues based on the identification of their degradation products. These results are discussed for further investigations and method developments for age determination of fingerprints, which is still a tremendous challenge because of several factors affecting the aging behavior of individual compounds in fingerprints. Graphical Abstract ᅟ.

  11. Fatty Acid Structure and Degradation Analysis in Fingerprint Residues

    NASA Astrophysics Data System (ADS)

    Pleik, Stefanie; Spengler, Bernhard; Schäfer, Thomas; Urbach, Dieter; Luhn, Steven; Kirsch, Dieter

    2016-09-01

    GC-MS investigations were carried out to elucidate the aging behavior of unsaturated fatty acids in fingerprint residues and to identify their degradation products in aged samples. For this purpose, a new sample preparation technique for fingerprint residues was developed that allows producing N-methyl- N-trimethylsilyl-trifluoroacetamide (MSTFA) derivatives of the analyzed unsaturated fatty acids and their degradation products. MSTFA derivatization catalyzed by iodotrimethylsilane enables the reliable identification of aldehydes and oxoacids as characteristic MSTFA derivatives in GCMS. The obtained results elucidate the degradation pathway of unsaturated fatty acids. Our study of aged fingerprint residues reveals that decanal is the main degradation product of the observed unsaturated fatty acids. Furthermore, oxoacids with different chain lengths are detected as specific degradation products of the unsaturated fatty acids. The detection of the degradation products and their chain length is a simple and effective method to determine the double bond position in unsaturated compounds. We can show that the hexadecenoic and octadecenoic acids found in fingerprint residues are not the pervasive fatty acids Δ9-hexadecenoic (palmitoleic acid) and Δ9-octadecenoic (oleic acid) acid but Δ6-hexadecenoic acid (sapienic acid) and Δ8-octadecenoic acid. The present study focuses on the structure identification of human sebum-specific unsaturated fatty acids in fingerprint residues based on the identification of their degradation products. These results are discussed for further investigations and method developments for age determination of fingerprints, which is still a tremendous challenge because of several factors affecting the aging behavior of individual compounds in fingerprints.

  12. LCMS analysis of fingerprints, the amino acid profile of 20 donors.

    PubMed

    de Puit, Marcel; Ismail, Mahado; Xu, Xiaoma

    2014-03-01

    The analysis of amino acids present in fingerprints has been studied several times. In this paper, we report a method for the analysis of amino acids using an fluorenylmethyloxycarbonyl chloride-derivatization for LC separation and MS detection. We have obtained good results with regard to the calibration curves and the limit of detection and LOQ for the target compounds. The extraction of the amino acids from the substrates used proved to be very efficient. Analysis of the derivatized amino acids enabled us to obtain full amino acid profiles for 20 donors. The intervariability is as expected rather large, with serine as the most abundant constituent, and when examining the total profile of the amino acids per donor, a characteristic pattern can be observed. Some amino acids were not detected in some donors, or fell out of the range of the calibration curve, where others showed a surprisingly high amount of material in the deposition analyses. Further investigations will have to address the intravariability of the amino acid profiles of the fingerprints from donors. By the development of the analytical method and the application to the analysis of fingerprints, we were able to gain insight in the variability of the constituents of fingerprints between the donors.

  13. Dietary intake and plasma metabolomic analysis of polyunsaturated fatty acids in bipolar subjects reveal dysregulation of linoleic acid metabolism.

    PubMed

    Evans, Simon J; Ringrose, Rachel N; Harrington, Gloria J; Mancuso, Peter; Burant, Charles F; McInnis, Melvin G

    2014-10-01

    Polyunsaturated fatty acids (PUFA) profiles associate with risk for mood disorders. This poses the hypothesis of metabolic differences between patients and unaffected healthy controls that relate to the primary illness or are secondary to medication use or dietary intake. However, dietary manipulation or supplementation studies show equivocal results improving mental health outcomes. This study investigates dietary patterns and metabolic profiles relevant to PUFA metabolism, in bipolar I individuals compared to non-psychiatric controls. We collected seven-day diet records and performed metabolomic analysis of fasted plasma collected immediately after diet recording. Regression analyses adjusted for age, gender and energy intake found that bipolar individuals had significantly lower intake of selenium and PUFAs, including eicosapentaenoic acid (EPA) (n-3), docosahexaenoic acid (DHA) (n-3), arachidonic acid (AA) (n-6) and docosapentaenoic acid (DPA) (n-3/n-6 mix); and significantly increased intake of the saturated fats, eicosanoic and docosanoic acid. Regression analysis of metabolomic data derived from plasma samples, correcting for age, gender, BMI, psychiatric medication use and dietary PUFA intake, revealed that bipolar individuals had reduced 13S-HpODE, a major peroxidation product of the n-6, linoleic acid (LA), reduced eicosadienoic acid (EDA), an elongation product of LA; reduced prostaglandins G2, F2 alpha and E1, synthesized from n-6 PUFA; and reduced EPA. These observations remained significant or near significant after Bonferroni correction and are consistent with metabolic variances between bipolar and control individuals with regard to PUFA metabolism. These findings suggest that specific dietary interventions aimed towards correcting these metabolic disparities may impact health outcomes for individuals with bipolar disorder.

  14. Immunolocalization of alpha-keratins and associated beta-proteins in lizard epidermis shows that acidic keratins mix with basic keratin-associated beta-proteins.

    PubMed

    Alibardi, Lorenzo

    2014-07-01

    The differentiation of the corneous layers of lizard epidermis has been analyzed by ultrastructural immunocytochemistry using specific antibodies against alpha-keratins and keratin associated beta-proteins (KAbetaPs, formerly indicated as beta-keratins). Both beta-cells and alpha-cells of the corneous layer derive from the same germinal layer. An acidic type I alpha-keratin is present in basal and suprabasal layers, early differentiating clear, oberhautchen, and beta-cells. Type I keratin apparently disappears in differentiated beta- and alpha-layers of the mature corneous layers. Conversely, a basic type II alpha-keratin rich in glycine is absent or very scarce in basal and suprabasal layers and this keratin likely does not pair with type I keratin to form intermediate filaments but is weakly detected in the pre-corneous and corneous alpha-layer. Single and double labeling experiments show that in differentiating beta-cells, basic KAbetaPs are added and replace type-I keratin to form the hard beta-layer. Epidermal alpha-keratins contain scarce cysteine (0.2-1.4 %) that instead represents 4-19 % of amino acids present in KAbetaPs. Possible chemical bonds formed between alpha-keratins and KAbetaPs may derive from electrostatic interactions in addition to cross-linking through disulphide bonds. Both the high content in glycine of keratins and KAbetaPs may also contribute to increase the hydrophobicy of the beta- and alpha-layers and the resistance of the corneous layer. The increase of gly-rich KAbetaPs amount and the bonds to the framework of alpha-keratins give rise to the inflexible beta-layer while the cys-rich KAbetaPs produce a pliable alpha-layer.

  15. A novel inhibitor of fatty acid synthase shows activity against HER2+ breast cancer xenografts and is active in anti-HER2 drug-resistant cell lines

    PubMed Central

    2011-01-01

    Introduction Inhibiting the enzyme Fatty Acid Synthase (FASN) leads to apoptosis of breast carcinoma cells, and this is linked to human epidermal growth factor receptor 2 (HER2) signaling pathways in models of simultaneous expression of FASN and HER2. Methods In a xenograft model of breast carcinoma cells that are FASN+ and HER2+, we have characterised the anticancer activity and the toxicity profile of G28UCM, the lead compound of a novel family of synthetic FASN inhibitors. In vitro, we analysed the cellular and molecular interactions of combining G28UCM with anti-HER drugs. Finally, we tested the cytotoxic ability of G28UCM on breast cancer cells resistant to trastuzumab or lapatinib, that we developed in our laboratory. Results In vivo, G28UCM reduced the size of 5 out of 14 established xenografts. In the responding tumours, we observed inhibition of FASN activity, cleavage of poly-ADPribose polymerase (PARP) and a decrease of p-HER2, p- protein kinase B (AKT) and p-ERK1/2, which were not observed in the nonresponding tumours. In the G28UCM-treated animals, no significant toxicities occurred, and weight loss was not observed. In vitro, G28UCM showed marked synergistic interactions with trastuzumab, lapatinib, erlotinib or gefitinib (but not with cetuximab), which correlated with increases in apoptosis and with decreases in the activation of HER2, extracellular signal-regulated kinase (ERK)1/2 and AKT. In trastuzumab-resistant and in lapatinib-resistant breast cancer cells, in which trastuzumab and lapatinib were not effective, G28UCM retained the anticancer activity observed in the parental cells. Conclusions G28UCM inhibits fatty acid synthase (FASN) activity and the growth of breast carcinoma xenografts in vivo, and is active in cells with acquired resistance to anti-HER2 drugs, which make it a candidate for further pre-clinical development. PMID:22177475

  16. Overexpression of a Protein Phosphatase 2C from Beech Seeds in Arabidopsis Shows Phenotypes Related to Abscisic Acid Responses and Gibberellin Biosynthesis1

    PubMed Central

    Reyes, David; Rodríguez, Dolores; González-García, Mary Paz; Lorenzo, Oscar; Nicolás, Gregorio; García-Martínez, José Luis; Nicolás, Carlos

    2006-01-01

    A functional abscisic acid (ABA)-induced protein phosphatase type 2C (PP2C) was previously isolated from beech (Fagus sylvatica) seeds (FsPP2C2). Because transgenic work is not possible in beech, in this study we overexpressed this gene in Arabidopsis (Arabidopsis thaliana) to provide genetic evidence on FsPP2C2 function in seed dormancy and other plant responses. In contrast with other PP2Cs described so far, constitutive expression of FsPP2C2 in Arabidopsis, under the cauliflower mosaic virus 35S promoter, produced enhanced sensitivity to ABA and abiotic stress in seeds and vegetative tissues, dwarf phenotype, and delayed flowering, and all these effects were reversed by gibberellic acid application. The levels of active gibberellins (GAs) were reduced in 35S:FsPP2C2 plants, although transcript levels of AtGA20ox1 and AtGA3ox1 increased, probably as a result of negative feedback regulation, whereas the expression of GASA1 was induced by GAs. Additionally, FsPP2C2-overexpressing plants showed a strong induction of the Responsive to ABA 18 (RAB18) gene. Interestingly, FsPP2C2 contains two nuclear targeting sequences, and transient expression assays revealed that ABA directed this protein to the nucleus. Whereas other plant PP2Cs have been shown to act as negative regulators, our results support the hypothesis that FsPP2C2 is a positive regulator of ABA. Moreover, our results indicate the existence of potential cross-talk between ABA signaling and GA biosynthesis. PMID:16815952

  17. Proteomic Analysis of Aortae from Human Lipoprotein(a) Transgenic Mice Shows an Early Metabolic Response Independent of Atherosclerosis

    PubMed Central

    Rodger, Euan J.; Suetani, Rachel J.; Jones, Gregory T.; Kleffmann, Torsten; Carne, Alan; Legge, Michael; McCormick, Sally P. A.

    2012-01-01

    Background Elevated low density lipoprotein (LDL) and lipoprotein(a) are independent risk factors for the development of atherosclerosis. Using a proteomic approach we aimed to determine early changes in arterial protein expression in transgenic mice containing both human LDL and lipoprotein(a) in circulation. Methods and Results Plasma lipid analyses showed the lipoprotein(a) transgenic mice had significantly higher lipid levels than wildtype, including a much increased LDL and high density lipoprotein (HDL) cholesterol. Analysis of aortae from lipoprotein(a) mice showed lipoprotein(a) accumulation but no lipid accumulation or foam cells, leaving the arteries essentially atherosclerosis free. Using two-dimensional gel electrophoresis and mass spectrometry, we identified 34 arterial proteins with significantly altered abundance (P<0.05) in lipoprotein(a) transgenic mice compared to wildtype including 17 that showed a ≥2 fold difference. Some proteins of interest showed a similarly altered abundance at the transcript level. These changes collectively indicated an initial metabolic response that included a down regulation in energy, redox and lipid metabolism proteins and changes in structural proteins at a stage when atherosclerosis had not yet developed. Conclusions Our study shows that human LDL and lipoprotein(a) promote changes in the expression of a unique set of arterial proteins which may be early indicators of the metabolic disturbances preceding atherosclerosis. PMID:22276189

  18. X-ray survival characteristics and genetic analysis for nine saccharomyces deletion mutants that show altered radiation sensitivity

    SciTech Connect

    Game, John C.; Williamson, Marsha S.; Baccari, Clelia

    2004-01-07

    The availability of a genome-wide set of Saccharomyces deletion mutants provides a chance to identify all the yeast genes involved in DNA repair. Using X-rays, we are screening these mutants to identify additional genes that show increased sensitivity to the lethal effects of ionizing radiation. For each mutant identified as sensitive, we are confirming that the sensitivity phenotype co-segregates with the deletion allele and are obtaining multipoint survival-versus-dose assays in at least two haploid and one homozygous diploid strains. We present data for deletion mutants involving the genes DOT1, MDM20, NAT3, SPT7, SPT20, GCN5, HFI1, DCC1 and VID21/EAF1, and discuss their potential roles in repair. Eight of these genes have a clear radiation-sensitive phenotype when deleted, but the ninth, GCN5, has at most a borderline phenotype. None of the deletions confer substantial sensitivity to ultra-violet radiation, although one or two may confer marginal sensitivity. The DOT1 gene is of interest because its only known function is to methylate one lysine residue in the core of the histone H3 protein. We find that histone H3 mutants (supplied by K. Struhl) in which this residue is replaced by other amino-acids are also X-ray sensitive, seeming to confirm that methylation of the lysine-79 residue is required for effective repair of radiation damage.

  19. Metagenomic analysis of the rhizosphere soil microbiome with respect to phytic acid utilization.

    PubMed

    Unno, Yusuke; Shinano, Takuro

    2013-01-01

    While phytic acid is a major form of organic phosphate in many soils, plant utilization of phytic acid is normally limited; however, culture trials of Lotus japonicus using experimental field soil that had been managed without phosphate fertilizer for over 90 years showed significant usage of phytic acid applied to soil for growth and flowering and differences in the degree of growth, even in the same culture pot. To understand the key metabolic processes involved in soil phytic acid utilization, we analyzed rhizosphere soil microbial communities using molecular ecological approaches. Although molecular fingerprint analysis revealed changes in the rhizosphere soil microbial communities from bulk soil microbial community, no clear relationship between the microbiome composition and flowering status that might be related to phytic acid utilization of L. japonicus could be determined. However, metagenomic analysis revealed changes in the relative abundance of the classes Bacteroidetes, Betaproteobacteria, Chlorobi, Dehalococcoidetes and Methanobacteria, which include strains that potentially promote plant growth and phytic acid utilization, and some gene clusters relating to phytic acid utilization, such as alkaline phosphatase and citrate synthase, with the phytic acid utilization status of the plant. This study highlights phylogenetic and metabolic features of the microbial community of the L. japonicus rhizosphere and provides a basic understanding of how rhizosphere microbial communities affect the phytic acid status in soil.

  20. Improved gas chromatography-flame ionization detector analytical method for the analysis of epoxy fatty acids.

    PubMed

    Mubiru, Edward; Shrestha, Kshitij; Papastergiadis, Antonios; De Meulenaer, Bruno

    2013-11-29

    In this study an improved method for analysis of epoxy fatty acids is reported. Data obtained from analysis of polar fatty acids has previously been presented, but due to the high number of compounds that co-elute in the polar fraction, the resultant chromatograms are complex which may lead to compromising the accuracy of the data. A three steps separation of fatty acid methyl esters (FAMEs) by solid-phase extraction (SPE) on a silica gel column to remove hydroxy fatty acid interferences was proposed. This approach is opposed to a two step separation procedure that has been often used to prevent analytical interferences caused by non-altered fatty acids. A gas chromatograph with a flame ionization detector (GC-FID) equipped with a polar CP-Sil 88™ column was used. Quantification was based on the use of methyl nonadecanoate (C19:0), as an internal standard. Individual mono epoxy fatty acids were well separated without co-eluting compounds. The optimized method was finally applied to screen epoxy fatty acids in 37 fresh oil samples. Results obtained for the total epoxy fatty acids were in the range 0.03-2mgg(-1) of oil with repeatability coefficient of variation (CV) ranging from 2.8 to 9.9% for duplicate analysis showing that the results obtained are repeatable.

  1. Mice lacking acid-sensing ion channels (ASIC) 1 or 2, but not ASIC3, show increased pain behaviour in the formalin test.

    PubMed

    Staniland, Amelia A; McMahon, Stephen B

    2009-07-01

    Extracellular acidification is a component of the inflammatory process and may be a factor driving the pain accompanying it. Acid-sensing ion channels (ASICs) are neuronal proton sensors and evidence suggests they are involved in signalling inflammatory pain. The aims of this study were to (1) clarify the role of ASICs in nociception and (2) confirm their involvement in inflammatory pain and determine whether this was subunit specific. This was achieved by (1) direct comparison of the sensitivity of ASIC1, ASIC2, ASIC3 and TRPV1 knockout mice versus wildtype littermates to acute thermal and mechanical noxious stimuli and (2) studying the behavioural responses of each transgenic strain to hind paw inflammation with either complete Freund's adjuvant (CFA) or formalin. Naïve ASIC1(-/-) and ASIC2(-/-) mice responded normally to acute noxious stimuli, whereas ASIC3(-/-) mice were hypersensitive to high intensity thermal stimuli. CFA injection decreased mechanical and thermal withdrawal thresholds for up to 8 days. ASIC2(-/-) mice had increased mechanical sensitivity on day 1 post-CFA compared to wildtype controls. TRPV1(-/-) mice had significantly reduced thermal, but not mechanical, hyperalgesia on all days after inflammation. Following formalin injection, ASIC1(-/-) and ASIC2(-/-), but not ASIC3(-/-) or TRPV1(-/-), mice showed enhanced pain behaviour, predominantly in the second phase of the test. These data suggest that whilst ASICs may play a role in mediating inflammatory pain, this role is likely to be modulatory and strongly dependent on channel subtype.

  2. Unambiguous typing of canine adenovirus isolates by deoxyribonucleic acid restriction-endonuclease analysis.

    PubMed Central

    Assaf, R; Marsolais, G; Yelle, J; Hamelin, C

    1983-01-01

    Viral deoxyribonucleic acid extracted from a limited number of cells infected with canine adenovirus type 1 or type 2 was cleaved with several restriction endonucleases. Agarose gel electrophoresis of the limit digests showed stable differences between the canine adenovirus type 1 and type 2 cleavage patterns. Rapid and accurate typing of large numbers of clinical isolates may thus be done by deoxyribonucleic acid restriction-endonuclease analysis. Images Fig. 1. Fig. 2. PMID:6321002

  3. [Analysis of oxalic acid and oxalates].

    PubMed

    Leskovar, P

    1979-08-01

    It is reported on individual methods for the estimation of the oxalic acid in body fluids, particularly in the urine. The case in question is a survey of the oxalate estimation methods, which, however, has no pretensions to completeness. The at present most actualestimation methods are brought somewhat more in detail. The data are not sufficient for the laboratorytechnical performance of the individual methods, this would transgress the possibilities of the work. However, the original papers are cited which contain all the necessary details. Some technical difficulties and disturbances in the individual estimation methods are also entered. Despite excellent work of several teams the problems of standardization, of the absolutely reliable reference methoda as well as of an objective consideration of advantages and disadvantages of individual, often subjectively judged methods is not yet solved. Comparing these methods, one gets the impression that several reliable methods of the same value are established. It seems that this estimation method brings the greatest progress which will reliably establish so small quantities of oxalate as they are in the blood or in the liquor. By this also the oxalate clearance and the renal oxalate treatment becomes more exactly establishable than up to now.

  4. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect

    States, David J.

    2004-07-28

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  5. Analysis of the generating action of the acid from PAG using acid sensitive dyes

    NASA Astrophysics Data System (ADS)

    Sekiguchi, Atsushi; Matsumoto, Yoko; Konishi, Hiroko; Moriyasu, Kengo; Morimoto, Yukihiro

    2011-04-01

    The use of acid sensitive dyes to determine the quantity of acid generated from PAG and in the analysis of acid-generating reaction is currently being studied. The method would allow an easy understanding of the PAG acid-generating reaction simply by adding an acid sensitive dye to the resist. In the conventional method, a resist containing a chromogenic substance is applied to a quartz substrate, which is then exposed. Following the exposure, the absorbance of chromogenic component near 530 nm is measured and evaluated with a spectroscope. The rate constant for acid generation (Dill's C parameter) during the exposure is determined based on the relationship between transmittance at 530 nm and the exposure dose. However, the chromogenic substance used in this method degrades over time (fading reaction) after the exposure, resulting in variations in transmittance measurements due to the effects of time between the completion of the exposure and the measurement of transmittance. We devised a prototype instrument capable of in situ measurements of absorbance at 530 nm while irradiating a 193-nm light beam. Using this instrument, we obtained rate constants for acid generation (Dill's C parameter) and examined the differing results obtained with ArF resist polymers of differing PAG concentrations and structures as well as dependence on the quantity of the chromogenic substance.

  6. Digital PCR analysis of circulating nucleic acids.

    PubMed

    Hudecova, Irena

    2015-10-01

    Detection of plasma circulating nucleic acids (CNAs) requires the use of extremely sensitive and precise methods. The commonly used quantitative real-time polymerase chain reaction (PCR) poses certain technical limitations in relation to the precise measurement of CNAs whereas the costs of massively parallel sequencing are still relatively high. Digital PCR (dPCR) now represents an affordable and powerful single molecule counting strategy to detect minute amounts of genetic material with performance surpassing many quantitative methods. Microfluidic (chip) and emulsion (droplet)-based technologies have already been integrated into platforms offering hundreds to millions of nanoliter- or even picoliter-scale reaction partitions. The compelling observations reported in the field of cancer research, prenatal testing, transplantation medicine and virology support translation of this technology into routine use. Extremely sensitive plasma detection of rare mutations originating from tumor or placental cells among a large background of homologous sequences facilitates unraveling of the early stages of cancer or the detection of fetal mutations. Digital measurement of quantitative changes in plasma CNAs associated with cancer or graft rejection provides valuable information on the monitoring of disease burden or the recipient's immune response and subsequent therapy treatment. Furthermore, careful quantitative assessment of the viral load offers great value for effective monitoring of antiviral therapy for immunosuppressed or transplant patients. The present review describes the inherent features of dPCR that make it exceptionally robust in precise and sensitive quantification of CNAs. Moreover, I provide an insight into the types of potential clinical applications that have been developed by researchers to date.

  7. Linkage Analysis in a Dutch Population Isolate Shows No Major Gene for Left-Handedness or Atypical Language Lateralization

    PubMed Central

    Ophoff, Roel A.; Aukes, Maartje F.; Cantor, Rita M.; Boks, Marco P.; Dauwan, Meenakshi; de Visser, Kees L.; Kahn, René S.; Sommer, Iris E.

    2015-01-01

    Cerebral dominance of language function and hand preference are suggested to be heritable traits with possible shared genetic background. However, joined genetic studies of these traits have never been conducted. We performed a genetic linkage study in 37 multigenerational human pedigrees of both sexes (consisting of 355 subjects) enriched with left-handedness in which we also measured language lateralization. Hand preference was measured with the Edinburgh Handedness Inventory, and language lateralization was measured with functional transcranial Doppler during language production. The estimated heritability of left-handedness and language lateralization in these pedigrees is 0.24 and 0.31, respectively. A parametric major gene model was tested for left-handedness. Nonparametric analyses were performed for left-handedness, atypical lateralization, and degree of language lateralization. We did not observe genome-wide evidence for linkage in the parametric or nonparametric analyses for any of the phenotypes tested. However, multiple regions showed suggestive evidence of linkage. The parametric model showed suggestive linkage for left-handedness in the 22q13 region [heterogeneity logarithm of odds (HLOD) = 2.18]. Nonparametric multipoint analysis of left-handedness showed suggestive linkage in the same region [logarithm of odds (LOD) = 2.80]. Atypical language lateralization showed suggestive linkage in the 7q34 region (LODMax = 2.35). For strength of language lateralization, we observed suggestive linkage in the 6p22 (LODMax = 2.54), 7q32 (LODMax = 1.93), and 9q33 (LODMax = 2.10) regions. We did not observe any overlap of suggestive genetic signal between handedness and the extent of language lateralization. The absence of significant linkage argues against the presence of a major gene coding for both traits; rather, our results are suggestive of these traits being two independent polygenic complex traits. PMID:26063907

  8. Analysis of the mouse mutant Cloth-ears shows a role for the voltage-gated sodium channel Scn8a in peripheral neural hearing loss.

    PubMed

    Mackenzie, F E; Parker, A; Parkinson, N J; Oliver, P L; Brooker, D; Underhill, P; Lukashkina, V A; Lukashkin, A N; Holmes, C; Brown, S D M

    2009-10-01

    Deafness is the most common sensory disorder in humans and the aetiology of genetic deafness is complex. Mouse mutants have been crucial in identifying genes involved in hearing. However, many deafness genes remain unidentified. Using N-ethyl N-nitrosourea (ENU) mutagenesis to generate new mouse models of deafness, we identified a novel semi-dominant mouse mutant, Cloth-ears (Clth). Cloth-ears mice show reduced acoustic startle response and mild hearing loss from approximately 30 days old. Auditory-evoked brainstem response (ABR) and distortion product otoacoustic emission (DPOAE) analyses indicate that the peripheral neural auditory pathway is impaired in Cloth-ears mice, but that cochlear function is normal. In addition, both Clth/Clth and Clth/+ mice display paroxysmal tremor episodes with behavioural arrest. Clth/Clth mice also show a milder continuous tremor during movement and rest. Longitudinal phenotypic analysis showed that Clth/+ and Clth/Clth mice also have complex defects in behaviour, growth, neurological and motor function. Positional cloning of Cloth-ears identified a point mutation in the neuronal voltage-gated sodium channel alpha-subunit gene, Scn8a, causing an aspartic acid to valine (D981V) change six amino acids downstream of the sixth transmembrane segment of the second domain (D2S6). Complementation testing with a known Scn8a mouse mutant confirmed that this mutation is responsible for the Cloth-ears phenotype. Our findings suggest a novel role for Scn8a in peripheral neural hearing loss and paroxysmal motor dysfunction.

  9. Do invasive species show higher phenotypic plasticity than native species and, if so, is it adaptive? A meta-analysis.

    PubMed

    Davidson, Amy Michelle; Jennions, Michael; Nicotra, Adrienne B

    2011-04-01

    Do invasive plant species have greater phenotypic plasticity than non-invasive species? And, if so, how does this affect their fitness relative to native, non-invasive species? What role might this play in plant invasions? To answer these long-standing questions, we conducted a meta-analysis using data from 75 invasive/non-invasive species pairs. Our analysis shows that invasive species demonstrate significantly higher phenotypic plasticity than non-invasive species. To examine the adaptive benefit of this plasticity, we plotted fitness proxies against measures of plasticity in several growth, morphological and physiological traits to test whether greater plasticity is associated with an improvement in estimated fitness. Invasive species were nearly always more plastic in their response to greater resource availability than non-invasives but this plasticity was only sometimes associated with a fitness benefit. Intriguingly, non-invasive species maintained greater fitness homoeostasis when comparing growth between low and average resource availability. Our finding that invasive species are more plastic in a variety of traits but that non-invasive species respond just as well, if not better, when resources are limiting, has interesting implications for predicting responses to global change.

  10. Analysis of a large dataset of mycorrhiza inoculation field trials on potato shows highly significant increases in yield.

    PubMed

    Hijri, Mohamed

    2016-04-01

    An increasing human population requires more food production in nutrient-efficient systems in order to simultaneously meet global food needs while reducing the environmental footprint of agriculture. Arbuscular mycorrhizal fungi (AMF) have the potential to enhance crop yield, but their efficiency has yet to be demonstrated in large-scale crop production systems. This study reports an analysis of a dataset consisting of 231 field trials in which the same AMF inoculant (Rhizophagus irregularis DAOM 197198) was applied to potato over a 4-year period in North America and Europe under authentic field conditions. The inoculation was performed using a liquid suspension of AMF spores that was sprayed onto potato seed pieces, yielding a calculated 71 spores per seed piece. Statistical analysis showed a highly significant increase in marketable potato yield (ANOVA, P < 0.0001) for inoculated fields (42.2 tons/ha) compared with non-inoculated controls (38.3 tons/ha), irrespective of trial year. The average yield increase was 3.9 tons/ha, representing 9.5 % of total crop yield. Inoculation was profitable with a 0.67-tons/ha increase in yield, a threshold reached in almost 79 % of all trials. This finding clearly demonstrates the benefits of mycorrhizal-based inoculation on crop yield, using potato as a case study. Further improvements of these beneficial inoculants will help compensate for crop production deficits, both now and in the future.

  11. Gas chromatographic analysis of infant formulas for total fatty acids, including trans fatty acids.

    PubMed

    Satchithanandam, Subramaniam; Fritsche, Jan; Rader, Jeanne I

    2002-01-01

    Twelve powdered and 13 liquid infant formulas were analyzed by using an extension of AOAC Official Method 996.01 for fat analysis in cereal products. Samples were hydrolyzed with 8 N HCl and extracted with ethyl and petroleum ethers. Fatty acid methyl esters were prepared by refluxing the mixed ether extracts with methanolic sodium hydroxide in the presence of 14% boron trifluoride in methanol. The extracts were analyzed by gas chromatography. In powdered formulas, saturated fatty acid (SFA) content (mean +/- SD; n = 12) was 41.05 +/- 3.94%, monounsaturated fatty acid (MUFA) content was 36.97 +/- 3.38%, polyunsaturated fatty acid (PUFA) content was 20.07 +/- 3.08%, and total trans fatty acid content was 1.30 +/- 1.27%. In liquid formulas, SFA content (mean +/- SD; n = 13) was 42.29 +/- 2.98%, MUFA content was 36.05 +/- 2.47%, PUFA content was 20.65 +/- 2.40%, and total trans fatty acid content was 0.88 +/- 0.54%. Total fat content in powdered formulas ranged from 4.4 to 5.5 g/100 kcal and linoleic acid content ranged from 868 to 1166 mg/100 kcal. In liquid formulas, total fat content ranged from 4.1 to 5.1 g/100 kcal and linoleic acid content ranged from 820 to 1100 mg/100 kcal. There were no significant differences between powdered and liquid infant formulas in concentrations of total fat, SFA, MUFA, PUFA, or trans fatty acids.

  12. Bile acids: analysis in biological fluids and tissues

    PubMed Central

    Griffiths, William J.; Sjövall, Jan

    2010-01-01

    The formation of bile acids/bile alcohols is of major importance for the maintenance of cholesterol homeostasis. Besides their functions in lipid absorption, bile acids/bile alcohols are regulatory molecules for a number of metabolic processes. Their effects are structure-dependent, and numerous metabolic conversions result in a complex mixture of biologically active and inactive forms. Advanced methods are required to characterize and quantify individual bile acids in these mixtures. A combination of such analyses with analyses of the proteome will be required for a better understanding of mechanisms of action and nature of endogenous ligands. Mass spectrometry is the basic detection technique for effluents from chromatographic columns. Capillary liquid chromatography-mass spectrometry with electrospray ionization provides the highest sensitivity in metabolome analysis. Classical gas chromatography-mass spectrometry is less sensitive but offers extensive structure-dependent fragmentation increasing the specificity in analyses of isobaric isomers of unconjugated bile acids. Depending on the nature of the bile acid/bile alcohol mixture and the range of concentration of individuals, different sample preparation sequences, from simple extractions to group separations and derivatizations, are applicable. We review the methods currently available for the analysis of bile acids in biological fluids and tissues, with emphasis on the combination of liquid and gas phase chromatography with mass spectrometry. PMID:20008121

  13. Geochemical analysis of potash mine seep oils, collapsed breccia pipe oil shows and selected crude oils, Eddy County, New Mexico

    USGS Publications Warehouse

    Palacas, J.G.; Snyder, R.P.; Baysinger, J.P.; Threlkeld, C.N.

    1982-01-01

    Oil shows, in the form of oil stains and bleeding oil, in core samples from two breccia pipes, Hills A and C, Eddy County, New Mexico, and seepage oils in a potash mine near Hill C breccia pipe are geochemically similar. The geochemical similarities strongly suggest that they belong to the same family of oils and were derived from similar sources. The oils are relatively high in sulfur (0.89 to 1.23 percent), rich in hydrocarbons (average 82 percent), relatively high in saturated hydrocarbon/aromatic hydrocarbon ratios (average 2.9), and based on analysis of seep oils alone, have a low API gravity (average 19.4?). The oils are for the most part severely biodegraded as attested by the loss of n-paraffin molecules. Geochemical comparison of seven crude oils collected in the vicinity of the breccia pipes indicates that the Yates oils are the likely source of the above family of oils. Six barrels of crude oil that were dumped into a potash exploration borehole near Hill C breccia pipe, to release stuck casing, are considered an unlikely source of the breccia pipe and mine seep oils. Volumetric and hydrodynamic constraints make it highly improbable that such a small volume of 'dumped' oil could migrate over distances ranging from about 600 feet to 2.5 miles to the sites of the oil shows.

  14. Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses.

    PubMed

    Brum, Jennifer R; Schenck, Ryan O; Sullivan, Matthew B

    2013-09-01

    Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world's oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world's oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51-92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.

  15. Research Advances. Image Pinpoints All 5 Million Atoms in Viral Coat; Bilirubin, "Animals-Only" Pigment, Found in Plants; New Evidence Shows Humans Make Salicylic Acid

    NASA Astrophysics Data System (ADS)

    King, Angela G.

    2009-08-01

    Recent "firsts" in chemical research: image of a viral capsid pinpointing 5 million atoms; isolation and identification of an "animal" pigment, bilirubin, from a plant source; evidence that humans make salicylic acid.

  16. Co-administration of hyaluronic acid with local anaesthetics shows lower cytotoxicity than local anaesthetic treatment alone in bovine articular chondrocytes

    PubMed Central

    Onur, T. S.; Sitron, C. S.; Dang, A.

    2013-01-01

    Objective To study the effect of hyaluronic acid (HA) on local anaesthetic chondrotoxicity in vitro. Methods Chondrocytes were harvested from bovine femoral condyle cartilage and isolated using collagenase-containing media. At 24 hours after seeding 15 000 cells per well onto a 96-well plate, chondrocytes were treated with media (DMEM/F12 + ITS), PBS, 1:1 lidocaine (2%):PBS, 1:1 bupivacaine (0.5%):PBS, 1:1 lidocaine (2%):HA, 1:1 bupivacaine (0. 5%):HA, or 1:1 HA:PBS for one hour. Following treatment, groups had conditions removed and 24-hour incubation. Cell viability was assessed using PrestoBlue and confirmed visually using fluorescence microscopy. Results Media-treated groups had a mean of 1.55×104 cells/well (sem 783). All treated cells showed statistically significant reduced viability when compared with media alone (all p < 0.003). Cells treated with bupivacaine + HA (6.70×103 cells/well (sem 1.10×103)) survived significantly more than bupivacaine (2.44×103 cells/well (sem 830)) (p < 0.001). Lidocaine + HA (1.45×103 cells/well (sem 596)) was not significantly more cytotoxic than lidocaine (2.24×103 cells/well (sem 341)) (p = 0.999). There was no statistical difference between the chondrotoxicities of PBS (8.49×103 cells/well (sem 730) cells/well) and HA (4.75×103 cells/well (sem 886)) (p = 0.294). Conclusions HA co-administration reduced anaesthetic cytotoxicity with bupivacaine but not lidocaine, suggesting different mechanisms of injury between the two. Co-administered intra-articular injections of HA with bupivacaine, but not lidocaine, may protect articular chondrocytes from local anaesthetic-associated death. Cite this article: Bone Joint Res 2013;2:270–5. PMID:24333946

  17. Computerized image analysis for acetic acid induced intraepithelial lesions

    NASA Astrophysics Data System (ADS)

    Li, Wenjing; Ferris, Daron G.; Lieberman, Rich W.

    2008-03-01

    Cervical Intraepithelial Neoplasia (CIN) exhibits certain morphologic features that can be identified during a visual inspection exam. Immature and dysphasic cervical squamous epithelium turns white after application of acetic acid during the exam. The whitening process occurs visually over several minutes and subjectively discriminates between dysphasic and normal tissue. Digital imaging technologies allow us to assist the physician analyzing the acetic acid induced lesions (acetowhite region) in a fully automatic way. This paper reports a study designed to measure multiple parameters of the acetowhitening process from two images captured with a digital colposcope. One image is captured before the acetic acid application, and the other is captured after the acetic acid application. The spatial change of the acetowhitening is extracted using color and texture information in the post acetic acid image; the temporal change is extracted from the intensity and color changes between the post acetic acid and pre acetic acid images with an automatic alignment. The imaging and data analysis system has been evaluated with a total of 99 human subjects and demonstrate its potential to screening underserved women where access to skilled colposcopists is limited.

  18. Global transcriptomic analysis of the response of Corynebacterium glutamicum to ferulic acid.

    PubMed

    Chen, Can; Pan, Junfeng; Yang, Xiaobing; Xiao, He; Zhang, Yaoling; Si, Meiru; Shen, Xihui; Wang, Yao

    2017-03-01

    Corynebacterium glutamicum can survive by using ferulic acid as the sole carbon source. In this study, we assessed the response of C. glutamicum to ferulic acid stress by means of a global transcriptional response analysis. The transcriptional data showed that several genes involved in degradation of ferulic acid were affected. Moreover, several genes related to the stress response; protein protection or degradation and DNA repair; replication, transcription and translation; and the cell envelope were differentially expressed. Deletion of the katA or sigE gene in C. glutamicum resulted in a decrease in cell viability under ferulic acid stress. These insights will facilitate further engineering of model industrial strains, with enhanced tolerance to ferulic acid to enable easy production of biofuels from lignocellulose.

  19. Quality Analysis of Chlorogenic Acid and Hyperoside in Crataegi fructus

    PubMed Central

    Weon, Jin Bae; Jung, Youn Sik; Ma, Choong Je

    2016-01-01

    Background: Crataegi fructus is a herbal medicine for strong stomach, sterilization, and alcohol detoxification. Chlorogenic acid and hyperoside are the major compounds in Crataegi fructus. Objective: In this study, we established novel high-performance liquid chromatography (HPLC)-diode array detection analysis method of chlorogenic acid and hyperoside for quality control of Crataegi fructus. Materials and Methods: HPLC analysis was achieved on a reverse-phase C18 column (5 μm, 4.6 mm × 250 mm) using water and acetonitrile as mobile phase with gradient system. The method was validated for linearity, precision, and accuracy. About 31 batches of Crataegi fructus samples collected from Korea and China were analyzed by using HPLC fingerprint of developed HPLC method. Then, the contents of chlorogenic acid and hyperoside were compared for quality evaluation of Crataegi fructus. Results: The results have shown that the average contents (w/w %) of chlorogenic acid and hyperoside in Crataegi fructus collected from Korea were 0.0438% and 0.0416%, respectively, and the average contents (w/w %) of 0.0399% and 0.0325%, respectively. Conclusion: In conclusion, established HPLC analysis method was stable and could provide efficient quality evaluation for monitoring of commercial Crataegi fructus. SUMMARY Quantitative analysis method of chlorogenic acid and hyperoside in Crataegi fructus is developed by high.performance liquid chromatography.(HPLC).diode array detectionEstablished HPLC analysis method is validated with linearity, precision, and accuracyThe developed method was successfully applied for quantitative analysis of Crataegi fructus sample collected from Korea and China. Abbreviations used: HPLC: High-performance liquid chromatography, GC: Gas chromatography, MS: Mass spectrometer, LOD: Limits of detection, LOQ: Limits of quantification, RSD: Relative standard deviation, RRT: Relative retention time, RPA: Relation peak area. PMID:27076744

  20. Brain Correlates of Cognitive Remediation in Schizophrenia: Activation Likelihood Analysis Shows Preliminary Evidence of Neural Target Engagement

    PubMed Central

    Ramsay, Ian S.; MacDonald, Angus W.

    2015-01-01

    Cognitive remediation training (CRT) for schizophrenia has been found to improve cognitive functioning and influence neural plasticity. However, with various training approaches and mixed findings, the mechanisms driving generalization of cognitive skills from CRT are unclear. In this meta-analysis of extant imaging studies examining CRT’s effects, we sought to clarify whether varying approaches to CRT suggest common neural changes and whether such mechanisms are restorative or compensatory. We conducted a literature search to identify studies appropriate for inclusion in an activation likelihood estimation (ALE) meta-analysis. Our criteria required studies to consist of training-based interventions designed to improve patients’ cognitive or social functioning, including generalization to untrained circumstances. Studies were also required to examine changes in pre- vs posttraining functional activation using functional magnetic resonance imaging or positron emission tomography. The literature search identified 162 articles, 9 of which were appropriate for inclusion. ALE analyses comparing pre- and posttraining brain activation showed increased activity in the lateral and medial prefrontal cortex (PFC), parietal cortex, insula, and the caudate and thalamus. Notably, activation associated with CRT in the left PFC and thalamus partially overlapped with previous meta-analytically identified areas associated with deficits in working memory, executive control, and facial emotion processing in schizophrenia. We conclude that CRT interventions from varying theoretic modalities elicit plasticity in areas that support cognitive and socioemotional processes in this early set of studies. While preliminary, these changes appear to be both restorative and compensatory, though thalamocortical areas previously associated with dysfunction may be common sources of plasticity for cognitive remediation in schizophrenia. PMID:25800249

  1. Expression analysis of human pterygium shows a predominance of conjunctival and limbal markers and genes associated with cell migration

    PubMed Central

    Aryankalayil-John, M.; Campos, M.M.; Fariss, R.N.; Rowsey, J.; Agarwalla, N.; Reid, T.W.; Dushku, N.; Cox, C.A.; Carper, D.; Wistow, G.

    2009-01-01

    Purpose Pterygium is a vision-impairing fibrovascular lesion that grows across the corneal surface and is associated with sunlight exposure. To increase our understanding of the cells types involved in pterygium, we have used expressed sequence tag analysis to examine the transcriptional repertoire of isolated pterygium and to identify marker genes for tissue origin and cell migration. Methods An unnormalized unamplified cDNA library was prepared from 15 pooled specimens of surgically removed pterygia as part of the NEIBank project. Gene expression patterns were compared with existing data for human cornea, limbus, and conjunctiva, and expression of selected genes was verified by immunofluorescence localization in normal eye ocular surface and in pterygium. Results Sequence analysis of 2,976 randomly selected clones produced over 1,800 unique clusters, potentially representing single genes. The most abundant complementary DNAs from pterygium include clusterin, keratins 13 (Krt13) and 4 (Krt4), S100A9/calgranulin B, and spermidine/spermine N1-acetyltransferase (SAT1). Markers for both conjunctiva (such as keratin 13/4 and AQP3) and corneal epithelium (such as keratin 12/3 and AQP5) were present. Immunofluorescence of Krt12 and 13 in the normal ocular surface showed specificity of Krt12 in cornea and Krt13 in conjunctival and limbal epithelia, with a fairly sharp boundary at the limbal–corneal border. In the pterygium there was a patchy distribution of both Krt12 and 13 up to a normal corneal epithelial region specific for Krt12. Immunoglobulins were also among the prominently expressed transcripts. Several of the genes expressed most abundantly in excised pterygium, particularly S100A9 and SAT1, have roles in cell migration. SAT1 exerts its effects through control of polyamine levels. IPENSpm, a polyamine analogue, showed a significant ability to reduce migration in primary cultures of pterygium. A number of genes highly expressed in cornea were not found in

  2. GENOMIC ANALYSIS OF THE TESTICULAR TOXICITY OF HALOACETIC ACIDS

    EPA Science Inventory

    Genomic analysis of the testicular toxicity of haloacetic acids

    David J. Dix and John C. Rockett
    Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, R...

  3. Age estimation in forensic sciences: Application of combined aspartic acid racemization and radiocarbon analysis

    SciTech Connect

    Alkass, K; Buchholz, B A; Ohtani, S; Yamamoto, T; Druid, H; Spalding, S L

    2009-11-02

    Age determination of unknown human bodies is important in the setting of a crime investigation or a mass disaster, since the age at death, birth date and year of death, as well as gender, can guide investigators to the correct identity among a large number of possible matches. Traditional morphological methods used by anthropologists to determine age are often imprecise, whereas chemical analysis of tooth dentin, such as aspartic acid racemization has shown reproducible and more precise results. In this paper we analyze teeth from Swedish individuals using both aspartic acid racemization and radiocarbon methodologies. The rationale behind using radiocarbon analysis is that above-ground testing of nuclear weapons during the cold war (1955-1963) caused an extreme increase in global levels of carbon-14 ({sup 14}C) which have been carefully recorded over time. Forty-four teeth from 41 individuals were analyzed using aspartic acid racemization analysis of tooth crown dentin or radiocarbon analysis of enamel and ten of these were split and subjected to both radiocarbon and racemization analysis. Combined analysis showed that the two methods correlated well (R2=0.66, p < 0.05). Radiocarbon analysis showed an excellent precision with an overall absolute error of 0.6 {+-} 04 years. Aspartic acid racemization also showed a good precision with an overall absolute error of 5.4 {+-} 4.2 years. Whereas radiocarbon analysis gives an estimated year of birth, racemization analysis indicates the chronological age of the individual at the time of death. We show how these methods in combination can also assist in the estimation of date of death of an unidentified victim. This strategy can be of significant assistance in forensic casework involving dead victim identification.

  4. Age estimation in forensic sciences: application of combined aspartic acid racemization and radiocarbon analysis.

    PubMed

    Alkass, Kanar; Buchholz, Bruce A; Ohtani, Susumu; Yamamoto, Toshiharu; Druid, Henrik; Spalding, Kirsty L

    2010-05-01

    Age determination of unknown human bodies is important in the setting of a crime investigation or a mass disaster because the age at death, birth date, and year of death as well as gender can guide investigators to the correct identity among a large number of possible matches. Traditional morphological methods used by anthropologists to determine age are often imprecise, whereas chemical analysis of tooth dentin, such as aspartic acid racemization, has shown reproducible and more precise results. In this study, we analyzed teeth from Swedish individuals using both aspartic acid racemization and radiocarbon methodologies. The rationale behind using radiocarbon analysis is that aboveground testing of nuclear weapons during the cold war (1955-1963) caused an extreme increase in global levels of carbon-14 ((14)C), which has been carefully recorded over time. Forty-four teeth from 41 individuals were analyzed using aspartic acid racemization analysis of tooth crown dentin or radiocarbon analysis of enamel, and 10 of these were split and subjected to both radiocarbon and racemization analysis. Combined analysis showed that the two methods correlated well (R(2) = 0.66, p < 0.05). Radiocarbon analysis showed an excellent precision with an overall absolute error of 1.0 +/- 0.6 years. Aspartic acid racemization also showed a good precision with an overall absolute error of 5.4 +/- 4.2 years. Whereas radiocarbon analysis gives an estimated year of birth, racemization analysis indicates the chronological age of the individual at the time of death. We show how these methods in combination can also assist in the estimation of date of death of an unidentified victim. This strategy can be of significant assistance in forensic casework involving dead victim identification.

  5. Simultaneous airborne nitric acid and formic acid measurements using a chemical ionization mass spectrometer around the UK: Analysis of primary and secondary production pathways

    NASA Astrophysics Data System (ADS)

    Le Breton, Michael; Bacak, Asan; Muller, Jennifer B. A.; Xiao, Ping; Shallcross, Beth M. A.; Batt, Rory; Cooke, Michael C.; Shallcross, Dudley E.; Bauguitte, S. J.-B.; Percival, Carl J.

    2014-02-01

    The first simultaneous measurements of formic and nitric acid mixing ratios around the United Kingdom were measured on the FAAM BAe-146 research aircraft with a chemical ionization mass spectrometer using I- reagent ions at 0.8 Hz. Analysis of the whole dataset shows that formic acid and nitric acid are positively correlated as illustrated by other studies (e.g. Veres et al., 2011). However, initial evidence indicates a prominent direct source of formic acid and also a significant source when O3 levels are high, suggesting the importance of the ozonolysis of 1-alkenes. A trajectory model was able to reproduce the formic acid concentrations by both the inclusion of a primary vehicle source and production via ozonolysis of propene equivalent 1-alkene levels. Inspection of data archives implies these levels of 1-alkene are possible after 11 am, but formic acid and nitric acid plumes early in the flight are too high for the model to replicate. These data show the relationship between nitric acid and formic acid cannot solely be attributed to related photochemical production. The simultaneous measurement of HCOOH and HNO3 has been implemented to estimate OH levels along the flight track assuming a relationship between formic and nitric acid in photochemical plumes and a constant source of 1-alkene.

  6. Using Demonstrations Involving Combustion and Acid-Base Chemistry to Show Hydration of Carbon Dioxide, Sulfur Dioxide, and Magnesium Oxide and Their Relevance for Environmental Climate Science

    ERIC Educational Resources Information Center

    Shaw, C. Frank, III; Webb, James W.; Rothenberger, Otis

    2016-01-01

    The nature of acidic and basic (alkaline) oxides can be easily illustrated via a series of three straightforward classroom demonstrations for high school and general chemistry courses. Properties of carbon dioxide, sulfur dioxide, and magnesium oxide are revealed inexpensively and safely. Additionally, the very different kinetics of hydration of…

  7. [New method of near infrared spectra analysis for the content of acid soluble lignin of Acacia].

    PubMed

    Liu, Sheng

    2014-01-01

    The near infrared spectra analysis model of the content of the acid soluble lignin and the model of the content of the Klason lignin were built by the iterative method separately at first. The results show that the prediction effect of the content of the Klason lignin is obviously better than that of the acid soluble lignin. Different from usual methods of building near infrared spectra analysis model, the approximate linear relation between the contents of the acid soluble lignin and the contents of the Klason lignin was used. Combined with the near infrared spectroscopy data of multi-wavelength, twenty sub models of prediction of the content of the acid soluble lignin were built with the help of the Klason lignin content whose prediction effect is better than that of the acid soluble lignin. By calculating the weighted mean value of the prediction values of these sub models, the new prediction value of the content of the acid soluble lignin of each acacia specimen was obtained at last. The prediction error of the new model is obviously less than that of the model built by the iterative method. It is possible that the method of modeling in the paper can be used to some chemical component contents when the predictions of them by usual methods are not very effective, and the effects of the near infrared spectra analysis of them will be improved.

  8. Mass spectrometric analysis of free fatty acids in infant milk powders by frozen pretreatment coupled with isotope-labeling derivatization.

    PubMed

    Zhou, Tianxiao; Leng, Jiapeng; Peng, Yaoshan; Zhang, Lei; Guo, Yinlong

    2016-03-01

    In combination with frozen pretreatment and carboxyl group derivatization, a novel workflow was developed for the determination of free fatty acids in milk powder. The workflow showed a significantly enhanced performance for comprehensive free fatty acid analysis owing to a highly efficient frozen extraction method. In addition, the advantages of the workflow also involved high sensitivity and great tolerance to a complex matrix. Characteristic fragment ions of derivatization reagents also provide clear evidence for the qualitative analysis of free fatty acids. Fourteen types of free fatty acids in a number of domestic and overseas infant milk powders have been successfully detected. The content of free fatty acids in the different samples was different, which probably indicates the diverse quality of infant milk powder. The workflow is expected to be a pragmatic tool for the analysis of free fatty acids in intricate matrices.

  9. Characterization of 22 Vibrio species by gas chromatography analysis of their cellular fatty acids.

    PubMed

    Urdaci, M C; Marchand, M; Grimont, P A

    1990-05-01

    The cellular fatty acid compositions of 51 Vibrio strains belonging to 22 species as well as five Aeromonas strains were determined by using capillary gas-liquid chromatography (GLC). The major fatty acids were most often hexadecenoic, hexadecanoic and octadecenoic acids. Heptadecenoic acid was present in significant amounts in V. alginolyticus, V. natriegens, V. parahaemolyticus and "Vibrio navarrensis". Twenty fatty acids including branched and hydroxy acids were detected in the genus Vibrio. Quantitative results were treated by principal component analysis to display groups of strains. The first three components (accounting for 69% of the variance) showed the type strains of V. fischeri, V. ordalii, V. damsela, V. mediterranei, V. tubiashii, V. campbellii, V. pelagius, V. gazogenes, and V. nereis to be unclustered. V. alginolyticus (4 strains) and V. parahaemolyticus (4 strains) showed some overlap and the type strain of V. natriegens was in their neighborhood. V. harveyi (4 strains) formed a cluster and V. vulnificus was in its vicinity. V. cholerae (5 strains) overlapped with V. diazotrophicus (3 strains) and was close to the type strain of V. mimicus and V. anguillarum. V. metschnikovii (3 strains) clustered with the type strain of V. cincinnatiensis. A decision tree was devised for the identification of Vibrio species based on qualitative characteristics of fatty acid patterns. However, the following three groups, V. alginolyticus-V. parahaemolyticus-V. natriegens, V. metschnikovii-V. cincinnatiensis and V. cholerae-V. mimicus could not be split into such a decision tree.

  10. Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain

    PubMed Central

    2014-01-01

    Background The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate are known to inhibit C. thermocellum and other microorganisms. To evaluate the biological impact of this type of hydrolysate, a transcriptomic analysis of growth in hydrolysate-containing medium was conducted on 17.5% v/v Populus hydrolysate-tolerant mutant (PM) and wild type (WT) strains of C. thermocellum. Results In two levels of Populus hydrolysate medium (0% and 10% v/v), the PM showed both gene specific increases and decreases of gene expression compared to the wild-type strain. The PM had increased expression of genes in energy production and conversion, and amino acid transport and metabolism in both standard and 10% v/v Populus hydrolysate media. In particular, expression of the histidine metabolism increased up to 100 fold. In contrast, the PM decreased gene expression in cell division and sporulation (standard medium only), cell defense mechanisms, cell envelope, cell motility, and cellulosome in both media. The PM downregulated inorganic ion transport and metabolism in standard medium but upregulated it in the hydrolysate media when compared to the WT. The WT differentially expressed 1072 genes in response to the hydrolysate medium which included increased transcription of cell defense mechanisms, cell motility, and cellulosome, and decreased expression in cell envelope, amino acid transport and metabolism, inorganic ion transport and metabolism, and lipid metabolism, while the PM only differentially expressed 92 genes. The PM tolerates up to 17.5% v/v Populus hydrolysate and growth in it elicited 489 genes with differential expression, which included increased expression in energy production and conversion, cellulosome production, and inorganic ion transport and metabolism and decreased expression in transcription and cell

  11. Recent advances in amino acid analysis by capillary electrophoresis.

    PubMed

    Poinsot, Véréna; Carpéné, Marie-Anne; Bouajila, Jalloul; Gavard, Pierre; Feurer, Bernard; Couderc, François

    2012-01-01

    This paper describes the most important articles that have been published on amino acid analysis using CE during the period from June 2009 to May 2011 and follows the format of the previous articles of Smith (Electrophoresis 1999, 20, 3078-3083), Prata et al. (Electrophoresis 2001, 22, 4129-4138) and Poinsot et al. (Electrophoresis 2003, 24, 4047-4062; Electrophoresis 2006, 27, 176-194; Electrophoresis 2008, 29, 207-223; Electrophoresis 2010, 31, 105-121). We present new developments in amino acid analysis with CE, which are reported describing the use of lasers or light emitting diodes for fluorescence detection, conductimetry electrochemiluminescence detectors, mass spectrometry applications, and lab-on-a-chip applications using CE. In addition, we describe articles concerning clinical studies and neurochemical applications of these techniques.

  12. In vitro quantitative analysis of Salmonella typhimurium preference for amino acids secreted by human breast tumor

    NASA Astrophysics Data System (ADS)

    Choi, Eunpyo; Maeng, Bohee; Lee, Jae-hun; Chang, Hyung-kwan; Park, Jungyul

    2016-12-01

    Bacterial therapies have been paid significant attentions by their ability to penetrate deep into the solid tumor tissue and its propensity to naturally accumulate in tumors of living animals. Understanding the actual mechanism for bacteria to target the tumor is therapeutically crucial but is poorly understood. We hypothesized that amino acids released from the specific tumors induced bacteria to those tumors and the experiments for chemotactic response of bacteria toward the cancer secreting amino acids was then performed by using the diffusion based multiple chemical gradient generator constructed by in situ self-assembly of microspheres. The quantitative analysis was carried out by comparison of intensity using green fluorescent protein (GFP) tagged Salmonella typhimurium ( S. typhimurium) in the gradient generator, which showed the clear preference to the released amino acids, especially from breast cancer patients. The understanding chemotaxis toward the cancer secreting amino acids is essential for controlling S. typhimurium targeting in tumors and will allow for the development of bacterial therapies.

  13. Analysis of sterols and fatty acids in natural and cultured Cordyceps by one-step derivatization followed with gas chromatography-mass spectrometry.

    PubMed

    Yang, F Q; Feng, K; Zhao, J; Li, S P

    2009-07-12

    Ten free fatty acids namely lauric acid, myristic acid, pentadecanoic acid, palmitoleic acid, palmitic acid, linoleic acid, oleic acid, stearic acid, docosanoic acid and lignoceric acid and four free sterols including ergosterol, cholesterol, campesterol and beta-sitosterol in natural (wild) Cordyceps sinensis, Cordyceps liangshanensis and Cordyceps gunnii, as well as cultured C. sinensis and Cordyceps militaris were first determined using pressurized liquid extraction (PLE), trimethylsilyl (TMS) derivatization and GC-MS analysis. The conditions such as the amount of reagent, temperature and time for TMS derivatization of analytes were optimized. Under the optimum conditions, all calibration curves showed good linearity within the tested ranges. The intra- and inter-day variations for 14 investigated compounds were less than 3.4% and 5.2%, respectively. The results showed that palmitic acid, linoleic acid, oleic acid, stearic acid and ergosterol are main components in natural and cultured Cordyceps which could be discriminated by hierarchical clustering analysis based on the contents of 14 investigated compounds or the 4 fatty acids, where the contents of palmitic acid and oleic acid in natural Cordyceps are significantly higher than those in the cultured ones.

  14. Simple enrichment and analysis of plasma lysophosphatidic acids.

    PubMed

    Wang, Jialu; Sibrian-Vazquez, Martha; Escobedo, Jorge O; Lowry, Mark; Wang, Lei; Chu, Yu-Hsuan; Moore, Richard G; Strongin, Robert M

    2013-11-21

    A simple and highly efficient technique for the analysis of lysophosphatidic acid (LPA) subspecies in human plasma is described. The streamlined sample preparation protocol furnishes the five major LPA subspecies with excellent recoveries. Extensive analysis of the enriched sample reveals only trace levels of other phospholipids. This level of purity not only improves MS analyses, but enables HPLC post-column detection in the visible region with a commercially available fluorescent phospholipids probe. Human plasma samples from different donors were analyzed using the above method and validated by LC-ESI/MS/MS.

  15. COPASAAR – A database for proteomic analysis of single amino acid repeats

    PubMed Central

    Depledge, Daniel P; Dalby, Andrew R

    2005-01-01

    Background Single amino acid repeats make up a significant proportion in all of the proteomes that have currently been determined. They have been shown to be functionally and medically significant, and are associated with cancers and neuro-degenerative diseases such as Huntington's Chorea, where a poly-glutamine repeat is responsible for causing the disease. The COPASAAR database is a new tool to facilitate the rapid analysis of single amino acid repeats at a proteome level. The database aims to simplify the comparison of repeat distributions between proteomes in order to provide a better understanding of their function and evolution. Results A comparative analysis of all proteomes in the database (currently 244) shows that single amino acid repeats account for about 12–14% of the proteome of any given species. They are more common in eukaryotes (14%) than in either archaea or bacteria (both 13%). Individual analyses of proteomes show that long single amino acid repeats (6+ residues) are much more common in the Eukaryotes and that longer repeats are usually made up of hydrophilic amino acids such as glutamine, glutamic acid, asparagine, aspartic acid and serine. Conclusion COPASAAR is a useful tool for comparative proteomics that provides rapid access to amino acid repeat data that can be readily data-mined. The COPASAAR database can be queried at the kingdom, proteome or individual protein level. As the amount of available proteome data increases this will be increasingly important in order to automate proteome comparison. The insights gained from these studies will give a better insight into the evolution of protein sequence and function. PMID:16078990

  16. Analysis of Saccharides by the Addition of Amino Acids

    NASA Astrophysics Data System (ADS)

    Ozdemir, Abdil; Lin, Jung-Lee; Gillig, Kent J.; Gulfen, Mustafa; Chen, Chung-Hsuan

    2016-06-01

    In this work, we present the detection sensitivity improvement of electrospray ionization (ESI) mass spectrometry of neutral saccharides in a positive ion mode by the addition of various amino acids. Saccharides of a broad molecular weight range were chosen as the model compounds in the present study. Saccharides provide strong noncovalent interactions with amino acids, and the complex formation enhances the signal intensity and simplifies the mass spectra of saccharides. Polysaccharides provide a polymer-like ESI spectrum with a basic subunit difference between multiply charged chains. The protonated spectra of saccharides are not well identified because of different charge state distributions produced by the same molecules. Depending on the solvent used and other ions or molecules present in the solution, noncovalent interactions with saccharides may occur. These interactions are affected by the addition of amino acids. Amino acids with polar side groups show a strong tendency to interact with saccharides. In particular, serine shows a high tendency to interact with saccharides and significantly improves the detection sensitivity of saccharide compounds.

  17. Regulatory impact analysis of the proposed acid-rain implementation regulations

    SciTech Connect

    Not Available

    1991-09-16

    This regulatory impact analysis (RIA) was developed in response to Executive Order (EO) 12291, which requires Federal Agencies to assess the costs, benefits, and impacts of all 'major' regulations. In compliance with EO 12291, this RIA assesses costs, benefits and impacts for the important provisions of Title IV. EPA divided its analysis of the Acid Rain Program into two parts. First, EPA analyzed the effects of the statute in the absence of any implementation regulations. In the second part of the analysis, EPA examined a 'regulatory' case that included both the SO2 reductions and the implementation regulations. By comparing costs under the regulatory case to those under the absent regulations case, EPA was able to isolate the incremental savings provided by the regulations. At the same time, by combining the two parts of the analysis, EPA was able to show the total costs imposed by the Acid Rain Program (the statute and the regulations) as a whole.

  18. Physicochemical characterization, fatty acid composition, and thermal analysis of Bertholletia excelsa HBK oil.

    PubMed

    Pena Muniz, Marcos Antônio; Ferreira Dos Santos, Marina Nídia; da Costa, Carlos Emmerson Ferreira; Morais, Luiz; Lamarão, Maria Louze Nobre; Ribeiro-Costa, Roseane Maria; Silva-Júnior, José Otávio Carréra

    2015-01-01

    The present study aimed at characterizing the oil extracted from Bertholletia excelsa H.B.K. almond, a native species from the Amazon region. Analytical methods used for oils and fats were employed through pharmacopoeia assays, AOCS (American Oil Chemists Society) standard methods as well as those recommended by ANVISA (National Health Surveillance Agency) such as acidity, peroxide value, saponification index, iodine value and refractive index, pH and relative density, and also thermoanalytical analyses (thermogravimetry, differential thermogravimetry and differential thermal analysis) as well as chromatographic analysis (gas chromatography). The characterization assessments of B. excelsa oil showed results indicating that the oil contains polyunsaturated fatty acids in large proportion. The termoanalytical tests indicated that B.excelsa oil showed thermal stability up to 220 °C, These results showed that the oil extracted from B. excelsa has acceptable characteristics and is of good quality.

  19. Physicochemical characterization, fatty acid composition, and thermal analysis of Bertholletia excelsa HBK oil

    PubMed Central

    Pena Muniz, Marcos Antônio; Ferreira dos Santos, Marina Nídia; da Costa, Carlos Emmerson Ferreira; Morais, Luiz; Lamarão, Maria Louze Nobre; Ribeiro-Costa, Roseane Maria; Silva-Júnior, José Otávio Carréra

    2015-01-01

    The present study aimed at characterizing the oil extracted from Bertholletia excelsa H.B.K. almond, a native species from the Amazon region. Analytical methods used for oils and fats were employed through pharmacopoeia assays, AOCS (American Oil Chemists Society) standard methods as well as those recommended by ANVISA (National Health Surveillance Agency) such as acidity, peroxide value, saponification index, iodine value and refractive index, pH and relative density, and also thermoanalytical analyses (thermogravimetry, differential thermogravimetry and differential thermal analysis) as well as chromatographic analysis (gas chromatography). The characterization assessments of B. excelsa oil showed results indicating that the oil contains polyunsaturated fatty acids in large proportion. The termoanalytical tests indicated that B.excelsa oil showed thermal stability up to 220 °C, These results showed that the oil extracted from B. excelsa has acceptable characteristics and is of good quality. PMID:25709225

  20. Spectroscopic and quantum chemical analysis of Isonicotinic acid methyl ester

    NASA Astrophysics Data System (ADS)

    Shoba, D.; Periandy, S.; Govindarajan, M.; Gayathri, P.

    2015-02-01

    In this present study, an organic compound Isonicotinic acid methyl ester (INAME) was structurally characterized by FTIR, FT-Raman, and NMR and UV spectroscopy. The optimized geometrical parameters and energies of all different and possible conformers of INAME are obtained from Density Functional Theory (DFT) by B3LYP/6-311++G(d,p) method. There are three conformers (SI, SII-1, and SII-2) for this molecule (ground state). The most stable conformer of INAME is SI conformer. The molecular geometry and vibrational frequencies of INAME in the ground state have been calculated by using HF and density functional method (B3LYP) 6-311++G (d,p) basis set. Detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The computed vibrational frequencies were compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. A study on the electronic properties, such as HOMO and LUMO energies were performed by time independent DFT approach. Besides, molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and first hyper polarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results show that the INAME molecule may have microscopic nonlinear optical (NLO) behavior with non zero values. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by gauge independent atomic orbital (GIAO) method.

  1. Comparative analysis of phenolic acids in mistletoe plants from various hosts.

    PubMed

    Luczkiewicz, M; Cisowski, W; Kaiser, P; Ochocka, R; Piotrowski, A

    2001-01-01

    Phenolic acids present in mistletoe plants collected from various hosts were analysed with the use of HPLC. The following numbers of compounds were found in the mistletoe plant material gathered from respective hosts: Sorbus aucuparia- 12 compounds; Acer plantanoides--14 compounds: Malus domestica, Pyrus communis and Populus nigra--13 compounds each; Quercus robur--15 compounds. Altogether 21 phenolic acids were chromatographically identified in the tested material. The compounds were either free or combined as esters or glycosides. Comparative chromatography revealed qualitative differences in the investigated compounds between the various plant materials. For example o-coumaric acid was only found in mistletoe hosted by Quercus robur. Digallic acid was only found in the plant material hosted by Acer plantanoides. Qualitative and quantitative composition of mistletoes hosted by Malus domestica and Pyrus communis showed considerable similarities as far as phenolic acids were concerned. Moreover. vanillic acid. absent in all other batches of plant material, seemed to be characteristic of the above mistletoes. Quantitative HPLC analysis demonstrated a considerable content of salicylic acid (39.55 mg%) in mistletoe hosted by Sorbus aucuparia. Apart from the above material, this compound was only present in small quantities in plants hosted by Populus nigra (15.63 mg%) and Quercus robur (2.63 mg%).

  2. Virulent strain of Lichtheimia corymbifera shows increased phagocytosis by macrophages as revealed by automated microscopy image analysis.

    PubMed

    Kraibooj, Kaswara; Park, Hea-Reung; Dahse, Hans-Martin; Skerka, Christine; Voigt, Kerstin; Figge, Marc Thilo

    2014-12-01

    Lichtheimia corymbifera is a ubiquitous soilborne zygomycete fungus, which is an opportunistic human pathogen in immunocompromised patients. The fungus can cause life-threatening diseases by attacking the lung during early stages of invasion and by disseminating during later phases causing systemic infection. Since infections have drastically increased during the last decades, it is a major goal to investigate the mechanisms underlying pathogenicity of L. corymbifera. One of the first barriers, which the fungus needs to cope with in the lung tissue, is phagocytosis by alveolar macrophages. Here, we report on phagocytosis assays for murine alveolar macrophages co-incubated with resting, swollen and opsonised spores of a virulent and an attenuated L. corymbifera strain. A major finding of this study is the significantly increased phagocytosis ratio of the virulent strain if compared to the attenuated strain. We quantify the phagocytosis by performing automated analysis of fluorescence microscopy images and by computing ratios for (i) fungal phagocytosis, (ii) fungal adhesion to phagocytes and (iii) fungal aggregation and spore cluster distribution in space. Automation of the image analysis yields objective results that overcome the disadvantages of manual analyses being time consuming, error-prone and subjective. Therefore, it can be expected that automated image analysis of confrontation assays will play a crucial role in future investigations of host-pathogen interactions.

  3. Functional Analysis of Leishmania Cyclopropane Fatty Acid Synthetase

    PubMed Central

    Oyola, Samuel O.; Evans, Krystal J.; Smith, Terry K.; Smith, Barbara A.; Hilley, James D.; Mottram, Jeremy C.; Kaye, Paul M.; Smith, Deborah F.

    2012-01-01

    The single gene encoding cyclopropane fatty acid synthetase (CFAS) is present in Leishmania infantum, L. mexicana and L. braziliensis but absent from L. major, a causative agent of cutaneous leishmaniasis. In L. infantum, usually causative agent of visceral leishmaniasis, the CFAS gene is transcribed in both insect (extracellular) and host (intracellular) stages of the parasite life cycle. Tagged CFAS protein is stably detected in intracellular L. infantum but only during the early log phase of extracellular growth, when it shows partial localisation to the endoplasmic reticulum. Lipid analyses of L. infantum wild type, CFAS null and complemented parasites detect a low abundance CFAS-dependent C19Δ fatty acid, characteristic of a cyclopropanated species, in wild type and add-back cells. Sub-cellular fractionation studies locate the C19Δ fatty acid to both ER and plasma membrane-enriched fractions. This fatty acid is not detectable in wild type L. major, although expression of the L. infantum CFAS gene in L. major generates cyclopropanated fatty acids, indicating that the substrate for this modification is present in L. major, despite the absence of the modifying enzyme. Loss of the L. infantum CFAS gene does not affect extracellular parasite growth, phagocytosis or early survival in macrophages. However, while endocytosis is also unaffected in the extracellular CFAS nulls, membrane transporter activity is defective and the null parasites are more resistant to oxidative stress. Following infection in vivo, L. infantum CFAS nulls exhibit lower parasite burdens in both the liver and spleen of susceptible hosts but it has not been possible to complement this phenotype, suggesting that loss of C19Δ fatty acid may lead to irreversible changes in cell physiology that cannot be rescued by re-expression. Aberrant cyclopropanation in L. major decreases parasite virulence but does not influence parasite tissue tropism. PMID:23251490

  4. ω-6 (18:2) and ω-3 (18:3) fatty acids in reconstituted high-density lipoproteins show different functionality of anti-atherosclerotic properties and embryo toxicity.

    PubMed

    Park, Ki-Hoon; Kim, Jae-Yong; Choi, Inho; Kim, Jae-Ryong; Cho, Kyung-Hyun

    2015-12-01

    Among unsaturated fatty acids, epidemiologic studies have demonstrated that ω-6 (linoleic acid) and ω-3 (linolenic acid) fatty acids show different associations with risk of cardiovascular disease (CVD), although its molecular mechanisms remain unclear. To determine why consumption of ω-3 fatty acid is associated with lower risk of CVD, we investigated the biological functions of ω-6 (linoleic acid) and ω-3 (linolenic acid) in reconstituted HDL (rHDL) after encapsulation using human cells and zebrafish embryo. Apolipoprotein A-I (apoA-I) is the principal protein behind the beneficial functions of HDL, which include potent anti-oxidant, anti-inflammatory, and anti-atherosclerotic activities in blood. Several rHDLs were synthesized with apoA-I and different molar ratio of ω-6 or ω-3 fatty acid. Both fatty acids showed similar solubility in rHDL up to a molar ratio of 95:5:1:10 (palmitoyloleoyl phosphatidylcholine:cholesterol:apoA-I:fatty acid). Although both rHDL showed similar structural properties and α-helical contents, ω-6-rHDL showed loss of anti-oxidant ability against LDL oxidation. Uptake of acetylated LDL into macrophages was inhibited by ω-3-rHDL but not ω-6-rHDL, suggesting that ω-6-rHDL has higher pro-atherosclerotic activity. ω-3-rHDL showed more enhanced cholesterol efflux activity with less accumulation of triglyceride in the macrophage. ω-6-rHDL caused more senescence in human dermal fibroblast cells with cytotoxicity, while ω-3-rHDL treatment inhibited the senescence. In zebrafish embryo survivability, ω-3-rHDL-injected embryos showed 86±3% survival, whereas ω-6-rHDL-injected ones showed 72±2% survival as well as an elevated inflammatory response in zebrafish embryos. In conclusion, ω-6-rHDL and ω-3-rHDL show different physiological activities in atherosclerosis, inflammation, and cellular senescence.

  5. Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins.

    PubMed

    Phillips, Nancy J; Steichen, Christopher T; Schilling, Birgit; Post, Deborah M B; Niles, Richard K; Bair, Thomas B; Falsetta, Megan L; Apicella, Michael A; Gibson, Bradford W

    2012-01-01

    Neisseria gonorrhoeae, the causative agent of gonorrhea, can form biofilms in vitro and in vivo. In biofilms, the organism is more resistant to antibiotic treatment and can serve as a reservoir for chronic infection. We have used stable isotope labeling by amino acids in cell culture (SILAC) to compare protein expression in biofilm and planktonic organisms. Two parallel populations of N. gonorrhoeae strain 1291, which is an arginine auxotroph, were grown for 48 h in continuous-flow chambers over glass, one supplemented with (13)C(6)-arginine for planktonic organisms and the other with unlabeled arginine for biofilm growth. The biofilm and planktonic cells were harvested and lysed separately, and fractionated into three sequential protein extracts. Corresponding heavy (H) planktonic and light (L) biofilm protein extracts were mixed and separated by 1D SDS-PAGE gels, and samples were extensively analyzed by liquid chromatography-mass spectrometry. Overall, 757 proteins were identified, and 152 unique proteins met a 1.5-fold cutoff threshold for differential expression with p-values <0.05. Comparing biofilm to planktonic organisms, this set included 73 upregulated and 54 downregulated proteins. Nearly a third of the upregulated proteins were involved in energy metabolism, with cell envelope proteins making up the next largest group. Of the downregulated proteins, the largest groups were involved in protein synthesis and energy metabolism. These proteomics results were compared with our previously reported results from transcriptional profiling of gonococcal biofilms using microarrays. Nitrite reductase and cytochrome c peroxidase, key enzymes required for anaerobic growth, were detected as highly upregulated in both the proteomic and transcriptomic datasets. These and other protein expression changes observed in the present study were consistent with a shift to anaerobic respiration in gonococcal biofilms, although changes in membrane proteins not explicitly related

  6. Virome analysis of antiretroviral-treated HIV patients shows no correlation between T-cell activation and anelloviruses levels

    PubMed Central

    Li, Linlin; Deng, Xutao; Da Costa, Antonio Charlys; Bruhn, Roberta; Deeks, Steven G.; Delwart, Eric

    2015-01-01

    Background Abnormally high levels of T-cell activation can persist in HIV-infected subjects despite effective anti-retroviral therapy (ART) and has been associated with negative health outcomes. The nature of the antigenic drivers or other causes of this residual T-cell activation remain uncertain. Anelloviruses are universally acquired soon after birth, resulting in persistent viremia, and considered part of the commensal human virome. Reduced immunocompetence results in increased anellovirus levels. Objectives To test whether increased levels of anelloviruses or other viruses in plasma are associated with higher levels of persistent T-cell activation during ART. Study design Two amplification methods combined with next generation sequencing were used to detect all viruses and estimate relative anellovirus levels in plasma from 19 adults on effective ART who exhibited a wide range of T-cell activation levels. Results Nucleic acids from HBV and HCV were detected in one patient each while pegivirus A (GBV-C) was found in three patients. Anellovirus DNA was detected in all patients with some individuals carrying up to eight different genotypes. Specific anellovirus genotypes or higher level of co-infections were not detected in subjects with higher levels of T-cell activation. No association was detected between relative plasma anellovirus DNA levels and the percentage of activated CD4 or CD8 T cells. Conclusions Human anelloviruses were detected in all HIV suppressed subjects, exhibited a wide range of viremia levels, and were genetically highly diverse. The level of persistent T-cell activation was not correlated with the level of viremia or genotypes present indicating that anellovirus antigens are unlikely to be a dominant source of antigens driving chronic T-cell activation. PMID:26479202

  7. Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids

    PubMed Central

    Bonacci, Gustavo; Asciutto, Eliana K.; Woodcock, Steven R.; Salvatore, Sonia R.; Freeman, Bruce A.; Schopfer, Francisco J.

    2012-01-01

    Nitro-fatty acids are electrophilic signaling mediators formed in increased amounts during inflammation by nitric oxide and nitrite-dependent redox reactions. A more rigorous characterization of endogenously-generated species requires additional understanding of their gas-phase induced fragmentation. Thus, collision induced dissociation (CID) of nitroalkane and nitroalkene groups in fatty acids were studied in the negative ion mode to provide mass spectrometric tools for their structural characterization. Fragmentation of nitroalkanes occurred mainly through loss of the NO2− anion or neutral loss of HNO2. The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional γ or δ unsaturation occurred through a multiple step cyclization reaction process, leading to 5 and 6 member ring heterocyclic products and carbon chain fragmentation. Cyclization products were not obtained during nitroalkane fragmentation, highlighting the role of double bond π electrons during NO2− rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of 13C and 15N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples. PMID:21953257

  8. RP-HPLC analysis of phenolic acids of selected Central European Carex L. (Cyperaceae) species and its implication for taxonomy.

    PubMed

    Bogucka-Kocka, Anna; Szewczyk, Katarzyna; Janyszek, Magdalena; Janyszek, Sławomir; Cieśla, Łukasz

    2011-01-01

    Eighteen species belonging to the Carex genus were checked for the presence and the amount of eight phenolic acids (p-hydroxybenzoic, vanillic, caffeic, syringic, protocatechuic, p-coumaric, sinapic, and ferulic) by means of HPLC. Both the free and bonded phenolic acids were analyzed. The majority of the analyzed acids occurred in the studied species in relatively high amounts. The highest concentrations found were caffeic acid and p-coumaric acid, for which the detected levels were negatively correlated. A very interesting feature was the occurrence of sinapic acid, a compound very rarely detected in plant tissues. Its distribution across the analyzed set of species can be hypothetically connected with the humidity of plants' habitats. Several attempted tests of aggregative cluster analysis showed no similarity to the real taxonomical structure of the genus Carex. Thus, the phenolic acids' composition cannot be considered as the major taxonomical feature for the genus Carex.

  9. Global gene analysis of oocytes from early stages in human folliculogenesis shows high expression of novel genes in reproduction.

    PubMed

    Markholt, S; Grøndahl, M L; Ernst, E H; Andersen, C Yding; Ernst, E; Lykke-Hartmann, K

    2012-02-01

    The pool of primordial follicles in humans is laid down during embryonic development and follicles can remain dormant for prolonged intervals, often decades, until individual follicles resume growth. The mechanisms that induce growth and maturation of primordial follicles are poorly understood but follicles once activated either continue growth or undergo atresia. We have isolated pure populations of oocytes from human primordial, intermediate and primary follicles using laser capture micro-dissection microscopy and evaluated the global gene expression profiles by whole-genome microarray analysis. The array data were confirmed by qPCR for selected genes. A total of 6301 unique genes were identified as significantly expressed representing enriched specific functional categories such as 'RNA binding', 'translation initiation' and 'structural molecule activity'. Several genes, some not previously known to be associated with early oocyte development, were identified with exceptionally high expression levels, such as the anti-proliferative transmembrane protein with an epidermal growth factor-like and two follistatin-like domains (TMEFF2), the Rho-GTPase-activating protein oligophrenin 1 (OPHN1) and the mitochondrial-encoded ATPase6 (ATP6). Thus, the present study provides not only a technique to capture and perform transcriptome analysis of the sparse material of human oocytes from the earliest follicle stages but further includes a comprehensive basis for our understanding of the regulatory factors and pathways present during early human folliculogenesis.

  10. Comparative Analysis of Clinical Samples Showing Weak Serum Reaction on AutoVue System Causing ABO Blood Typing Discrepancies

    PubMed Central

    Jo, Su Yeon; Lee, Ju Mi; Kim, Hye Lim; Sin, Kyeong Hwa; Lee, Hyeon Ji; Chang, Chulhun Ludgerus

    2017-01-01

    Background ABO blood typing in pre-transfusion testing is a major component of the high workload in blood banks that therefore requires automation. We often experienced discrepant results from an automated system, especially weak serum reactions. We evaluated the discrepant results by the reference manual method to confirm ABO blood typing. Methods In total, 13,113 blood samples were tested with the AutoVue system; all samples were run in parallel with the reference manual method according to the laboratory protocol. Results The AutoVue system confirmed ABO blood typing of 12,816 samples (97.7%), and these results were concordant with those of the manual method. The remaining 297 samples (2.3%) showed discrepant results in the AutoVue system and were confirmed by the manual method. The discrepant results involved weak serum reactions (<2+ reaction grade), extra serum reactions, samples from patients who had received stem cell transplants, ABO subgroups, and specific system error messages. Among the 98 samples showing ≤1+ reaction grade in the AutoVue system, 70 samples (71.4%) showed a normal serum reaction (≥2+ reaction grade) with the manual method, and 28 samples (28.6%) showed weak serum reaction in both methods. Conclusions ABO blood tying of 97.7% samples could be confirmed by the AutoVue system and a small proportion (2.3%) needed to be re-evaluated by the manual method. Samples with a 2+ reaction grade in serum typing do not need to be evaluated manually, while those with ≤1+ reaction grade do. PMID:28028997

  11. Analysis of the Relationship Between Predictors of No-Show Appointment Behavior and the Benefit of Automated Patient Reminders

    DTIC Science & Technology

    2006-05-31

    number of patients who miss their appointment, clinics have been able to achieve greater efficiency through demand forecasting (Dove and Schneider, 1981 ... 1981 ). Lending further creditability to the predictive value of patient specific characteristics, Goldman, Freidin, Cook, Eigner and Grich ( 1981 ) found...independently correlated with no-show behavior (Goldman et al., 1981 ). As administrators and clinicians grapple with the best method for curbing the

  12. Analysis and survival of amino acids in Martian regolith analogs

    NASA Astrophysics Data System (ADS)

    Garry, James R. C.; Loes Ten Kate, Inge; Martins, Zita; Nørnberg, Per; Ehrenfreund, Pascale

    2006-03-01

    We have investigated the native amino acid composition of two analogs of Martian soil, JSC Mars-1 and Salten Skov. A Mars simulation chamber has been built and used to expose samples of these analogs to temperature and lighting conditions similar to those found at low latitudes on the Martian surface. The effects of the simulated conditions have been examined using high-performance liquid chromatography (HPLC). Exposure to energetic ultraviolet (UV) light in vacuum appears to cause a modest increase in the concentration of certain amino acids within the materials, which is interpreted as resulting from the degradation of microorganisms. The influence of low temperatures shows that the accretion of condensed water on the soils leads to the destruction of amino acids, supporting the idea that reactive chemical processes involving H2O are at work within the Martian soil. We discuss the influence of UV radiation, low temperatures, and gaseous CO2 on the intrinsic amino acid composition of Martian soil analogs and describe, with the help of a simple model, how these studies fit within the framework of life detection on Mars and the practical tasks of choosing and using Martian regolith analogs in planetary research.

  13. Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway.

    PubMed

    Muñoz-Ramírez, Zilia Y; Mendez-Tenorio, Alfonso; Kato, Ikuko; Bravo, Maria M; Rizzato, Cosmeri; Thorell, Kaisa; Torres, Roberto; Aviles-Jimenez, Francisco; Camorlinga, Margarita; Canzian, Federico; Torres, Javier

    2017-01-01

    Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.

  14. Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway

    PubMed Central

    Muñoz-Ramírez, Zilia Y.; Mendez-Tenorio, Alfonso; Kato, Ikuko; Bravo, Maria M.; Rizzato, Cosmeri; Thorell, Kaisa; Torres, Roberto; Aviles-Jimenez, Francisco; Camorlinga, Margarita; Canzian, Federico; Torres, Javier

    2017-01-01

    Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk. PMID:28293542

  15. [Fast analysis of common fatty acids in edible vegetable oils by ultra-performance convergence chromatography-mass spectrometry].

    PubMed

    Lin, Chunhua; Xie, Xianqing; Fan, Naili; Tu, Yuanhong; Chen, Yan; Liao, Weilin

    2015-04-01

    A fast analytical method for five common fatty acids in six edible vegetable oils was developed by ultra-performance convergence chromatography-mass spectrometry (UPC2-MS). The five fatty acids are palmitic acid, stearic acid, oleic acid, linoleic acid and linolenic acid. Their contents in the corn oil, sunflower oil, soybean oil, tea oil, rapeseed oil and peanut oil were compared. The chromatographic separation was performed on an ACQUITY UPC2 BEH 2-EP column (100 mm x 2.1 mm, 1.7 µm) using the mobile phases of carbon dioxide and methanol/acetonitrile (1:1, v/v) with gradient elution. The separated compounds were detected by negative electrospray ionization ESF-MS. The results showed that the reasonable linearities were achieved for all the analytes over the range of 0.5-100 mg/L with the correlation coefficients (R2) of 0.9985-0.9998. The limits of quantification (S/N ≥ 10) of the five fatty acids were 0.15-0.50 mg/L. The recoveries of the five fatty acids at three spiked levels were in the range of 89.61%-108.50% with relative standard deviations of 0.69%-3.01%. The developed method showed high performance, good resolution and fast analysis for the underivatized fatty acids. It has been successfully used to detect the five fatty acids from corn oil, sunflower oil, soybean oil, tea oil rapeseed oil and peanut oil.

  16. Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

    PubMed Central

    Lees, John A.; Kremer, Philip H. C.; Manso, Ana S.; Croucher, Nicholas J.; Ferwerda, Bart; Serón, Mercedes Valls; Oggioni, Marco R.; Parkhill, Julian; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2017-01-01

    Recent studies have provided evidence for rapid pathogen genome diversification, some of which could potentially affect the course of disease. We have previously described such variation seen between isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis. Here, we performed whole-genome sequencing of paired isolates from the blood and CSF of 869 meningitis patients to determine whether such variation frequently occurs between these two niches in cases of bacterial meningitis. Using a combination of reference-free variant calling approaches, we show that no genetic adaptation occurs in either invaded niche during bacterial meningitis for two major pathogen species, Streptococcus pneumoniae and Neisseria meningitidis. This study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood–brain barrier. Our findings place the focus back on bacterial evolution between nasopharyngeal carriage and invasion, or diversity of the host, as likely mechanisms for determining invasiveness. PMID:28348877

  17. Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions

    NASA Astrophysics Data System (ADS)

    Vatansever, Sezen; Gümüş, Zeynep H.; Erman, Burak

    2016-11-01

    K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach –conditional time-delayed correlations (CTC) – using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations. Analyzing nucleotide-dependent intrinsic K-Ras motions with the new approach yields predictions that agree with the literature, showing that GTP-binding stabilizes K-Ras motions and leads to residue correlations with relatively long characteristic decay times. Furthermore, our study is the first to identify driver-follower relationships in correlated motions of K-Ras residue pairs, revealing the direction of information flow during allosteric modulation of its nucleotide-dependent intrinsic activity: active K-Ras Switch-II region motions drive Switch-I region motions, while α-helix-3L7 motions control both. Our results provide novel insights for strategies that directly target mutant K-Ras.

  18. Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions

    PubMed Central

    Vatansever, Sezen; Gümüş, Zeynep H.; Erman, Burak

    2016-01-01

    K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach –conditional time-delayed correlations (CTC) – using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations. Analyzing nucleotide-dependent intrinsic K-Ras motions with the new approach yields predictions that agree with the literature, showing that GTP-binding stabilizes K-Ras motions and leads to residue correlations with relatively long characteristic decay times. Furthermore, our study is the first to identify driver-follower relationships in correlated motions of K-Ras residue pairs, revealing the direction of information flow during allosteric modulation of its nucleotide-dependent intrinsic activity: active K-Ras Switch-II region motions drive Switch-I region motions, while α-helix-3L7 motions control both. Our results provide novel insights for strategies that directly target mutant K-Ras. PMID:27845397

  19. Tomato PYR/PYL/RCAR abscisic acid receptors show high expression in root, differential sensitivity to the abscisic acid agonist quinabactin, and the capability to enhance plant drought resistance.

    PubMed

    González-Guzmán, Miguel; Rodríguez, Lesia; Lorenzo-Orts, Laura; Pons, Clara; Sarrión-Perdigones, Alejandro; Fernández, Maria A; Peirats-Llobet, Marta; Forment, Javier; Moreno-Alvero, Maria; Cutler, Sean R; Albert, Armando; Granell, Antonio; Rodríguez, Pedro L

    2014-08-01

    Abscisic acid (ABA) plays a crucial role in the plant's response to both biotic and abiotic stress. Sustainable production of food faces several key challenges, particularly the generation of new varieties with improved water use efficiency and drought tolerance. Different studies have shown the potential applications of Arabidopsis PYR/PYL/RCAR ABA receptors to enhance plant drought resistance. Consequently the functional characterization of orthologous genes in crops holds promise for agriculture. The full set of tomato (Solanum lycopersicum) PYR/PYL/RCAR ABA receptors have been identified here. From the 15 putative tomato ABA receptors, 14 of them could be grouped in three subfamilies that correlated well with corresponding Arabidopsis subfamilies. High levels of expression of PYR/PYL/RCAR genes was found in tomato root, and some genes showed predominant expression in leaf and fruit tissues. Functional characterization of tomato receptors was performed through interaction assays with Arabidopsis and tomato clade A protein phosphatase type 2Cs (PP2Cs) as well as phosphatase inhibition studies. Tomato receptors were able to inhibit the activity of clade A PP2Cs differentially in an ABA-dependent manner, and at least three receptors were sensitive to the ABA agonist quinabactin, which inhibited tomato seed germination. Indeed, the chemical activation of ABA signalling induced by quinabactin was able to activate stress-responsive genes. Both dimeric and monomeric tomato receptors were functional in Arabidopsis plant cells, but only overexpression of monomeric-type receptors conferred enhanced drought resistance. In summary, gene expression analyses, and chemical and transgenic approaches revealed distinct properties of tomato PYR/PYL/RCAR ABA receptors that might have biotechnological implications.

  20. Tomato PYR/PYL/RCAR abscisic acid receptors show high expression in root, differential sensitivity to the abscisic acid agonist quinabactin, and the capability to enhance plant drought resistance

    PubMed Central

    González-Guzmán, Miguel; Rodríguez, Lesia; Lorenzo-Orts, Laura; Pons, Clara; Sarrión-Perdigones, Alejandro; Fernández, Maria A.; Peirats-Llobet, Marta; Forment, Javier; Moreno-Alvero, Maria; Cutler, Sean R.; Albert, Armando; Granell, Antonio; Rodríguez, Pedro L.

    2014-01-01

    Abscisic acid (ABA) plays a crucial role in the plant’s response to both biotic and abiotic stress. Sustainable production of food faces several key challenges, particularly the generation of new varieties with improved water use efficiency and drought tolerance. Different studies have shown the potential applications of Arabidopsis PYR/PYL/RCAR ABA receptors to enhance plant drought resistance. Consequently the functional characterization of orthologous genes in crops holds promise for agriculture. The full set of tomato (Solanum lycopersicum) PYR/PYL/RCAR ABA receptors have been identified here. From the 15 putative tomato ABA receptors, 14 of them could be grouped in three subfamilies that correlated well with corresponding Arabidopsis subfamilies. High levels of expression of PYR/PYL/RCAR genes was found in tomato root, and some genes showed predominant expression in leaf and fruit tissues. Functional characterization of tomato receptors was performed through interaction assays with Arabidopsis and tomato clade A protein phosphatase type 2Cs (PP2Cs) as well as phosphatase inhibition studies. Tomato receptors were able to inhibit the activity of clade A PP2Cs differentially in an ABA-dependent manner, and at least three receptors were sensitive to the ABA agonist quinabactin, which inhibited tomato seed germination. Indeed, the chemical activation of ABA signalling induced by quinabactin was able to activate stress-responsive genes. Both dimeric and monomeric tomato receptors were functional in Arabidopsis plant cells, but only overexpression of monomeric-type receptors conferred enhanced drought resistance. In summary, gene expression analyses, and chemical and transgenic approaches revealed distinct properties of tomato PYR/PYL/RCAR ABA receptors that might have biotechnological implications. PMID:24863435

  1. Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils

    PubMed Central

    Quideau, Sylvie A.; McIntosh, Anne C.S.; Norris, Charlotte E.; Lloret, Emily; Swallow, Mathew J.B.; Hannam, Kirsten

    2016-01-01

    Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about the overall structure of terrestrial microbial communities. PLFA profiling has been extensively used in a range of ecosystems as a biological index of overall soil quality, and as a quantitative indicator of soil response to land management and other environmental stressors. The standard method presented here outlines four key steps: 1. lipid extraction from soil samples with a single-phase chloroform mixture, 2. fractionation using solid phase extraction columns to isolate phospholipids from other extracted lipids, 3. methanolysis of phospholipids to produce fatty acid methyl esters (FAMEs), and 4. FAME analysis by capillary gas chromatography using a flame ionization detector (GC-FID). Two standards are used, including 1,2-dinonadecanoyl-sn-glycero-3-phosphocholine (PC(19:0/19:0)) to assess the overall recovery of the extraction method, and methyl decanoate (MeC10:0) as an internal standard (ISTD) for the GC analysis. PMID:27685177

  2. Analysis of HCV genotypes from blood donors shows three new HCV type 6 subgroups exist in Myanmar.

    PubMed

    Shinji, Toshiyuki; Kyaw, Yi Yi; Gokan, Katsunori; Tanaka, Yasuhito; Ochi, Koji; Kusano, Nobuchika; Mizushima, Takaaki; Fujioka, Shin-ichi; Shiraha, Hidenori; Lwin, Aye Aye; Shiratori, Yasushi; Mizokami, Masashi; Khin, Myo; Miyahara, Masayuki; Okada, Shigeru; Koide, Norio

    2004-06-01

    The prevalence of hepatitis C virus (HCV) genotypes in Myanmar in comparison with the rest of Southeast Asia is not well known. Serum samples were obtained from 201 HCV antibody-positive volunteer blood donors in and around the Myanmar city of Yangon. Of these, the antibody titers of 101 samples were checked by serial dilution using HCV antibody PA test II and Terasaki microplate as a low-cost method. To compare antibody titers by this method and RNA identification, we also checked HCV-RNA using the Amplicor 2.0 test. Most high-titer groups were positive for HCV-RNA. Of the 201 samples, 110 were successfully polymerase chain reaction (PCR) amplified. Among them, 35 (31.8%) were of genotype 1, 52 (47.3%) were of genotype 3, and 23 (20.9%) were of type 6 variants, and phylogenetic analysis of these type 6 variants revealed that 3 new type 6 subgroups exist in Myanmar. We named the subgroups M6-1, M6-2, and M6-3. M6-1 and M6-2 were relatively close to types 8 and 9, respectively. M6-3, though only found in one sample, was a brand-new subgroup. These subtypes were not seen in Vietnam, where type 6 group variants are widely spread. These findings may be useful for analyzing how and when these subgroups were formed.

  3. Phylogenetic analysis shows that Neolithic slate plaques from the southwestern Iberian Peninsula are not genealogical recording systems.

    PubMed

    García Rivero, Daniel; O'Brien, Michael J

    2014-01-01

    Prehistoric material culture proposed to be symbolic in nature has been the object of considerable archaeological work from diverse theoretical perspectives, yet rarely are methodological tools used to test the interpretations. The lack of testing is often justified by invoking the opinion that the slippery nature of past human symbolism cannot easily be tackled by the scientific method. One such case, from the southwestern Iberian Peninsula, involves engraved stone plaques from megalithic funerary monuments dating ca. 3,500-2,750 B.C. (calibrated age). One widely accepted proposal is that the plaques are ancient mnemonic devices that record genealogies. The analysis reported here demonstrates that this is not the case, even when the most supportive data and techniques are used. Rather, we suspect there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula, with little or no geographic patterning. This would entail a cultural system in which plaque design was based on a fundamental core idea, with a number of mutable and variable elements surrounding it.

  4. Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull

    PubMed Central

    Esteve-Altava, Borja; Boughner, Julia C.; Diogo, Rui; Villmoare, Brian A.; Rasskin-Gutman, Diego

    2015-01-01

    Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon’s general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates. PMID:25992690

  5. Anatomical network analysis shows decoupling of modular lability and complexity in the evolution of the primate skull.

    PubMed

    Esteve-Altava, Borja; Boughner, Julia C; Diogo, Rui; Villmoare, Brian A; Rasskin-Gutman, Diego

    2015-01-01

    Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon's general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates.

  6. Phylogenetic Analysis Shows That Neolithic Slate Plaques from the Southwestern Iberian Peninsula Are Not Genealogical Recording Systems

    PubMed Central

    García Rivero, Daniel; O'Brien, Michael J.

    2014-01-01

    Prehistoric material culture proposed to be symbolic in nature has been the object of considerable archaeological work from diverse theoretical perspectives, yet rarely are methodological tools used to test the interpretations. The lack of testing is often justified by invoking the opinion that the slippery nature of past human symbolism cannot easily be tackled by the scientific method. One such case, from the southwestern Iberian Peninsula, involves engraved stone plaques from megalithic funerary monuments dating ca. 3,500–2,750 B.C. (calibrated age). One widely accepted proposal is that the plaques are ancient mnemonic devices that record genealogies. The analysis reported here demonstrates that this is not the case, even when the most supportive data and techniques are used. Rather, we suspect there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula, with little or no geographic patterning. This would entail a cultural system in which plaque design was based on a fundamental core idea, with a number of mutable and variable elements surrounding it. PMID:24558384

  7. Meta-analysis of quantification methods shows that archaea and bacteria have similar abundances in the subseafloor.

    PubMed

    Lloyd, Karen G; May, Megan K; Kevorkian, Richard T; Steen, Andrew D

    2013-12-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined "yield" to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.

  8. Metabolism of Seriola lalandi during Starvation as Revealed by Fatty Acid Analysis and Compound-Specific Analysis of Stable Isotopes within Amino Acids

    PubMed Central

    Barreto-Curiel, Fernando; Focken, Ulfert; D’Abramo, Louis R.

    2017-01-01

    Fish starvation is defined as food deprivation for a long period of time, such that physiological processes become confined to basal metabolism. Starvation provides insights in physiological processes without interference from unknown factors in digestion and nutrient absorption occurring in fed state. Juveniles of amberjack Seriola lalandi were isotopically equilibrated to a formulated diet for 60 days. One treatment consisted of fish that continued to be fed and fish in the other treatment were not fed for 35 days. The isotopic signatures prior to the beginning of and after the starvation period, for fish in the starvation and control treatments, were analysed for lipid content, fatty acid composition and isotopic analysis of bulk (EA-IRMS) and of amino acids (compound specific isotope analysis, CSIA). There were three replicates for the starvation group. Fatty acid content in muscle and liver tissue before and after starvation was determined to calculate percent change. Results showed that crude lipid was the most used source of energy in most cases; the PUFAs and LC-PUFAs were highly conserved. According to the protein signature in bulk (δ15N) and per amino acid (δ13C and δ15N), in muscle tissue, protein synthesis did not appear to occur substantially during starvation, whereas in liver, increases in δ13C and δ15N indicate that protein turnover occurred, probably for metabolic routing to energy-yielding processes. As a result, isotopic values of δ15N in muscle tissue do not change, whereas CSIA net change occurred in the liver tissue. During the study period of 35 days, muscle protein was largely conserved, being neither replenished from amino acid pools in the plasma and liver nor catabolized. PMID:28095488

  9. Structure and function analysis of protein-nucleic acid complexes

    NASA Astrophysics Data System (ADS)

    Kuznetsova, S. A.; Oretskaya, T. S.

    2016-05-01

    The review summarizes published data on the results and achievements in the field of structure and function analysis of protein-nucleic acid complexes by means of main physical and biochemical methods, including X-ray diffraction, nuclear magnetic resonance spectroscopy, electron and atomic force microscopy, small-angle X-ray and neutron scattering, footprinting and cross-linking. Special attention is given to combined approaches. The advantages and limitations of each method are considered, and the prospects of their application for wide-scale structural studies in vivo are discussed. The bibliography includes 145 references.

  10. Genetic analysis shows that morphology alone cannot distinguish asian carp eggs from those of other cyprinid species

    USGS Publications Warehouse

    Larson, James H.; McCalla, Sunnie; Chapman, Duane C.; Rees, Christopher B.; Knights, Brent C.; Vallazza, Jon; George, Amy E.; Richardson, William B.; Amberg, Jon

    2016-01-01

    Fish eggs and embryos (hereafter collectively referred to as “eggs”) were collected in the upper Mississippi River main stem (~300 km upstream of previously reported spawning by invasive Asian carp) during summer 2013. Based on previously published morphological characteristics, the eggs were identified as belonging to Asian carp. A subsample of the eggs was subsequently analyzed by using molecular methods to determine species identity. Genetic identification using the cytochrome-c oxidase 1 gene was attempted for a total of 41 eggs. Due to the preservation technique used (formalin) and the resulting DNA degradation, sequences were recovered from only 17 individual eggs. In all 17 cases, cyprinids other than Asian carp (usually Notropis sp.) were identified as the most likely species. In previously published reports, a key characteristic that distinguished Asian carp eggs from those of other cyprinids was size: Asian carp eggs exhibited diameters ranging from 4.0 to 6.0 mm and were thought to be much larger than the otherwise similar eggs of native species. Eggs from endemic cyprinids were believed to rarely reach 3.0 mm and had not been observed to exceed 3.3 mm. However, many of the eggs that were genetically identified as originating from native cyprinids were as large as 4.0 mm in diameter (at early developmental stages) and were therefore large enough to over- lap with the lower end of the size range observed for Asian carp eggs. Researchers studying the egg stages of Asian carp and other cyprinids should plan on preserving subsets of eggs for genetic analysis to confirm morphological identifications.

  11. Efficacy of extended thrombo-prophylaxis in major abdominal surgery: what does the evidence show? A meta-analysis.

    PubMed

    Bottaro, Federico Jorge; Elizondo, Maria Cristina; Doti, Carlos; Bruetman, Julio Enrique; Perez Moreno, Pablo Diego; Bullorsky, Eduardo Oscar; Ceresetto, Jose Manuel

    2008-06-01

    Venous thromboembolism (VTE) is a frequent complication following major abdominal surgery. The use of low-molecular-weight heparins (LMWH) to prevent thrombotic events in these patients is a common and well documented practice. However, there is some controversy surrounding the duration of the prophylaxis, as it has been suggested that the risk persists for several weeks after surgery. The objective of this meta-analysis is to systematically review the clinical studies that compared safety and efficacy of extended use of LMWH (for three to four weeks after surgery) versus conventional in-hospital prophylaxis. An electronic data base search was performed. Only randomized, controlled studies were eligible. Data on the incidence of deep vein thrombosis (DVT), VTE and bleeding were extracted. Only three studies fulfilled the inclusion criteria. The indication for surgery was neoplastic disease in 70.6% (780/1104) of patients. The administration of extended LMWH prophylaxis significantly reduced the incidence of VTE, 5.93% (23/388) versus 13.6% (55/405), RR 0.44 (CI 95% 0.28 - 0.7); DVT 5.93% (23/388) versus 12.9% (52/402), RR 0.46 (CI 95% 0.29 - 0.74); proximal DVT 1% (4/388) versus 4.72% (19/402), RR 0.24 (CI 95% 0.09 - 0.67). We found no significant difference in major or minor bleeding between the two groups: 3.85% (21/545) in the extended thrombo-prophylaxis (ETP) group versus 3.48% (19/559) in the conventional prophylaxis group; RR 1.12 (CI 95% 0.61 - 2.06). There was no heterogeneity between the studies. We conclude that ETP with LMWH should be considered as a safe and useful strategy to prevent VTE in high-risk major abdominal surgery.

  12. Selection Indices and Multivariate Analysis Show Similar Results in the Evaluation of Growth and Carcass Traits in Beef Cattle

    PubMed Central

    Brito Lopes, Fernando; da Silva, Marcelo Corrêa; Magnabosco, Cláudio Ulhôa; Goncalves Narciso, Marcelo; Sainz, Roberto Daniel

    2016-01-01

    This research evaluated a multivariate approach as an alternative tool for the purpose of selection regarding expected progeny differences (EPDs). Data were fitted using a multi-trait model and consisted of growth traits (birth weight and weights at 120, 210, 365 and 450 days of age) and carcass traits (longissimus muscle area (LMA), back-fat thickness (BF), and rump fat thickness (RF)), registered over 21 years in extensive breeding systems of Polled Nellore cattle in Brazil. Multivariate analyses were performed using standardized (zero mean and unit variance) EPDs. The k mean method revealed that the best fit of data occurred using three clusters (k = 3) (P < 0.001). Estimates of genetic correlation among growth and carcass traits and the estimates of heritability were moderate to high, suggesting that a correlated response approach is suitable for practical decision making. Estimates of correlation between selection indices and the multivariate index (LD1) were moderate to high, ranging from 0.48 to 0.97. This reveals that both types of indices give similar results and that the multivariate approach is reliable for the purpose of selection. The alternative tool seems very handy when economic weights are not available or in cases where more rapid identification of the best animals is desired. Interestingly, multivariate analysis allowed forecasting information based on the relationships among breeding values (EPDs). Also, it enabled fine discrimination, rapid data summarization after genetic evaluation, and permitted accounting for maternal ability and the genetic direct potential of the animals. In addition, we recommend the use of longissimus muscle area and subcutaneous fat thickness as selection criteria, to allow estimation of breeding values before the first mating season in order to accelerate the response to individual selection. PMID:26789008

  13. Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs

    PubMed Central

    Edwards, Ceiridwen J; Bollongino, Ruth; Scheu, Amelie; Chamberlain, Andrew; Tresset, Anne; Vigne, Jean-Denis; Baird, Jillian F; Larson, Greger; Ho, Simon Y.W; Heupink, Tim H; Shapiro, Beth; Freeman, Abigail R; Thomas, Mark G; Arbogast, Rose-Marie; Arndt, Betty; Bartosiewicz, László; Benecke, Norbert; Budja, Mihael; Chaix, Louis; Choyke, Alice M; Coqueugniot, Eric; Döhle, Hans-Jürgen; Göldner, Holger; Hartz, Sönke; Helmer, Daniel; Herzig, Barabara; Hongo, Hitomi; Mashkour, Marjan; Özdogan, Mehmet; Pucher, Erich; Roth, Georg; Schade-Lindig, Sabine; Schmölcke, Ulrich; Schulting, Rick J; Stephan, Elisabeth; Uerpmann, Hans-Peter; Vörös, István; Voytek, Barbara; Bradley, Daniel G; Burger, Joachim

    2007-01-01

    The extinct aurochs (Bos primigenius primigenius) was a large type of cattle that ranged over almost the whole Eurasian continent. The aurochs is the wild progenitor of modern cattle, but it is unclear whether European aurochs contributed to this process. To provide new insights into the demographic history of aurochs and domestic cattle, we have generated high-confidence mitochondrial DNA sequences from 59 archaeological skeletal finds, which were attributed to wild European cattle populations based on their chronological date and/or morphology. All pre-Neolithic aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. We also report one new and highly divergent haplotype in a Neolithic aurochs sample from Germany, which points to greater variability during the Pleistocene. Furthermore, the Neolithic and Bronze Age samples that were classified with confidence as European aurochs using morphological criteria all carry P haplotype mitochondrial DNA, suggesting continuity of Late Glacial and Early Holocene aurochs populations in Europe. Bayesian analysis indicates that recent population growth gives a significantly better fit to our data than a constant-sized population, an observation consistent with a postglacial expansion scenario, possibly from a single European refugial population. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This, in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria, lends persuasive support to a scenario whereby gracile Near Eastern domestic populations, carrying predominantly T haplotypes, replaced P haplotype-carrying robust autochthonous aurochs populations in Europe, from the Early Neolithic onward. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare. PMID

  14. Morphometric analysis of molars in a Middle Pleistocene population shows a mosaic of ‘modern’ and Neanderthal features

    PubMed Central

    Martinón-Torres, María; Spěváčková, Petra; Gracia-Téllez, Ana; Martínez, Ignacio; Bruner, Emiliano; Arsuaga, Juan Luis; Bermúdez de Castro, José María

    2013-01-01

    Previous studies of upper first molar (M1) crown shape have shown significant differences between Homo sapiens and Homo neanderthalensis that were already present in the European Middle Pleistocene populations, including the large dental sample from Atapuerca-Sima de los Huesos (SH). Analysis of other M1 features such as the total crown base area, cusp proportions, cusp angles and occlusal polygon have confirmed the differences between both lineages, becoming a useful tool for the taxonomic assignment of isolated teeth from Late Pleistocene sites. However, until now the pattern of expression of these variables has not been known for the SH sample. This fossil sample, the largest collection from the European Middle Pleistocene, is generally interpreted as being from the direct ancestors of Neanderthals, and thus is a reference sample for assessing the origin of the Neanderthal morphologies. Surprisingly, our study reveals that SH M1s present a unique mosaic of H. neanderthalensis and H. sapiens features. Regarding the cusp angles and the relative occlusal polygon area, SH matches the H. neanderthalensis pattern. However, regarding the total crown base area and relative cusps size, SH M1s are similar to H. sapiens, with a small crown area, a strong hypocone reduction and a protocone enlargement, although the protocone expansion in SH is significantly larger than in any other group studied. The SH dental sample calls into question the uniqueness of some so-called modern traits. Our study also sounds a note of caution on the use of M1 occlusal morphology for the alpha taxonomy of isolated M1s. PMID:23914934

  15. Selection Indices and Multivariate Analysis Show Similar Results in the Evaluation of Growth and Carcass Traits in Beef Cattle.

    PubMed

    Brito Lopes, Fernando; da Silva, Marcelo Corrêa; Magnabosco, Cláudio Ulhôa; Goncalves Narciso, Marcelo; Sainz, Roberto Daniel

    2016-01-01

    This research evaluated a multivariate approach as an alternative tool for the purpose of selection regarding expected progeny differences (EPDs). Data were fitted using a multi-trait model and consisted of growth traits (birth weight and weights at 120, 210, 365 and 450 days of age) and carcass traits (longissimus muscle area (LMA), back-fat thickness (BF), and rump fat thickness (RF)), registered over 21 years in extensive breeding systems of Polled Nellore cattle in Brazil. Multivariate analyses were performed using standardized (zero mean and unit variance) EPDs. The k mean method revealed that the best fit of data occurred using three clusters (k = 3) (P < 0.001). Estimates of genetic correlation among growth and carcass traits and the estimates of heritability were moderate to high, suggesting that a correlated response approach is suitable for practical decision making. Estimates of correlation between selection indices and the multivariate index (LD1) were moderate to high, ranging from 0.48 to 0.97. This reveals that both types of indices give similar results and that the multivariate approach is reliable for the purpose of selection. The alternative tool seems very handy when economic weights are not available or in cases where more rapid identification of the best animals is desired. Interestingly, multivariate analysis allowed forecasting information based on the relationships among breeding values (EPDs). Also, it enabled fine discrimination, rapid data summarization after genetic evaluation, and permitted accounting for maternal ability and the genetic direct potential of the animals. In addition, we recommend the use of longissimus muscle area and subcutaneous fat thickness as selection criteria, to allow estimation of breeding values before the first mating season in order to accelerate the response to individual selection.

  16. Morphometric analysis of molars in a Middle Pleistocene population shows a mosaic of 'modern' and Neanderthal features.

    PubMed

    Martinón-Torres, María; Spěváčková, Petra; Gracia-Téllez, Ana; Martínez, Ignacio; Bruner, Emiliano; Arsuaga, Juan Luis; Bermúdez de Castro, José María

    2013-10-01

    Previous studies of upper first molar (M1) crown shape have shown significant differences between Homo sapiens and Homo neanderthalensis that were already present in the European Middle Pleistocene populations, including the large dental sample from Atapuerca-Sima de los Huesos (SH). Analysis of other M1 features such as the total crown base area, cusp proportions, cusp angles and occlusal polygon have confirmed the differences between both lineages, becoming a useful tool for the taxonomic assignment of isolated teeth from Late Pleistocene sites. However, until now the pattern of expression of these variables has not been known for the SH sample. This fossil sample, the largest collection from the European Middle Pleistocene, is generally interpreted as being from the direct ancestors of Neanderthals, and thus is a reference sample for assessing the origin of the Neanderthal morphologies. Surprisingly, our study reveals that SH M(1) s present a unique mosaic of H. neanderthalensis and H. sapiens features. Regarding the cusp angles and the relative occlusal polygon area, SH matches the H. neanderthalensis pattern. However, regarding the total crown base area and relative cusps size, SH M(1) s are similar to H. sapiens, with a small crown area, a strong hypocone reduction and a protocone enlargement, although the protocone expansion in SH is significantly larger than in any other group studied. The SH dental sample calls into question the uniqueness of some so-called modern traits. Our study also sounds a note of caution on the use of M(1) occlusal morphology for the alpha taxonomy of isolated M(1) s.

  17. Transcriptomic analysis of inbreeding depression in cold-sensitive Drosophila melanogaster shows upregulation of the immune response.

    PubMed

    Vermeulen, C J; Sørensen, P; Kirilova Gagalova, K; Loeschcke, V

    2013-09-01

    In sexually reproducing species, increased homozygosity often causes a decline in fitness, called inbreeding depression. Recently, researchers started describing the functional genomic changes that occur during inbreeding, both in benign conditions and under environmental stress. To further this aim, we have performed a genome-wide gene expression study of inbreeding depression, manifesting as cold sensitivity and conditional lethality. Our focus was to describe general patterns of gene expression during inbreeding depression and to identify specific processes affected in our line. There was a clear difference in gene expression between the stressful restrictive environment and the benign permissive environment in both the affected inbred line and the inbred control line. We noted a strong inbreeding-by-environment interaction, whereby virtually all transcriptional differences between lines were found in the restrictive environment. Functional annotation showed enrichment of transcripts coding for serine proteases and their inhibitors (serpins and BPTI/Kunitz family), which indicates activation of the innate immune response. These genes have previously been shown to respond transcriptionally to cold stress, suggesting the conditional lethal effect is associated with an exaggerated cold stress response. The set of differentially expressed genes significantly overlapped with those found in three other studies of inbreeding depression, demonstrating that it is possible to detect a common signature across different genetic backgrounds.

  18. An actuarial analysis shows that offering lung cancer screening as an insurance benefit would save lives at relatively low cost.

    PubMed

    Pyenson, Bruce S; Sander, Marcia S; Jiang, Yiding; Kahn, Howard; Mulshine, James L

    2012-04-01

    Lung cancer screening is not established as a public health practice, yet the results of a recent large randomized controlled trial showed that screening with low-dose spiral computed tomography reduces lung cancer mortality. Using actuarial models, this study estimated the costs and benefits of annual lung cancer screening offered as a commercial insurance benefit in the high-risk US population ages 50-64. Assuming current commercial reimbursement rates for treatment, we found that screening would cost about $1 per insured member per month in 2012 dollars. The cost per life-year saved would be below $19,000, an amount that compares favorably with screening for cervical, breast, and colorectal cancers. Our results suggest that commercial insurers should consider lung cancer screening of high-risk individuals to be high-value coverage and provide it as a benefit to people who are at least fifty years old and have a smoking history of thirty pack-years or more. We also believe that payers and patients should demand screening from high-quality, low-cost providers, thus helping set an example of efficient system innovation.

  19. Comparative analysis of zygotic developmental genes in Rhodnius prolixus genome shows conserved features on the tracheal developmental pathway.

    PubMed

    Lavore, A; Pascual, A; Salinas, F M; Esponda-Behrens, N; Martinez-Barnetche, J; Rodriguez, M; Rivera-Pomar, R

    2015-09-01

    Most of the in-depth studies on insect developmental genetic have been carried out in the fruit fly Drosophila melanogaster, an holometabolous insect, so much more still remains to be studied in hemimetabolous insects. Having Rhodnius prolixus sequenced genome available, we search for orthologue genes of zygotic signaling pathways, segmentation, and tracheogenesis in the R. prolixus genome and in three species of Triatoma genus transcriptomes, concluding that there is a high level of gene conservation. We also study the function of two genes required for tracheal system development in D. melanogaster - R. prolixus orthologues: trachealess (Rp-trh) and empty spiracles (Rp-ems). From that we see that Rp-trh is required for early tracheal development since Rp-trh RNAi shows that the primary tracheal branches fail to form. On the other hand, Rp-ems is implied in the proper formation of the posterior tracheal branches, in a similar way to D. melanogaster. These results represent the initial characterization of the genes involved in the tracheal development of an hemimetabolous insect building a bridge between the current genomic era and V. Wigglesworth's classical studies on insects' respiratory system physiology.

  20. Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products.

    PubMed

    Holloway, David M; Harrison, Lionel G; Kosman, David; Vanario-Alonso, Carlos E; Spirov, Alexander V

    2006-11-01

    We analyze the relation between maternal gradients and segmentation in Drosophila, by quantifying spatial precision in protein patterns. Segmentation is first seen in the striped expression patterns of the pair-rule genes, such as even-skipped (eve). We compare positional precision between Eve and the maternal gradients of Bicoid (Bcd) and Caudal (Cad) proteins, showing that Eve position could be initially specified by the maternal protein concentrations but that these do not have the precision to specify the mature striped pattern of Eve. By using spatial trends, we avoid possible complications in measuring single boundary precision (e.g., gap gene patterns) and can follow how precision changes in time. During nuclear cleavage cycles 13 and 14, we find that Eve becomes increasingly correlated with egg length, whereas Bcd does not. This finding suggests that the change in precision is part of a separation of segmentation from an absolute spatial measure, established by the maternal gradients, to one precise in relative (percent egg length) units.

  1. Gas chromatography-vacuum ultraviolet spectroscopy for analysis of fatty acid methyl esters.

    PubMed

    Fan, Hui; Smuts, Jonathan; Bai, Ling; Walsh, Phillip; Armstrong, Daniel W; Schug, Kevin A

    2016-03-01

    A new vacuum ultraviolet (VUV) detector for gas chromatography was recently developed and applied to fatty acid methyl ester (FAME) analysis. VUV detection features full spectral acquisition in a wavelength range of 115-240nm, where virtually all chemical species absorb. VUV absorption spectra of 37 FAMEs, including saturated, monounsaturated, and polyunsaturated types were recorded. Unsaturated FAMEs show significantly different gas phase absorption profiles than saturated ones, and these classes can be easily distinguished with the VUV detector. Another advantage includes differentiating cis/trans-isomeric FAMEs (e.g. oleic acid methyl ester and linoleic acid methyl ester isomers) and the ability to use VUV data analysis software for deconvolution of co-eluting signals. As a universal detector, VUV also provides high specificity, sensitivity, and a fast data acquisition rate, making it a powerful tool for fatty acid screening when combined with gas chromatography. The fatty acid profile of several food oil samples (olive, canola, vegetable, corn, sunflower and peanut oils) were analyzed in this study to demonstrate applicability to real world samples.

  2. Mercury analysis of various types of coal using acid extraction and pyrolysis methods

    SciTech Connect

    Jae Young Park; Jong Hyun Won; Tai Gyu Lee

    2006-12-15

    The mercury contents of various types of coal currently consumed in Korea were analyzed using acid extraction and pyrolysis methods. The results of analysis by acid extraction and pyrolysis methods were compared and discussed. Generally, high mercury concentrations of 105.6 to 434.5 ng/g (by acid extraction) and 125.7 to 475.4 ng/g (by pyrolysis) were obtained for tested anthracite coals in this study. For bituminous coals, the mercury contents were 11.5-48 ng/g (by acid extraction) and 12.5-52.4 ng/g (by pyrolysis). For coal samples, much simpler and far less time-consuming pyrolysis method tends to give higher values for the Hg concentration than the acid extraction method (by less than 10%) because of the interference from a UV absorption by SOx generated during thermal destruction of coal matrix. Also, further analysis shows that coals with higher densities have higher mercury contents and that the sulfur and mercury contents of coals are positively correlated with each other. 10 refs., 4 figs., 2 tabs.

  3. Comparative proteomic analysis of engineered Saccharomyces cerevisiae with enhanced free fatty acid accumulation.

    PubMed

    Chen, Liwei; Lee, Jaslyn Jie Lin; Zhang, Jianhua; Chen, Wei Ning

    2016-02-01

    The engineered Saccharomyces cerevisiae strain △faa1△faa4 [Acot5s] was demonstrated to accumulate more free fatty acids (FFA) previously. Here, comparative proteomic analysis was performed to get a global overview of metabolic regulation in the strain. Over 500 proteins were identified, and 82 of those proteins were found to change significantly in the engineered strains. Proteins involved in glycolysis, acetate metabolism, fatty acid synthesis, TCA cycle, glyoxylate cycle, the pentose phosphate pathway, respiration, transportation, and stress response were found to be upregulated in △faa1△faa4 [Acot5s] as compared to the wild type. On the other hand, proteins involved in glycerol, ethanol, ergosterol, and cell wall synthesis were downregulated. Taken together with our metabolite analysis, our results showed that the disruption of Faa1 and Faa4 and expression of Acot5s in the engineered strain △faa1△faa4 [Acot5s] not only relieved the feedback inhibition of fatty acyl-CoAs on fatty acid synthesis, but also caused a major metabolic rearrangement. The rearrangement redirected carbon flux toward the pathways which generate the essential substrates and cofactors for fatty acid synthesis, such as acetyl-CoA, ATP, and NADPH. Therefore, our results help shed light on the mechanism for the increased production of fatty acids in the engineered strains, which is useful in providing information for future studies in biofuel production.

  4. A Nationwide Analysis of Outcomes of Weekend Admissions for Intracerebral Hemorrhage Shows Disparities Based on Hospital Teaching Status

    PubMed Central

    Patel, Achint A.; Benjo, Alexandre; Pathak, Ambarish; Kar, Jitesh; Jani, Vishal B.; Annapureddy, Narender; Agarwal, Shiv Kumar; Sabharwal, Manpreet S.; Simoes, Priya K.; Konstantinidis, Ioannis; Yacoub, Rabi; Javed, Fahad; El Hayek, Georges; Menon, Madhav C.; Nadkarni, Girish N.

    2015-01-01

    Background and Purpose: With the “weekend effect” being well described, the Brain Attack Coalition released a set of “best practice” guidelines in 2005, with the goal to uniformly provide standard of care to patients with stroke. We attempted to define a “weekend effect” in outcomes among patients with intracranial hemorrhage (ICH) over the last decade, utilizing the Nationwide Inpatient Sample (NIS) data. We also attempted to analyze the trend of such an effect. Materials and Methods: We determined the association of ICH weekend admissions with hospital outcomes including mortality, adverse discharge, length of stay, and cost compared to weekday admissions using multivariable logistic regression. We extracted our study cohort from the NIS, the largest all-payer data set in the United States. Results: Of 485 329 ICH admissions from 2002 to 2011, 27.5% were weekend admissions. Overall, weekend admissions were associated with 11% higher odds of in-hospital mortality. When analyzed in 3-year groups, excess mortality of weekend admissions showed temporal decline. There was higher mortality with weekend admissions in nonteaching hospitals persisted (odds ratios 1.16, 1.13, and 1.09, respectively, for 3-year subgroups). Patients admitted during weekends were also 9% more likely to have an adverse discharge (odds ratio 1.09; 95% confidence interval: 1.07-1.11; P < .001) with no variation by hospital status. There was no effect of a weekend admission on either length of stay or cost of care. Conclusion: Nontraumatic ICH admissions on weekends have higher in-hospital mortality and adverse discharge. This demonstrates need for in-depth review for elucidating this discrepancy and stricter adherence to standard-of-care guidelines to ensure uniform care. PMID:27053981

  5. Transcriptome Analysis of Enterococcus faecalis during Mammalian Infection Shows Cells Undergo Adaptation and Exist in a Stringent Response State

    PubMed Central

    Frank, Kristi L.; Colomer-Winter, Cristina; Grindle, Suzanne M.; Lemos, José A.; Schlievert, Patrick M.; Dunny, Gary M.

    2014-01-01

    As both a commensal and a major cause of healthcare-associated infections in humans, Enterococcus faecalis is a remarkably adaptable organism. We investigated how E. faecalis adapts in a mammalian host as a pathogen by characterizing changes in the transcriptome during infection in a rabbit model of subdermal abscess formation using transcriptional microarrays. The microarray experiments detected 222 and 291 differentially regulated genes in E. faecalis OG1RF at two and eight hours after subdermal chamber inoculation, respectively. The profile of significantly regulated genes at two hours post-inoculation included genes involved in stress response, metabolism, nutrient acquisition, and cell surface components, suggesting genome-wide adaptation to growth in an altered environment. At eight hours post-inoculation, 88% of the differentially expressed genes were down-regulated and matched a transcriptional profile consistent with a (p)ppGpp-mediated stringent response. Subsequent subdermal abscess infections with E. faecalis mutants lacking the (p)ppGpp synthetase/hydrolase RSH, the small synthetase RelQ, or both enzymes, suggest that intracellular (p)ppGpp levels, but not stringent response activation, influence persistence in the model. The ability of cells to synthesize (p)ppGpp was also found to be important for growth in human serum and whole blood. The data presented in this report provide the first genome-wide insights on E. faecalis in vivo gene expression and regulation measured by transcriptional profiling during infection in a mammalian host and show that (p)ppGpp levels affect viability of E. faecalis in multiple conditions relevant to mammalian infection. The subdermal abscess model can serve as a novel experimental system for studying the E. faecalis stringent response in the context of the mammalian immune system. PMID:25545155

  6. Compound Specific Isotope Analysis of Fatty Acids in Southern African Aerosols

    NASA Astrophysics Data System (ADS)

    Billmark, K. A.; Macko, S. A.; Swap, R. J.

    2003-12-01

    This study, conducted as a part of the Southern African Regional Science Initiative (SAFARI 2000), applied compound specific isotope analysis to describe aerosols at source regions and rural locations. Stable carbon isotopic compositions of individual fatty acids were determined for aerosol samples collected at four sites throughout southern Africa. Mongu, Zambia and Skukuza, South Africa were chosen for their location within intense seasonal Miombo woodland savanna and bushveld savanna biomass burning source regions, respectively. Urban aerosols were collected at Johannesburg, South Africa and rural samples were collected at Sua Pan, Botswana. Fatty acid isotopic compositions varied temporally. Urban aerosols showed significant isotopic enrichment of selected short chain fatty acids (C < 20) compared to aerosols produced during biomass combustion. Sua Pan short chain fatty acid signatures were significantly different from the other non-urban sites, which suggests that sources other than biomass combustion products, such as organic eolian material, impact the Sua Pan aerosol profile. However, a high degree of correlation between Sua Pan and Skukuza long chain fatty acid δ 13C values confirm atmospheric linkages between the two areas and that isotopic signatures of combusted fatty acids are unaltered during atmospheric transport highlighting their potential for use as a conservative tracer.

  7. Transcriptome analysis of bitter acid biosynthesis and precursor pathways in hop (Humulus lupulus)

    PubMed Central

    2013-01-01

    Background Bitter acids (e.g. humulone) are prenylated polyketides synthesized in lupulin glands of the hop plant (Humulus lupulus) which are important contributors to the bitter flavour and stability of beer. Bitter acids are formed from acyl-CoA precursors derived from branched-chain amino acid (BCAA) degradation and C5 prenyl diphosphates from the methyl-D-erythritol 4-phosphate (MEP) pathway. We used RNA sequencing (RNA-seq) to obtain the transcriptomes of isolated lupulin glands, cones with glands removed and leaves from high α-acid hop cultivars, and analyzed these datasets for genes involved in bitter acid biosynthesis including the supply of major precursors. We also measured the levels of BCAAs, acyl-CoA intermediates, and bitter acids in glands, cones and leaves. Results Transcripts encoding all the enzymes of BCAA metabolism were significantly more abundant in lupulin glands, indicating that BCAA biosynthesis and subsequent degradation occurs in these specialized cells. Branched-chain acyl-CoAs and bitter acids were present at higher levels in glands compared with leaves and cones. RNA-seq analysis showed the gland-specific expression of the MEP pathway, enzymes of sucrose degradation and several transcription factors that may regulate bitter acid biosynthesis in glands. Two branched-chain aminotransferase (BCAT) enzymes, HlBCAT1 and HlBCAT2, were abundant, with gene expression quantification by RNA-seq and qRT-PCR indicating that HlBCAT1 was specific to glands while HlBCAT2 was present in glands, cones and leaves. Recombinant HlBCAT1 and HlBCAT2 catalyzed forward (biosynthetic) and reverse (catabolic) reactions with similar kinetic parameters. HlBCAT1 is targeted to mitochondria where it likely plays a role in BCAA catabolism. HlBCAT2 is a plastidial enzyme likely involved in BCAA biosynthesis. Phylogenetic analysis of the hop BCATs and those from other plants showed that they group into distinct biosynthetic (plastidial) and catabolic (mitochondrial

  8. Characterizing estuarine plume discharge into the coastal ocean using fatty acid biomarkers and pigment analysis.

    PubMed

    Fischer, Andrew M; Ryan, John P; Levesque, Christian; Welschmeyer, Nicholas

    2014-08-01

    The transformation of estuaries by human activities continues to alter the biogeochemical balance of the coastal ocean. The disruption of this balance can negatively impact the provision of goods and services, including fisheries, commerce and transportation, recreation and esthetic enjoyment. Here we examine a link, between the Elkhorn Slough and the coastal ocean in Monterey Bay, California (USA) using a novel application of fatty acid and pigment analysis. Fatty acid analysis of filtered water samples showed biologically distinct water types between the Elkhorn Slough plume and the receiving waters of the coastal ocean. A remarkable feature of the biological content of the plume entering the coastal ocean was the abundance of bacteria-specific fatty acids, which correlated well with concentrations of colored dissolved organic matter (CDOM). Pigment analysis showed that plume waters contained higher concentrations of diatoms and cryptophytes, while the coastal ocean waters showed higher relative concentrations of dinoflagellates. Bacteria and cryptophytes can provide a source of labile, energy-rich organic matter that may be locally important as a source of food for pelagic and benthic communities. Surface and depth surveys of the plume show that the biogeochemical constituents of the slough waters are injected into the coastal waters and become entrained in the northward flowing, nearshore current of Monterey Bay. Transport of these materials to the northern portion of the bay can fuel a bloom incubator, which exists in this region. This study shows that fatty acid markers can reveal the biogeochemical interactions between estuaries and the coastal ocean and highlights how man-made changes have the potential to influence coastal ecological change.

  9. Multivariate factor analysis of detailed milk fatty acid profile: Effects of dairy system, feeding, herd, parity, and stage of lactation.

    PubMed

    Mele, M; Macciotta, N P P; Cecchinato, A; Conte, G; Schiavon, S; Bittante, G

    2016-12-01

    We investigated the potential of using multivariate factor analysis to extract metabolic information from data on the quantity and quality of milk produced under different management systems. We collected data from individual milk samples taken from 1,158 Brown Swiss cows farmed in 85 traditional or modern herds in Trento Province (Italy). Factor analysis was carried out on 47 individual fatty acids, milk yield, and 5 compositional milk traits (fat, protein, casein, and lactose contents, somatic cell score). According to a previous study on multivariate factor analysis, a variable was considered to be associated with a specific factor if the absolute value of its correlation with the factor was ≥0.60. The extracted factors were representative of the following 12 groups of fatty acids or functions: de novo fatty acids, branched fatty acid-milk yield, biohydrogenation, long-chain fatty acids, desaturation, short-chain fatty acids, milk protein and fat contents, odd fatty acids, conjugated linoleic acids, linoleic acid, udder health, and vaccelenic acid. Only 5 fatty acids showed small correlations with these groups. Factor analysis suggested the existence of differences in the metabolic pathways for de novo short- and medium-chain fatty acids and Δ(9)-desaturase products. An ANOVA of factor scores highlighted significant effects of the dairy farming system (traditional or modern), season, herd/date, parity, and days in milk. Factor behavior across levels of fixed factors was consistent with current knowledge. For example, compared with cows farmed in modern herds, those in traditional herds had higher scores for branched fatty acids, which were inversely associated with milk yield; primiparous cows had lower scores than older cows for de novo fatty acids, probably due to a larger contribution of lipids mobilized from body depots on milk fat yield. The statistical approach allowed us to reduce a large number of variables to a few latent factors with biological

  10. Gene identification and functional analysis of methylcitrate synthase in citric acid-producing Aspergillus niger WU-2223L.

    PubMed

    Kobayashi, Keiichi; Hattori, Takasumi; Honda, Yuki; Kirimura, Kohtaro

    2013-01-01

    Methylcitrate synthase (EC 2.3.3.5; MCS) is a key enzyme of the methylcitric acid cycle localized in the mitochondria of eukaryotic cells and related to propionic acid metabolism. In this study, cloning of the gene mcsA encoding MCS and heterologous expression of it in Escherichia coli were performed for functional analysis of the MCS of citric acid-producing Aspergillus niger WU-2223L. Only one copy of mcsA (1,495 bp) exists in the A. niger WU-2223L chromosome. It encodes a 51-kDa polypeptide consisting of 465 amino acids containing mitochondrial targeting signal peptides. Purified recombinant MCS showed not only MCS activity (27.6 U/mg) but also citrate synthase (EC 2.3.3.1; CS) activity (26.8 U/mg). For functional analysis of MCS, mcsA disruptant strain DMCS-1, derived from A. niger WU-2223L, was constructed. Although A. niger WU-2223L showed growth on propionate as sole carbon source, DMCS-1 showed no growth. These results suggest that MCS is an essential enzyme in propionic acid metabolism, and that the methylcitric acid cycle operates functionally in A. niger WU-2223L. To determine whether MCS makes a contribution to citric acid production, citric acid production tests on DMCS-1 were performed. The amount of citric acid produced from glucose consumed by DMCS-1 in citric acid production medium over 12 d of cultivation was on the same level to that by WU-2223L. Thus it was found that MCS made no contribution to citric acid production from glucose in A. niger WU-2223L, although MCS showed CS activity.

  11. Culture-independent analysis of lactic acid bacteria diversity associated with mezcal fermentation.

    PubMed

    Narváez-Zapata, J A; Rojas-Herrera, R A; Rodríguez-Luna, I C; Larralde-Corona, C P

    2010-11-01

    Mezcal is an alcoholic beverage obtained from the distillation of fermented juices of cooked Agave spp. plant stalks (agave must), and each region in Mexico with denomination of origin uses defined Agave species to prepare mezcal with unique organoleptic characteristics. During fermentation to produce mezcal in the state of Tamaulipas, not only alcohol-producing yeasts are involved, but also a lactic acid bacterial community that has not been characterized yet. In order to address this lack of knowledge on this traditional Mexican beverage, we performed a DGGE-16S rRNA analysis of the lactic acid bacterial diversity and metabolite accumulation during the fermentation of a typical agave must that is rustically produced in San Carlos County (Tamaulipas, Mexico). The analysis of metabolite production indicated a short but important malolactic fermentation stage not previously described for mezcal. The denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes showed a distinctive lactic acid bacterial community composed mainly of Pediococcus parvulus, Lactobacillus brevis, Lactobacillus composti, Lactobacillus parabuchneri, and Lactobacillus plantarum. Some atypical genera such as Weissella and Bacillus were also found in the residual must. Our results suggest that the lactic acid bacteria could strongly be implicated in the organoleptic attributes of this traditional Mexican distilled beverage.

  12. Comparative analysis of the cytotoxicity of homopolymeric amino acids.

    PubMed

    Oma, Yoko; Kino, Yoshihiro; Sasagawa, Noboru; Ishiura, Shoichi

    2005-05-15

    Many human proteins have homopolymeric amino acid (HPAA) tracts, although the physiological significance or cellular effects of their presence is poorly understood. We previously reported that 20 kinds of HPAAs show characteristic intracellular localization and that among those, hydrophobic HPAAs aggregate strongly and form high molecular weight proteins when expressed in cultured cells. In this study, we investigated the cytotoxicity of 20 kinds of HPAAs. HPAA tracts of approximately 30 residues fused to the C-terminus of YFP were expressed in COS-7 cells. Cells expressing homopolymeric-Cys, -Ile, -Leu, and -Val showed low viability in Trypan Blue assay. Caspase-3 activity, which is usually upregulated in dying cells, was determined by measuring the cleavage of the peptide substrate Ac-DEVD-MCA and by detecting the cleaved active form of the caspase-3 by Western blotting. The activity of caspase-3 was drastically elevated in cells expressing those HPAAs which showed low viability in Trypan Blue assay. Interestingly, it was found that there is a correlation between the hydrophobicity of a single amino acid and the cytotoxicity of the corresponding HPAA as a homopolymer. These results indicate that the hydrophobicity of HPAAs may cause cytotoxicity.

  13. Field enhancement sample stacking for analysis of organic acids in traditional Chinese medicine by capillary electrophoresis.

    PubMed

    Zhu, Qianqian; Xu, Xueqin; Huang, Yuanyuan; Xu, Liangjun; Chen, Guonan

    2012-07-13

    A technique known as field enhancement sample stacking (FESS) and capillary electrophoresis (CE) separation has been developed to analyze and detect organic acids in the three traditional Chinese medicines (such as Portulaca oleracea L., Crataegus pinnatifida and Aloe vera L.). In FESS, a reverse electrode polarity-stacking mode (REPSM) was applied as on-line preconcentration strategy. Under the optimized condition, the baseline separation of eight organic acids (linolenic acid, lauric acid, p-coumaric acid, ascorbic acid, benzoic acid, caffeic acid, succinic acid and fumaric acid) could be achieved within 20 min. Validation parameters of this method (such as detection limits, linearity and precision) were also evaluated. The detection limits ranged from 0.4 to 60 ng/mL. The results indicated that the proposed method was effective for the separation of mixtures of organic acids. Satisfactory recoveries were also obtained in the analysis of these organic acids in the above traditional Chinese medicine samples.

  14. [Principal component analysis of mineral elements and fatty acids composition in flaxseed from ten different regions].

    PubMed

    Xing, Li; Zhao, Feng-Min; Cao, You-Fu; Wang, Mei; Mei, Shuai; Li, Shao-Ping; Cai, Zhi-Yong

    2014-09-01

    Flaxseed is a kind of biomass with high edible and medical value. It is rich in many kinds of nutrients and mineral elements. China is one of the important producing places of flaxseed. In order to explore the main characteristic constituents of mineral elements and fatty acids in flaxseed, the study of analyzing the mineral elements and fatty acid composition from 10 different regions was carried out. The contents of seventeen kinds of mineral elements in flaxseed were determined by inductively coupled plasma mass spectrometry (ICP-MS). The contents of fatty acids of the flaxseed oil obtained under the same conditions were determined by gas chromatography-mass spectrometer (GC-MS). The principal component analysis (PCA) method was applied to the study of analyzing the mineral elements and fatty acid compositions in flaxseeds. The difference in mineral elements and fatty acids of flaxseed from different regions were discussed. The main characteristic constituents of mineral elements and fatty acids were analyzed. The results showed that K, Sr, Mg, Ni, Co, Cr, Cd, Se, Zn and Cu were the main characteristic constituents of the mineral elements. At the same time, C16:0, C18:0, C18: 2, C18:3, C20:0 and C20:1 were the main characteristic constituents of the fatty acids. The combination of ICP-MS, GS-MS and PCA can reveal the characteristics and difference of mineral elements and fatty acids from different regions. The results would provide important theoretical basis for the reasonable and effective utilization of flaxseed.

  15. Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

    SciTech Connect

    Myers, G.; Foley, B.; Korber, B.; Mellors, J.W.; Jeang, K.T.; Wain-Hobson, S.

    1997-04-01

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.

  16. Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by Salicylic Acid (SA) and Jasmonic Acid (JA).

    PubMed

    Gao, Zhengquan; Li, Yan; Wu, Guanxun; Li, Guoqiang; Sun, Haifeng; Deng, Suzhen; Shen, Yicheng; Chen, Guoqiang; Zhang, Ruihao; Meng, Chunxiao; Zhang, Xiaowen

    2015-01-01

    Haematococcus pluvialis is an astaxanthin-rich microalga that can increase its astaxanthin production by salicylic acid (SA) or jasmonic acid (JA) induction. The genetic transcriptome details of astaxanthin biosynthesis were analyzed by exposing the algal cells to 25 mg/L of SA and JA for 1, 6 and 24 hours, plus to the control (no stress). Based on the RNA-seq analysis, 56,077 unigenes (51.7%) were identified with functions in response to the hormone stress. The top five identified subcategories were cell, cellular process, intracellular, catalytic activity and cytoplasm, which possessed 5600 (~9.99%), 5302 (~9.45%), 5242 (~9.35%), 4407 (~7.86%) and 4195 (~7.48%) unigenes, respectively. Furthermore, 59 unigenes were identified and assigned to 26 putative transcription factors (TFs), including 12 plant-specific TFs. They were likely associated with astaxanthin biosynthesis in Haematococcus upon SA and JA stress. In comparison, the up-regulation of differential expressed genes occurred much earlier, with higher transcript levels in the JA treatment (about 6 h later) than in the SA treatment (beyond 24 h). These results provide valuable information for directing metabolic engineering efforts to improve astaxanthin biosynthesis in H. pluvialis.

  17. Trophic hierarchies illuminated via amino acid isotopic analysis.

    PubMed

    Steffan, Shawn A; Chikaraishi, Yoshito; Horton, David R; Ohkouchi, Naohiko; Singleton, Merritt E; Miliczky, Eugene; Hogg, David B; Jones, Vincent P

    2013-01-01

    Food web ecologists have long sought to characterize the trophic niches of animals using stable isotopic analysis. However, distilling trophic position from isotopic composition has been difficult, largely because of the variability associated with trophic discrimination factors (inter-trophic isotopic fractionation and routing). We circumvented much of this variability using compound-specific isotopic analysis (CSIA). We examined the (15)N signatures of amino acids extracted from organisms reared in pure culture at four discrete trophic levels, across two model communities. We calculated the degree of enrichment at each trophic level and found there was a consistent trophic discrimination factor (~7.6‰). The constancy of the CSIA-derived discrimination factor permitted unprecedented accuracy in the measurement of animal trophic position. Conversely, trophic position estimates generated via bulk-(15)N analysis significantly underestimated trophic position, particularly among higher-order consumers. We then examined the trophic hierarchy of a free-roaming arthropod community, revealing the highest trophic position (5.07) and longest food chain ever reported using CSIA. High accuracy in trophic position estimation brings trophic function into sharper focus, providing greater resolution to the analysis of food webs.

  18. Trophic Hierarchies Illuminated via Amino Acid Isotopic Analysis

    PubMed Central

    Steffan, Shawn A.; Chikaraishi, Yoshito; Horton, David R.; Ohkouchi, Naohiko; Singleton, Merritt E.; Miliczky, Eugene; Hogg, David B.; Jones, Vincent P.

    2013-01-01

    Food web ecologists have long sought to characterize the trophic niches of animals using stable isotopic analysis. However, distilling trophic position from isotopic composition has been difficult, largely because of the variability associated with trophic discrimination factors (inter-trophic isotopic fractionation and routing). We circumvented much of this variability using compound-specific isotopic analysis (CSIA). We examined the 15N signatures of amino acids extracted from organisms reared in pure culture at four discrete trophic levels, across two model communities. We calculated the degree of enrichment at each trophic level and found there was a consistent trophic discrimination factor (~7.6‰). The constancy of the CSIA-derived discrimination factor permitted unprecedented accuracy in the measurement of animal trophic position. Conversely, trophic position estimates generated via bulk-15N analysis significantly underestimated trophic position, particularly among higher-order consumers. We then examined the trophic hierarchy of a free-roaming arthropod community, revealing the highest trophic position (5.07) and longest food chain ever reported using CSIA. High accuracy in trophic position estimation brings trophic function into sharper focus, providing greater resolution to the analysis of food webs. PMID:24086703

  19. In silico Analysis for Predicting Fatty Acids of Black Cumin Oil as Inhibitors of P-Glycoprotein

    PubMed Central

    Ali, Babar; Jamal, Qazi Mohd. Sajid; Mir, Showkat R.; Shams, Saiba; Al-Wabel, Naser A.; Kamal, Mohammad A.

    2015-01-01

    glycoprotein as a receptor.Rat P-gp structure quality shows 88.5% residues in favored region obtained by Ramchandran plot analysis.Docking analysis revealed that Some amino acids common for all compounds like Ser221, Pro222, Ile224, Gly225, Ser228, Ala229, Lys233, Tyr302, Tyr309, Ile337, Leu338 and Thr341 in the P-gp and ligands binding patterns.Eicosadeinoic acid has highest binding affinity with P-gp as the amount of energy needed to bind with P-gp was lowest (-11.92 kcal/mol). Abbreviations used: P-gp: P-glycoprotein PMID:27013802

  20. [Quantitative analysis of seven phenolic acids in eight Yinqiao Jiedu serial preparations by quantitative analysis of multi-components with single-marker].

    PubMed

    Wang, Jun-jun; Zhang, Li; Guo, Qing; Kou, Jun-ping; Yu, Bo-yang; Gu, Dan-hua

    2015-04-01

    The study aims to develop a unified method to determine seven phenolic acids (neochlorogenic acid, chlorogenic acid, 4-caffeoylquinic acid, caffeic acid, isochlorogenic acid B, isochlorogenic acid A and isochlorogenic acid C) contained in honeysuckle flower that is the monarch drug of all the eight Yinqiao Jiedu serial preparations using quantitative analysis of multi-components by single-marker (QAMS). Firstly, chlorogenic acid was used as a reference to get the average relative correction factors (RCFs) of the other phenolic acids in ratios to the reference; columns and instruments from different companies were used to validate the durability of the achieved RCFs in different levels of standard solutions; and honeysuckle flower extract was used as the reference substance to fix the positions of chromatographic peaks. Secondly, the contents of seven phenolic acids in eight different Yinqiao Jiedu serial preparations samples were calculated based on the RCFs durability. Finally, the quantitative results were compared between QAMS and the external standard (ES) method. The results have showed that the durability of the achieved RCFs is good (RSD during 0.80% - 2.56%), and there are no differences between the quantitative results of QAMS and ES (the relative average deviation < 0.93%). So it can be successfully used to the quantitative control of honeysuckle flower principally prescribed in Yinqiao Jiedu serial preparations.

  1. DFT computation and experimental analysis of vibrational and electronic spectra of phenoxy acetic acid herbicides

    NASA Astrophysics Data System (ADS)

    Arul Dhas, D.; Hubert Joe, I.; Roy, S. D. D.; Balachandran, S.

    2013-05-01

    An absolute vibrational analysis has been attempted on the basis of experimental FTIR and NIR-FT Raman spectra with calculated vibrational wavenumbers and intensities of phenoxy acetic acids. The equilibrium geometry, bonding features and harmonic vibrational wavenumbers have been calculated with the help of B3LYP method with Dunning correlation consistent basis set aug-cc-pVTZ. The electronic structures of molecular fragments were described in terms of natural bond orbital analysis, which shows intermolecular Osbnd H⋯O and intramolecular Csbnd H⋯O hydrogen bonds. The electronic absorption spectra with different solvents have been investigated in combination with time-dependent density functional theory calculation. The pKa values of phenoxy acetic acids were compared.

  2. Hyperdimensional Analysis of Amino Acid Pair Distributions in Proteins

    PubMed Central

    Henriksen, Svend B.; Arnason, Omar; Söring, Jón; Petersen, Steffen B.

    2011-01-01

    Our manuscript presents a novel approach to protein structure analyses. We have organized an 8-dimensional data cube with protein 3D-structural information from 8706 high-resolution non-redundant protein-chains with the aim of identifying packing rules at the amino acid pair level. The cube contains information about amino acid type, solvent accessibility, spatial and sequence distance, secondary structure and sequence length. We are able to pose structural queries to the data cube using program ProPack. The response is a 1, 2 or 3D graph. Whereas the response is of a statistical nature, the user can obtain an instant list of all PDB-structures where such pair is found. The user may select a particular structure, which is displayed highlighting the pair in question. The user may pose millions of different queries and for each one he will receive the answer in a few seconds. In order to demonstrate the capabilities of the data cube as well as the programs, we have selected well known structural features, disulphide bridges and salt bridges, where we illustrate how the queries are posed, and how answers are given. Motifs involving cysteines such as disulphide bridges, zinc-fingers and iron-sulfur clusters are clearly identified and differentiated. ProPack also reveals that whereas pairs of Lys residues virtually never appear in close spatial proximity, pairs of Arg are abundant and appear at close spatial distance, contrasting the belief that electrostatic repulsion would prevent this juxtaposition and that Arg-Lys is perceived as a conservative mutation. The presented programs can find and visualize novel packing preferences in proteins structures allowing the user to unravel correlations between pairs of amino acids. The new tools allow the user to view statistical information and visualize instantly the structures that underpin the statistical information, which is far from trivial with most other SW tools for protein structure analysis. PMID:22174733

  3. Clinical benefit using sperm hyaluronic acid binding technique in ICSI cycles: a systematic review and meta-analysis.

    PubMed

    Beck-Fruchter, Ronit; Shalev, Eliezer; Weiss, Amir

    2016-03-01

    The human oocyte is surrounded by hyaluronic acid, which acts as a natural selector of spermatozoa. Human sperm that express hyaluronic acid receptors and bind to hyaluronic acid have normal shape, minimal DNA fragmentation and low frequency of chromosomal aneuploidies. Use of hyaluronic acid binding assays in intracytoplasmic sperm injection (ICSI) cycles to improve clinical outcomes has been studied, although none of these studies had sufficient statistical power. In this systematic review and meta-analysis, electronic databases were searched up to June 2015 to identify studies of ICSI cycles in which spermatozoa able to bind hyaluronic acid was selected. The main outcomes were fertilization rate and clinical pregnancy rate. Secondary outcomes included cleavage rate, embryo quality, implantation rate, spontaneous abortion and live birth rate. Seven studies and 1437 cycles were included. Use of hyaluronic acid binding sperm selection technique yielded no improvement in fertilization and pregnancy rates. A meta-analysis of all available studies showed an improvement in embryo quality and implantation rate; an analysis of prospective studies only showed an improvement in embryo quality. Evidence does not support routine use of hyaluronic acid binding assays in all ICSI cycles. Identification of patients that might benefit from this technique needs further study.

  4. Incomplete oxidation of ethylenediaminetetraacetic acid in chemical oxygen demand analysis.

    PubMed

    Anderson, James E; Mueller, Sherry A; Kim, Byung R

    2007-09-01

    Ethylenediaminetetraacetic acid (EDTA) was found to incompletely oxidize in chemical oxygen demand (COD) analysis, leading to incorrect COD values for water samples containing relatively large amounts of EDTA. The degree of oxidation depended on the oxidant used, its concentration, and the length of digestion. The COD concentrations measured using COD vials with a potassium dichromate concentration of 0.10 N (after dilution by sample and sulfuric acid) were near theoretical oxygen demand values. However, COD measured with dichromate concentrations of 0.010 N and 0.0022 N were 30 to 40% lower than theoretical oxygen demand values. Similarly, lower COD values were observed with manganic sulfate as oxidant at 0.011 N. Extended digestion yielded somewhat higher COD values, suggesting incomplete and slower oxidation of EDTA, as a result of lower oxidant concentrations. For wastewater in which EDTA is a large fraction of COD, accurate COD measurement may not be achieved with methods using dichromate concentrations less than 0.1 N.

  5. Determination of pyruvic acid by using enzymic fluorescence capillary analysis.

    PubMed

    Zhao, Yuan-Yuan; Gao, Xiu-Feng; Li, Yong-Sheng; Ju, Xiang; Zhang, Jia; Zheng, Jia

    2008-07-15

    A new method (P-LE-FCA) for the determination of pyruvic acid was proposed based on liquid enzyme method (LE) and fluorescence capillary analysis (FCA). The optimum experimental conditions were as follows: the excitation and emission wavelengths were 350 and 460 nm, respectively; the reaction time and temperature were 20 min and 38 degrees C, respectively; the pH of phosphate buffer solution was 7.5; the concentrations of nicotinamide adenine dinucleotide and lactate dehydrogenase were 1.0 mmol L(-1) and 5.0 k UL(-1), respectively. The linear range of this method was 0.2-1.2 mmol L(-1) (Delta F=327.13C-10.018, r=0.9942). Its detection limit was 0.012 mmol L(-1). And its relative standard deviation was 0.86%. Only 18 microL of total reaction solution is enough for the detection. P-LE-FCA has some merits such as lower cost, simple operation procedure and micro determination. It has been used for the determination of pyruvic acid content in human urine samples.

  6. Folic acid fortification of grain: an economic analysis.

    PubMed Central

    Romano, P S; Waitzman, N J; Scheffler, R M; Pi, R D

    1995-01-01

    OBJECTIVES. The purpose of this study was to compare the economic costs and benefits of fortifying grain with folic acid to prevent neural tube defects. METHODS. A cost-benefit analysis based on the US population, using the human capital approach to estimate the costs associated with preventable neural tube defects, was conducted. RESULTS. Under a range of assumptions about discount rates, baseline folate intake, the effectiveness of folate in preventing neural tube defects, the threshold dose that minimizes risk, and the cost of surveillance, fortification would likely yield a net economic benefit. The best estimate of this benefit is $94 million with low-level (140 micrograms [mcg] per 100 g grain) fortification and $252 million with high-level (350 mcg/100 g) fortification. The benefit-to-cost ratio is estimated at 4.3:1 for low-level and 6.1:1 for high-level fortification. CONCLUSIONS. By averting costly birth defects, folic acid fortification of grain in the United States may yield a substantial economic benefit. We may have underestimated net benefits because of unmeasured costs of neural tube defects and unmeasured benefits of higher folate intake. We may have overestimated net benefits if the cost of neurologic sequelae related to delayed diagnosis of vitamin B12 deficiency exceeds our projection. PMID:7733427

  7. Development of gas chromatography analysis of fatty acids in marine organisms.

    PubMed

    Tang, Baokun; Row, Kyung Ho

    2013-08-01

    The gas chromatographic analysis of fatty acids has attracted considerable interest. In this analysis, the common derivatives of fatty acids, such as fatty acid methyl esters, can be detected using a flame ionization detector and the mass spectra can indicate the true structure of fatty acids. This paper reviews gas chromatographic methods for obtaining fatty acids from marine organisms. The stationary phase and detector for applications in gas chromatography are discussed. This article also reviews the components of fatty acids in marine animals, marine plants and marine microorganisms.

  8. Analysis of the interactions of sulfur-containing amino acids in membrane proteins.

    PubMed

    Gómez-Tamayo, José C; Cordomí, Arnau; Olivella, Mireia; Mayol, Eduardo; Fourmy, Daniel; Pardo, Leonardo

    2016-08-01

    The interactions of Met and Cys with other amino acid side chains have received little attention, in contrast to aromatic-aromatic, aromatic-aliphatic or/and aliphatic-aliphatic interactions. Precisely, these are the only amino acids that contain a sulfur atom, which is highly polarizable and, thus, likely to participate in strong Van der Waals interactions. Analysis of the interactions present in membrane protein crystal structures, together with the characterization of their strength in small-molecule model systems at the ab-initio level, predicts that Met-Met interactions are stronger than Met-Cys ≈ Met-Phe ≈ Cys-Phe interactions, stronger than Phe-Phe ≈ Phe-Leu interactions, stronger than the Met-Leu interaction, and stronger than Leu-Leu ≈ Cys-Leu interactions. These results show that sulfur-containing amino acids form stronger interactions than aromatic or aliphatic amino acids. Thus, these amino acids may provide additional driving forces for maintaining the 3D structure of membrane proteins and may provide functional specificity.

  9. Method comparison study for weak acid dissociation cyanide analysis.

    PubMed

    Evans, Joseph D; Thompson, Leslie; Clark, Patrick J; Beckman, Scott W

    2003-02-01

    Method comparison studies of two different methods for the analysis of weak acid dissociable (WAD) cyanide revealed analytical flaws and/or matrix interference problems with both procedures. EPA "draft" method 1677 using a Perstorp 3202 CN analyzer was compared to Standard Method 4500 CN I. It was discovered that the Perstorp analyzer produced more precise and more accurate results once appropriate and necessary procedural steps from the EPA draft method were modified. Comparison of these two methods, was based on "real world" samples collected from a mine-tailing solution. The mine-tailing solution contained high concentrations of cyanide and metals. Inconsistencies in method procedures were traced to sulfide interferences and high concentrations of WAD metals. Conclusions were based upon a large sample base collected from a mine site over a 90-day period.

  10. Comparison and analysis of fatty acids, sterols, and tocopherols in eight vegetable oils.

    PubMed

    Li, Changmo; Yao, Yunping; Zhao, Guozhong; Cheng, Wen; Liu, Huilin; Liu, Chunyang; Shi, Zhen; Chen, Yao; Wang, Shuo

    2011-12-14

    The similarities and differences of eight vegetable oils produced in China were investigated in terms of their fatty acid, sterol, and tocopherol compositions and subsequent data processing by hierarchical clustering analysis and principal component analysis. The lipid profiles, acquired by analytical techniques tailored to each lipid class, revealed great similarities among the fatty acid profiles of corn and sesame oil as well as few differences in their sterol profiles. It turns out that not only was there great similarity between the fatty acid profiles of corn oil and sesame oil but also there were not too many differences for the sterol profiles. Sunflower and tea-seed oil showed similar sterol compositions, while the tea-seed oil tocopherol was very similar to palm oil. The results demonstrated that the use of only one of these profiles was unreliable for indentifying oil origin and authenticity. In contrast, the use of the sterol or tocopherol profile together with the fatty acid profile more accurately discriminates these oils.

  11. Transcriptome analysis of Rhizopus oryzae in response to xylose during fumaric acid production.

    PubMed

    Xu, Qing; Liu, Ying; Li, Shuang; Jiang, Ling; Huang, He; Wen, Jianping

    2016-08-01

    Xylose is one of the most abundant lignocellulosic components, but it cannot be used by R. oryzae for fumaric acid production. Here, we applied high-throughput RNA sequencing to generate two transcriptional maps of R. oryzae following fermentation in glucose or xylose. The differential expression analysis showed that, genes involved in amino acid metabolism, fatty acid metabolism, and gluconeogenesis, were up-regulated in response to xylose. Moreover, we discovered the potential presence of oxidative stress in R. oryzae during xylose fermentation. To adapt to this unfavorable condition, R. oryzae displayed reduced growth and induce of a number of antioxidant enzymes, including genes involved in glutathione, trehalose synthesis, and the proteasomal pathway. These responses might divert the flow of carbon required for the accumulation of fumaric acid. Furthermore, using high-throughput RNA sequencing, we identified a large number of novel transcripts and a substantial number of genes that underwent alternative splicing. Our analysis provides remarkable insight into the mechanisms underlying xylose fermentation by R. oryzae. These results may reveal potential target genes or strategies to improve xylose fermentation.

  12. [Comparative genomics and evolutionary analysis of CRISPR loci in acetic acid bacteria].

    PubMed

    Kai, Xia; Xinle, Liang; Yudong, Li

    2015-12-01

    The clustered regularly interspaced short palindromic repeat (CRISPR) is a widespread adaptive immunity system that exists in most archaea and many bacteria against foreign DNA, such as phages, viruses and plasmids. In general, CRISPR system consists of direct repeat, leader, spacer and CRISPR-associated sequences. Acetic acid bacteria (AAB) play an important role in industrial fermentation of vinegar and bioelectrochemistry. To investigate the polymorphism and evolution pattern of CRISPR loci in acetic acid bacteria, bioinformatic analyses were performed on 48 species from three main genera (Acetobacter, Gluconacetobacter and Gluconobacter) with whole genome sequences available from the NCBI database. The results showed that the CRISPR system existed in 32 species of the 48 strains studied. Most of the CRISPR-Cas system in AAB belonged to type I CRISPR-Cas system (subtype E and C), but type II CRISPR-Cas system which contain cas9 gene was only found in the genus Acetobacter and Gluconacetobacter. The repeat sequences of some CRISPR were highly conserved among species from different genera, and the leader sequences of some CRISPR possessed conservative motif, which was associated with regulated promoters. Moreover, phylogenetic analysis of cas1 demonstrated that they were suitable for classification of species. The conservation of cas1 genes was associated with that of repeat sequences among different strains, suggesting they were subjected to similar functional constraints. Moreover, the number of spacer was positively correlated with the number of prophages and insertion sequences, indicating the acetic acid bacteria were continually invaded by new foreign DNA. The comparative analysis of CRISR loci in acetic acid bacteria provided the basis for investigating the molecular mechanism of different acetic acid tolerance and genome stability in acetic acid bacteria.

  13. Sensitive Amino Acid Composition and Chirality Analysis with the Mars Organic Analyzer (MOA)

    NASA Technical Reports Server (NTRS)

    Skelley, Alison M.; Scherer, James R.; Aubrey, Andrew D.; Grover, William H.; Ivester, Robin H. C.; Ehrenfreund, Pascale; Grunthaner, Frank J.; Bada, Jeffrey L.; Mathies, Richard A.

    2005-01-01

    Detection of life on Mars requires definition of a suitable biomarker and development of sensitive yet compact instrumentation capable of performing in situ analyses. Our studies are focused on amino acid analysis because amino acids are more resistant to decomposition than other biomolecules, and because amino acid chirality is a well-defined biomarker. Amino acid composition and chirality analysis has been previously demonstrated in the lab using microfabricated capillary electrophoresis (CE) chips. To analyze amino acids in the field, we have developed the Mars Organic Analyzer (MOA), a portable analysis system that consists of a compact instrument and a novel multi-layer CE microchip.

  14. Phytochemical Analysis, Antioxidant Activity, Fatty Acids Composition, and Functional Group Analysis of Heliotropium bacciferum

    PubMed Central

    Ahmad, Sohail; Ahmad, Shabir; Bibi, Ahtaram; Ishaq, Muhammad Saqib; Afridi, Muhammad Siddique; Kanwal, Farina; Zakir, Muhammad; Fatima, Farid

    2014-01-01

    Heliotropium bacciferum is paramount in medicinal perspective and belongs to Boraginaceae family. The crude and numerous fractions of leaves, stem, and roots of the plant were investigated for phytochemical analysis and DPPH radical scavenging activity. Phytochemical analysis of crude and fractions of the plant revealed the presence of alkaloids, saponins, tannins, steroids, terpenoids, flavonoids, glycosides, and phenols. The antioxidant (free radical scavenging) activity of various extracts of the Heliotropium bacciferum was resolute against 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical with the avail of UV spectrophotometer at 517 nm. The stock solution (1000 mg/mL) and then several dilutions (50, 100, 150, 200, and 250 mg/mL) of the crude and fractions were prepared. Ascorbic acid was used as a standard. The plant leaves (52.59 ± 0.84 to 90.74 ± 1.00), stem (50.19 ± 0.92 to 89.42 ± 1.10), and roots extracts (49.19 ± 0.52 to 90.01 ± 1.02) divulged magnificent antioxidant activities. For the ascertainment of the fatty acid constituents a gas chromatograph hyphenated to mass spectrometer was used. The essential fatty acids for growth maintenance such as linoleic acid (65.70%), eicosadienoic acid (15.12%), oleic acid (8.72%), and palmitic acid (8.14%) were found in high percentage. The infrared spectra of all extracts of the plant were recorded by IR Prestige-21 FTIR model. PMID:25489605

  15. GLC analysis of Indian rapeseed-mustard to study the variability of fatty acid composition.

    PubMed

    Kaushik, N; Agnihotri, A

    2000-12-01

    Rapeseed-mustard is one of the most economically important oilseed crops in India. Speciality oils having high amounts of a specific fatty acid are of immense importance for both nutritional and industrial purposes. Oil high in oleic acid has demand in commercial food-service applications due to a long shelf-life and cholesterol-reducing properties. Both linoleic and linolenic acids are essential fatty acids; however, less than 3% linolenic acid is preferred for oil stability. High erucic acid content is beneficial for the polymer industry, whereas low erucic acid is recommended for food purposes. Therefore, it is important to undertake systematic characterization of the available gene pool for its variable fatty acid profile to be utilized for specific purposes. In the present study the Indian rapeseed-mustard germplasm and some newly developed low-erucic-acid strains were analysed by GLC to study the fatty acid composition in these lines. The GLC analysis revealed that the rapeseed-mustard varieties being commonly grown in India are characterized by high erucic acid content (30-51%) in the oil with low levels of oleic acid (13-23%). However, from among the recently developed low-erucic-acid strains, several lines were identified with comparatively high oleic acid (60-70%), moderate to high linoleic acid (13-40%) and low linolenic acid (< 10%) contents. Work is in progress at TERI (New Delhi, India) to utilize these lines for development of strains with particular fatty acid compositions for specific purposes.

  16. Gas Chromatographic Analysis of Acidic Indole Auxins in Nicotiana1

    PubMed Central

    Bayer, Margret H.

    1969-01-01

    Acidic indole auxins have been extracted from N. glauca, N. langsdorffii and their 2 tumor-prone 4n- and 2n-hybrids. After purification of the extracts and thin-layer chromatography, acidic indoles were subjected to esterification and gas chromatography. The esters of 4 indole acids were detected and determined: indole-3-acetic acid, indole-3-carboxylic acid, indole-3-propionic acid and indole-3-butyric acid. The indolic nature of fractionated samples was confirmed by spectrophotofluorometry and the physiological significance of the indole esters proven in a biotest. A substantial increase in extractable indole-3-butyric acid in the tumor-prone hybrids suggests an additional pathway of auxin synthesis in these tissues. PMID:5774173

  17. Electromembrane extraction and HPLC analysis of haloacetic acids and aromatic acetic acids in wastewater.

    PubMed

    Alhooshani, Khalid; Basheer, Chanbasha; Kaur, Jagjit; Gjelstad, Astrid; Rasmussen, Knut E; Pedersen-Bjergaard, Stig; Lee, Hian Kee

    2011-10-30

    For the first time, haloacetic acids and aromatic acetic acids were extracted from wastewater samples using electromembrane extraction (EME). A thin layer of toluene immobilized on the walls of a polypropylene membrane envelope served as an artificial supported liquid membrane (SLM). The haloacetic acids (HAAs) (chloroacetic acid, dichloroacetic acid, and trifluoroacetic acid) and aromatic acetic acids (phenylacetic acid and p-hydroxyphenylacetic acid) were extracted through the SLM and into an alkalized aqueous buffer solution. The buffer solution was located inside the membrane envelope. The electrical potential difference sustained over the membrane acted as the driving force for the transport of haloacetic acids into the membrane by electrokinetic migration. After extraction, the extracts were analyzed by high-performance liquid chromatography-ultraviolet detection. The detection limits were between 0.072 and 40.3 ng L(-1). The calibration plot linearity was in the range of 5 and 200 μg L(-1) while the correlation coefficients for the analytes ranged from 0.9932 to 0.9967. Relative recoveries were in the range of 87-106%. The extraction efficiency was found to be comparable to that of solid-phase extraction.

  18. Nucleic acid analysis using terminal-phosphate-labeled nucleotides

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2008-04-22

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  19. Quantitative analysis of 17 amino acids in tobacco leaves using an amino acid analyzer and chemometric resolution.

    PubMed

    Zeng, Yihang; Cai, Wensheng; Shao, Xueguang

    2015-06-01

    A method was developed for quantifying 17 amino acids in tobacco leaves by using an A300 amino acid analyzer and chemometric resolution. In the method, amino acids were eluted by the buffer solution on an ion-exchange column. After reacting with ninhydrin, the derivatives of amino acids were detected by ultraviolet detection. Most amino acids are separated by the elution program. However, five peaks of the derivatives are still overlapping. A non-negative immune algorithm was employed to extract the profiles of the derivatives from the overlapping signals, and then peak areas were adopted for quantitative analysis of the amino acids. The method was validated by the determination of amino acids in tobacco leaves. The relative standard deviations (n = 5) are all less than 2.54% and the recoveries of the spiked samples are in a range of 94.62-108.21%. The feasibility of the method was proved by analyzing the 17 amino acids in 30 tobacco leaf samples.

  20. Characterizing the interaction between uranyl ion and fulvic acid using regional integration analysis (RIA) and fluorescence quenching.

    PubMed

    Zhu, Bingqi; Ryan, David K

    2016-03-01

    The development of chemometric methods has substantially improved the quantitative usefulness of the fluorescence excitation-emission matrix (EEM) in the analysis of dissolved organic matter (DOM). In this study, Regional Integration Analysis (RIA) was used to quantitatively interpret EEMs and assess fluorescence quenching behavior in order to study the binding between uranyl ion and fulvic acid. Three fulvic acids including soil fulvic acid (SFA), Oyster River fulvic acid (ORFA) and Suwannee River fulvic acid (SRFA) were used and investigated by the spectroscopic techniques. The EEM spectra obtained were divided into five regions according to fluorescence structural features and two distinct peaks were observed in region III and region V. Fluorescence quenching analysis was conducted for these two regions with the stability constants, ligand concentrations and residual fluorescence values calculated using the Ryan-Weber model. Results indicated a relatively strong binding ability between uranyl ion and fulvic acid samples at low pH (log K value varies from 4.11 to 4.67 at pH 3.50). Fluorophores in region III showed a higher binding ability with fewer binding sites than in region V. Stability constants followed the order, SFA > ORFA > SRFA, while ligand concentrations followed the reverse order, SRFA > ORFA > SFA. A comparison between RIA and Parallel Factor Analysis (PARAFAC) data treatment methods was also performed and good agreement between these two methods (less than 4% difference in log K values) demonstrates the reliability of the RIA method in this study.

  1. Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme

    SciTech Connect

    Matte, Allan; Grosse, Stephan; Bergeron, Hélène; Abokitse, Kofi; Lau, Peter C.K.

    2012-04-30

    The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavoring and polymer industries. Here, the crystal structure of phenolic acid decarboxylase (PAD) from Bacillus pumilus strain UI-670 is reported. The enzyme is a 161-residue polypeptide that forms dimers both in the crystal and in solution. The structure of PAD as determined by X-ray crystallography revealed a -barrel structure and two -helices, with a cleft formed at one edge of the barrel. The PAD structure resembles those of the lipocalin-fold proteins, which often bind hydrophobic ligands. Superposition of structurally related proteins bound to their cognate ligands shows that they and PAD bind their ligands in a conserved location within the -barrel. Analysis of the residue-conservation pattern for PAD-related sequences mapped onto the PAD structure reveals that the conservation mainly includes residues found within the hydrophobic core of the protein, defining a common lipocalin-like fold for this enzyme family. A narrow cleft containing several conserved amino acids was observed as a structural feature and a potential ligand-binding site.

  2. Compound-Specific Amino Acid Isotopic Analysis of Benthic Food Webs in the Chukchi Sea

    NASA Astrophysics Data System (ADS)

    Zhang, M.; Cooper, L. W.; Biasatti, D. M.; Grebmeier, J. M.

    2014-12-01

    The Chukchi Sea is known for locally high standing stocks of benthic macrofauna and strong coupling between pelagic-benthic components of the ecosystem. However, benthic food structure is not fully understood, due to varied sources of particulate organic matter (POM) and the high diversity of benthic invertebrates. We provide the first demonstration of the application of compound-specific amino acid isotope analysis to study the dietary sources and trophic structure for this Arctic marginal sea. About 20 stations in Chukchi Sea were sampled during cruises in August of 2012 and 2013. At each station, phytoplankton, POM and benthic fauna were collected, processed and analyzed using GC-C-IRMS (gas chromatography-combustion-isotope ratio mass spectrometry). Among benthic fauna, dominant species included the following taxonomic groups: Ophiuroidea, Amphipoda, Polychaeta, Gastropoda, Bivalvia, and Cnidaria. The benthic fauna showed similar patterns of individual amino acid δ13C, with glycine the most enriched in 13C and leucine the most depleted in 13C. Specific amino acids including phenylalanine showed spatial variability in δ13C and δ15N values within the sampled area, indicating contributions of different dietary sources including phytoplankton, sea ice algae, benthic algae and terrestrial organic materials. δ15N values of individual amino acids such as the difference between glutamic acid and phenylalanine, i.e. Δ15Nglu-phe (δ15Nglu - δ15Nphe), were also used to identify trophic levels of benthic invertebrates relative to estimates available from bulk δ15N values. These data will ultimately be used to evaluate the spatial variability of organic carbon sources and trophic level interactions of dominant benthic species in the Chukchi Sea.

  3. Quantitative Analysis and In vitro Anti-inflammatory Effects of Gallic Acid, Ellagic Acid, and Quercetin from Radix Sanguisorbae

    PubMed Central

    Seo, Chang-Seob; Jeong, Soo-Jin; Yoo, Sae-Rom; Lee, Na-Ri; Shin, Hyeun-Kyoo

    2016-01-01

    Background: Radix Sanguisorbae has long been used to treat diarrhea, enteritis, duodenal ulcers, and internal hemorrhage. Objective: We investigated the in vitro anti-inflammatory effects of Radix Sanguisorbae and performed quantitative analyses of three marker components, namely gallic acid, ellagic acid, and quercetin, using high-performance liquid chromatography coupled with a photodiode array detector. Materials and Methods: The three marker components were separated using a reversed-phase Gemini C18 analytical column maintained at 40°C by the gradient elution with two solvent systems. We examined the biological effects of the three marker compounds, gallic acid, ellagic acid, and quercetin, by determining their anti-inflammatory activities in the murine macrophage cell line RAW 264.7. Results: All of the marker compounds exhibited inhibitory effects on prostaglandin E2 production in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages, with no cytotoxicity. Particularly, ellagic acid significantly inhibited production of the proinflammatory cytokines tumor necrosis factor alpha and interleukin-6 in LPS-treated RAW 264.7 cells. Conclusion: Our results suggest that ellagic acid is the most potent bioactive phytochemical component of radix Sanguisorbae in the treatment of inflammatory diseases. SUMMARY Established high-performance liquid chromatography method was applied in the quantitative analysis of gallic acid, ellagic acid, and quercetin present in an extract from radix SanguisorbaeAmong the three compounds, the ellagic acid.(7.65.mg/g) is main component in radix SanguisorbaeEllagic acid significantly inhibited production of the proinflammatory cytokines tumor necrosis factor alpha and interleukin-6 in lipopolysaccharide-treated RAW 264.7 cells. Abbreviations used: HPLC: High-performance liquid chromatography, PDA: Photodiode array, TNF-α: Tumor necrosis factor alpha, IL: Interleukin, LPS: Lipopolysaccharide, PGE2: Prostaglandin E2, NSAIDs

  4. Transcriptomic Analysis of Murine Embryos Lacking Endogenous Retinoic Acid Signaling

    PubMed Central

    Paschaki, Marie; Schneider, Carole; Rhinn, Muriel; Thibault-Carpentier, Christelle; Dembélé, Doulaye; Niederreither, Karen; Dollé, Pascal

    2013-01-01

    Retinoic acid (RA), an active derivative of the liposoluble vitamin A (retinol), acts as an important signaling molecule during embryonic development, regulating phenomenons as diverse as anterior-posterior axial patterning, forebrain and optic vesicle development, specification of hindbrain rhombomeres, pharyngeal arches and second heart field, somitogenesis, and differentiation of spinal cord neurons. This small molecule directly triggers gene activation by binding to nuclear receptors (RARs), switching them from potential repressors to transcriptional activators. The repertoire of RA-regulated genes in embryonic tissues is poorly characterized. We performed a comparative analysis of the transcriptomes of murine wild-type and Retinaldehyde Dehydrogenase 2 null-mutant (Raldh2−/−) embryos — unable to synthesize RA from maternally-derived retinol — using Affymetrix DNA microarrays. Transcriptomic changes were analyzed in two embryonic regions: anterior tissues including forebrain and optic vesicle, and posterior (trunk) tissues, at early stages preceding the appearance of overt phenotypic abnormalities. Several genes expected to be downregulated under RA deficiency appeared in the transcriptome data (e.g. Emx2, Foxg1 anteriorly, Cdx1, Hoxa1, Rarb posteriorly), whereas reverse-transcriptase-PCR and in situ hybridization performed for additional selected genes validated the changes identified through microarray analysis. Altogether, the affected genes belonged to numerous molecular pathways and cellular/organismal functions, demonstrating the pleiotropic nature of RA-dependent events. In both tissue samples, genes upregulated were more numerous than those downregulated, probably due to feedback regulatory loops. Bioinformatic analyses highlighted groups (clusters) of genes displaying similar behaviors in mutant tissues, and biological functions most significantly affected (e.g. mTOR, VEGF, ILK signaling in forebrain tissues; pyrimidine and purine metabolism

  5. Analysis of seasonal variation of stratospheric nitric acid

    NASA Astrophysics Data System (ADS)

    Gruzdev, A. N.

    1998-11-01

    Data from the draft COSPAR reference model for stratospheric nitric acid (HNO3) are analysed. Eight months of LIMS HNO3 measurements allow the analysis of dynamics of regimes associated with the annual HNO3 maximum followed by the HNO3 decrease in the Northern Hemisphere and the annual HNO3 minimum followed by the HNO3 increase in the Southern Hemisphere. The HNO3 minimum is noted earlier (in November) in the Southern Hemisphere subtropical upper stratosphere, from where the regime of minimum HNO3 values propagates to the southern high-latitude middle stratosphere, and then (in Austral summer) the equatorward propagation of the regime is observed, with a persistent downward component. The regime of the HNO3 annual maximum in the Northern Hemisphere propagates from the Arctic lower stratosphere (in autumn) and from the tropical middle stratosphere (in late summer), so that in the mid-latitude middle stratosphere the downward propagation of the regime is observed. Evolution of areas with HNO3 increase and decrease by 1 ppbv against the January HNO3 distribution quantifies intensity of the HNO3 decrease in winter-spring in the Northern Hemisphere and the HNO3 increase in Austral summer-autumn in the Southern Hemisphere.

  6. Simulating realistic predator signatures in quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.

    2015-01-01

    Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

  7. An isobolographic analysis of the antinociceptive effect of xylopic acid in combination with morphine or diclofenac

    PubMed Central

    Woode, Eric; Ameyaw, Elvis Ofori; Abotsi, Wonder Kofi Mensah; Boakye-Gyasi, Eric

    2015-01-01

    Background: A common practice of managing pain globally is the combination of analgesics and this is aimed at facilitating patient compliance, simplifying prescription, and improving efficacy without increasing adverse effects. Fruit extracts of Xylopia aethiopica are used traditionally in the management of pain disorders and xylopic acid (XA) present in the fruit extract have been shown to possess analgesic properties in animals. There is the likelihood of concomitant use of XA and the commonly used analgesics in traditional settings. This study, therefore, evaluated the pharmacologic interaction between XA/morphine and xylopic/diclofenac combinations. Methods: The formalin test and acetic acid writhing test were used to study the antinociceptive activity of XA, morphine, and diclofenac. The isobolographic analysis was used to study the antinociceptive interactions between XA co-administered with morphine or diclofenac. Results: Results obtained revealed that XA (10–100 mg/kg), morphine (1–10 mg/kg), and diclofenac (1–10 mg/kg) produced dose-related antinociception with different potencies in the formalin and acetic acid writhing tests. Isobolographic analysis of XA/morphine and XA/diclofenac combinations revealed potentiation of their antinociceptive effects. The degree of potentiation calculated as interaction index showed synergism for both combinations in all the nociceptive tests. Conclusion: In conclusion, the present study demonstrated synergism for the co-administration of XA with morphine or diclofenac. PMID:26692735

  8. [Analysis of aliphatic carboxylic acids in anaerobic digestion process waters by ion-exclusion chromatography].

    PubMed

    Ito, Kazuaki; Sakamoto, Jun; Nagaoka, Kazuya; Takayama, Yohichi; Kanahori, Takashi; Sunahara, Hiroshi; Hayashi, Tsuneo; Sato, Shinji; Hirokawa, Takeshi; Tanaka, Kazuhiko

    2012-04-01

    The analysis of seven aliphatic carboxylic acids (formic, acetic, propionic, iso-butyric, n-butyric, iso-valeric and n-valeric acid) in anaerobic digestion process waters for biogas production was examined by ion-exclusion chromatography with dilute acidic eluents (benzoic acid, perfluorobutyric acid (PFBA) and sulfuric acid) and non-suppressed conductivity/ultraviolet (UV) detection. The columns used were a styrene/divinylbenzene-based strongly acidic cation-exchange resin column (TSKgel SCX) and a polymethacrylate-based weakly acidic cation-exchange resin column (TSKgel Super IC-A/C). Good separation was performed on the TSKgel SCX in shorter retention times. For the TSKgel Super IC-A/C, peak shape of the acids was sharp and symmetrical in spite of longer retention times. In addition, the mutual separation of the acids was good except for iso- and n-butyric acids. The better separation and good detection was achieved by using the two columns (TSKgel SCX and TSKgel Super IC-A/C connected in series), lower concentrations of PFBA and sulfuric acid as eluents, non-suppressed conductivity detection and UV detection at 210 nm. This analysis was applied to anaerobic digestion process waters. The chromatograms with conductivity detection were relatively simpler compared with those of UV detection. The use of two columns with different selectivities for the aliphatic carboxylic acids and the two detection modes was effective for the determination and identification of the analytes in anaerobic digestion process waters containing complex matrices.

  9. Determination of acid ionization constants for weak acids by osmometry and the instrumental analysis self-evaluation feedback approach to student preparation of solutions

    NASA Astrophysics Data System (ADS)

    Kakolesha, Nyanguila

    One focus of this work was to develop of an alternative method to conductivity for determining the acid ionization constants. Computer-controlled osmometry is one of the emerging analytical tools in industrial research and clinical laboratories. It is slowly finding its way into chemistry laboratories. The instrument's microprocessor control ensures shortened data collection time, repeatability, accuracy, and automatic calibration. The equilibrium constants of acetic acid, chloroacetic acid, bromoacetic acid, cyanoacetic acid, and iodoacetic acid have been measured using osmometry and their values compared with the existing literature values obtained, usually, from conductometric measurements. Ionization constant determined by osmometry for the moderately strong weak acids were in reasonably good agreement with literature values. The results showed that two factors, the ionic strength and the osmotic coefficient, exert opposite effects in solutions of such weak acids. Another focus of the work was analytical chemistry students solution preparation skills. The prevailing teacher-structured experiments leave little room for students' ingenuity in quantitative volumetric analysis. The purpose of this part of the study was to improve students' skills in making solutions using instrument feedback in a constructivist-learning model. After making some solutions by weighing and dissolving solutes or by serial dilution, students used the spectrophotometer and the osmometer to compare their solutions with standard solutions. Students perceived the instrument feedback as a nonthreatening approach to monitoring the development of their skill levels and liked to clarify their understanding through interacting with an instructor-observer. An assessment of the instrument feedback and the constructivist model indicated that students would assume responsibility for their own learning if given the opportunity. This study involved 167 students enrolled in Quantitative Chemical

  10. Effects of Omega-3 Fatty Acid in Nonalcoholic Fatty Liver Disease: A Meta-Analysis

    PubMed Central

    Lu, Wenxia; Li, Sainan; Li, Jingjing; Wang, Jianrong; Zhang, Rong; Zhou, Yuqing; Yin, Qin; Wang, Fan; Xia, Yujing; Liu, Tong; Lu, Jie; Zhou, Yingqun

    2016-01-01

    A meta-analysis was conducted to assess the effect of omega-3 fatty acid supplementation (n-3 PUFAs) in lowering liver fat, liver enzyme (alanine aminotransferase (ALT), aspartate aminotransferase (AST), and gamma-glutamyltransferase (GGT) levels), and blood lipids (triglyceride (TG), total cholesterol (TC), high density lipoprotein (HDL), and low density lipoprotein (LDL)) in patients with nonalcoholic fatty liver disease (NAFLD) or nonalcoholic steatohepatitis (NASH). Methods. MEDLINE/PubMed, EMBASE, the Cochrane Central Register of Controlled Trials, CINAHL, Science Citation Index (ISI Web of Science), Chinese Biomedical Literature Database (CBM), and Chinese National Knowledge Infrastructure (CNKI) were searched for relevant randomized controlled trials on the effects of n-3 polyunsaturated fatty acids (PUFAs) in patients with NAFLD from inception to May 2015. Ten studies were included in this meta-analysis. Results. 577 cases of NAFLD/NASH in ten randomized controlled trials (RCTs) were included. The results of the meta-analysis showed that benefit changes in liver fat favored PUFA treatment, and it was also beneficial for GGT, but it was not significant on ALT, AST, TC, and LDL. Conclusions. In this meta-analysis, omega-3 PUFAs improved liver fat, GGT, TG, and HDL in patients with NAFLD/NASH. Therefore, n-3 PUFAs may be a new treatment option for NAFLD. PMID:27651787

  11. Diffusion tensor MRI shows progressive changes in the hippocampus and dentate gyrus after status epilepticus in rat - histological validation with Fourier-based analysis.

    PubMed

    Salo, Raimo A; Miettinen, Tuukka; Laitinen, Teemu; Gröhn, Olli; Sierra, Alejandra

    2017-03-04

    Imaging markers for monitoring disease progression, recovery, and treatment efficacy are a major unmet need for many neurological diseases, including epilepsy. Recent evidence suggests that diffusion tensor imaging (DTI) provides high microstructural contrast even outside major white matter tracts. We hypothesized that in vivo DTI could detect progressive microstructural changes in the dentate gyrus and the hippocampal CA3bc in the rat brain after status epilepticus (SE). To test this hypothesis, we induced SE with systemic kainic acid or pilocarpine in adult male Wistar rats and subsequently scanned them using in vivo DTI at five time-points: prior to SE, and 10, 20, 34, and 79 days post SE. In order to tie the DTI findings to changes in the tissue microstructure, myelin- and glial fibrillary acidic protein (GFAP)-stained sections from the same animals underwent Fourier analysis. We compared the Fourier analysis parameters, anisotropy index and angle of myelinated axons or astrocyte processes, to corresponding DTI parameters, fractional anisotropy (FA) and the orientation angle of the principal eigenvector. We found progressive detectable changes in DTI parameters in both the dentate gyrus (FA, axial diffusivity [D||], linear anisotropy [CL] and spherical anisotropy [CS], p<0.001, linear mixed-effects model [LMEM]) and the CA3bc (FA, D||, CS, and angle, p<0.001, LMEM; CL and planar anisotropy [CP], p<0.01, LMEM) post SE. The Fourier analysis revealed that both myelinated axons and astrocyte processes played a role in the water diffusion anisotropy changes detected by DTI in individual portions of the dentate gyrus (suprapyramidal blade, mid-portion, and infrapyramidal blade). In the whole dentate gyrus, myelinated axons markedly contributed to the water diffusion changes. In CA3bc as well as in CA3b and CA3c, both myelinated axons and astrocyte processes contributed to water diffusion anisotropy and orientation. Our study revealed that DTI is a promising method

  12. EFFECTS OF NITRIC ACID ON CRITICALITY SAFETY ANALYSIS

    SciTech Connect

    Williamson, B.

    2011-08-18

    As nitric acid molarity is increased, there are two competing phenomena affecting the reactivity of the system. First, there is interaction between each of the 10 wells in the basket-like insert. As the molarity of the nitric acid solution is increased (it moves from 100% water to 100% HNO{sub 3}), the hydrogen atom density decreases by about 80%. However, it remains a relatively efficient moderator. The moderating ratio of nitric acid is about 90% that of water. As the media between the wells is changed from 100% water to 100% nitric acid, the density of the media increases by 50%. A higher density typically leads to a better reflector. However, when the macroscopic scattering cross sections are considered, nitric acid is a much worse reflector than water. The effectiveness of nitric acid as a reflector is about 40% that of water. Since the media between the wells become a worse reflector and still remains an effective moderator, interaction between the wells increases. This phenomenon will cause reactivity to increase as nitric acid molarity increases. The seond phenomenon is due to the moderating ratio changing in the high concentration fissile-nitric acid solution in the 10 wells. Since the wells contain relatively small volumes of high concentration solutions, a small decrease in moderating power has a large effect on reactivity. This is due to the fact that neutrons are more likely to escape the high concentration fissile solution before causing another fission event. The result of this phenomenon is that as nitric acid molarity increases, reactivity decreases. Recent studies have shown that the second phenomenon is indeed the dominating force in determining reactivity changes in relation to nitric acid molarity changes. When considering the system as a whole, as nitric acid molarity increases, reactivity decreases.

  13. [Microsequencing, analysis of molecular weight and amino acid composition for pyrimidine 5'-nucleotidase I of human erythrocytes].

    PubMed

    Pan, Zhu-Lin; Li, Jin-Ying; Min, Bi-He; Ying, Kang; Zhou, Hong; Xu, Xiao-Ping; Shong, Xian-Min; Han, Feng-Lai; Zhang, Wei-Ping; Zhang, Xian

    2003-02-01

    To further explore the mechanism of congenital pyrimidine 5'-nuleotidase I (P5'N-I) deficiency, on the basis of purification of the protein, the molecular weight and amino acid composition were analysed by mass-spectrograph and amino-acid analyzer, microsequencing and bioinformation analysis of P5'N-I were performed after it was hydrolysed by trypsin. The results showed that three fractions were found in the purified P5'N-I and their molecular weights were 26,952.9, 55,476 and 110,938, respectively. The sequence from one of the peptide fragments was I-E-G-P-T-I-R-Q-I-E. The homologous sequence was not found after comparision with the ten-amino-acid sequence in GenBank by blast procedure. Amino acid analysis indicated that P5'N-I was composed of 18 amino acids at least, and 243 amino acid residues. In conclusion, the enzyme might be an allosteric enzyme, there might be homologous dimer or tetramer in physiological status of normal human erythrocyte, the microsequence could be designed as the probe for fishing the genes of interest. The composition of amino acid might be an important information in determination of its protein primary structure.

  14. Spectrophotometric determination of acidity constant of some indicators in various micellar media solutions by rank annihilation factor analysis

    NASA Astrophysics Data System (ADS)

    Niazi, Ali; Zolgharnein, Javad; Davoodabadi, Mohammad Reza

    2008-07-01

    Rank annihilation factor analysis (RAFA) was used to the spectrophotometric studies of the acidity constant of methyl orange, methyl red and methyl violet in water and different micellar solutions at 25 °C and an ionic strength of 0.1 M. When the acidity constants (surfactant concentration dependent acidity constant) acts as an optimizing object, and simply combined with the pure spectrum of acidic and basic forms, the rank of original data matrix can be reduced. The residual standard deviation (R.S.D.) of the residual matrix after bi-linearization of the background matrix is regarded as the evaluation function. Results show that the acidity constant of these indicators are influenced as the percentages of neutral, cationic and anionic surfactant such as Triton X-100 (poly(oxyethylene)(9.5) p-(1,1,3,3-tetramethyl), sodiumdodecylsulfate (SDS) and cethyltrimethylammonium (CTAB), respectively, added to the solution of these reagents. Also, RAFA is an efficient chemometrics algorithm for completely analysis of acid-base equilibrium systems by spectrophotometric method. Effects of surfactant on acidity constant and absorption spectra are also discussed.

  15. Spectrophotometric determination of acidity constant of some indicators in various micellar media solutions by rank annihilation factor analysis.

    PubMed

    Niazi, Ali; Zolgharnein, Javad; Davoodabadi, Mohammad Reza

    2008-07-01

    Rank annihilation factor analysis (RAFA) was used to the spectrophotometric studies of the acidity constant of methyl orange, methyl red and methyl violet in water and different micellar solutions at 25 degrees C and an ionic strength of 0.1M. When the acidity constants (surfactant concentration dependent acidity constant) acts as an optimizing object, and simply combined with the pure spectrum of acidic and basic forms, the rank of original data matrix can be reduced. The residual standard deviation (R.S.D.) of the residual matrix after bi-linearization of the background matrix is regarded as the evaluation function. Results show that the acidity constant of these indicators are influenced as the percentages of neutral, cationic and anionic surfactant such as Triton X-100 (poly(oxyethylene)(9.5)p-(1,1,3,3-tetramethyl), sodiumdodecylsulfate (SDS) and cethyltrimethylammonium (CTAB), respectively, added to the solution of these reagents. Also, RAFA is an efficient chemometrics algorithm for completely analysis of acid-base equilibrium systems by spectrophotometric method. Effects of surfactant on acidity constant and absorption spectra are also discussed.

  16. Deoxyribonucleic Acid Polymerase of Rous Sarcoma Virus: Reaction Conditions and Analysis of the Reaction Product Nucleic Acids

    PubMed Central

    Bishop, D. H. L.; Ruprecht, Ruth; Simpson, R. W.; Spiegelman, S.

    1971-01-01

    Reaction conditions for Rous sarcoma virus ribonucleic acid (RNA)-instructed deoxyribonucleic acid (DNA) polymerase activity are described whereby the viral RNA is relatively protected from endogenous or added nuclease activity. Three analyses of reaction product nucleic acids (3H-RNA, 32P-DNA) were compared, namely, gel electrophoresis, Cs2SO4 gradient centrifugation, and hydroxyapatite column chromatography. It was found that hydroxyapatite analysis could be misleading unless the state of the template RNA was monitored concomitantly with the DNA analysis. Gel electrophoresis and Cs2SO4 gradient centrifugation gave comparable results. It was concluded that analyses of the product of reverse transcriptase reactions should not only refer to the template RNA and product DNA species, but also be performed with virus or viral RNA which do not have or obtain nicks in the 60S RNA. Otherwise, interpretation of the results would have the ambiguity of potential artifacts caused by those degraded RNA molecules. PMID:4332143

  17. Proteome Analysis using Selective Incorporation of Isotopically Labeled Amino Acids

    SciTech Connect

    Veenstra, Timothy D.; Martinovic, Suzana; Anderson, Gordon A.; Pasa-Tolic, Liljiana; Smith, Richard D.

    2000-01-01

    A method is described for identifying intact proteins from genomic databases using a combination of accurate molecular mass measurements and partial amino acid content. An initial demonstration was conducted for proteins isolated from Escherichia coli (E. coli) using a multiple auxotrophic strain of K12. Proteins were extracted from the organism grown in natural isotopic abundance minimal medium and also minimal medium containing isotopically labeled leucine (Leu-D10), were mixed and analyzed by capillary isoelectric focusing (CIEF) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR). The incorporation of the isotopically labeled Leu residue has no effect on the CIEF separation of the protein, therefore both versions of the protein are observed within the same FTICR spectrum. The difference in the molecular mass of the natural isotopic abundance and Leu-D10 isotopically labeled proteins is used to determine the number of Leu residues present in that particular protein. Knowledge of the molecular mass and number of Leu residues present can be used to unambiguously identify the intact protein. Preliminary results show the efficacy of using this method to unambiguously identify proteins isolated from E. coli.

  18. Robust analysis of underivatized free amino acids in soil by hydrophilic interaction liquid chromatography coupled with electrospray tandem mass spectrometry.

    PubMed

    Gao, Jiajia; Helmus, Rick; Cerli, Chiara; Jansen, Boris; Wang, Xiang; Kalbitz, Karsten

    2016-06-03

    Amino acids are an important and highly dynamic fraction of organic N in soils and their determination in soil without derivatization is challenging due to the difficulties in separation and detection of trace amounts of these polar analytes. In the present work, we developed an analytical method to quantify 20 free amino acids in aqueous soil extracts without derivatization. The method employed hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) technique combined with a cation exchange solid phase extraction (SPE). Four stable isotope labelled amino acids were used as internal standards to improve the method performance. Good separation of 20 underivatized amino acids was achieved within 12min. The limit of detection (LODs) and limit of quantification (LOQs) were in the range of 13-384ngg(-1) and 43-1267ngg(-1) (dry soil basis), respectively. The results showed that overall recoveries with high precision were obtained for the extracted free amino acids from ten different soils. The overall recoveries of 18 amino acids were similar for the ten soils used, which differed substantially in organic C content and in other properties as soil texture and pH. For most of the amino acids, the average recoveries from soil extracts were between 74% and 117%, with the exception of Met (31%), Pro (52%) and Arg (68%). Variability was within acceptable limits (relative standard deviations were between 4% and 13%), with the exception of Met (relative standard deviation=90%) and Arg (relative standard deviation=53%). Thus the proposed method with high throughout and high analyte specificity shows great promise for consistent analysis of free amino acids extracted from soils and offers new horizons for the analysis of amino acids in terrestrial and aquatic ecosystem.

  19. Analysis of methylphosphonic acid, ethyl methylphosphonic acid and isopropyl methylphosphonic acid at low microgram per liter levels in groundwater.

    PubMed

    Sega, G A; Tomkins, B A; Griest, W H

    1997-11-28

    A method is described for determining methylphosphonic acid, ethyl methylphosphonic acid and isopropyl methylphosphonic acid, which are hydrolysis products of the nerve agents VX (S-2-diisopropylaminoethyl O-ethyl methylphosphonothiolate) and GB (sarin, isopropylmethyl phosphonofluoridate). The analytes are extracted from 50 ml groundwater using a solid-phase extraction column packed with 500 mg of silica with a bonded quaternary amine phase, and are eluted and derivatized with methanolic trimethylphenylammonium hydroxide. Separation and quantitation are achieved using a capillary column gas chromatograph equipped with a flame photometric detector operated in its phosphorus-selective mode. Two independent statistically-unbiased procedures were employed to determine the detection limits, which ranged between 3 and 9 micrograms/l, for the three analytes.

  20. Advanced Technologies in Sialic Acid and Sialoglycoconjugate Analysis.

    PubMed

    Kitajima, Ken; Varki, Nissi; Sato, Chihiro

    2015-01-01

    Although the structural diversity of sialic acid (Sia) is rapidly expanding, understanding of its biological significance has lagged behind. Advanced technologies to detect and probe diverse structures of Sia are absolutely necessary not only to understand further biological significance but also to pursue medicinal and industrial applications. Here we describe analytical methods for detection of Sia that have recently been developed or improved, with a special focus on 9-O-acetylated N-acetylneuraminic acid (Neu5,9Ac), N-glycolylneuraminic acid (Neu5Gc), deaminoneuraminic acid (Kdn), O-sulfated Sia (SiaS), and di-, oligo-, and polysialic acid (diSia/oligoSia/polySia) in glycoproteins and glycolipids. Much more attention has been paid to these Sia and sialoglycoconjugates during the last decade, in terms of regulation of the immune system, neural development and function, tumorigenesis, and aging.

  1. Extraction, purification, methylation and GC-MS analysis of short-chain carboxylic acids for metabolic flux analysis.

    PubMed

    Tivendale, Nathan D; Jewett, Erin M; Hegeman, Adrian D; Cohen, Jerry D

    2016-08-15

    Dynamic metabolic flux analysis requires efficient and effective methods for extraction, purification and analysis of a plethora of naturally-occurring compounds. One area of metabolism that would be highly informative to study using metabolic flux analysis is the tricarboxylic acid (TCA) cycle, which consists of short-chain carboxylic acids. Here, we describe a newly-developed method for extraction, purification, derivatization and analysis of short-chain carboxylic acids involved in the TCA cycle. The method consists of snap-freezing the plant material, followed by maceration and a 12-15h extraction at -80 °C. The extracts are then subject to reduction (to stabilize β-keto acids), purified by strong anion exchange solid phase extraction and methylated with methanolic HCl. This method could also be readily adapted to quantify many other short-chain carboxylic acids.

  2. Focal point analysis of torsional isomers of acrylic acid

    NASA Astrophysics Data System (ADS)

    Alev Çiftçioğlu, Gökçen; Trindle, Carl; Yavuz, Ilhan

    2010-10-01

    The thermochemistry of acrylic acid has presented challenges owing to its high reactivity, tendency to dimerize in the gas phase, and the existence of two very nearly equal energy conformational isomers. Well-tested thermochemical schemes including G2, G3, G4, and CBS-QB3 agree in the prediction that the s-cis syn structure is the most stable of the torsional isomers, with the s-cis anti form lying 3 kJ mol-1 or less higher in energy. Microwave spectra suggest a value of 0.63 kJ mol-1. The energy barrier between these forms is in the neighbourhood of 25 kJ mol-1 according to a MP2/cc-pVDZ calculation. We present estimates of the relative energies of all four torsional isomers and the rotational barrier based on a variant of the Focal Point Analysis developed by Császár and co-workers. These calculations, extending to the CCSD(T)/cc-pV5Z level, predict that the s-cis anti torsional isomer is the most stable form, in contrast to prior estimates. The s-cis syn form lies about 2.9 kJ mol-1 higher, while the s-trans syn and anti forms lie at about 21.7 and 23.3 kJ mol-1, respectively. We estimate the rotational barrier between the s-cis trans and s-cis anti structures to be about 23.9 kJ mol-1. Error ranges derived from the fit to extrapolation forms suggest that our estimates have an uncertainty of about 0.1 kJ mol-1.

  3. Proteomic analysis of MOLT-4 cells treated by valproic acid.

    PubMed

    Vávrová, Jirina; Janovská, Sylva; Rezácová, Martina; Hernychová, Lenka; Tichá, Zuzana; Vokurková, Doris; Záskodová, Darina; Lukásová, Emilie

    2007-09-01

    The effect of valproic acid (VA) on protein expression in human T-lymphocytic leukemia cells MOLT-4 was studied. VA is an inhibitor of histonedeacetylases and has a potential use as antitumor agent in leukemia treatment. The authors in this work prove that 4 h long incubation with 2 mmol/l VA causes phosphorylation of histone H2A.X and its colocalization with 53BP1 in nuclear foci. Their co-localization is typical for DSB signaling machinery. These foci were detected in cells after 4 h exposure without increase of Annexin V positive apoptotic cells. Slight increase in apoptosis (Annexin V positivity) after 24 h is accompanied by more intensive increase in phosphorylation of H2A.X and also by formation of nuclear foci containing gammaH2A.X and 53BP1. Treatment of cells with 2 mmol/l VA resulted in induction of apoptosis affecting about 30% of cells after incubation for 72 h. The changes in protein expression were examined after cell incubation with 2 mmol/l VA for 4 h. Proteins were separated by two-dimensional electrophoresis and quantified using image evaluation system. Those exhibiting significant VA-induced abundance alterations were identified by mass spectrometry. Changes in expression of 22 proteins were detected, of which 15 proteins were down-regulated. Proteomic analysis resulted in successful identification of three proteins involving alfa-tubulin 3, tubulin-specific chaperone and heterogeneous nuclear ribonucloprotein F. Expression of seven proteins was up-regulated, including heterogeneous nuclear ribonucloprotein A/B. Identified proteins are related to microtubular system and hnRNP family. Suppression of microtubular proteins and changes of balance among hnRNPs can contribute to proliferation arrest and apoptosis induction.

  4. Analysis of Vaginal Acetic Acid in Patients Undergoing Treatment for Bacterial Vaginosis

    PubMed Central

    Chaudry, Amjad N.; Travers, Paul J.; Yuenger, Jeffrey; Colletta, Lorraine; Evans, Phillip; Zenilman, Jonathan M.; Tummon, Andrew

    2004-01-01

    A “gold standard” method for the diagnosis of bacterial vaginosis (BV) is lacking. The clinical criteria described by the Amsel technique are subjective and difficult to quantify. Alternatively, the reading of Gram-stained vaginal smears by scoring techniques such as those that use the Nugent or Hay-Ison scoring systems is again subjective, requires expert personnel to perform the reading, and is infrequently used clinically. Recently, a new diagnostic device, the Osmetech Microbial Analyzer—Bacterial Vaginosis (OMA-BV), which determines a patient's BV status on the basis of measurement of the amount of acetic acid present in a vaginal swab specimen, was approved by the Food and Drug Administration. The present study uses the conducting polymer gas-sensing technology of OMA-BV to measure the concentration of acetic acid in the headspace above vaginal swab specimens from patients undergoing treatment for BV with metronidazole. In 97.8% of the cases the level of acetic acid detected fell sharply during the treatment period, crossing from above to below the diagnostic threshold of 900 ppm. The diagnosis obtained on the basis of the level of vaginal acetic acid was compared with the diagnoses obtained by use of the Amsel criteria and the Nugent scoring system both at the time of initial entry into the study and at the repeat samplings on days 7 and 14. The results obtained with OMA-BV showed overall agreements compared with the results of the Amsel and Nugent tests of 98 and 94%, respectively, for the 34 patients monitored through the treatment process. This provides further evidence that the measurement of vaginal acetic acid by headspace analysis with conducting polymer sensors is a valid alternative to present tests for the diagnosis of BV. PMID:15528711

  5. Quantitative metabolomics analysis of amino acid metabolism in recombinant Pichia pastoris under different oxygen availability conditions

    PubMed Central

    2012-01-01

    Background Environmental and intrinsic stress factors can result in the global alteration of yeast physiology, as evidenced by several transcriptional studies. Hypoxia has been shown to have a beneficial effect on the expression of recombinant proteins in Pichia pastoris growing on glucose. Furthermore, transcriptional profiling analyses revealed that oxygen availability was strongly affecting ergosterol biosynthesis, central carbon metabolism and stress responses, in particular the unfolded protein response. To contribute to the better understanding of the effect and interplay of oxygen availability and foreign protein secretion on central metabolism, a first quantitative metabolomic analysis of free amino acids pools in a recombinant P. pastoris strain growing under different oxygen availability conditions has been performed. Results The values obtained indicate significant variations in the intracellular amino acid pools due to different oxygen availability conditions, showing an overall increase of their size under oxygen limitation. Notably, even while foreign protein productivities were relatively low (about 40–80 μg Fab/gDCW·h), recombinant protein production was found to have a limited but significant impact on the intracellular amino acid pools, which were generally decreased in the producing strain compared with the reference strain. However, observed changes in individual amino acids pools were not correlated with their corresponding relative abundance in the recombinant protein sequence, but to the overall cell protein amino acid compositional variations. Conclusions Overall, the results obtained, combined with previous transcriptomic and proteomic analyses provide a systematic metabolic fingerprint of the oxygen availability impact on recombinant protein production in P. pastoris. PMID:22704468

  6. Polymalic acid fermentation by Aureobasidium pullulans for malic acid production from soybean hull and soy molasses: Fermentation kinetics and economic analysis.

    PubMed

    Cheng, Chi; Zhou, Yipin; Lin, Meng; Wei, Peilian; Yang, Shang-Tian

    2017-01-01

    Polymalic acid (PMA) production by Aureobasidium pullulans ZX-10 from soybean hull hydrolysate supplemented with corn steep liquor (CSL) gave a malic acid yield of ∼0.4g/g at a productivity of ∼0.5g/L·h. ZX-10 can also ferment soy molasses, converting all carbohydrates including the raffinose family oligosaccharides to PMA, giving a high titer (71.9g/L) and yield (0.69g/g) at a productivity of 0.29g/L·h in fed-batch fermentation under nitrogen limitation. A higher productivity of 0.64g/L·h was obtained in repeated batch fermentation with cell recycle and CSL supplementation. Cost analysis for a 5000 MT plant shows that malic acid can be produced at $1.10/kg from soy molasses, $1.37/kg from corn, and $1.74/kg from soybean hull. At the market price of $1.75/kg, malic acid production from soy molasses via PMA fermentation offers an economically competitive process for industrial production of bio-based malic acid.

  7. Capillary Electrophoresis Analysis of Organic Amines and Amino Acids in Saline and Acidic Samples Using the Mars Organic Analyzer

    NASA Astrophysics Data System (ADS)

    Stockton, Amanda M.; Chiesl, Thomas N.; Lowenstein, Tim K.; Amashukeli, Xenia; Grunthaner, Frank; Mathies, Richard A.

    2009-11-01

    The Mars Organic Analyzer (MOA) has enabled the sensitive detection of amino acid and amine biomarkers in laboratory standards and in a variety of field sample tests. However, the MOA is challenged when samples are extremely acidic and saline or contain polyvalent cations. Here, we have optimized the MOA analysis, sample labeling, and sample dilution buffers to handle such challenging samples more robustly. Higher ionic strength buffer systems with pKa values near pH 9 were developed to provide better buffering capacity and salt tolerance. The addition of ethylaminediaminetetraacetic acid (EDTA) ameliorates the negative effects of multivalent cations. The optimized protocol utilizes a 75 mM borate buffer (pH 9.5) for Pacific Blue labeling of amines and amino acids. After labeling, 50 mM (final concentration) EDTA is added to samples containing divalent cations to ameliorate their effects. This optimized protocol was used to successfully analyze amino acids in a saturated brine sample from Saline Valley, California, and a subcritical water extract of a highly acidic sample from the Río Tinto, Spain. This work expands the analytical capabilities of the MOA and increases its sensitivity and robustness for samples from extraterrestrial environments that may exhibit pH and salt extremes as well as metal ions.

  8. Capillary electrophoresis analysis of organic amines and amino acids in saline and acidic samples using the Mars organic analyzer.

    PubMed

    Stockton, Amanda M; Chiesl, Thomas N; Lowenstein, Tim K; Amashukeli, Xenia; Grunthaner, Frank; Mathies, Richard A

    2009-11-01

    The Mars Organic Analyzer (MOA) has enabled the sensitive detection of amino acid and amine biomarkers in laboratory standards and in a variety of field sample tests. However, the MOA is challenged when samples are extremely acidic and saline or contain polyvalent cations. Here, we have optimized the MOA analysis, sample labeling, and sample dilution buffers to handle such challenging samples more robustly. Higher ionic strength buffer systems with pK(a) values near pH 9 were developed to provide better buffering capacity and salt tolerance. The addition of ethylaminediaminetetraacetic acid (EDTA) ameliorates the negative effects of multivalent cations. The optimized protocol utilizes a 75 mM borate buffer (pH 9.5) for Pacific Blue labeling of amines and amino acids. After labeling, 50 mM (final concentration) EDTA is added to samples containing divalent cations to ameliorate their effects. This optimized protocol was used to successfully analyze amino acids in a saturated brine sample from Saline Valley, California, and a subcritical water extract of a highly acidic sample from the Río Tinto, Spain. This work expands the analytical capabilities of the MOA and increases its sensitivity and robustness for samples from extraterrestrial environments that may exhibit pH and salt extremes as well as metal ions.

  9. Myrtus communis berry color morphs: a comparative analysis of essential oils, fatty acids, phenolic compounds, and antioxidant activities.

    PubMed

    Messaoud, Chokri; Boussaid, Mohamed

    2011-02-01

    Extracts of mature dark blue and white berries from two Tunisian Myrtus communis morphs growing at the same site were assessed for their essential-oil and fatty-acid compositions, phenolic contents, and antioxidant activities. The GC and GC/MS analyses of the essential oils allowed the identification of 33 constituents. The oils from the dark blue fruits showed high percentages of α-pinene (11.1%), linalool (11.6%), α-terpineol (15.7%), methyl eugenol (6.2%), and geraniol (3.7%). Myrtenyl acetate (20.3%) was found to be the major compound in the oils from white berries. GC Analysis of the pericarp and seed fatty acids showed that the polyunsaturated fatty acids constituted the major fraction (54.3-78.1%). The highest percentages of linoleic acid (78.0%) and oleic acid (20.0%) were observed in the seeds and the pericarps of the white fruits, respectively. The total phenol, flavonoid, and flavonol contents and the concentration of the eight anthocyanins, identified by HPLC analysis, were significantly higher in the dark blue fruits. All extracts showed a substantial antioxidant activity, assessed by the free radical-scavenging activity and the ferric reducing power, with the dark blue fruit extracts being more effective.

  10. Quantitative gas chromatographic analysis of volatile fatty acids in spent culture media and body fluids.

    PubMed Central

    van den Bogaard, A E; Hazen, M J; Van Boven, C P

    1986-01-01

    Gas chromatographic analysis of volatile fatty acids for identification of obligately anaerobic bacteria and for presumptive diagnosis of anaerobic infections is now widely practiced. However, it is difficult to compare data because only a qualitative analysis is done or only chromatograms are presented instead of quantitative data on volatile fatty acid production. We compared three stationary phases for volatile fatty acid analysis of aqueous solutions and four methods of pretreating samples for gas chromatography. Quantitative analysis could be done accurately by using Carbowax as the stationary phase after pretreatment of spent culture media with Dowex columns. If only qualitative analysis is required (e.g., for presumptive diagnosis of anaerobic infections), ether extraction and headspace analysis are equally suitable. The overall variation coefficient for volatile fatty acid production by four reference strains of obligately anaerobic bacteria after 24 h of incubation was approximately 10%. PMID:3958144

  11. Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck)

    PubMed Central

    Huang, Dingquan; Zhao, Yihong; Cao, Minghao; Qiao, Liang; Zheng, Zhi-Liang

    2016-01-01

    Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control. PMID:27092171

  12. Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck).

    PubMed

    Huang, Dingquan; Zhao, Yihong; Cao, Minghao; Qiao, Liang; Zheng, Zhi-Liang

    2016-01-01

    Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control.

  13. Validation of two methods for fatty acids analysis in eggs.

    PubMed

    Mazalli, Mônica R; Bragagnolo, Neura

    2007-05-01

    A comparative study between two methods (lipid extraction followed by saponification and methylation, and direct methylation) to determine the fatty acids in egg yolk was evaluated. Direct methylation of the samples resulted in lower fatty acid content and greater variation in the results than the lipid extraction followed by saponification and methylation. The low repeatability observed for the direct HCl methylation method was probably due to a less efficient extraction and conversion of the fatty acids into their methyl esters as compared to the same procedure starting with the lipid extract. As the lipid extraction followed by esterification method was shown to be more precise it was validated using powdered egg certified as reference material (RM 8415, NIST) and applied to samples of egg, egg enriched with polyunsaturated omega-3 fatty acids (n-3 PUFA), and commercial spray-dried whole egg powder.

  14. Simultaneous analysis of tea catechins, caffeine, gallic acid, theanine and ascorbic acid by micellar electrokinetic capillary chromatography.

    PubMed

    Aucamp, J P; Hara, Y; Apostolides, Z

    2000-04-21

    A micellar electrokinetic capillary chromatography (MEKC) method for the simultaneous analysis of five tea catechins, theanine, caffeine, gallic acid and ascorbic acid has been developed. The catechins are (-)-epicatechin, (+)-catechin, (-)-epigallocatechin, (-)-epicatechin gallate and (-)-epigallocatechin gallate. p-Nitrophenol serves as both reference and internal standard. All the components are separated within 13 min with a 57 cm uncoated fused-silica column. On-column detection was carried out at 200 nm. This method has been used to measure these compounds in fresh tea leaves and tea liquor. The limit of detection for all analytes ranged from 1 to 20 microg/ml.

  15. Modeling anaerobic digestion of blue algae: stoichiometric coefficients of amino acids acidogenesis and thermodynamics analysis.

    PubMed

    Yuan, Xian-Zheng; Shi, Xiao-Shuang; Yuan, Chun-Xin; Wang, Yu-Ping; Qiu, Yan-Ling; Guo, Rong-Bo; Wang, Li-Sheng

    2014-02-01

    In order to facilitate the application of Anaerobic Digestion Model No. 1 (ADM1), an approach for a detailed calculation of stoichiometric coefficients for amino acids acidogenesis during the anaerobic digestion of blue algae is presented. The simulation results obtained support the approach by good predictions of the dynamic behavior of cumulative methane production, pH values as well as the concentrations of acetate, propionate, butyrate, valerate and inorganic nitrogen. The sensitivity analysis based on Monte Carlo simulation showed that the stoichiometric coefficients for amino acids acidogenesis had high sensitivities to the outputs of the model. The model further indicated that the Gibbs free energies from the uptake of long-chain fatty acids (LCFA), valerate and butyrate were positive through the digestion, while the free energies for other components were negative. During the digestion, the cumulative heat productions from microbial activities and methane were 77.69 kJ and 185.76 kJ, respectively. This result suggested that proper heat preservation of anaerobic digesters could minimize the external heating needs due to the heat produced from microbial activities.

  16. Accurate analysis of taurine, anserine, carnosine and free amino acids in a cattle muscle biopsy sample.

    PubMed

    Imanari, Mai; Higuchi, Mikito; Shiba, Nobuya; Watanabe, Akira

    2010-06-01

    We have established an analysis method for some free amino acids (FAAs), as well as taurine (Tau), anserine (Ans) and carnosine (Car), in a fresh biopsy sample from cattle muscle. A series of model biopsy samples, corresponding to the mixtures of lean meat, fat and connective tissue, was prepared and showed high correlation coefficients between the compound concentration and the 3-methylhistidine (3-MeHis) content derived from hydrolysis of the biopsy sample (r = 0.74-0.95, P < 0.01). Interference from blood contamination could not be neglected, because the concentration of some FAAs in blood was comparable to that in muscle. However, it was possible to control the contamination of Tau, Ans, Car, glutamic acid, glutamine, asparatic acid and alanine to less than 5.0% when the blood contamination was controlled to less than 23%.These results suggest the necessity of measuring 3-MeHis as an index of lean meat and hemoglobin as an index of blood contamination when compounds in muscle biopsy samples are evaluated. We have carried out a series of these analyses using one biopsy sample and reveal differences in Tau, Ans, Car and some FAAs in beef muscle after different feeding regimes.

  17. Salts of phenylacetic acid and 4-hydroxyphenylacetic acid with Cinchona alkaloids: Crystal structures, thermal analysis and FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Amombo Noa, Francoise M.; Jacobs, Ayesha

    2016-06-01

    Seven salts were formed with phenylacetic acid (PAA), 4-hydroxyphenylacetic acid (HPAA) and the Cinchona alkaloids; cinchonidine (CIND), quinidine (QUID) and quinine (QUIN). For all the structures the proton was transferred from the carboxylic acid of the PAA/HPAA to the quinuclidine nitrogen of the respective Cinchona alkaloid. For six of the salts, water was included in the crystal structures with one of these also incorporating an isopropanol solvent molecule. However HPAA co-crystallised with quinine to form an anhydrous salt, (HPAA-)(QUIN+). The thermal stability of the salts were determined and differential scanning calorimetry revealed that the (HPAA-)(QUIN+) salt had the highest thermal stability compared to the other salt hydrates. The salts were also characterized using Fourier transform infrared spectroscopy. (PAA-)(QUID+)·H2O and (PAA-)(QUIN+)·H2O are isostructural and Hirshfeld surface analysis was completed to compare the intermolecular interactions in these two structures.

  18. Prediction of anticancer property of bowsellic acid derivatives by quantitative structure activity relationship analysis and molecular docking study

    PubMed Central

    Satpathy, Raghunath; Guru, R. K.; Behera, R.; Nayak, B.

    2015-01-01

    Context: Boswellic acid consists of a series of pentacyclic triterpene molecules that are produced by the plant Boswellia serrata. The potential applications of Bowsellic acid for treatment of cancer have been focused here. Aims: To predict the property of the bowsellic acid derivatives as anticancer compounds by various computational approaches. Materials and Methods: In this work, all total 65 derivatives of bowsellic acids from the PubChem database were considered for the study. After energy minimization of the ligands various types of molecular descriptors were computed and corresponding two-dimensional quantitative structure activity relationship (QSAR) models were obtained by taking Andrews coefficient as the dependent variable. Statistical Analysis Used: Different types of comparative analysis were used for QSAR study are multiple linear regression, partial least squares, support vector machines and artificial neural network. Results: From the study geometrical descriptors shows the highest correlation coefficient, which indicates the binding factor of the compound. To evaluate the anticancer property molecular docking study of six selected ligands based on Andrews affinity were performed with nuclear factor-kappa protein kinase (Protein Data Bank ID 4G3D), which is an established therapeutic target for cancers. Along with QSAR study and docking result, it was predicted that bowsellic acid can also be treated as a potential anticancer compound. Conclusions: Along with QSAR study and docking result, it was predicted that bowsellic acid can also be treated as a potential anticancer compound. PMID:25709332

  19. [Analysis on the components of rat urinary stone induced by terephthalic acid].

    PubMed

    Qi, Shaoting; Wang, Xinru; Xu, Xikun; Yao, Hongwei

    2002-04-01

    In order to analyze the components of rat urinary stone and to explore the possible mechanism of chemically induced bladder cancer, terephthalic acid (TPA) is orally administrated to rats at the doses of 5000 and 500 mg/kg/BW/everyday for consecutive 90 days and stones in bladder and kidney are collected. Inductive Coupled Plasma Quantomer (ICP), Element Analyzer (EA) and Fourier Transform Infared Spectrometer (FT-IR) are applied for the analysis on the components of stone in bladder and kidney. The results showed that the main components of the stone are calcium, carbon, nitrogen, hydrogen and phosphorus. The FT-IR showed that the stones both in bladder and kidney might contain nitrous, carbonate, ammonium salt, and para-position replaced benzene-ring compounds, but no original TPA is detected. The findings indicate that TPA might have a metabolic turnover inside the rat body, and, at least, might not be completely excreted in its original form.

  20. Validation of acid washes as critical control points in hazard analysis and critical control point systems.

    PubMed

    Dormedy, E S; Brashears, M M; Cutter, C N; Burson, D E

    2000-12-01

    A 2% lactic acid wash used in a large meat-processing facility was validated as an effective critical control point (CCP) in a hazard analysis and critical control point (HACCP) plan. We examined the microbial profiles of beef carcasses before the acid wash, beef carcasses immediately after the acid wash, beef carcasses 24 h after the acid wash, beef subprimal cuts from the acid-washed carcasses, and on ground beef made from acid-washed carcasses. Total mesophilic, psychrotrophic, coliforms, generic Escherichia coli, lactic acid bacteria, pseudomonads, and acid-tolerant microorganisms were enumerated on all samples. The presence of Salmonella spp. was also determined. Acid washing significantly reduced all counts except for pseudomonads that were present at very low numbers before acid washing. All other counts continued to stay significantly lower (P < 0.05) than those on pre-acid-washed carcasses throughout all processing steps. Total bacteria, coliforms, and generic E. coli enumerated on ground beef samples were more than 1 log cycle lower than those reported in the U.S. Department of Agriculture Baseline data. This study suggests that acid washes may be effective CCPs in HACCP plans and can significantly reduce the total number of microorganisms present on the carcass and during further processing.

  1. Comparative analysis of multilineage properties of mesenchymal stromal cells derived from fetal sources shows an advantage of mesenchymal stromal cells isolated from cord blood in chondrogenic differentiation potential

    PubMed Central

    Pievani, Alice; Scagliotti, Valeria; Russo, Francesca Maria; Azario, Isabella; Rambaldi, Benedetta; Sacchetti, Benedetto; Marzorati, Simona; Erba, Eugenio; Giudici, Giovanni; Riminucci, Mara; Biondi, Andrea; Vergani, Patrizia; Serafini, Marta

    2014-01-01

    Background aims Cord blood (CB) and amniotic fluid (AF) could represent new and attractive mesenchymal stromal cell (MSC) sources, but their potential therapeutic applications are still limited by lack of standardized protocols for isolation and differentiation. In particular, chondrogenic differentiation has never been deeply investigated. Methods MSCs were obtained from CB and AF samples collected during cesarean sections at term and compared for their biological and differentiation properties, with particular interest in cartilage differentiation, in which quantitative real-time polymerase chain reaction and immunohistochemical analyses were performed to evaluate the expression of type 2 collagen, type 10 collagen, SRY-box9 and aggrecan. Results We were able to isolate MSCs from 12 of 30 (40%) and 5 of 20 (25%) CB and AF units, respectively. Fluorescence in situ hybridization analysis indicated the fetal origin of isolated MSC strains. Both populations expressed mesenchymal but not endothelial and hematopoietic markers, even though we observed a lower expression of human leukocyte antigen (HLA) I in CB-MSCs. No differences in proliferation rate and cell cycle analysis could be detected. After osteogenic induction, both populations showed matrix mineralization and typical marker expression. Under chondrogenic conditions, pellets derived from CB-MSCs, in contrast with AF-MSCs pellets, were significantly larger, showed cartilage-like morphology and resulted positive for chondrocyte-associated markers, such as type 2 collagen, type 10 collagen, SRY-box9 and aggrecan. Conclusions Our results show that CB-MSCs and AF-MSCs collected at term differ from each other in their biological and differentiation properties. In particular, only CB-MSCs showed a clear chondrogenic potential and thus could represent an ideal candidate for cartilage-tissue engineering. PMID:24794181

  2. Spectrophotometric Analysis of the Cyanide Metabolite 1-Aminothiazoline-6-Carboxylic Acid

    DTIC Science & Technology

    2006-01-01

    besides the possibility of using ATCA as an improved REFERENCES marker of cyanide intoxication , if ATCA is found to play a Ballantyne, B. 1977. In...Open Literature 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Spectrophotometric analysis of the cyanide metabolite 2-aminothiazoline-4-carboxylic acid 5b...See reprint. 15. SUBJECT TERMS Cyanide metabolite, 2-aminothiazoline-4-carboxylic acid, ATCA, 2-Iminothiazolidine-4-carboxylic acid, ITCA

  3. Transcriptomic Analysis of Carboxylic Acid Challenge in Escherichia coli: Beyond Membrane Damage

    PubMed Central

    Royce, Liam A.; Boggess, Erin; Fu, Yao; Liu, Ping; Shanks, Jacqueline V.; Dickerson, Julie; Jarboe, Laura R.

    2014-01-01

    Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0 to probe mechanisms of toxicity. This analysis highlights the intracellular acidification and membrane damage caused by C8 challenge. Network component analysis identified transcription factors with altered activity including GadE, the activator of the glutamate-dependent acid resistance system (AR2) and Lrp, the amino acid biosynthesis regulator. The intracellular acidification was quantified during exogenous challenge, but was not observed in a carboxylic acid producing strain, though this may be due to lower titers than those used in our exogenous challenge studies. We developed a framework for predicting the proton motive force during adaptation to strong inorganic acids and carboxylic acids. This model predicts that inorganic acid challenge is mitigated by cation accumulation, but that carboxylic acid challenge inverts the proton motive force and requires anion accumulation. Utilization of native acid resistance systems was not useful in terms of supporting growth or alleviating intracellular acidification. AR2 was found to be non-functional, possibly due to membrane damage. We proposed that interaction of Lrp and C8 resulted in repression of amino acid biosynthesis. However, this hypothesis was not supported by perturbation of lrp expression or amino acid supplementation. E. coli strains were also engineered for altered cyclopropane fatty acid content in the membrane, which had a dramatic effect on membrane properties, though C8 tolerance was not increased. We conclude that achieving higher production titers requires circumventing the membrane damage. As higher titers are achieved, acidification may become problematic. PMID:24586888

  4. Citric acid traps to replace sulphuric acid in the ammonia diffusion of dilute water samples for 15N analysis.

    PubMed

    Schleppi, Patrick; Bucher-Wallin, Inga; Saurer, Matthias; Jäggi, Maya; Landolt, Werner

    2006-01-01

    The analysis of 15N in aqueous samples requires the concentration of dissolved nitrogen (N) into a small volume that can be analysed by mass spectrometry. This is conveniently achieved by the NH3 diffusion technique, where NH4+ is captured on small acidified filters enclosed in PTFE. NO3- can be analysed the same way by reducing it to NH4+ with Devarda's alloy. H2SO4 is commonly used for the acidification of the filters. During combustion, however, this acid leads to the production of SO2 and elemental sulphur, which both have detrimental effects on the mass spectrometer. We propose here to replace H2SO4 with citric acid because it is combusted completely to CO2 and H2O in the elemental analyser before entering the mass spectrometer. Citric acid was found to give comparable results in terms of N recovery and 15N values, both for NH4+ and for NO3- samples. Blank samples revealed that N contamination was slightly lower using citric instead of sulphuric acid as acidifier of the glass filters. NH4+ samples first concentrated over cation-exchange columns were strongly acidic and several methods were tested to raise the pH for the subsequent diffusion. These samples gave incomplete N recoveries, but this problem was independent of the acid used on the filters and of the final pH of the sample. Complete recovery was achieved only by increasing the volume of the eluate from the columns. Citric acid can thus generally be recommended instead of H2SO4 for ammonia diffusion.

  5. Topological analysis of the electronic charge density in the ethene protonation reaction catalyzed by acidic zeolite.

    PubMed

    Zalazar, M Fernanda; Peruchena, Nélida M

    2007-08-16

    In the present work, the distribution of the electronic charge density in the ethene protonation reaction by a zeolite acid site is studied within the framework of the density functional theory and the atoms in molecules (AIM) theory. The key electronic effects such as topological distribution of the charge density involved in the reaction are presented and discussed. The results are obtained at B3LYP/6-31G(**) level theory. Attention is focused on topological parameters such as electron density, its Laplacian, kinetic energy density, potential energy density, and electronic energy density at the bond critical points (BCP) in all bonds involved in the interaction zone, in the reactants, pi-complex, transition state, and alkoxy product. In addition, the topological atomic properties are determined on the selected atoms in the course of the reaction (average electron population, N(Omega), atomic net charge, q(Omega), atomic energy, E(Omega), atomic volume, v(Omega), and first moment of the atomic charge distribution, M(Omega)) and their changes are analyzed exhaustively. The topological study clearly shows that the ethene interaction with the acid site of the zeolite cluster, T5-OH, in the ethene adsorbed, is dominated by a strong O-H...pi interaction with some degree of covalence. AIM analysis based on DFT calculation for the transition state (TS) shows that the hydrogen atom from the acid site in the zeolitic fragment is connected to the carbon atom by a covalent bond with some contribution of electrostatic interaction and to the oxygen atom by closed shell interaction with some contribution of covalent character. The C-O bond formed in the alkoxy product can be defined as a weaker shared interaction. Our results show that in the transition state, the dominant interactions are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the concentration and accumulation of the charge density along the bond path between

  6. Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges.

    PubMed

    Qing, Taiping; He, Dinggeng; He, Xiaoxiao; Wang, Kemin; Xu, Fengzhou; Wen, Li; Shangguan, Jingfang; Mao, Zhengui; Lei, Yanli

    2016-04-01

    Owing to their highly efficient catalytic effects and substrate specificity, the nucleic acid tool enzymes are applied as 'nano-tools' for manipulating different nucleic acid substrates both in the test-tube and in living organisms. In addition to the function as molecular scissors and molecular glue in genetic engineering, the application of nucleic acid tool enzymes in biochemical analysis has also been extensively developed in the past few decades. Used as amplifying labels for biorecognition events, the nucleic acid tool enzymes are mainly applied in nucleic acids amplification sensing, as well as the amplification sensing of biorelated variations of nucleic acids. With the introduction of aptamers, which can bind different target molecules, the nucleic acid tool enzymes-aided signal amplification strategies can also be used to sense non-nucleic targets (e.g., ions, small molecules, proteins, and cells). This review describes and discusses the amplification strategies of nucleic acid tool enzymes-aided biosensors for biochemical analysis applications. Various analytes, including nucleic acids, ions, small molecules, proteins, and cells, are reviewed briefly. This work also addresses the future trends and outlooks for signal amplification in nucleic acid tool enzymes-aided biosensors.

  7. Students' Understanding of Acid, Base and Salt Reactions in Qualitative Analysis.

    ERIC Educational Resources Information Center

    Tan, Kim-Chwee Daniel; Goh, Ngoh-Khang; Chia, Lian-Sai; Treagust, David F.

    2003-01-01

    Uses a two-tier, multiple-choice diagnostic instrument to determine (n=915) grade 10 students' understanding of the acid, base, and salt reactions involved in basic qualitative analysis. Reports that many students did not understand the formation of precipitates and the complex salts, acid/salt-base reactions, and thermal decomposition involved in…

  8. Analysis of Steam Heating of a Two-Layer TBP/N-Paraffin/Nitric Acid Mixtures

    SciTech Connect

    Laurinat, J.E.; Hassan, N.M.; Rudisill, T.S.; Askew, N.M.

    1998-07-22

    This report presents an analysis of steam heating of a two-layer tri-n-butyl phosphate (TBP)/n-paraffin-nitric acid mixture.The purpose of this study is to determine if the degree of mixing provided by the steam jet or by bubbles generated by the TBP/nitric acid reaction is sufficient to prevent a runaway reaction.

  9. MICROARRAY ANALYSIS OF DICHLOROACETIC ACID-INDUCED CHANGES IN GENE EXPRESSION

    EPA Science Inventory


    MICROARRAY ANALYSIS OF DICHLOROACETIC ACID-INDUCED CHANGES IN GENE EXPRESSION

    Dichloroacetic acid (DCA) is a major by-product of water disinfection by chlorination. Several studies have demonstrated the hepatocarcinogenicity of DCA in rodents when administered in dri...

  10. Analysis and properties of the decarboxylation products of oleic acid by catalytic triruthenium dodecacarbonyl

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recently, ruthenium-catalyzed isomerization-decarboxylation of fatty acids to give alkene mixtures was reported. When the substrate was oleic acid, the reaction yielded a mixture consisting of heptadecene isomers. In this work, we report the compositional analysis of the mixture obtained by triruthe...

  11. Genome Wide Analysis of Fatty Acid Desaturation and Its Response to Temperature1[OPEN

    PubMed Central

    Menard, Guillaume N.; Moreno, Jose Martin; Bryant, Fiona M.; Munoz-Azcarate, Olaya; Hassani-Pak, Keywan; Kurup, Smita

    2017-01-01

    Plants modify the polyunsaturated fatty acid content of their membrane and storage lipids in order to adapt to changes in temperature. In developing seeds, this response is largely controlled by the activities of the microsomal ω-6 and ω-3 fatty acid desaturases, FAD2 and FAD3. Although temperature regulation of desaturation has been studied at the molecular and biochemical levels, the genetic control of this trait is poorly understood. Here, we have characterized the response of Arabidopsis (Arabidopsis thaliana) seed lipids to variation in ambient temperature and found that heat inhibits both ω-6 and ω-3 desaturation in phosphatidylcholine, leading to a proportional change in triacylglycerol composition. Analysis of the 19 parental accessions of the multiparent advanced generation intercross (MAGIC) population showed that significant natural variation exists in the temperature responsiveness of ω-6 desaturation. A combination of quantitative trait locus (QTL) analysis and genome-wide association studies (GWAS) using the MAGIC population suggests that ω-6 desaturation is largely controlled by cis-acting sequence variants in the FAD2 5′ untranslated region intron that determine the expression level of the gene. However, the temperature responsiveness of ω-6 desaturation is controlled by a separate QTL on chromosome 2. The identity of this locus is unknown, but genome-wide association studies identified potentially causal sequence variants within ∼40 genes in an ∼450-kb region of the QTL. PMID:28108698

  12. Vibrational spectroscopy and chemometrics for rapid, quantitative analysis of bitter acids in hops (Humulus lupulus).

    PubMed

    Killeen, Daniel P; Andersen, David H; Beatson, Ron A; Gordon, Keith C; Perry, Nigel B

    2014-12-31

    Hops, Humulus lupulus, are grown worldwide for use in the brewing industry to impart characteristic flavor and aroma to finished beer. Breeders produce many varietal crosses with the aim of improving and diversifying commercial hops varieties. The large number of crosses critical to a successful breeding program imposes high demands on the supporting chemical analytical laboratories. With the aim of reducing the analysis time associated with hops breeding, quantitative partial least-squares regression (PLS-R) models have been produced, relating reference data acquired by the industrial standard HPLC and UV methods, to vibrational spectra of the same, chemically diverse hops sample set. These models, produced from rapidly acquired infrared (IR), near-infrared (NIR), and Raman spectra, were appraised using standard statistical metrics. Results demonstrated that all three spectroscopic methods could be used for screening hops for α-acid, total bitter acids, and cohumulone concentrations in powdered hops. Models generated from Raman and IR spectra also showed potential for use in screening hops varieties for xanthohumol concentrations. NIR analysis was performed using both a standard benchtop spectrometer and a portable NIR spectrometer, with comparable results obtained by both instruments. Finally, some important vibrational features of cohumulone, colupulone, and xanthohumol were assigned using DFT calculations, which allow more insightful interpretation of PLS-R latent variable plots.

  13. Effects of acids used in the microabrasion technique: Microhardness and confocal microscopy analysis

    PubMed Central

    Pini, Núbia-Inocencya-Pavesi; Ambrosano, Gláucia-Maria-Bovi; da Silva, Wander-José; Aguiar, Flávio-Henrique-Baggio; Lovadino, José-Roberto

    2015-01-01

    Background This study evaluated the effects of the acids used in the microabrasion on enamel. Material and Methods Seventy enamel/dentine blocks (25 mm2) of bovine incisors were divided into 7 groups (n=10). Experimental groups were treated by active/passive application of 35% H3PO4 (E1/E2) or 6.6% HCl (E3/E4). Control groups were treated by microabrasion with H3PO4+pumice (C5), HCl+silica (C6), or no treatment (C7). The superficial (SMH) and cross-sectional (CSMH; depths of 10, 25, 50, and 75 µm) microhardness of enamel were analyzed. Morphology was evaluated by confocal laser-scanning microscopy (CLSM). Data were analyzed by analysis of variance (Proc Mixed), Tukey, and Dunnet tests (α=5%). Results Active application (E1 and E3) resulted in higher microhardness than passive application (E2 and E4), with no difference between acids. For most groups, the CSMH decreased as the depth increased. All experimental groups and negative controls (C5 and C6) showed significantly reduced CSMH values compared to the control. A significantly higher mean CSMH result was obtained with the active application of H3PO4 (E1) compared to HCl (E3). Passive application did not result in CSMH differences between acids. CLSM revealed the conditioning pattern for each group. Conclusions Although the acids displayed an erosive action, use of microabrasive mixture led to less damage to the enamel layers. Key words:Enamel microabrasion, enamel microhardness, confocal laser scanning microscopy. PMID:26535098

  14. Characterization and analysis of the cotton cyclopropane fatty acid synthase family and their contribution to cyclopropane fatty acid synthesis

    SciTech Connect

    Yu X. H.; Shanklin J.; Rawat, R.

    2011-05-01

    Cyclopropane fatty acids (CPA) have been found in certain gymnosperms, Malvales, Litchi and other Sapindales. The presence of their unique strained ring structures confers physical and chemical properties characteristic of unsaturated fatty acids with the oxidative stability displayed by saturated fatty acids making them of considerable industrial interest. While cyclopropenoid fatty acids (CPE) are well-known inhibitors of fatty acid desaturation in animals, CPE can also inhibit the stearoyl-CoA desaturase and interfere with the maturation and reproduction of some insect species suggesting that in addition to their traditional role as storage lipids, CPE can contribute to the protection of plants from herbivory. Three genes encoding cyclopropane synthase homologues GhCPS1, GhCPS2 and GhCPS3 were identified in cotton. Determination of gene transcript abundance revealed differences among the expression of GhCPS1, 2 and 3 showing high, intermediate and low levels, respectively, of transcripts in roots and stems; whereas GhCPS1 and 2 are both expressed at low levels in seeds. Analyses of fatty acid composition in different tissues indicate that the expression patterns of GhCPS1 and 2 correlate with cyclic fatty acid (CFA) distribution. Deletion of the N-terminal oxidase domain lowered GhCPS's ability to produce cyclopropane fatty acid by approximately 70%. GhCPS1 and 2, but not 3 resulted in the production of cyclopropane fatty acids upon heterologous expression in yeast, tobacco BY2 cell and Arabidopsis seed. In cotton GhCPS1 and 2 gene expression correlates with the total CFA content in roots, stems and seeds. That GhCPS1 and 2 are expressed at a similar level in seed suggests both of them can be considered potential targets for gene silencing to reduce undesirable seed CPE accumulation. Because GhCPS1 is more active in yeast than the published Sterculia CPS and shows similar activity when expressed in model plant systems, it represents a strong candidate gene for

  15. Circulating nucleic acids: An analysis of their occurrence in malignancies.

    PubMed

    Suraj, Shankar; Dhar, Chirag; Srivastava, Sweta

    2017-01-01

    Through a regulated or fortuitous phenomenon, small portions of cell nucleic acids are thrown into circulation. Since the discovery of these circulating nucleic acids (CNAs) in 1948, numerous studies have been published to elucidate their clinical implications in multifarious diseases. Scientists have now discovered disease-specific genetic aberrations, such as mutations, microsatellite alterations, epigenetic modulations (including aberrant methylation), as well as viral DNA/RNA from nucleic acids in plasma and serum. CNAs have become increasingly popular due to their potential for use as a liquid biopsy, which is a tool for non-invasive diagnosis and monitoring of diseases, such as cancer, stroke, trauma, myocardial infarction, autoimmune disorders, and pregnancy-associated complications. While the diagnostic potential of CNAs has been investigated extensively, there is a paucity of understanding of their pathophysiological functions. Are these CNAs part of the cell's regular framework of functioning? Or do they act as molecular players in disease initiation and progression? The aim of this review is to investigate the origins and functions of the circulating cell-free nucleic acids in the plasma and serum of patients with various malignancies, and propose areas of study, which may elucidate the novel underlying mechanisms that are functioning during cancer initiation/progression.

  16. Soil Studies: Applying Acid-Base Chemistry to Environmental Analysis.

    ERIC Educational Resources Information Center

    West, Donna M.; Sterling, Donna R.

    2001-01-01

    Laboratory activities for chemistry students focus attention on the use of acid-base chemistry to examine environmental conditions. After using standard laboratory procedures to analyze soil and rainwater samples, students use web-based resources to interpret their findings. Uses CBL probes and graphing calculators to gather and analyze data and…

  17. HPLC Analysis of [Alpha]- and [Beta]-Acids in Hops

    ERIC Educational Resources Information Center

    Danenhower, Travis M.; Force, Leyna J.; Petersen, Kenneth J.; Betts, Thomas A.; Baker, Gary A.

    2008-01-01

    Hops have been used for centuries to impart aroma and bitterness to beer. The cones of the female hop plant contain both essential oils, which include many of the fragrant components of hops, and a collection of compounds known as [alpha]- and [beta]-acids that are the precursors to bittering agents. In order for brewers to predict the ultimate…

  18. Circulating nucleic acids: An analysis of their occurrence in malignancies

    PubMed Central

    Suraj, Shankar; Dhar, Chirag; Srivastava, Sweta

    2017-01-01

    Through a regulated or fortuitous phenomenon, small portions of cell nucleic acids are thrown into circulation. Since the discovery of these circulating nucleic acids (CNAs) in 1948, numerous studies have been published to elucidate their clinical implications in multifarious diseases. Scientists have now discovered disease-specific genetic aberrations, such as mutations, microsatellite alterations, epigenetic modulations (including aberrant methylation), as well as viral DNA/RNA from nucleic acids in plasma and serum. CNAs have become increasingly popular due to their potential for use as a liquid biopsy, which is a tool for non-invasive diagnosis and monitoring of diseases, such as cancer, stroke, trauma, myocardial infarction, autoimmune disorders, and pregnancy-associated complications. While the diagnostic potential of CNAs has been investigated extensively, there is a paucity of understanding of their pathophysiological functions. Are these CNAs part of the cell's regular framework of functioning? Or do they act as molecular players in disease initiation and progression? The aim of this review is to investigate the origins and functions of the circulating cell-free nucleic acids in the plasma and serum of patients with various malignancies, and propose areas of study, which may elucidate the novel underlying mechanisms that are functioning during cancer initiation/progression. PMID:28123700

  19. Comparing models for perfluorooctanoic acid pharmacokinetics using Bayesian analysis

    EPA Science Inventory

    Selecting the appropriate pharmacokinetic (PK) model given the available data is investigated for perfluorooctanoic acid (PFOA), which has been widely analyzed with an empirical, one-compartment model. This research examined the results of experiments [Kemper R. A., DuPont Haskel...

  20. Analysis of Organic Acids, Deacetyl Asperulosidic Acid and Polyphenolic Compounds as a Potential Tool for Characterization of Noni (Morinda citrifolia) Products.

    PubMed

    Bittová, Miroslava; Hladůkova, Dita; Roblová, Vendula; Krácmar, Stanislav; Kubán, Petr; Kubán, Vlastimil

    2015-11-01

    Organic acids, deacetyl asperulosidic acid (DAA) and polyphenolic compounds in various noni (Morinda citrifolia L.) products (4 juices, 4 dry fruit powders and 2 capsules with dry fruit powder) were analyzed. Reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with a variable wavelength detector (VWD) and electrospray ionization time-of-flight mass spectrometer (ESI-TOF MS) was applied for simultaneous analysis of organic acids (malic, lactic, citric and succinic acid) and DAA. An RP-HPLC method with diode-array detector (DAD) was developed for the analysis of polyphenolic compound content (rutin, catechin, quercitrin, kaempferol, gallic acid, caffeic acid and p-coumaric acid). The developed methods can contribute to better characterization of available noni products that is required from the consumers. In our study, we discovered significant dissimilarities in the content of DAA, citric acid and several phenolic compounds in some samples.

  1. Titration of strong and weak acids by sequential injection analysis technique.

    PubMed

    Maskula, S; Nyman, J; Ivaska, A

    2000-05-31

    A sequential injection analysis (SIA) titration method has been developed for acid-base titrations. Strong and weak acids in different concentration ranges have been titrated with a strong base. The method is based on sequential aspiration of an acidic sample zone and only one zone of the base into a carrier stream of distilled water. On their way to the detector, the sample and the reagent zones are partially mixed due to the dispersion and thereby the base is partially neutralised by the acid. The base zone contains the indicator. An LED-spectrophotometer is used as detector. It senses the colour of the unneutralised base and the signal is recorded as a typical SIA peak. The peak area of the unreacted base was found to be proportional to the logarithm of the acid concentration. Calibration curves with good linearity were obtained for a strong acid in the concentration ranges of 10(-4)-10(-2) and 0.1-3 M. Automatic sample dilution was implemented when sulphuric acid at concentration of 6-13 M was titrated. For a weak acid, i.e. acetic acid, a linear calibration curve was obtained in the range of 3x10(-4)-8x10(-2) M. By changing the volumes of the injected sample and the reagent, different acids as well as different concentration ranges of the acids can be titrated without any other adjustments in the SIA manifold or the titration protocol.

  2. Compound-Specific Isotope Analysis of Amino Acids for Stardust-Returned Samples

    NASA Technical Reports Server (NTRS)

    Cook, Jamie; Elsila, Jamie E.; Stern J. C.; Glavin, D. P.; Dworkin, J. P.

    2008-01-01

    Significant portions of the early Earth's prebiotic organic inventory , including amino acids, could have been delivered to the Earth's sur face by comets and their fragments. Analysis of comets via spectrosc opic observations has identified many organic molecules, including me thane, ethane, arnmonia, cyanic acid, formaldehyde, formamide, acetal ehyde, acetonitrile, and methanol. Reactions between these identifie d molecules could allow the formation of more complex organics such a s amino acids. Isotopic analysis could reveal whether an extraterrest rial signature is present in the Stardust-exposed amines and amino ac ids. Although bulk isotopic analysis would be dominated by the EACA contaminant's terrestrial signature, compoundspecific isotope analysi s (CSIA) could determine the signature of each of the other individua l amines. Here, we report on progress made towards CSIA of the amino acids glycine and EACA in Stardustreturned samples.

  3. Molten Carbonate and Phosphoric Acid Stationary Fuel Cells: Overview and Gap Analysis

    SciTech Connect

    Remick, R.; Wheeler, D.

    2010-09-01

    This report describes the technical and cost gap analysis performed to identify pathways for reducing the costs of molten carbonate fuel cell (MCFC) and phosphoric acid fuel cell (PAFC) stationary fuel cell power plants.

  4. Fatty acid analysis tool (FAAT): An FT-ICR MS lipid analysis algorithm.

    PubMed

    Leavell, Michael D; Leary, Julie A

    2006-08-01

    Electrospray ionization mass spectrometry is becoming an established tool for the investigation of lipids. As the methods for lipid analysis become more mature and their throughput increases, computer algorithms for the interpretation of such data will become a necessity. Toward this end, an algorithm dedicated to the analysis of Fourier transform mass spectral data from lipid extracts has been developed. The algorithm, Fatty Acid Analysis Tool, termed FAAT, has been successfully used to investigate complex lipid extracts containing thousands of components, from various species of mycobacteria including M. tuberculosis and M. abscessus. FAAT is rapid, generally taking tens of seconds to interpret multiple spectra, and accessible to most users as it is implemented in Microsoft Excel Visual Basic Software. In the reduction of data, FAAT begins by scaling spectra (i.e., to account for dilution factors), identifying monoisotopic ions, and assigning isotope packets. Unique features of FAAT include the following: (1) overlapping saturated and unsaturated lipid species can be distinguished, (2) known ions are assigned from a user-defined library including species that possess methylene heterogeneity, (3) and isotopic shifts from stable isotope labeling experiments are identified and assigned (up to a user-defined maximum). In addition, abundance differences between samples grown under normal and stressed conditions can be determined. In the analysis of mycobacterial lipid extracts, FAAT has successfully identified isotopic shifts from incorporation of 15N in M. abscessus. Additionally, FAAT has been used to successfully determine differences in lipid abundances between M. tuberculosis wild-type and mutant strains.

  5. An air-pressure-free elastomeric valve for integrated nucleic acid analysis by capillary electrophoresis

    NASA Astrophysics Data System (ADS)

    Jung, Wooseok; Barrett, Matthew; Brooks, Carla; Rivera, Andrew; Birdsell, Dawn N.; Wagner, David M.; Zenhausern, Frederic

    2015-12-01

    We present a new elastomeric valve for integrated nucleic acid analysis by capillary electrophoresis. The valve functions include metering to capture a designated volume of biological sample into a polymerase chain reaction (PCR) chamber, sealing to preserve the sample during PCR cycling, and transfer of the PCR-products and on-chip formamide post-processing for the analysis of DNA fragments by capillary gel electrophoresis. This new valve differs from prior art polydimethylsiloxane (PDMS) valves in that the valve is not actuated externally by air-pressure or vacuum so that it simplifies a DNA analysis system by eliminating the need for an air-pressure or vacuum source, and off-cartridge solenoid valves, control circuit boards and software. Instead, the new valve is actuated by a thermal cycling peltier assembly integrated within the hardware instrument that tightly comes in contact with a microfluidic cartridge for thermal activation during PCR, so that it spontaneously closes the valve without an additional actuator system. The valve has bumps in the designated locations so that it has a self-alignment that does not require precise alignment of a valve actuator. Moreover, the thickness of the new valve is around 600 μm with an additional bump height of 400 μm so that it is easy to handle and very feasible to fabricate by injection molding compared to other PDMS valves whose thicknesses are around 30-100 μm. The new valve provided over 95% of metering performance in filling the fixed volume of the PCR chamber, preserved over 97% of the sample volume during PCR, and showed very comparable capillary electrophoresis peak heights to the benchtop assay tube controls with very consistent transfer volume of the PCR-product and on-chip formamide. The new valve can perform a core function for integrated nucleic acid analysis by capillary electrophoresis.

  6. Techno-economic Analysis for the Thermochemical Conversion of Lignocellulosic Biomass to Ethanol via Acetic Acid Synthesis

    SciTech Connect

    Zhu, Yunhua; Jones, Susanne B.

    2009-04-01

    Biomass is a renewable energy resource that can be converted into liquid fuel suitable for transportation applications. As a widely available biomass form, lignocellulosic biomass can have a major impact on domestic transportation fuel supplies and thus help meet the Energy Independence and Security Act renewable energy goals (U.S. Congress 2007). This study performs a techno-economic analysis of the thermo chemical conversion of biomass to ethanol, through methanol and acetic acid, followed by hydrogenation of acetic acid to ethanol. The conversion of syngas to methanol and methanol to acetic acid are well-proven technologies with high conversions and yields. This study was undertaken to determine if this highly selective route to ethanol could provide an already established economically attractive route to ethanol. The feedstock was assumed to be wood chips at 2000 metric ton/day (dry basis). Two types of gasification technologies were evaluated: an indirectly-heated gasifier and a directly-heated oxygen-blown gasifier. Process models were developed and a cost analysis was performed. The carbon monoxide used for acetic acid synthesis from methanol and the hydrogen used for hydrogenation were assumed to be purchased and not derived from the gasifier. Analysis results show that ethanol selling prices are estimated to be $2.79/gallon and $2.81/gallon for the indirectly-heated gasifier and the directly-heated gasifier systems, respectively (1stQ 2008$, 10% ROI). These costs are above the ethanol market price for during the same time period ($1.50 - $2.50/gal). The co-production of acetic acid greatly improves the process economics as shown in the figure below. Here, 20% of the acetic acid is diverted from ethanol production and assumed to be sold as a co-product at the prevailing market prices ($0.40 - $0.60/lb acetic acid), resulting in competitive ethanol production costs.

  7. Trajectory analysis of acid deposition data from the new jersey pine barrens

    NASA Astrophysics Data System (ADS)

    Budd, William W.

    This research provides an example of the application of a simple method for evaluating regional interrelationships using air parcel trajectory analysis. An assessment of trajectories associated with storms affecting McDonald's Branch watershed (39°50'N, 74°30'W) is presented. A simple classification system is used to examine regional contributions of acid precursors. The results of the work suggest that major regional sources of acid precursor emissions dominated precipitation acidity for the Pine Barrens region from 1978 to 1981. An incremental approach to acid precipitation policy is suggested.

  8. RFLP and AFLP analysis of inter- and intraspecific variation of Brassica rapa and B. napus shows that B. rapa is an important genetic resource for B. napus improvement.

    PubMed

    Liu, Ren-Hu; Meng, Jin-Ling

    2006-09-01

    Fingerprinting of 29 accessions of oilseed rape, including seven accessions of Brassica napus, and 22 accessions of B. rapa (B. campestris) from Europe, North America, and China was analyzed using RFLP and AFLP markers. In total, 1,477 polymorphic RFLP bands and 183 polymorphic AFLP bands from 166 enzyme-probe combinations and two pairs of AFLP primers, respectively, were scored for the 29 accessions. On average, RFLP analysis showed that the Arabidopsis EST probe detected more polymorphic bands in Brassica than the random genomic probe performed. More polymorphic RFLP markers were detected with the digestion of EcoR I or BamH I than HindIII. According to the number of bands amplified from each accession, the copy numbers of each gene in the genomes of B. rapa and B. napus were estimated. The average copy numbers in B. rapa of China, B. rapa of Europe, and B. napus, were 3.2, 3.1, and 2.9, respectively. Genetic distance based on the AFLP data was well correlated with that based on the RFLP data (r = 0.72, P<0.001), but 0.39 smaller on average. Genetic diversity analysis showed that Chinese B. rapa was more polymorphic than Chinese B. napus and European materials. Some European B. napus accessions were clustered into European B. rapa, which were distinctly different from Chinese B. napus. The larger variations of Chinese accessions of B. rapa suggest that they are valuable in oilseed rape breeding. Novel strategies to use intersubgenomic heterosis between genome of B. rapa (A(r)A(r)) and genome of B. napus (A(n)A(n)C(n)C(n)) were elucidated.

  9. Allele specific-PCR and melting curve analysis showed relatively high frequency of β-casein gene A1 allele in Iranian Holstein, Simmental and native cows.

    PubMed

    Gholami, M; Hafezian, S H; Rahimi, G; Farhadi, A; Rahimi, Z; Kahrizi, D; Kiani, S; Karim, H; Vaziri, S; Muhammadi, S; Veisi, F; Ghadiri, K; Shetabi, H; Zargooshi, J

    2016-10-31

    There are two allelic forms of A1 and A2 of β-casein gene in dairy cattle. Proteolytic digestion of bovine β-casein A1 type produces bioactive peptide of β-casomorphin-7 known as milk devil. β-casomorphin-7 causes many diseases, including type 1 diabetes, cardiovascular disease syndrome, sudden death and madness. The aim of the present study was to determine the different allelic forms of β-casein gene in Iranian Holstein, Simmental and native cattle in order to identify A1 and A2 variants. The blood samples were collected randomly and DNA was extracted using modified salting out method. An 854 bp fragment including part of exon 7 and part of intron 6 of β-casein gene was amplified by allele specific polymerase chain reaction (AS-PCR). Also, the accuracy of AS-PCR genotyping has been confirmed by melting temperature curve analysis using Real-time PCR machinery. The comparison of observed allele and genotype frequency among the studied breeds was performed using the Fisher exact and Chi-squared test, respectively by SAS program. Obtained results showed the A1 allele frequencies of 50, 51.57, 54.5, 49.4 and 46.6% in Holstein, Simmental, Sistani, Taleshi and Mazandarani cattle populations, respectively. The chi-square test was shown that no any populations were in Hardy-Weinberg equilibrium for studied marker locus. Comparison and analysis of the test results for allelic frequency showed no any significant differences between breeds (P>0.05). The frequency of observed genotypes only differs significantly between Holstein and Taleshi breeds but no any statistically significant differences were found for other breeds (P>0.05). A relatively high frequency of β-casein A1 allele was observed in Iranian native cattle. Therefore, determine the genotypes and preference alleles A2 in these native and commercial cattle is recommended.

  10. A propensity score analysis shows that empirical treatment with linezolid does not increase the thirty-day mortality rate in patients with Gram-negative bacteremia.

    PubMed

    Ternavasio-de la Vega, Hugo-Guillermo; Mateos-Díaz, Ana-María; Martinez, Jose-Antonio; Almela, Manel; Cobos-Trigueros, Nazaret; Morata, Laura; De-la-Calle, Cristina; Sala, Marta; Mensa, Josep; Marcos, Miguel; Soriano, Alex

    2014-12-01

    The role of linezolid in empirical therapy of suspected bacteremia remains unclear. The aim of this study was to evaluate the influence of empirical use of linezolid or glycopeptides in addition to other antibiotics on the 30-day mortality rates in patients with Gram-negative bacteremia. For this purpose, 1,126 patients with Gram-negative bacteremia in the Hospital Clinic of Barcelona from 2000 to 2012 were included in this study. In order to compare the mortality rates between patients who received linezolid or glycopeptides, the propensity scores on baseline variables were used to balance the treatment groups, and both propensity score matching and propensity-adjusted logistic regression were used to compare the 30-day mortality rates between the groups. The overall 30-day mortality rate was 16.0% during the study period. Sixty-eight patients received empirical treatment with linezolid, and 1,058 received glycopeptides. The propensity score matching included 64 patients in each treatment group. After matching, the mortality rates were 14.1% (9/64) in patients who received glycopeptides and 21.9% (14/64) in those who received linezolid, and a nonsignificant association between empirical linezolid treatment and mortality rate (odds ratio [OR], 1.63; 95% confidence interval [CI], 0.69 to 3.82; P = 0.275, McNemar's test) was found. This association remained nonsignificant when variables that remained unbalanced after matching were included in a conditional logistic regression model. Further, the stratified propensity score analysis did not show any significant relationship between empirical linezolid treatment and the mortality rate after adjustment by propensity score quintiles or other variables potentially associated with mortality. In conclusion, the propensity score analysis showed that empirical treatment with linezolid compared with that with glycopeptides was not associated with 30-day mortality rates in patients with Gram-negative bacteremia.

  11. Television Quiz Show Simulation

    ERIC Educational Resources Information Center

    Hill, Jonnie Lynn

    2007-01-01

    This article explores the simulation of four television quiz shows for students in China studying English as a foreign language (EFL). It discusses the adaptation and implementation of television quiz shows and how the students reacted to them.

  12. Gene expression analysis of two extensively drug-resistant tuberculosis isolates show that two-component response systems enhance drug resistance.

    PubMed

    Yu, Guohua; Cui, Zhenling; Sun, Xian; Peng, Jinfu; Jiang, Jun; Wu, Wei; Huang, Wenhua; Chu, Kaili; Zhang, Lu; Ge, Baoxue; Li, Yao

    2015-05-01

    Global analysis of expression profiles using DNA microarrays was performed between a reference strain H37Rv and two clinical extensively drug-resistant isolates in response to three anti-tuberculosis drug exposures (isoniazid, capreomycin, and rifampicin). A deep analysis was then conducted using a combination of genome sequences of the resistant isolates, resistance information, and related public microarray data. Certain known resistance-associated gene sets were significantly overrepresented in upregulated genes in the resistant isolates relative to that observed in H37Rv, which suggested a link between resistance and expression levels of particular genes. In addition, isoniazid and capreomycin response genes, but not rifampicin, either obtained from published works or our data, were highly consistent with the differentially expressed genes of resistant isolates compared to those of H37Rv, indicating a strong association between drug resistance of the isolates and genes differentially regulated by isoniazid and capreomycin exposures. Based on these results, 92 genes of the studied isolates were identified as candidate resistance genes, 10 of which are known resistance-related genes. Regulatory network analysis of candidate resistance genes using published networks and literature mining showed that three two-component regulatory systems and regulator CRP play significant roles in the resistance of the isolates by mediating the production of essential envelope components. Finally, drug sensitivity testing indicated strong correlations between expression levels of these regulatory genes and sensitivity to multiple anti-tuberculosis drugs in Mycobacterium tuberculosis. These findings may provide novel insights into the mechanism underlying the emergence and development of drug resistance in resistant tuberculosis isolates and useful clues for further studies on this issue.

  13. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group.

    PubMed

    Pánek, Tomáš; Zadrobílková, Eliška; Walker, Giselle; Brown, Matthew W; Gentekaki, Eleni; Hroudová, Miluše; Kang, Seungho; Roger, Andrew J; Tice, Alexander K; Vlček, Čestmír; Čepička, Ivan

    2016-05-01

    Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.

  14. Molecular analysis of transgenic melon plants showing virus resistance conferred by direct repeat of movement gene of Cucumber green mottle mosaic virus.

    PubMed

    Ali, Emran Md; Emran, Ali; Tabei, Yutaka; Kobayashi, Kappei; Yamaoka, Naoto; Nishiguchi, Masamichi

    2012-08-01

    Cucumber green mottle mosaic virus (CGMMV) is a major limiting factor in the production of melon plants worldwide. For effective control of this virus using the transgenic approach, the direct repeat of the movement protein gene of CGMMV was used for transforming melon plants by Agrobacterium tumefaciens. PCR and Southern blot analyses of T₃ confirmed that they carried the transgene. Northern blot analysis with total RNA showed that transgene transcript RNA as well as siRNA was observed in all plants tested. Separate leaves or individual plants were inoculated with CGMMV and subjected to ELISA and RNA blot analysis using the coat protein gene probe of the virus. Compared to nontransgenic control, these plants were shown to have high virus resistance. Furthermore, cytosine of the transgene DNA in the plants was methylated. Thus, these results reveal that the transgenic lines were highly resistant to the virus through RNA silencing. Key message High virus resistance was obtained in transgenic melon plants with direct repeat of movement protein gene of Cucumber green mottle mosaic tobamovirus through RNA silencing.

  15. Analysis of conservative tracer measurement results using the Frechet distribution at planted horizontal subsurface flow constructed wetlands filled with coarse gravel and showing the effect of clogging processes.

    PubMed

    Dittrich, Ernő; Klincsik, Mihály

    2015-11-01

    A mathematical process, developed in Maple environment, has been successful in decreasing the error of measurement results and in the precise calculation of the moments of corrected tracer functions. It was proved that with this process, the measured tracer results of horizontal subsurface flow constructed wetlands filled with coarse gravel (HSFCW-C) can be fitted more accurately than with the conventionally used distribution functions (Gaussian, Lognormal, Fick (Inverse Gaussian) and Gamma). This statement is true only for the planted HSFCW-Cs. The analysis of unplanted HSFCW-Cs needs more research. The result of the analysis shows that the conventional solutions (completely stirred series tank reactor (CSTR) model and convection-dispersion transport (CDT) model) cannot describe these types of transport processes with sufficient accuracy. These outcomes can help in developing better process descriptions of very difficult transport processes in HSFCW-Cs. Furthermore, a new mathematical process can be developed for the calculation of real hydraulic residence time (HRT) and dispersion coefficient values. The presented method can be generalized to other kinds of hydraulic environments.

  16. Analysis of the aspartic acid metabolic pathway using mutant genes.

    PubMed

    Azevedo, R A

    2002-01-01

    Amino acid metabolism is a fundamental process for plant growth and development. Although a considerable amount of information is available, little is known about the genetic control of enzymatic steps or regulation of several pathways. Much of the information about biochemical pathways has arisen from the use of mutants lacking key enzymes. Although mutants were largely used already in the 60's, by bacterial and fungal geneticists, it took plant research a long time to catch up. The advance in this area was rapid in the 80's, which was followed in the 90's by the development of techniques of plant transformation. In this review we present an overview of the aspartic acid metabolic pathway, the key regulatory enzymes and the mutants and transgenic plants produced for lysine and threonine metabolism. We also discuss and propose a new study of high-lysine mutants.

  17. Reduction reaction analysis of nanoparticle copper oxide for copper direct bonding using formic acid

    NASA Astrophysics Data System (ADS)

    Fujino, Masahisa; Akaike, Masatake; Matsuoka, Naoya; Suga, Tadatomo

    2017-04-01

    Copper direct bonding is required for electronics devices, especially power devices, and copper direct bonding using formic acid is expected to lower the bonding temperature. In this research, we analyzed the reduction reaction of copper oxide using formic acid with a Pt catalyst by electron spin resonance analysis and thermal gravimetry analysis. It was found that formic acid was decomposed and radicals were generated under 200 °C. The amount of radicals generated was increased by adding the Pt catalyst. Because of these radicals, both copper(I) oxide and copper(II) oxide start to be decomposed below 200 °C, and the reduction of copper oxide is accelerated by reactants such as H2 and CO from the decomposition of formic acid above 200 °C. The Pt catalyst also accelerates the reaction of copper oxide reduction. Herewith, it is considered that the copper surface can be controlled more precisely by using formic acid to induce direct bonding.

  18. Proteomic analysis of salicylic acid-induced resistance to Magnaporthe oryzae in susceptible and resistant rice.

    PubMed

    Li, Yunfeng; Zhang, Zhihui; Nie, Yanfang; Zhang, Lianhui; Wang, Zhenzhong

    2012-08-01

    To probe salicylic acid (SA)-induced sequential events at translational level and factors associated with SA response, we conducted virulence assays and proteomic profiling analysis on rice resistant and susceptible cultivars against Magnaporthe oryzae at various time points after SA treatment. The results showed that SA significantly enhanced rice resistance against M. oryzae. Proteomic analysis of SA-treated leaves unveiled 36 differentially expressed proteins implicated in various functions, including defense, antioxidative enzymes, and signal transduction. Majority of these proteins were induced except three antioxidative enzymes, which were negatively regulated by SA. Consistent with the above findings, SA increased the level of reactive oxygen species (ROS) with resistant cultivar C101LAC showing faster response to SA and producing higher level of ROS than susceptible cultivar CO39. Furthermore, we showed that nucleoside diphosphate kinase 1, which is implicated in regulation of ROS production, was strongly induced in C101LAC but not in CO39. Taken together, the findings suggest that resistant rice cultivar might possess a more sensitive SA signaling system or effective pathway than susceptible cultivar. In addition, our results indicate that SA also coordinates other cellular activities such as photosynthesis and metabolism to facilitate defense response and recovery, highlighting the complexity of SA-induced resistance mechanisms.

  19. Analysis of tellurium thin films electrodeposition from acidic citric bath

    NASA Astrophysics Data System (ADS)

    Kowalik, Remigiusz; Kutyła, Dawid; Mech, Krzysztof; Żabiński, Piotr

    2016-12-01

    This work presents the description of the electrochemical process of formation thin tellurium layers from citrate acidic solution. The suggested methodology consists in the preparation of stable acidic baths with high content of tellurium, and with the addition of citrate acid. In order to analyse the mechanism of the process of tellurium deposition, the electroanalytical tests were conducted. The tests of cyclic voltammetry and hydrodynamic ones were performed with the use of polycrystalline gold disk electrode. The range of potentials in which deposition of tellurium in direct four-electron process is possible was determined as well as the reduction of deposited Te° to Te2- and its re-deposition as a result of the comproportionation reaction. On the basis of the obtained results, the deposition of tellurium was conducted by the potentiostatic method. The influence of a deposition potential and a concentration of TeO2 in the solution on the rate of tellurium coatings deposition was examined. The presence of tellurium was confirmed by X-ray spectrofluorometry and electron probe microanalysis. In order to determine the phase composition and the morphology, the obtained coatings were analysed with the use of x-ray diffraction and scanning electron microscopy.

  20. Conformational analysis and vibrational assignments of benzohydroxamic acid and benzohydrazide

    NASA Astrophysics Data System (ADS)

    Al-Saadi, Abdulaziz A.

    2012-09-01

    The structures of benzohydroxamic acid (BHA) and benzohydrazide (BH) were investigated at the B3LYP, MP2 and MP4(SDQ) levels of theory and compared to the corresponding structures of formyl analogs. All levels of theory predicted the two molecules to exist predominantly in a near-planar structure adopting a cis conformation where the hydroxyl group of the acid and the amino group of the hydrazide eclipse the carbonyl bond. The stability of the near-planar structure is explained on the basis of mutual conjugation between the phenyl and the Nsbnd H moieties with the Cdbnd O group. The intramolecular interaction between the carbonyl group and the hydrogen atom of the hydroxyl group of the acid or the amino group of the hydrazide plays a significant role in stabilizing the near-cis form in both molecules. The degree of the non-planarity was predicted to increase as going from BHA to BH molecules. The computed vibrational frequencies of the near-cis structure were combined with experimental infrared and Raman data to provide reliable vibrational assignments for the two molecules.

  1. Analysis of large new South African dataset using two host-specificity indices shows generalism in both adult and larval ticks of mammals.

    PubMed

    Espinaze, Marcela P A; Hellard, Eléonore; Horak, Ivan G; Cumming, Graeme S

    2016-03-01

    Ticks and tick-borne pathogens can have considerable impacts on the health of livestock, wildlife and people. Knowledge of tick-host preferences is necessary for both tick and pathogen control. Ticks were historically considered as specialist parasites, but the range of sampled host species has been limited, infestation intensity has not been included in prior analyses, and phylogenetic distances between hosts have not been previously considered. We used a large dataset of 35 604 individual collections and two host-specificity indices to assess the specificity of 61 South African tick species, as well as distinctions between adult and juvenile ticks, for 95 mammalian hosts. When accounting for host phylogeny, most adult and juvenile ticks behaved as generalists, with juveniles being significantly more generalist than adults. When we included the intensity of tick infestation, ticks exhibited a wider diversity of specificity in all life stages. Our results show that ticks of mammals in South Africa tend to behave largely as generalists and that adult ticks are more host-specific. More generally, our analysis shows that the incorporation of life-stage differences, infestation intensity and phylogenetic distances between hosts, as well as the use of more than one specificity index, can all contribute to a deeper understanding of host-parasite interactions.

  2. Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

    PubMed

    Ley, A C; Hardy, O J

    2013-04-01

    AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species.

  3. Single Amino Acid Substitutions at Specific Positions of the Heptad Repeat Sequence of Piscidin-1 Yielded Novel Analogs That Show Low Cytotoxicity and In Vitro and In Vivo Antiendotoxin Activity

    PubMed Central

    Kumar, Amit; Tripathi, Amit Kumar; Kathuria, Manoj; Shree, Sonal; Tripathi, Jitendra Kumar; Purshottam, R. K.; Ramachandran, Ravishankar; Mitra, Kalyan

    2016-01-01

    Piscidin-1 possesses significant antimicrobial and cytotoxic activities. To recognize the primary amino acid sequence(s) in piscidin-1 that could be important for its biological activity, a long heptad repeat sequence located in the region from amino acids 2 to 19 was identified. To comprehend the possible role of this motif, six analogs of piscidin-1 were designed by selectively replacing a single isoleucine residue at a d (5th) position or at an a (9th or 16th) position with either an alanine or a valine residue. Two more analogs, namely, I5F,F6A-piscidin-1 and V12I-piscidin-1, were designed for investigating the effect of interchanging an alanine residue at a d position with an adjacent phenylalanine residue and replacing a valine residue with an isoleucine residue at another d position of the heptad repeat of piscidin-1, respectively. Single alanine-substituted analogs exhibited significantly reduced cytotoxicity against mammalian cells compared with that of piscidin-1 but appreciably retained the antibacterial and antiendotoxin activities of piscidin-1. All the single valine-substituted piscidin-1 analogs and I5F,F6A-piscidin-1 showed cytotoxicity greater than that of the corresponding alanine-substituted analogs, antibacterial activity marginally greater than or similar to that of the corresponding alanine-substituted analogs, and also antiendotoxin activity superior to that of the corresponding alanine-substituted analogs. Interestingly, among these peptides, V12I-piscidin-1 showed the highest cytotoxicity and antibacterial and antiendotoxin activities. Lipopolysaccharide (12 mg/kg of body weight)-treated mice, further treated with I16A-piscidin-1, the piscidin-1 analog with the highest therapeutic index, at a single dose of 1 or 2 mg/kg of body weight, showed 80 and 100% survival, respectively. Structural and functional characterization of these peptides revealed the basis of their biological activity and demonstrated that nontoxic piscidin-1 analogs with

  4. How to eliminate the formation of chlorogenic acids artefacts during plants analysis? Sea sand disruption method (SSDM) in the HPLC analysis of chlorogenic acids and their native derivatives in plants.

    PubMed

    Wianowska, Dorota; Typek, Rafał; Dawidowicz, Andrzej L

    2015-09-01

    The analytical procedures for determining plant constituents involve the application of sample preparation methods to fully isolate and/or pre-concentrate the analyzed substances. High-temperature liquid extraction is still applied most frequently for this purpose. The present paper shows that high-temperature extraction cannot be applied for the analysis of chlorogenic acids (CQAs) and their derivatives in plants as it causes the CQAs transformation leading to erroneous quantitative estimations of these compounds. Experiments performed on different plants (black elder, hawthorn, nettle, yerba maté, St John's wort and green coffee) demonstrate that the most appropriate method for the estimation of CQAs/CQAs derivatives is sea sand disruption method (SSDM) because it does not induce any transformation and/or degradation processes in the analyzed substances. Owing to the SSDM method application we found that the investigated plants, besides four main CQAs, contain sixteen CQAs derivatives, among them three quinic acids. The application of SSDM in plant analysis not only allows to establish a true concentration of individual CQAs in the examined plants but also to determine which chlorogenic acids derivatives are native plant components and what is their concentration level. What is even more important, the application of SSDM in plant analysis allows to eliminate errors that may arise or might have arisen in the study of chlorogenic acids and their derivatives in plant metabolism.

  5. (13)C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids.

    PubMed

    Ghosh, Amit; Ando, David; Gin, Jennifer; Runguphan, Weerawat; Denby, Charles; Wang, George; Baidoo, Edward E K; Shymansky, Chris; Keasling, Jay D; García Martín, Héctor

    2016-01-01

    Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined (13)C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption. These genetic modifications were applied to S. cerevisiae WRY2, a strain that is capable of producing 460 mg/L of free fatty acids. With the addition of ATP citrate lyase and downregulation of malate synthase, the engineered strain produced 26% more free fatty acids. Further increases in free fatty acid production of 33% were obtained by knocking out the cytoplasmic glycerol-3-phosphate dehydrogenase, which flux analysis had shown was competing for carbon flux upstream with the carbon flux through the acetyl-CoA production pathway in the cytoplasm. In total, the genetic interventions applied in this work increased fatty acid production by ~70%.

  6. Pyrolysis characteristics and kinetics of acid tar waste from crude benzol refining: A thermogravimetry-mass spectrometry analysis.

    PubMed

    Chihobo, Chido H; Chowdhury, Arindrajit; Kuipa, Pardon K; Simbi, David J

    2016-12-01

    Pyrolysis is an attractive thermochemical conversion technology that may be utilised as a safe disposal option for acid tar waste. The kinetics of acid tar pyrolysis were investigated using thermogravimetry coupled with mass spectrometry under a nitrogen atmosphere at different heating rates of 10, 15 and 20 K min(-1) The thermogravimetric analysis shows three major reaction peaks centred around 178 °C, 258 °C, and 336 °C corresponding to the successive degradation of water soluble lower molecular mass sulphonic acids, sulphonated high molecular mass hydrocarbons, and high molecular mass hydrocarbons. The kinetic parameters were evaluated using the iso-conversional Kissinger-Akahira-Sunose method. A variation in the activation energy with conversion revealed that the pyrolysis of the acid tar waste progresses through complex multi-step kinetics. Mass spectrometry results revealed a predominance of gases such as hydrogen, methane and carbon monoxide, implying that the pyrolysis of acid tar waste is potentially an energy source. Thus the pyrolysis of acid tar waste may present a viable option for its environmental treatment. There are however, some limitations imposed by the co-evolution of corrosive gaseous components for which appropriate considerations must be provided in both pyrolysis reactor design and selection of construction materials.

  7. Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry

    PubMed Central

    Torde, Richard G.; Therrien, Andrew J.; Shortreed, Michael R.; Smith, Lloyd M.; Lamos, Shane M.

    2014-01-01

    Binary stable isotope labeling couple with LC-ESI-MS has been used as a powerful non-targeted approach for the relative quantification of lipids, amino acids, and many other important metabolite classes. A multiplexed approach using three or more isotopic labeling reagents greatly reduces analytical run-time while maintaining excellent sensitivity and reproducibility. Three isotopic cholamine labeling reagents have been developed to take advantage of the pre-ionized character of cholamine, for ESI, and the ease by which stable isotopes can be incorporated into the cholamine structure. These three cholamine labeling reagents have been used to relatively quantify three fatty acid samples simultaneously. The quantification resulted in the observation of 12 fatty acids that had an average absolute error of 0.9% and an average coefficient of variation of 6.1%. Caged versus cage-free isotope labeling experiments showed that cage-free eggs have an increased level of omega-3 fatty acids as compared to caged eggs. This multiplexed fatty acid analysis provides an inexpensive and expedited tool for broad-based lipid profiling that will further aid discoveries in the mechanisms of fatty acid action in cells. PMID:24317525

  8. 13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids

    PubMed Central

    Ghosh, Amit; Ando, David; Gin, Jennifer; Runguphan, Weerawat; Denby, Charles; Wang, George; Baidoo, Edward E. K.; Shymansky, Chris; Keasling, Jay D.; García Martín, Héctor

    2016-01-01

    Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here, we used flux-based modeling approaches to improve yields of fatty acids in Saccharomyces cerevisiae. We combined 13C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Yarrowia lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for downregulation in terms of acetyl-CoA consumption. These genetic modifications were applied to S. cerevisiae WRY2, a strain that is capable of producing 460 mg/L of free fatty acids. With the addition of ATP citrate lyase and downregulation of malate synthase, the engineered strain produced 26% more free fatty acids. Further increases in free fatty acid production of 33% were obtained by knocking out the cytoplasmic glycerol-3-phosphate dehydrogenase, which flux analysis had shown was competing for carbon flux upstream with the carbon flux through the acetyl-CoA production pathway in the cytoplasm. In total, the genetic interventions applied in this work increased fatty acid production by ~70%. PMID:27761435

  9. Analysis of Potential Amino Acid Biomarkers in Brain Tissue and the Effect of Galangin on Cerebral Ischemia.

    PubMed

    Yang, Ruocong; Chen, Kun; Zhao, Yanyan; Tian, Pengpeng; Duan, Feipeng; Sun, Wenli; Liu, Yuxin; Yan, Zhiyong; Li, Shaojing

    2016-04-06

    Galangin, a potent scavenger of free radicals, has been used as an herbal medicine for various ailments for centuries in Asia. With complex pathophysiology, ischemic stroke is one of the most frequent causes of death and disability worldwide. We have reported that galangin provides direct protection against ischemic injury as a potential neuroprotective agent and has potential therapeutic effects on the changes of serum amino acids in ischemic stroke; however, the mechanism of the changes of amino acids in the ischemic brain tissue has not yet been clarified. In this paper, we explored brain tissue amino acid biomarkers in the acute phase of cerebral ischemia and the effect of galangin on those potential biomarkers. Finally, we identified that glutamic acid, alanine and aspartic acid showed significant changes (p < 0.05 or p < 0.01) in galangin-treated groups compared with vehicle-treated rats and the four enzymes associated with these three AAs' metabolic pathways; GLUD1, SLC16A10, SLC1A1 and GPT were identified by multiplex interactions with the three amino acids. By metabolite-protein network analysis and molecular docking, six of 28 proteins were identified and might become potential galangin biomarkers for acute ischemic stroke. The data in our study provides thoughts for exploring the mechanism of disease, discovering new targets for drug candidates and elucidating the related regulatory signal network.

  10. [Gene cloning and bioinformatics analysis of new gene for chlorogenic acid biosynthesis of Lonicera hypoglauca].

    PubMed

    Yu, Shu-lin; Huang, Lu-qi; Yuan, Yuan; Qi, Lin-jie; Liu, Da-hui

    2015-03-01

    To obtain the key genes for chlorogenic acid biosynthesis of Lonicera hypoglauca, four new genes ware obtained from the our dataset of L. hypoglauca. And we also predicted the structure and function of LHPAL4, LHHCT1 , LHHCT2 and LHHCT3 proteins. The phylogenetic tree showed that LHPAL4 was closely related with LHPAL1, LHHCT1 was closely related with LHHCT3, LHHCT2 clustered into a single group. By Real-time PCR to detect the gene expressed level in different organs of L. hypoglauca, we found that the transcripted level of LHPAL4, LHHCT1 and LHHCT3 was the highest in defeat flowers, and the transcripted level of LHHCT2 was the highest in leaves. These result provided a basis to further analysis the mechanism of active ingredients in different organs, as well as the element for in vitro biosynthesis of active ingredients.

  11. Enantiomer labelling, a method for the quantitative analysis of amino acids.

    PubMed

    Frank, H; Nicholson, G J; Bayer, E

    1978-12-21

    Enantiomer labelling a method for the quntitative analysis of optically active natural compounds by gas chromatography, involves the use of the unnatural enantiomer as an internal standard. With Chirasil-Val, a chiral stationary phase that is thermally stable up to up to 240 degrees, the enantiomers of amino acids and a variety of other compounds can be separated and quantitated. Incomplete recovery from the sample, incomplete derivatization, hydrolysis and thermal decomposition of the derivative and shifting response factors can be compensated for by adding the unnatural enantiomer. The accuracy of amino acid analysis by enantiomer labelling is equal or superior to that of hitherto known methods. The procedure affords a complete analysis of peptides with respect to both amino acid composition and the optical purity of each amino acid.

  12. Biological agent identification by nucleic acid base-pair analysis using surface-enhanced Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Farquharson, Stuart; Smith, Wayne W.; Elliott, Susan; Sperry, Jay F.

    1999-01-01

    Recently, a number of analytical methods have been successfully developed which use nucleic acid sequencing to identify biological warfare agents. However, the effectiveness of these methods, towards the safety and protection of US Armed Forces and their allies are limited by the period required to enumerate the nucleic acid through polymerase chain reactions or culture growth to produce sufficient quantities for analysis. To overcome this limitation, we have been investigating the ability of surface-enhanced Raman spectroscopy to detect nucleic acids with sufficient sensitivity and selectivity to eliminate the need for enumeration. The design of a small volume electrolytic sample cell will be presented along with analysis of the nucleic acid bases and preliminary analysis of model bacteria.

  13. Strategies for comprehensive analysis of amino acid biomarkers of oxidative stress.

    PubMed

    Ptolemy, A S; Lee, R; Britz-McKibbin, P

    2007-07-01

    Despite the wide interest in using modified amino acids as putative biomarkers of oxidative stress, many issues remain as to their overall reliability for early detection and diagnosis of diseases. In contrast to conventional single biomarker studies, comprehensive analysis of biomarkers offers an unbiased strategy for global assessment of modified amino acid metabolism due to reactive oxygen and nitrogen species. This review examines recent analytical techniques amenable for analysis of modified amino acids in biological samples reported during 2003-2007. Particular attention is devoted to the need for validated methods applicable to high-throughput analysis of multiple amino acid biomarkers, as well as consideration of sample pretreatment protocols on artifact formation for improved clinical relevance.

  14. Synthesis, Preliminary Bioevaluation and Computational Analysis of Caffeic Acid Analogues

    PubMed Central

    Liu, Zhiqian; Fu, Jianjun; Shan, Lei; Sun, Qingyan; Zhang, Weidong

    2014-01-01

    A series of caffeic acid amides were designed, synthesized and evaluated for anti-inflammatory activity. Most of them exhibited promising anti-inflammatory activity against nitric oxide (NO) generation in murine macrophage RAW264.7 cells. A 3D pharmacophore model was created based on the biological results for further structural optimization. Moreover, predication of the potential targets was also carried out by the PharmMapper server. These amide analogues represent a promising class of anti-inflammatory scaffold for further exploration and target identification. PMID:24857914

  15. Preparation and dielectric analysis of microphase-separated poly(acrylonitrile-co-acrylamide-co-acrylic acid) hydrogels

    SciTech Connect

    Hu, D.Shiaw-Guang; Lin, Yow-Shi

    1993-12-31

    The acidic hydrolysis of polyacrylonitrile was carried out to yield a variety of terpolymers made up of nitriles, amides and acids. The formation of block structure was shown to follow a ripper mechanism occurring to acrylamide groups, that is more pronounced for a certain range of acrylamide content, evidenced by the composition analysis using {sup 1}H-NMR and base titration. The rates of formation of acrylamide fraction and acid fraction in the consecutive mode are approximately the same, yielding the content of ionic groups from 0.8 to 2.2. mole percent, dependent on the time of hydrolysis. The dielectric relaxation measurement on swollen gels shows three relaxation transitions, {alpha}, {beta}, {gamma}, over -150{degrees}C to 0{degrees}C, as influenced by the chemical composition and water absorption. The {beta} and {gamma} are associated with the polymer-water interaction and short-range motion of polymers and water.

  16. CoMFA and CoMSIA 3D-QSAR analysis on hydroxamic acid derivatives as urease inhibitors.

    PubMed

    Ul-Haq, Zaheer-; Wadood, Abdul; Uddin, Reaz

    2009-02-01

    Urease (EC 3.5.1.5) serves as a virulence factor in pathogens that are responsible for the development of many diseases in humans and animals. Urease allows soil microorganisms to use urea as a source of nitrogen and aid in the rapid break down of urea-based fertilizers resulting in phytopathicity. It has been well established that hydroxamic acids are the potent inhibitors of urease activity. The 3D-QSAR studies on thirty five hydroxamic acid derivatives as known urease inhibitors were performed by Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods to determine the factors required for the activity of these compounds. The CoMFA model produced statistically significant results with cross-validated (q(2)) 0.532 and conventional (r(2)) correlation coefficients 0.969.The model indicated that the steric field (70.0%) has greater influence on hydroxamic acid inhibitors than the electrostatic field (30.0%). Furthermore, five different fields: steric, electrostatic, hydrophobic, H-bond donor and H-bond acceptor assumed to generate the CoMSIA model, which gave q(2) 0.665 and r(2) 0.976.This model showed that steric (43.0%), electrostatic (26.4%) and hydrophobic (20.3%) properties played a major role in urease inhibition. The analysis of CoMFA and CoMSIA contour maps provided insight into the possible modification of the hydroxamic acid derivatives for improved activity.

  17. Genome-wide analysis of AP2/ERF family genes from Lotus corniculatus shows LcERF054 enhances salt tolerance.

    PubMed

    Sun, Zhan-Min; Zhou, Mei-Liang; Xiao, Xing-Guo; Tang, Yi-Xiong; Wu, Yan-Min

    2014-09-01

    Lotus corniculatus is used in agriculture as a main forage plant. Members of the Apetala2/ethylene response factor (AP2/ERF) family play important roles in regulating gene expression in response to many forms of stress, including drought and salt. Here, starting from database of the L. corniculatus var. japonicus genome, we identified 127 AP2/ERF genes by insilico cloning method. The phylogeny, gene structures, and putative conserved motifs in L. corniculatus var. japonicus ERF proteins were analyzed. Based on the number of AP2/ERF domains and the function of the genes, 127 AP2/ERF genes from L. corniculatus var. japonicus were classified into five subfamilies named the AP2, dehydration-responsive element binding factor (DREB), ERF, RAV, and a soloist. Outside the AP2/ERF domain, many L. corniculatus var. japonicus-specific conserved motifs were detected. Expression profile analysis of AP2/ERF genes by quantitative real-time PCR revealed that 19 LcERF genes, including LcERF054 (KJ004728), were significantly induced by salt stress. The results showed that the LcERF054 gene encodes a nuclear transcription activator. Overexpression of LcERF054 in Arabidopsis enhanced the tolerances to salt stress, showed higher germination ratio of seeds, and had elevated levels of relative moisture contents, soluble sugars, proline, and lower levels of malondialdehyde under stress conditions compared to wild-type plants. The expression of hyperosmotic salinity response genes COR15A, LEA4-5, P5CS1, and RD29A was found to be elevated in the LcERF054-overexpressing Arabidopsis plants compared to wild type. These results revealed that the LcERF genes play important roles in L. corniculatus cv Leo under salt stress and that LcERFs are attractive engineering targets in applied efforts to improve abiotic stress tolerances in L. corniculatus cv Leo or other crops.

  18. Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes.

    PubMed

    Zhan, Yinxiu; Mariani, Luca; Barozzi, Iros; Schulz, Edda G; Blüthgen, Nils; Stadler, Michael; Tiana, Guido; Giorgetti, Luca

    2017-03-01

    Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions. Here, we present a novel algorithm named CaTCH that identifies hierarchical trees of chromosomal domains in Hi-C maps, stratified through their reciprocal physical insulation, which is a single and biologically relevant parameter. By applying CaTCH to published Hi-C data sets, we show that previously reported folding layers appear at different insulation levels. We demonstrate that although no structurally privileged folding level exists, TADs emerge as a functionally privileged scale defined by maximal boundary enrichment in CTCF and maximal cell-type conservation. By measuring transcriptional output in embryonic stem cells and neural precursor cells, we show that the likelihood that genes in a domain are coregulated during differentiation is also maximized at the scale of TADs. Finally, we observe that regulatory sequences occur at genomic locations corresponding to optimized mutual interactions at the same scale. Our analysis suggests that the architectural functionality of TADs arises from the interplay between their ability to partition interactions and the specific genomic position of regulatory sequences.

  19. An electrochemical clamp assay for direct, rapid analysis of circulating nucleic acids in serum

    NASA Astrophysics Data System (ADS)

    Das, Jagotamoy; Ivanov, Ivaylo; Montermini, Laura; Rak, Janusz; Sargent, Edward H.; Kelley, Shana O.

    2015-07-01

    The analysis of cell-free nucleic acids (cfNAs), which are present at significant levels in the blood of cancer patients, can reveal the mutational spectrum of a tumour without the need for invasive sampling of the tissue. However, this requires differentiation between the nucleic acids that originate from healthy cells and the mutated sequences shed by tumour cells. Here we report an electrochemical clamp assay that directly detects mutated sequences in patient serum. This is the first successful detection of cfNAs without the need for enzymatic amplification, a step that normally requires extensive sample processing and is prone to interference. The new chip-based assay reads out the presence of mutations within 15 minutes using a collection of oligonucleotides that sequester closely related sequences in solution, and thus allow only the mutated sequence to bind to a chip-based sensor. We demonstrate excellent levels of sensitivity and specificity and show that the clamp assay accurately detects mutated sequences in a collection of samples taken from lung cancer and melanoma patients.

  20. Serum Uric Acid Levels and Diabetic Peripheral Neuropathy in Type 2 Diabetes: a Systematic Review and Meta-analysis.

    PubMed

    Yu, Shuai; Chen, Ying; Hou, Xu; Xu, Donghua; Che, Kui; Li, Changgui; Yan, Shengli; Wang, Yangang; Wang, Bin

    2016-03-01

    Previous studies suggested a possible association between serum uric acid levels and peripheral neuropathy in patients with type 2 diabetes, but no definite evidence was available. A systematic review and meta-analysis of relevant studies were performed to comprehensively estimate the association. Pubmed, Web of Science, Embase, and China Biology Medicine (CBM) databases were searched for eligible studies. Study-specific data were combined using random-effect or fixed-effect models of meta-analysis according to between-study heterogeneity. Twelve studies were finally included into the meta-analysis, which involved a total of 1388 type 2 diabetic patients with peripheral neuropathy and 4746 patients without peripheral neuropathy. Meta-analysis showed that there were obvious increased serum uric acid levels in diabetic patients with peripheral neuropathy (weighted mean difference [WMD] = 50.03 μmol/L, 95% confidence interval [95%CI] 22.14-77.93, P = 0.0004). Hyperuricemia was also significantly associated with increased risk of peripheral neuropathy in patients with type 2 diabetes (risk ratio [RR] = 2.83, 95%CI 2.13-3.76, P < 0.00001). Meta-analysis of two studies with adjusted risk estimates showed that hyperuricemia was independently associated with increased risk of peripheral neuropathy in type 2 diabetic patients (RR = 1.95, 95%CI 1.23-3.11, P = 0.005). Type 2 diabetic patients with peripheral neuropathy have obvious increased serum uric acid levels, and hyperuricemia is associated with increased risk of peripheral neuropathy. Further prospective cohort studies are needed to validate the impact of serum uric acid levels on peripheral neuropathy risk.

  1. Linking concepts in the ecology and evolution of invasive plants: network analysis shows what has been most studied and identifies knowledge gaps.

    PubMed

    Vanderhoeven, Sonia; Brown, Cynthia S; Tepolt, Carolyn K; Tsutsui, Neil D; Vanparys, Valérie; Atkinson, Sheryl; Mahy, Grégory; Monty, Arnaud

    2010-03-01

    In recent decades, a growing number of studies have addressed connections between ecological and evolutionary concepts in biologic invasions. These connections may be crucial for understanding the processes underlying invaders' success. However, the extent to which scientists have worked on the integration of the ecology and evolution of invasive plants is poorly documented, as few attempts have been made to evaluate these efforts in invasion biology research. Such analysis can facilitate recognize well-documented relationships and identify gaps in our knowledge. In this study, we used a network-based method for visualizing the connections between major aspects of ecology and evolution in the primary research literature. Using the family Poaceae as an example, we show that ecological concepts were more studied and better interconnected than were evolutionary concepts. Several possible connections were not documented at all, representing knowledge gaps between ecology and evolution of invaders. Among knowledge gaps, the concepts of plasticity, gene flow, epigenetics and human influence were particularly under-connected. We discuss five possible research avenues to better understand the relationships between ecology and evolution in the success of Poaceae, and of alien plants in general.

  2. Characteristic constants of 2,2',4'-trihydroxyazobenzene-5-sulfonic acid, a reagent for spectrophotometric analysis

    USGS Publications Warehouse

    Fletcher, Mary H.

    1960-01-01

    The dye 2,2',4'-trihydroxyazobenzene-5-sulfonic acid, has shown promise as a reagent for the determination of zirconium. As the literature contains very little information about this dye, basic data pertinent to its use as a reagent were determined. The sulfonic acid group and all three of the hydroxy groups show acidic characteristics. Apparent dissociation constants were determined for the three more labile protons and the approximate order of magnitude for the fourth constant was estimated. Absorption spectra for the different ionization species are given. A curve is also included which shows the fraction of dye in the different ionization forms at acidities from 10.35M hydrochloric acid to pH 11.9. A sixth dye species was found in 1.0 to 8.4M potassium hydroxide solutions, but its nature is unknown.

  3. Rapid analysis of fatty acid profiles in raw nuts and seeds by microwave-ultrasonic synergistic in situ extraction-derivatisation and gas chromatography-mass spectrometry.

    PubMed

    Liu, Rui-Lin; Song, Shuang-Hong; Wu, Mei; He, Tian; Zhang, Zhi-Qi

    2013-12-15

    Based on microwave-ultrasonic synergistic in situ extraction-derivatisation (MUED), gas chromatography-mass spectrometry was proposed for rapid analysis of fatty acid profiles in raw nut and seed materials. Several critical experimental parameters for MUED, including reaction temperature, microwave power, amounts of catalyst and derivatisation reagent, have been optimised using response surface methodology. The results showed that the chromatographic peak areas of total fatty acids and the content of total unsaturated fatty acids obtained with MUED were markedly higher than those obtained by the conventional method (P<0.05 and P<0.01, respectively). The MUED method simplified the handling steps compared to the conventional procedure, shortened the sample preparation time whilst improving the extraction and derivatisation efficiency of lipids, and reduced oxidisation and decomposition of the unsaturated fatty acids. The simplicity, robustness and practicality of this method highlighted its significant potential for application in the rapid analysis of fatty acids in natural food resource samples.

  4. Analysis of heavy oils: Method development and application to Cerro Negro heavy petroleum detailed separation and analysis of acidic compounds

    SciTech Connect

    Green, J.B.; Yu, S.K.T.; Green, J.A.; Doughty, D.A.; Vogh, J.W.; Grigsby, R.D.

    1989-10-01

    An HPLC method for fractionation of whole acid concentrates into nominal compound class subfractions is described. The method utilizes silica columns and gradient elution with eluents containing a strong base, tetramethyl-ammonium hydroxide. The performance of the method is evaluated through analysis of subfractions obtained from a coal liquid, Wilmington, CA, petroleum and Cerro Negro heavy oil. Methods developed specifically for analysis of whole acid concentrates and subfractions are described in detail. These include: (1) an infrared method for determination of total hydroxyl and carboxyl groups after their conversion to trifluoroacetate and 2,2,2-trifluoresters, respectively. (2) an NMR method for functional group analysis based on methylation of acidic groups with {sup 13}C-enriched methyl iodide, (3) a nonaqueous titration procedure employing the potassium salt of dimethyl sulfoxide as a titrant for acidic compounds, (4) GC/MS analysis of hydroxyaromatic compounds after their conversion to trifluoroacetate esters, and (5) probe microdistillation high resolution mass spectrometric analysis of acid fractions exhibiting low volatility. 146 refs., 38 figs., 27 tabs.

  5. Promoter Analysis of the Human Ascorbic Acid Transporters SVCT1 & 2: Mechanisms of Adaptive Regulation in Liver Epithelial Cells

    PubMed Central

    Reidling, Jack C.; Rubin, Stanley A.

    2010-01-01

    Ascorbic acid, the active form of vitamin C, is a vital antioxidant in the human liver, yet the molecular mechanisms involved in the regulation of ascorbic acid transporters (hSVCT1 and hSVCT2) in liver cells are poorly understood. Therefore, we characterized the minimal promoter regions of hSVCT1 & 2 in cultured human liver epithelial cells (HepG2) and examined the effects of ascorbic acid deprivation and supplementation on activity and regulation of the transport systems. Identified minimal promoters required for basal activity were found to include multiple cis-regulatory elements, whereas mutational analysis demonstrated that HNF-1 sites in the hSVCT1 promoter and KLF/Sp1 sites in the hSVCT2 promoter were essential for activities. When cultured in ascorbic acid deficient or supplemented media, HepG2 cells demonstrated significant (P < 0.01) and specific reciprocal changes in [14C]-Ascorbic acid uptake, and in hSVCT1 mRNA and protein levels as well as hSVCT1 promoter activity. However, no significant changes in hSVCT2 expression or promoter activity were observed during ascorbic acid deficient or supplemented conditions. We mapped the ascorbic acid responsive region in the hSVCT1 promoter and determined that HNF-1 sites are important for the adaptive regulation response. The results of these studies further characterize the hSVCT1 and 2 promoters, establish that ascorbic acid uptake by human liver epithelial cells is adaptively regulated, and show that transcriptional mechanisms via HNF-1 in the hSVCT1 promoter may, in part, be involved in this regulation. PMID:20471816

  6. Expression Analysis of Phenylalanine Ammonia Lyase Gene and Rosmarinic Acid Production in Salvia officinalis and Salvia virgata Shoots Under Salicylic Acid Elicitation.

    PubMed

    Ejtahed, Roghayeh Sadat; Radjabian, Tayebeh; Hoseini Tafreshi, Sayed Ali

    2015-08-01

    Partial fragments of phenylalanine ammonia lyase (PAL) genes were cloned and characterized from Salvia officinalis (SoPAL) and Salvia virgata (SvPAL). Different concentrations (250 and 500 μM) of exogenous salicylic acid (SA) were used when correlation between PAL expression and rosmarinic acid (RA) accumulation was compared. The results showed that the deduced cDNA sequences of the partial genes had high similarities with those of known PAL gene from other plant species. Semi-quantitative reverse transcription PCR (RT-PCR) analysis revealed that exogenous application of SA led to up-regulating of the PAL expression. Further analysis showed that in S. virgata, at higher concentration of SA, higher accumulation of RA was achieved, while in S. officinalis, the higher RA accumulation was observed at lower concentration of SA. It was concluded that there was no positive correlation between the intensity of PAL transcription and the RA accumulation in the studied species. Therefore, despite of the increase in transcription rate of the PAL at the higher concentration of SA, the lower amounts of RA were accumulated in the case of S. officinalis. Consequently, the hypothesis that PAL is the rate-determining step in RA biosynthesis is not always valid and probably some other unknown factors participate in the synthesis of phenolics.

  7. Improved Proteomic Analysis Following Trichloroacetic Acid Extraction of Bacillus anthracis Spore Proteins

    SciTech Connect

    Kaiser, Brooke LD; Wunschel, David S.; Sydor, Michael A.; Warner, Marvin G.; Wahl, Karen L.; Hutchison, Janine R.

    2015-08-07

    Proteomic analysis of bacterial samples provides valuable information about cellular responses and functions under different environmental pressures. Proteomic analysis is dependent upon efficient extraction of proteins from bacterial samples without introducing bias toward extraction of particular protein classes. While no single method can recover 100% of the bacterial proteins, selected protocols can improve overall protein isolation, peptide recovery, or enrich for certain classes of proteins. The method presented here is technically simple and does not require specialized equipment such as a mechanical disrupter. Our data reveal that for particularly challenging samples, such as B. anthracis Sterne spores, trichloroacetic acid extraction improved the number of proteins identified within a sample compared to bead beating (714 vs 660, respectively). Further, TCA extraction enriched for 103 known spore specific proteins whereas bead beating resulted in 49 unique proteins. Analysis of C. botulinum samples grown to 5 days, composed of vegetative biomass and spores, showed a similar trend with improved protein yields and identification using our method compared to bead beating. Interestingly, easily lysed samples, such as B. anthracis vegetative cells, were equally as effectively processed via TCA and bead beating, but TCA extraction remains the easiest and most cost effective option. As with all assays, supplemental methods such as implementation of an alternative preparation method may provide additional insight to the protein biology of the bacteria being studied.

  8. 5-(Bis(3-(2-hydroxyethyl)-1H-indol-2-yl)methyl)-2-hydroxybenzoic acid (BHIMHA): showing a strategy of designing drug to block lung metastasis of tumors

    PubMed Central

    Gan, Taiping; Wang, Yuji; Zhao, Ming; Wu, Jianhui; Yang, Jian; Peng, Shiqi

    2016-01-01

    Early metastasis is still the most recalcitrant factor in the treatment of lung cancer patients. By analyzing the structures and comparing the docking scores of the known pharmacophores, the authors of this paper designed 5-(bis(3-(2-hydroxyethyl)-1H-indol-2-yl)methyl)-2-hydroxybenzoic acid (BHIMHA) as a promising lead compound to develop metastasis inhibitors. In vitro 5, 10, and 20 µM of BHIMHA concentration dependently inhibited the migration and invasion of A549 cells. In vivo 0.4, 2.0, and 8.9 µmol/kg of BHIMHA dose dependently inhibited the metastasis of LLC (Lewis Lung Carcinoma) toward lung. In vivo, 2 µmol/kg of BHIMHA showed additional actions of slowing the growth of the primary tumor of C57BL/6 mice and S180 mice as well as inhibiting xylene-induced ear edema of the mice. Therefore, BHIMHA simultaneously blocked tumor metastasis toward lung, slowed the primary tumor growth, and limited the inflammation. These pharmacological actions were correlated with the inhibition of PKCα and NF-κB expression. PMID:26937173

  9. Analysis of single nucleic acid molecules in micro- and nano-fluidics.

    PubMed

    Friedrich, Sarah M; Zec, Helena C; Wang, Tza-Huei

    2016-03-07

    Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.

  10. Human retroviruses and aids, 1992. A compilation and analysis of nucleic acid and amino acid sequences

    SciTech Connect

    Myers, G.; Korber, B.; Berzofsky, J.A.; Pavlakis, G.N.; Smith, R.F.

    1992-10-01

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) HIV and SIV Nucleotide Sequences; (H) Amino Acid Sequences; (III) Analyses; (IV) Related Sequences; and (V) Database Communications. information within all the parts is updated at least twice in each year, which accounts for the modes of binding and pagination in the compendium. While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions below of the parts of the compendium, the user should read the individual introductions for each part.

  11. Visualized analysis of cellular fatty acid profiles of Vibrio parahaemolyticus strains under cold stress.

    PubMed

    Jia, Juntao; Chen, Ying; Jiang, Yinghui; Tang, Jing; Yang, Lijun; Liang, Chengzhu; Jia, Zhen; Zhao, Liqing

    2014-08-01

    Vibrio parahaemolyticus is a common foodborne bacterial pathogen, which survives in cold environments and is sometimes difficult to culture. Fatty acid analysis under cold stress was conducted for several V. parahaemolyticus strains using gas chromatography/mass spectrometry, and the results were compared with those of the controls. All the fatty acid profiles obtained were visualized by multidimensional scaling (MDS) and self-organized map (SOM). It was observed that the fatty acid profiles of V. parahaemolyticus substantially changed under cold stress. The percentage of methyl palmitate remarkably decreased and that of methyl palmitoleate (except for two strains) and methyl oleate increased. These findings demonstrate the role of fatty acids in cold stress. The changes in the fatty acid profiles illustrated by MDS and SOM could differentiate strains under cold stress from the controls and can potentially lead to a method of detecting injured cold-stressed V. parahaemolyticus.

  12. [Quantitative analysis of deacylgymnemic acid by high-performance liquid chromatography].

    PubMed

    Suzuki, K; Ishihara, S; Uchida, M; Komoda, Y

    1993-04-01

    A method of the quantitative analysis was established for the determination of deacylgymnemic acid (DAGA) in the alkaline hydrolysate of the sample containing gymnemic acids which are ingredients of Gymnema sylvestre R. BR. leaves, by means of high-performance liquid chromatography. This method was used for comparing the contents of gymnemic acids in various samples. The amount of gymnemic acids analyzed as DAGA in 70% ethanol extract of dry leaves was about twice that in hot water extract. The commercial health-supplemental foods of five companies were investigated for the contents of gymnemic acids as DAGA and there were large differences from 38 to 251 mg in the dosage per day recommended by each company.

  13. Comparison of two gas-liquid chromatograph columns for the analysis of fatty acids in ruminant meat.

    PubMed

    Alves, Susana P; Bessa, Rui J B

    2009-06-26

    Two gas-liquid chromatograph capillary columns for the analysis of fatty acids (FA) in ruminant fat are compared. Those columns are the CP-Sil 88 of 100 m long with a highly polar stationary phase and the Omegawax 250 of 30 m long with a stationary phase of intermediate polarity. Fatty acid methyl ester (FAME) patterns of branched-chain, cis and trans octadecenoate isomers, as well as conjugated and non-conjugated 18:2 and 18:3 isomers are fairly different between columns, even though most of the FAME could be separated on either column. However, the CP-Sil 88 showed better resolution of 18:1 isomers than Omegawax 250. The analysis of 96 samples of ruminant meat fat in both chromatographic systems showed that averages obtained for total FA content and for most of the individual FA did not differ between columns. Moreover, regression analysis of Omegawax and CP-Sil 88 data is highly correlated. Quantitative differences between chromatographic systems were detected for samples containing more than 66 mg fatty acids per gram of muscle dry matter.

  14. Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein.

    PubMed

    Shaikh, Afshan S; Tang, Yinjie J; Mukhopadhyay, Aindrila; Martín, Héctor García; Gin, Jennifer; Benke, Peter I; Keasling, Jay D

    2010-01-01

    Microbial production of many commercially important secondary metabolites occurs during stationary phase, and methods to measure metabolic flux during this growth phase would be valuable. Metabolic flux analysis is often based on isotopomer information from proteinogenic amino acids. As such, flux analysis primarily reflects the metabolism pertinent to the growth phase during which most proteins are synthesized. To investigate central metabolism and amino acids synthesis activity during stationary phase, addition of fully (13)C-labeled glucose followed by induction of green fluorescent protein (GFP) expression during stationary phase was used. Our results indicate that Escherichia coli was able to produce new proteins (i.e., GFP) in the stationary phase, and the amino acids in GFP were mostly from degraded proteins synthesized during the exponential growth phase. Among amino acid biosynthetic pathways, only those for serine, alanine, glutamate/glutamine, and aspartate/asparagine had significant activity during the stationary phase.

  15. Study of Stationary Phase Metabolism Via Isotopomer Analysis of Amino Acids from an Isolated Protein

    SciTech Connect

    Shaikh, AfshanS.; Tang, YinjieJ.; Mukhopadhyay, Aindrila; Martin, Hector Garcia; Gin, Jennifer; Benke, Peter; Keasling, Jay D.

    2009-09-14

    Microbial production of many commercially important secondary metabolites occurs during stationary phase, and methods to measure metabolic flux during this growth phase would be valuable. Metabolic flux analysis is often based on isotopomer information from proteinogenic amino acids. As such, flux analysis primarily reflects the metabolism pertinent to the growth phase during which most proteins are synthesized. To investigate central metabolism and amino acids synthesis activity during stationary phase, addition of fully 13C-labeled glucose followed by induction of green fluorescent protein (GFP) expression during stationary phase was used. Our results indicate that Escherichia coli was able to produce new proteins (i.e., GFP) in the stationary phase, and the amino acids in GFP were mostly from degraded proteins synthesized during the exponential growth phase. Among amino acid biosynthetic pathways, only those for serine, alanine, glutamate/glutamine, and aspartate/asparagine had significant activity during the stationary phase.

  16. Analysis of amino acids in latent fingerprint residue by capillary electrophoresis-mass spectrometry.

    PubMed

    Atherton, Tom; Croxton, Ruth; Baron, Mark; Gonzalez-Rodriguez, Jose; Gámiz-Gracia, Laura; García-Campaña, Ana M

    2012-11-01

    The analysis of the chemical composition of fingerprints is important for the development and improvement of existing fingerprint enhancement techniques. This study demonstrates the first analysis of a latent fingerprint sample, using an optimized CE-MS method. In total 12 amino acids were detected in the fingerprint sample. MS/MS fragmentation was used to provide additional identity confirmation, for which eight of the twelve detected amino acids generated confirmatory product ions. Nine amino acids were quantified and their relative abundances were consistent with previous studies with serine and glycine being the most abundant. The successful detection of amino acids from latent fingerprints demonstrates that CE-MS is a potential future technique for further study of such compounds in fingerprint samples.

  17. A method for analysis of vanillic acid in polar ice cores

    NASA Astrophysics Data System (ADS)

    Grieman, M. M.; Greaves, J.; Saltzman, E. S.

    2015-02-01

    Biomass burning generates a wide range of organic compounds that are transported via aerosols to the polar ice sheets. Vanillic acid is a product of conifer lignin combustion, which has previously been observed in laboratory and ambient biomass burning aerosols. In this study a method was developed for analysis of vanillic acid in melted polar ice core samples. Vanillic acid was chromatographically separated using reversed-phase liquid chromatography (HPLC) and detected using electrospray ionization-triple quadrupole mass spectrometry (ESI-MS/MS). Using a 100 μL injection loop and analysis time of 4 min, we obtained a detection limit of 77 ppt (parts per trillion by mass) and an analytical precision of ±10%. Measurements of vanillic acid in Arctic ice core samples from the Siberian Akademii Nauk core are shown as an example application of the method.

  18. Showing What They Know

    ERIC Educational Resources Information Center

    Cech, Scott J.

    2008-01-01

    Having students show their skills in three dimensions, known as performance-based assessment, dates back at least to Socrates. Individual schools such as Barrington High School--located just outside of Providence--have been requiring students to actively demonstrate their knowledge for years. The Rhode Island's high school graduating class became…

  19. The Ozone Show.

    ERIC Educational Resources Information Center

    Mathieu, Aaron

    2000-01-01

    Uses a talk show activity for a final assessment tool for students to debate about the ozone hole. Students are assessed on five areas: (1) cooperative learning; (2) the written component; (3) content; (4) self-evaluation; and (5) peer evaluation. (SAH)

  20. What Do Maps Show?

    ERIC Educational Resources Information Center

    Geological Survey (Dept. of Interior), Reston, VA.

    This curriculum packet, appropriate for grades 4-8, features a teaching poster which shows different types of maps (different views of Salt Lake City, Utah), as well as three reproducible maps and reproducible activity sheets which complement the maps. The poster provides teacher background, including step-by-step lesson plans for four geography…

  1. Show Me the Way

    ERIC Educational Resources Information Center

    Dicks, Matthew J.

    2005-01-01

    Because today's students have grown up steeped in video games and the Internet, most of them expect feedback, and usually gratification, very soon after they expend effort on a task. Teachers can get quick feedback to students by showing them videotapes of their learning performances. The author, a 3rd grade teacher describes how the seemingly…

  2. Chemistry Game Shows

    NASA Astrophysics Data System (ADS)

    Campbell, Susan; Muzyka, Jennifer

    2002-04-01

    We present a technological improvement to the use of game shows to help students review for tests. Our approach uses HTML files interpreted with a browser on a computer attached to an LCD projector. The HTML files can be easily modified for use of the game in a variety of courses.

  3. Honored Teacher Shows Commitment.

    ERIC Educational Resources Information Center

    Ratte, Kathy

    1987-01-01

    Part of the acceptance speech of the 1985 National Council for the Social Studies Teacher of the Year, this article describes the censorship experience of this honored social studies teacher. The incident involved the showing of a videotape version of the feature film entitled "The Seduction of Joe Tynan." (JDH)

  4. Talk Show Science.

    ERIC Educational Resources Information Center

    Moore, Mitzi Ruth

    1992-01-01

    Proposes having students perform skits in which they play the roles of the science concepts they are trying to understand. Provides the dialog for a skit in which hot and cold gas molecules are interviewed on a talk show to study how these properties affect wind, rain, and other weather phenomena. (MDH)

  5. Stage a Water Show

    ERIC Educational Resources Information Center

    Frasier, Debra

    2008-01-01

    In the author's book titled "The Incredible Water Show," the characters from "Miss Alaineus: A Vocabulary Disaster" used an ocean of information to stage an inventive performance about the water cycle. In this article, the author relates how she turned the story into hands-on science teaching for real-life fifth-grade students. The author also…

  6. Characterization and stability analysis of zinc oxide nanoencapsulated conjugated linoleic acid.

    PubMed

    Choy, Jin-Ho; Shin, Jiwon; Lim, Seung-Yong; Oh, Jae-Min; Oh, Mi-Hwa; Oh, Sangsuk

    2010-08-01

    Nanoencapsulation technology has a diverse range of applications, including drug-delivery systems (DDS) and cosmetic and chemical carriers, because it can deliver various bio- and organic-molecules and improve their stabilities. Conjugated linoleic acid (CLA) has health benefits, including being an anticancer agent, but it decreases flavor due to volatiles from oxidation. To improve the stability of CLA for food applications, nanoencapsulated CLA was synthesized for use in zinc basic salt (ZBS) and characterized by powder X-ray diffractometry, thermogravimetric analysis (TGA), elemental CHN analysis, inductively coupled plasma (ICP) analysis, UV/VIS spectroscopy, and FTIR spectroscopy. The thermal stability of nanoencapsulated CLA at 180 degrees C, a temperature similar to that used in cooking, was analyzed by gas chromatography. The gallery height of nanoencapsulated CLA was determined to be approximately 26 A through powder X-ray diffractometry; therefore, the CLA molecules were closely packed with zig-zag form between the intracrystalline spaces of nano particles. Elemental CHN analysis and ICP data determined the chemical composition of nanoencapsulated CLA to be Zn(4.86)(OH)(8.78)(CLA)(0.94). By TGA, it was determined about 45% (wt/wt) of weight loss corresponded to CLA, which is good agreement with the 42.13% (wt/wt) determined from high-performance liquid chromatography (HPLC) and elemental CHN analysis. UV/VIS spectroscopy and Fourier-transformed infrared (FTIR) spectroscopy showed encapsulated CLA maintained a conjugated diene structure, supporting the presence of CLA. Nanoencapsulation improved the thermal stability of CLA by about 25%, compared to pristine CLA. Practical Application: This system can be used for protection of encapsulated negatively-charged food ingredients from thermal processing.

  7. Biometrics from the carbon isotope ratio analysis of amino acids in human hair.

    PubMed

    Jackson, Glen P; An, Yan; Konstantynova, Kateryna I; Rashaid, Ayat H B

    2015-01-01

    This study compares and contrasts the ability to classify individuals into different grouping factors through either bulk isotope ratio analysis or amino-acid-specific isotope ratio analysis of human hair. Using LC-IRMS, we measured the isotope ratios of 14 amino acids in hair proteins independently, and leucine/isoleucine as a co-eluting pair, to provide 15 variables for classification. Multivariate analysis confirmed that the essential amino acids and non-essential amino acids were mostly independent variables in the classification rules, thereby enabling the separation of dietary factors of isotope intake from intrinsic or phenotypic factors of isotope fractionation. Multivariate analysis revealed at least two potential sources of non-dietary factors influencing the carbon isotope ratio values of the amino acids in human hair: body mass index (BMI) and age. These results provide evidence that compound-specific isotope ratio analysis has the potential to go beyond region-of-origin or geospatial movements of individuals-obtainable through bulk isotope measurements-to the provision of physical and characteristic traits about the individuals, such as age and BMI. Further development and refinement, for example to genetic, metabolic, disease and hormonal factors could ultimately be of great assistance in forensic and clinical casework.

  8. Structural analysis of the alcohol acyltransferase protein family from Cucumis melo shows that enzyme activity depends on an essential solvent channel.

    PubMed

    Galaz, Sebastián; Morales-Quintana, Luis; Moya-León, María Alejandra; Herrera, Raúl

    2013-03-01

    Alcohol acyltransferases (AAT) play a key role in ester biosynthesis. In Cucumis melo var. cantalupensis, AATs are encoded by a gene family of four members (CmAAT1-4). CmAAT1, CmAAT3 and CmAAT4 are capable of synthesizing esters, with CmAAT1 the most active. CmAAT2 is inactive and has an Ala268 residue instead of a threonine which is present in all other active AATs, although the role of this residue is still unclear. The present work aims to understand the molecular mechanism involved in ester biosynthesis in melon fruit and to clarify the importance of the Ala268 residue. First, structural models for each protein were built by comparative modelling methodology. Afterwards, conformational interaction between the protein and several ligands, alcohols and acyl-CoAs was explored by molecular docking and molecular dynamics simulation. Structural analysis showed that CmAATs share a similar structure. Also, well-defined solvent channels were described in the CmAATs except for CmAAT2 which does not have a proper channel and instead has a small pocket around Ala268. Residues of the catalytic HxxxD motif interact with substrates within the solvent channel, with Ser363 also important. Strong binding interaction energies were described for the best substrate couple of each CmAAT (hexyl-, benzyl- and cinnamyl-acetate for CmAAT1, 3 and 4 respectively). CmAAT1 and CmAAT2 protein surfaces share similar electrostatic potentials; nevertheless the entrance channels for the substrates differ in location and electrostatic character, suggesting that Ala268 might be responsible for that. This could partly explain the major differences in activity reported for these two enzymes.

  9. Fine Resolution Analysis of Lake Malawi Sediment Record Shows No Significant Climatic Impacts from the Mount Toba Super-Eruption of ~75ky

    NASA Astrophysics Data System (ADS)

    Jackson, L. J.; Stone, J.; Cohen, A. S.

    2014-12-01

    Debate over long, and short-term climatic impacts of the Mt. Toba super-eruption circa 75ky is often focused on East Africa. A severe drop in anatomically modern human populations has been hypothesized to be synchronous with a volcanic winter caused by the Toba super-eruption. If the Toba eruption caused a volcanic winter in East Africa, climatologically-sensitive ecosystems, such as Lake Malawi and its immediate watershed should show a direct and observable response in the sediment record. Cooler temperatures would cause a reduction of density contrast between epilimnion and hypolimnion waters, allowing for increased mixing and oxygenation of normally anoxic bottom waters. Enhanced mixing would cause noticeable changes in lake fly and algal communities. Cooler temperatures might also affect precipitation and the fire regime in the surrounding watershed. We analyzed two Lake Malawi cores at the finest practical resolution. Core 2A-10H-2 was analyzed in less than 6-year intervals and core 1C-8H-1 in 7-year intervals surrounding the Youngest Toba Tephra (YTT) for microfaunal abundance and variability, sediment composition, and evidence of changes in the occurrence of fires or watershed precipitation. Our analysis included point counts of diatoms and other algae, lake flies, charcoal, and siliciclastics. Changes in microfossil assemblage, variability, and abundance, as well as sediment composition around the YTT in Core 2A and 1C do not indicate that increased mixing or cooler temperatures occurred in either the central or northern basins of Lake Malawi. Similarly, charcoal counts do not suggest a change in fire regime. Our results indicate that at a subdecadal scale there was no substantial response in Lake Malawi or its immediate watershed to the Mt. Toba super-eruption, in contrast to predictions from the volcanic winter hypothesis.

  10. Sampling and analysis of hexavalent chromium during exposure to chromic acid mist and welding fumes.

    PubMed

    Blomquist, G; Nilsson, C A; Nygren, O

    1983-12-01

    Sampling and analysis of hexavalent chromium during exposure to chromic acid mist and welding fumes. Scand j work environ & health 9 (1983) 489-495. In view of the serious health effects of hexavalent chromium, the problems involved in its sampling and analysis in workroom air have been the subject of much concern. In this paper, the stability problems arising from the reduction of hexavalent to trivalent chromium during sampling, sample storage, and analysis are discussed. Replacement of sulfuric acid by a sodium acetate buffer (pH 4) as a leaching solution prior to analysis with the diphenylcarbazide (DPC) method is suggested and is demonstrated to be necessary in order to avoid reduction. Field samples were taken from two different industrial processes-manual metal arc welding on stainless steel without shield gas and chromium plating. A comparison was made of the DPC method, acidic dissolution with atomic absorption spectrophotometric (AAS) analysis, and the carbonate method. For chromic acid mist, the DPC method and AAS analysis were shown to give the same results. In the analysis of welding fumes, the modified DPC method gave the same results as the laborious and less sensitive carbonate method.

  11. Knee Viscosupplementation: Cost-Effectiveness Analysis between Stabilized Hyaluronic Acid in a Single Injection versus Five Injections of Standard Hyaluronic Acid.

    PubMed

    Estades-Rubio, Francisco J; Reyes-Martín, Alvaro; Morales-Marcos, Victor; García-Piriz, Mercedes; García-Vera, Juan J; Perán, Macarena; Marchal, Juan A; Montañez-Heredia, Elvira

    2017-03-17

    Given the wide difference in price per vial between various presentations of hyaluronic acid, this study seeks to compare the effectiveness and treatment cost of stabilized hyaluronic acid (NASHA) in a single injection with standard preparations of hyaluronic acid (HA) in five injections in osteoarthritis (OA) of the knee. Fifty-four patients with knee osteoarthritis (Kellgren-Lawrence Grade II and III) and the Western Ontario and McMaster Universities Arthritis Index (WOMAC) pain score greater than 7, with a homogeneous distribution of age, sex, BMI, and duration of disease, were included in this study. Patients were randomized into two groups: Group I was treated with NASHA (Durolane(®)) and Group II with HA (Go-ON(®)). Patient's evolution was followed up at the 1st, 2nd, 4th, 8th, 12th, and 26th week after treatment. A statistically significant improvement in WOMAC score was observed for patients treated with NASHA versus those who received HA at Week 26. In addition, the need for analgesia was significantly reduced at Week 26 in the NASHA-treated group. Finally, the economic analysis showed an increased cost of overall treatment with HA injections. Our data support the use of the NASHA class of products in the treatment of knee OA.

  12. Knee Viscosupplementation: Cost-Effectiveness Analysis between Stabilized Hyaluronic Acid in a Single Injection versus Five Injections of Standard Hyaluronic Acid

    PubMed Central

    Estades-Rubio, Francisco J.; Reyes-Martín, Alvaro; Morales-Marcos, Victor; García-Piriz, Mercedes; García-Vera, Juan J.; Perán, Macarena; Marchal, Juan A.; Montañez-Heredia, Elvira

    2017-01-01

    Given the wide difference in price per vial between various presentations of hyaluronic acid, this study seeks to compare the effectiveness and treatment cost of stabilized hyaluronic acid (NASHA) in a single injection with standard preparations of hyaluronic acid (HA) in five injections in osteoarthritis (OA) of the knee. Fifty-four patients with knee osteoarthritis (Kellgren–Lawrence Grade II and III) and the Western Ontario and McMaster Universities Arthritis Index (WOMAC) pain score greater than 7, with a homogeneous distribution of age, sex, BMI, and duration of disease, were included in this study. Patients were randomized into two groups: Group I was treated with NASHA (Durolane®) and Group II with HA (Go-ON®). Patient’s evolution was followed up at the 1st, 2nd, 4th, 8th, 12th, and 26th week after treatment. A statistically significant improvement in WOMAC score was observed for patients treated with NASHA versus those who received HA at Week 26. In addition, the need for analgesia was significantly reduced at Week 26 in the NASHA-treated group. Finally, the economic analysis showed an increased cost of overall treatment with HA injections. Our data support the use of the NASHA class of products in the treatment of knee OA. PMID:28304363

  13. Comparison of two derivatization methods for the analysis of fatty acids and trans fatty acids in bakery products using gas chromatography.

    PubMed

    Salimon, Jumat; Omar, Talal A; Salih, Nadia

    2014-01-01

    Two different procedures for the methylation of fatty acids (FAs) and trans fatty acids (TFAs) in food fats were compared using gas chromatography (GC-FID). The base-catalyzed followed by an acid-catalyzed method (KOCH3/HCl) and the base-catalyzed followed by (trimethylsilyl)diazomethane (TMS-DM) method were used to prepare FA methyl esters (FAMEs) from lipids extracted from food products. In general, both methods were suitable for the determination of cis/trans FAs. The correlation coefficients (r) between the methods were relatively small (ranging from 0.86 to 0.99) and had a high level of agreement for the most abundant FAs. The significant differences (P = 0.05) can be observed for unsaturated FAs (UFAs), specifically for TFAs. The results from the KOCH3/HCl method showed the lowest recovery values (%R) and higher variation (from 84% to 112%), especially for UFAs. The TMS-DM method had higher R values, less variation (from 90% to 106%), and more balance between variation and %RSD values in intraday and interday measurements (less than 4% and 6%, resp.) than the KOCH3/HCl method, except for C12:0, C14:0, and C18:0. Nevertheless, the KOCH3/HCl method required shorter time and was less expensive than the TMS-DM method which is more convenient for an accurate and thorough analysis of rich cis/trans UFA samples.

  14. Hydrolysis study of organic acid anhydrides by differential thermal analysis-I Pyromellitic dianhydride.

    PubMed

    Rosenfeld, J M; Loncrini, D F; Murphy, C B

    1966-08-01

    A technique for following the hydrolysis of pyromellitic acid dianhydride (PMDA) by differential thermal analysis (DTA) is described. On exposure of PMDA to moisture, an endothennic peak is initiated between 190 and 200 degrees . As the degree of hydrolysis increases, this peak becomes more intense and shifts to higher temperatures. The formation of pyromellitic acid (PMA) during the hydrolysis of PMDA can be determined qualitatively by DTA.

  15. A rapid, sensitive method for quantitative analysis of underivatized amino acids by liquid chromatography-tandem mass spectrometry (LC-MS/MS).

    PubMed

    Le, Anthony; Ng, Angelina; Kwan, Tony; Cusmano-Ozog, Kristina; Cowan, Tina M

    2014-01-01

    The quantitation of free amino acids from physiologic samples is essential for diagnosing and monitoring patients with inherited metabolic disorders. Current methods are hindered by long preparative and/or analysis times, expensive reagents, and often suboptimal performance characteristics. To overcome these challenges, a improved method for amino acid analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been developed and validated. Samples were deproteinized with sulfosalicylic acid and supernatants diluted with tridecafluoroheptanoic acid. Chromatographic separation of amino acids occurred using two columns, with conditions favoring resolution of isobaric compounds and minimizing ion suppression. Eluted compounds were detected by selective reaction monitoring, and quantitated by relating peak areas of amino acids to externally run standards. Validation studies evaluated linearity, within- and between-run imprecision, lower limits of detection and quantification for 33 amino acids, and correlation with the Biochrom 30 Amino Acid Analyzer. Total run time including re-equilibration was 15min per sample. Within-run precision averaged 2.8% for all compounds, with an average linear correlation coefficient of 0.995. The majority of compounds were reliably quantitated at ≤0.1μM. Between-run precision averaged 4.0%. Results showed excellent correlation with the Biochrom 30 amino acid analyzer with an average overall correlation of 0.908. We conclude that our method is extremely sensitive, specific and reproducible and represents an improvement over other currently available technologies.

  16. Vibrational spectroscopic study and NBO analysis on tranexamic acid using DFT method

    NASA Astrophysics Data System (ADS)

    Muthu, S.; Prabhakaran, A.

    2014-08-01

    In this work, we reported the vibrational spectra of tranexamic acid (TA) by experimental and quantum chemical calculation. The solid phase FT-Raman and FT-IR spectra of the title compound were recorded in the region 4000 cm-1 to 100 cm-1 and 4000 cm-1 to 400 cm-1 respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of TA in the ground state have been calculated by using density functional theory (DFT) B3LYP method with standard 6-31G(d,p) basis set. The scaled theoretical wavenumber showed very good agreement with the experimental values. The vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes. Stability of the molecule, arising from hyperconjugative interactions and charge delocalization, has been analyzed using Natural Bond Orbital (NBO) analysis. The results show that ED in the σ* and π* antibonding orbitals and second order delocalization energies E(2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. The electrostatic potential mapped onto an isodensity surface has been obtained. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

  17. Spectrofluorometric analysis of amino acid mixtures: Implications for future space missions

    NASA Astrophysics Data System (ADS)

    Chan, Hoi S.; Martins, Zita; Sephton, Mark A.

    2012-01-01

    Efficient detection of organic molecules is fundamental for the success of future life detection missions. Spectrofluorometric analysis is one of the many techniques that may be used to detect organic molecules in extraterrestrial settings. A particularly important class of organic molecules to target is the amino acids on which all terrestrial life depends. This study aims to identify the optimum fluorescence excitation and emission wavelengths for 17 amino acid standards to examine the effects of amino acid concentrations, mixtures and fluorescence quenching. The results and interpretations can guide the design and operation of life detection protocols on future space missions.

  18. Trophic hierarchies revealed via amino acid isotopic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Despite the potential of isotopic methods to illuminate trophic function, accurate estimates of lifetime feeding tendencies have remained elusive. A relatively new approach—referred to as compound-specific isotopic analysis (CSIA)—has emerged, centering on the measurement of 15N:14N ratios in amino ...

  19. Serum uric acid levels in patients with Parkinson’s disease: A meta-analysis

    PubMed Central

    Wen, Min; Zhou, Bo; Chen, Yun-Hua; Ma, Zhao-Lei; Gou, Yun; Zhang, Chun-Lin; Yu, Wen-Feng; Jiao, Ling

    2017-01-01

    Background Lower serum uric acid (UA) levels have been reported as a risk factor in Parkinson’s disease (PD). However, the results have been inconsistent so far. Objectives The aim of the present study was to clarify the potential relationship of uric acid with PD. Methods Comprehensive electronic search in pubmed, web of science, and the Cochrane Library database to find original articles about the association between PD and serum uric acid levels published before Dec 2015. Literature quality assessment was performed with the Newcastle-Ottawa Scale. Random-effects model was used to estimate the standardized mean differences (SMDs) with 95% confidence intervals (CIs). Heterogeneity across studies was assessed using I2 and H2 statistics. Sensitivity analyses to assess the influence of individual studies on the pooled estimate. Publication bias was investigated using funnel plots and Egger’s regression test. Analyses were performed by using Review Manager 5.3 and Stata 11.0. Results Thirteen studies with a total of 4646 participants (2379 PD patients and 2267 controls) were included in this meta-analysis. The current results showed that the serum UA levels in PD patients were significantly lower compared to sex and age-matched healthy controls (SMD: -0.49, 95% CI: [-0.67, -0.30], Z = 5.20, P < 0.001) and these results showed no geographic regional (Asia: SMD = −0.65, 95% CI [−0.84, −0.46], Z = 6.75, p <0.001; Non-Asia: SMD = −0.25, 95% CI [−0.43, −0.07], Z = 2.70, p = 0.007) and sex differences (women: SMD = −0.53, 95% CI [−0.70, −0.35], z = 5.98, p <0.001; men: SMD = −0.66, 95% CI [−0.87, −0.44], z = 6.03, p <0.001). Serum UA levels in middle-late stage PD patients with higher H&Y scales were significantly lower than early stage PD patients with lower H&Y scales (SMD = 0.63, 95% CI [0.36,0.89], z = 4.64, p <0.001). Conclusions Our study showed that the serum UA levels are significantly lower in PD and the level is further decreased as the

  20. Transcriptional Analysis of Lactobacillus brevis to N-Butanol and Ferulic Acid Stress Responses

    PubMed Central

    Winkler, James; Kao, Katy C.

    2011-01-01

    Background The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates pose significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. Simultaneously, product toxicity must also be overcome to allow for efficient production of next generation biofuels such as n-butanol, isopropanol, and others from these low cost feedstocks. Methodology and Principal Findings This study explores the high ferulic acid and n-butanol tolerance in Lactobacillus brevis, a lactic acid bacterium often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis reveals that the presence of ferulic acid triggers the expression of currently uncharacterized membrane proteins, possibly in an effort to counteract ferulic acid induced changes in membrane fluidity and ion leakage. In contrast to the ferulic acid stress response, n-butanol challenges to growing cultures primarily induce genes within the fatty acid synthesis pathway and reduced the proportion of 19∶1 cyclopropane fatty acid within the L. brevis membrane. Both inhibitors also triggered generalized stress responses. Separate attempts to alter flux through the Escherichia coli fatty acid synthesis by overexpressing acetyl-CoA carboxylase subunits and deleting cyclopropane fatty acid synthase (cfa) both failed to improve n-butanol tolerance in E. coli, indicating that additional components of the stress response are required to confer n-butanol resistance. Conclusions Several promising routes for understanding both ferulic acid and n-butanol tolerance have been identified from L. brevis gene expression data. These insights may be used to guide further engineering of

  1. Intelligent machine learning analysis for phosphoric acid fuel cell operations

    SciTech Connect

    Hoyt, W.; Foote, J.P.; Murphy, R.W.; Chen, F.C.

    1998-07-01

    Several fuel cell types are available and are in various stages of technology development. The complex nature of the balance of plant and fuel cell interface poses many technical challenges to achieve proper system control under commercial operating conditions. Real-time predictive diagnostic computer systems based on advanced intelligent machine learning technologies offer a means to facilitate the detection, understanding, and control of fuel cell subsystems to avoid system instabilities and failures that can result in costly plant shutdowns. The objectives reported herein are the development of physical and empirical computer models for application and testing of predictive control strategies based on intelligent machine learning techniques for fuel cells. A physical/empirical model was built and validated using available operating data from commercial fuel cells. Neural networks were then used to build an empirical model from the original physical/empirical model. Using the neural network model, a predictive, feedforward strategy was developed to control the fuel flow for a phosphoric acid fuel cell physical/empirical model. The predictive control strategy was compared to traditional proportional integral derivative control schemes.

  2. Genome level analysis of bacteriocins of lactic acid bacteria.

    PubMed

    Singh, Neetigyata Pratap; Tiwari, Abhay; Bansal, Ankiti; Thakur, Shruti; Sharma, Garima; Gabrani, Reema

    2015-06-01

    Bacteriocins are antimicrobial peptides which are ribosomally synthesized by mainly all bacterial species. LABs (lactic acid bacteria) are a diverse group of bacteria that include around 20 genera of various species. Though LABs have a tremendous potential for production of anti-microbial peptides, this group of bacteria is still underexplored for bacteriocins. To study the diversity among bacteriocin encoding clusters and the putative bacteriocin precursors, genome mining was performed on 20 different species of LAB not reported to be bacteriocin producers. The phylogenetic tree of gyrB, rpoB, and 16S rRNA were constructed using MEGA6 software to analyze the diversity among strains. Putative bacteriocins operons identified were found to be diverse and were further characterized on the basis of physiochemical properties and the secondary structure. The presence of at least two cysteine residues in most of the observed putative bacteriocins leads to disulphide bond formation and provide stability. Our data suggests that LABs are prolific source of low molecular weight non modified peptides.

  3. A mutational analysis of the cytosolic domain of the tomato Cf-9 disease-resistance protein shows that membrane-proximal residues are important for Avr9-dependent necrosis.

    PubMed

    Chakrabarti, Apratim; Velusamy, Thilaga; Tee, Choon Yang; Jones, David A

    2016-05-01

    The tomato Cf-9 gene encodes a membrane-anchored glycoprotein that imparts race-specific resistance against the tomato leaf mould fungus Cladosporium fulvum in response to the avirulence protein Avr9. Although the N-terminal half of the extracellular leucine-rich repeat (eLRR) domain of the Cf-9 protein determines its specificity for Avr9, the C-terminal half, including its small cytosolic domain, is postulated to be involved in signalling. The cytosolic domain of Cf-9 carries several residues that are potential sites for ubiquitinylation or phosphorylation, or signals for endocytic uptake. A targeted mutagenesis approach was employed to investigate the roles of these residues and cellular processes in Avr9-dependent necrosis triggered by Cf-9. Our results indicate that the membrane-proximal region of the cytosolic domain of Cf-9 plays an important role in Cf-9-mediated necrosis, and two amino acids within this region, a threonine (T835) and a proline (P838), are particularly important for Cf-9 function. An alanine mutation of T835 had no effect on Cf-9 function, but an aspartic acid mutation, which mimics phosphorylation, reduced Cf-9 function. We therefore postulate that phosphorylation/de-phosphorylation of T835 could act as a molecular switch to determine whether Cf-9 is in a primed or inactive state. Yeast two-hybrid analysis was used to show that the cytosolic domain of Cf-9 interacts with the cytosolic domain of tomato VAP27. This interaction could be disrupted by an alanine mutation of P838, whereas interaction with CITRX remained unaffected. We therefore postulate that a proline-induced kink in the membrane-proximal region of the cytosolic domain of Cf-9 may be important for interaction with VAP27, which may, in turn, be important for Cf-9 function.

  4. Nutrient uptake by marine invertebrates: cloning and functional analysis of amino acid transporter genes in developing sea urchins (Strongylocentrotus purpuratus).

    PubMed

    Meyer, Eli; Manahan, Donal T

    2009-08-01

    Transport of amino acids from low concentrations in seawater by marine invertebrates has been extensively studied, but few of the genes involved in this physiological process have been identified. We have characterized three amino acid transporter genes cloned from embryos of the sea urchin Strongylocentrotus purpuratus. These genes show phylogenetic proximity to classical amino acid transport systems, including Gly and B0+, and the inebriated gene (INE). Heterologous expression of these genes in frog oocytes induced a 40-fold increase in alanine transport above endogenous levels, demonstrating that these genes mediate alanine transport. Antibodies specific to one of these genes (Sp-AT1) inhibited alanine transport, confirming the physiological activity of this gene in larvae. Whole-mount antibody staining of larvae revealed expression of Sp-AT1 in the ectodermal tissues associated with amino acid transport, as independently demonstrated by autoradiographic localization of radioactive alanine. Maximum rates of alanine transport increased 6-fold during early development, from embryonic to larval stages. Analysis of gene expression during this developmental period revealed that Sp-AT1 transcript abundance remained nearly constant, while that of another transporter gene (Sp-AT2) increased 11-fold. The functional characterization of these genes establishes a molecular biological basis for amino acid transport by developmental stages of marine invertebrates.

  5. Characterization and phylogenetic analysis of a thermostable N-carbamoyl- l-amino acid amidohydrolase from Bacillus kaustophilus CCRC11223.

    PubMed

    Hu, Hui-Yu; Hsu, Wen-Hwei; Chien, Hungchien Roger

    2003-04-01

    A thermostable N-carbamoyl- l-amino acid amidohydrolase ( l-N-carbamoylase) gene composed of an 1,230-bp ORF encoding a 44.3-kDa protein was cloned from the thermophile Bacillus kaustophilus CCRC11223. This l-N-carbamoylase contained six cysteine residues that form three disulfide bridges. The purified l-N-carbamoylase was stringently l-specific and exhibited high activity in the hydrolysis of N-carbamoyl- l-homophenylalanine. N-carbamoyl derivatives of beta-alanine, beta-aminoisobutyric acids, l-tryptophan, and d-specific amino acids were not recognized as substrates. The l-N-carbamoylase required the divalent metal ions Mn(2+), Co(2+), and Ni(2+) for increasing activity. The pH and temperature optima of the enzyme were pH 7.4 and 70 degrees C, respectively. This enzyme was completely thermostable at 50 degrees C for 36 days in the presence of d- and/or l-specific substrates. Phylogenetic analysis of the available amino acid sequences of N-carbamoyl and N-acyl amino acid amidohydrolases from the three main kingdoms of life showed that they can be divided into four distinct families. The B. kaustophilus enzyme could be classified into the family of l-N-carbamoylases and some beta-ureidopropionases, but did not hydrolyze beta-ureidopropionates.

  6. Comparison of amino acid derivatization reagents for LC-ESI-MS analysis. Introducing a novel phosphazene-based derivatization reagent.

    PubMed

    Rebane, Riin; Oldekop, Maarja-Liisa; Herodes, Koit

    2012-09-01

    Amino acid analysis with high performance liquid chromatography with electrospray ionization mass spectrometry (LC-ESI-MS) is an emerging method. For more sensitive analysis, derivatization is used and next to commercially available derivatization reagents such as dansyl chloride (DNS), 9-fluorenylmethyl chloroformate (FMOC-Cl) and diethyl ethoxymethylenemalonate (DEEMM), new derivatization reagents are designed specially for LC-ESI-MS, like p-N,N,N-trimethylammonioanilyl N'-hydroxysuccinimidyl carbamate iodide (TAHS) which provides very low limits of detection. In this work, a novel phosphazene based derivatization reagent (FOSF) that provides comparable limits of quantitation (LoQ) to TAHS is introduced. Moreover, a thorough comparison between FOSF, TAHS, DNS, FMOC-Cl and DEEMM is carried out for 7 different amino acids - Arg, Asp, Gly, β-Ala, Pro, Trp and Phe. This is a first time that thorough comparison is carried out on the same instrument for amino acid derivatization reagents. Results on the same instrument for five amino acid derivatization reagents show that novel reagents are sensitive with LoQ values around 80 fmol but have disadvantages such as problematic chromatographic separation. Next to novel reagents, DEEMM offers very good LoQ-s (average of 150 fmol) and wide dynamic linear range.

  7. Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on 13C-metabolic flux analysis.

    PubMed

    He, Lian; Xiao, Yi; Gebreselassie, Nikodimos; Zhang, Fuzhong; Antoniewiez, Maciek R; Tang, Yinjie J; Peng, Lifeng

    2014-03-01

    We engineered a fatty acid overproducing Escherichia coli strain through overexpressing tesA (“pull”) and fadR (“push”) and knocking out fadE (“block”). This “pull-push-block” strategy yielded 0.17 g of fatty acids (C12–C18) per gram of glucose (equivalent to 48% of the maximum theoretical yield) in batch cultures during the exponential growth phase under aerobic conditions. Metabolic fluxes were determined for the engineered E. coli and its control strain using tracer ([1,2-13C]glucose) experiments and 13C-metabolic flux analysis. Cofactor (NADPH) and energy (ATP) balances were also investigated for both strains based on estimated fluxes. Compared to the control strain, fatty acid overproduction led to significant metabolic responses in the central metabolism: (1) Acetic acid secretion flux decreased 10-fold; (2) Pentose phosphate pathway and Entner–Doudoroff pathway fluxes increased 1.5- and 2.0-fold, respectively; (3) Biomass synthesis flux was reduced 1.9-fold; (4) Anaplerotic phosphoenolpyruvate carboxylation flux decreased 1.7-fold; (5) Transhydrogenation flux converting NADH to NADPH increased by 1.7-fold. Real-time quantitative RT-PCR analysis revealed the engineered strain increased the transcription levels of pntA (encoding the membrane-bound transhydrogenase) by 2.1-fold and udhA (encoding the soluble transhydrogenase) by 1.4-fold, which is in agreement with the increased transhydrogenation flux. Cofactor and energy balances analyses showed that the fatty acid overproducing E. coli consumed significantly higher cellular maintenance energy than the control strain. We discussed the strategies to future strain development and process improvements for fatty acid production in E. coli.

  8. Processing and analysis of chitosan nanocomposites reinforced with chitin whiskers and tannic acid as a crosslinker.

    PubMed

    Rubentheren, V; Ward, Thomas A; Chee, Ching Yern; Tang, Chee Kuang

    2015-01-22

    Chitosan film reinforced with nano-sized chitin whiskers and crosslinked using tannic acid was synthesized by the casting-vaporation method. The mechanical and physicochemical properties of several film samples (consisting of different ratio of chitin and tannic acid) were compared with neat chitosan. Tensile tests show that the addition of chitin improves the nanocomposite films mechanical properties up to 137% compared to neat chitosan, but this is slightly degraded when tannic acid is introduced. However, tannic acid and chitin whisker content greatly reduced moisture content by 294% and water solubility by 13%. Transmission electron microscopy (TEM) and Fourier-transform-infrared spectroscopy (FTIR) were used to investigate the morphology and molecular interaction of film. X-ray diffraction results indicated that the samples with chitin whiskers had a more rigid structure. The addition of tannic acid changed the structure into an anhydrous crystalline conformation when compared to neat chitosan film.

  9. Selective removal of phosphate for analysis of organic acids in complex samples.

    PubMed

    Deshmukh, Sandeep; Frolov, Andrej; Marcillo, Andrea; Birkemeyer, Claudia

    2015-04-03

    Accurate quantitation of compounds in samples of biological origin is often hampered by matrix interferences one of which occurs in GC-MS analysis from the presence of highly abundant phosphate. Consequently, high concentrations of phosphate need to be removed before sample analysis. Within this context, we screened 17 anion exchange solid-phase extraction (SPE) materials for selective phosphate removal using different protocols to meet the challenge of simultaneous recovery of six common organic acids in aqueous samples prior to derivatization for GC-MS analysis. Up to 75% recovery was achieved for the most organic acids, only the low pKa tartaric and citric acids were badly recovered. Compared to the traditional approach of phosphate removal by precipitation, SPE had a broader compatibility with common detection methods and performed more selectively among the organic acids under investigation. Based on the results of this study, it is recommended that phosphate removal strategies during the analysis of biologically relevant small molecular weight organic acids consider the respective pKa of the anticipated analytes and the detection method of choice.

  10. Human cell toxicogenomic analysis linking reactive oxygen species to the toxicity of monohaloacetic acid drinking water disinfection byproducts.

    PubMed

    Pals, Justin; Attene-Ramos, Matias S; Xia, Menghang; Wagner, Elizabeth D; Plewa, Michael J

    2013-01-01

    Chronic exposure to drinking water disinfection byproducts has been linked to adverse health risks. The monohaloacetic acids (monoHAAs) are generated as byproducts during the disinfection of drinking water and are cytotoxic, genotoxic, mutagenic, and teratogenic. Iodoacetic acid toxicity was mitigated by antioxidants, suggesting the involvement of oxidative stress. Other monoHAAs may share a similar mode of action. Each monoHAA generated a significant concentration-response increase in the expression of a β-lactamase reporter under the control of the antioxidant response element (ARE). The monoHAAs generated oxidative stress with a rank order of iodoacetic acid (IAA) > bromoacetic acid (BAA) ≫ chloroacetic acid (CAA); this rank order was observed with other toxicological end points. Toxicogenomic analysis was conducted with a nontransformed human intestinal epithelial cell line (FHs 74 Int). Exposure to the monoHAAs altered the transcription levels of multiple oxidative stress responsive genes, indicating that each exposure generated oxidative stress. The transcriptome profiles showed an increase in thioredoxin reductase 1 (TXNRD1) and sulfiredoxin (SRXN1), suggesting peroxiredoxin proteins had been oxidized during monoHAA exposures. Three possible sources of reactive oxygen species were identified, the hypohalous acid generating peroxidase enzymes lactoperoxidase (LPO) and myeloperoxidase (MPO), nicotinamide adenine dinucleotide phosphate (NADPH)-dependent oxidase 5 (NOX5), and PTGS2 (COX-2) mediated arachidonic acid metabolism. Each monoHAA exposure caused an increase in COX-2 mRNA levels. These data provide a functional association between monoHAA exposure and adverse health outcomes such as oxidative stress, inflammation, and cancer.

  11. Analysis of free amino acids in natural waters by liquid chromatography-tandem mass spectrometry.

    PubMed

    How, Zuo Tong; Busetti, Francesco; Linge, Kathryn L; Kristiana, Ina; Joll, Cynthia A; Charrois, Jeffrey W A

    2014-11-28

    This paper reports a new analytical method for the analysis of 18 amino acids in natural waters using solid-phase extraction (SPE) followed by liquid chromatography-electrospray tandem mass spectrometry (LC-MS/MS) operated in multiple reaction monitoring mode. Two different preconcentration methods, solid-phase extraction and concentration under reduced pressure, were tested in development of this method. Although concentration under reduced pressure provided better recoveries and method limits of detection for amino acids in ultrapure water, SPE was a more suitable extraction method for real samples due to the lower matrix effects for this method. Even though the strong cation exchange resin used in SPE method introduced exogenous matrix interferences into the sample extracts (inorganic salt originating from the acid-base reaction during the elution step), the SPE method still incorporates a broad sample clean-up and minimised endogenous matrix effects by reducing interferences originating from real water samples. The method limits of quantification (MLQ) for the SPE LC-MS/MS method in ultrapure water ranged from 0.1 to 100 μg L(-1) as N for the different amino acids. The MLQs of the early eluting amino acids were limited by the presence of matrix interfering species, such as inorganic salts in natural water samples. The SPE LC-MS/MS method was successfully applied to the analysis of amino acids in 3 different drinking water source waters: the average total free amino acid content in these waters was found to be 19 μg L(-1) as N, while among the 18 amino acids analysed, the most abundant amino acids were found to be tyrosine, leucine and isoleucine.

  12. Not a "reality" show.

    PubMed

    Wrong, Terence; Baumgart, Erica

    2013-01-01

    The authors of the preceding articles raise legitimate questions about patient and staff rights and the unintended consequences of allowing ABC News to film inside teaching hospitals. We explain why we regard their fears as baseless and not supported by what we heard from individuals portrayed in the filming, our decade-long experience making medical documentaries, and the full un-aired context of the scenes shown in the broadcast. The authors don't and can't know what conversations we had, what documents we reviewed, and what protections we put in place in each televised scene. Finally, we hope to correct several misleading examples cited by the authors as well as their offhand mischaracterization of our program as a "reality" show.

  13. Analysis of serum metabolites for the discovery of amino acid biomarkers and the effect of galangin on cerebral ischemia.

    PubMed

    Gao, Jian; Yang, Hongjun; Chen, Jianxin; Fang, Jiansong; Chen, Chang; Liang, Rixin; Yang, Gengliang; Wu, Hongwei; Wu, Chuanhong; Li, Shaojing

    2013-09-01

    Ischemic stroke, a devastating disease with a complex pathophysiology, is a leading cause of death and disability worldwide. In our previous study, we reported that galangin provided direct protection against ischemic injury and acted as a potential neuroprotective agent. However, its associated neuroprotective mechanism has not yet been clarified. In this paper, we explored the potential AA biomarkers in the acute phase of cerebral ischemia and the effect of galangin on those potential biomarkers. In our study, 12 AAs were quantified in rat serum and found to be impaired by middle cerebral artery occlusion (MCAO)-induced focal cerebral ischemia. Using partial least squares discriminate analysis (PLS-DA), we identified the following amino acids as potential biomarkers of cerebral ischemia: glutamic acid (Glu), homocysteine (Hcy), methionine (Met), tryptophan (Trp), aspartic acid (Asp), alanine (Ala) and tyrosine (Tyr). Moreover, four amino acids (Hcy, Met, Glu and Trp) showed significant change in galangin-treated (100 and 50 mg kg(-1)) groups compared to vehicle groups. Furthermore, we identified three pathway-related enzymes tyrosine aminotransferase (TAT), glutamine synthetase (GLUL) and monocarboxylate transporter (SLC16A10) by multiplex interactions with Glu and Hcy, which have been previously reported to be closely related to cerebral ischemia. Through an analysis of the metabolite-protein network analysis, we identified 16 proteins that were associated with two amino acids by multiple interactions with three enzymes; five of them may become potential biomarkers of galangin for acute ischemic stroke as the result of molecule docking. Our results may help develop novel strategies to explore the mechanism of cerebral ischemia, discover potential targets for drug candidates and elucidate the related regulatory signal network.

  14. Determination of phosphate in natural waters by activation analysis of tungstophosphoric acid

    USGS Publications Warehouse

    Allen, Herbert E.; Hahn, Richard B.

    1969-01-01

    Activation analysis may be used to determine quantitatively traces of phosphate in natural waters. Methods based on the reaction 31P(n,γ)32P are subject to interference by sulfur and chlorine which give rise to 32P through n,p and n,α reactions. If the ratio of phosphorus to sulfur or chlorine is small, as it is in most natural waters, accurate analyses by these methods are difficult to achieve. In the activation analysis method, molybdate and tungstate ions are added to samples containing phosphate ion to form tungstomolybdophosphoric acid. The complex is extracted with 2,6-dimethyl-4-heptanone. After activation of an aliquot of the organic phase for 1 hour at a flux of 1013 neutrons per cm2, per second, the gamma spectrum is essentially that of tungsten-187. The induced activity is proportional to the concentration of phosphate in the sample. A test of the method showed it to give accurate results at concentrations of 4 to at least 200 p.p.b. of phosphorus when an aliquot of 100 μl. was activated. By suitable reagent purification, counting for longer times, and activation of larger aliquots, the detection limit could be lowered several hundredfold.

  15. Development of an alternative eluent system for Ag+-HPLC analysis of conjugated linoleic acid isomers.

    PubMed

    Müller, André; Düsterloh, Kaja; Ringseis, Robert; Eder, Klaus; Steinhart, Hans

    2006-02-01

    In this study, 13 different eluent systems containing n-hexane, n-heptane and iso-octane as main solvents and ACN, propionitrile (PCN) and butyronitrile (BCN) in concentrations between 0.1 and 0.2% as modifiers were tested for their influence on retention time shifts (RTS) and resolution of conjugated linoleic acid (CLA) methyl esters using two ChromSpher 5 Lipids columns (250 mm x 4.6 mm, 5 microm) in series. The eluent system n-hexane/PCN 0.2% showed the highest stability with an obtained RTS of 0.26 min for the cis/trans-group after 14 consecutive injections of a CLA isomer mix compared to the reference system of n-hexane/ACN 0.15% (RTS of 2.35 min). This enhanced stability is due to better solubility of PCN in n-hexane compared to ACN. The enhanced stability coincided with a negligible loss in resolution for the cis,trans/trans,cis- and the cis,cis-groups. As shown for the analysis of human aortic endothelial cells spiked with t10c12-CLA, data from CLA-analysis by Ag+-HPLC-DAD must be judged very carefully, especially at low concentrations, as coeluting matrix compounds may give false-positive results. Therefore, results should be confirmed by GC-FID and GC-MS.

  16. Fractal analysis of polyferric chloride-humic acid (PFC-HA) flocs in different topological spaces.

    PubMed

    Wang, Yili; Lu, Jia; Baiyu, Du; Shi, Baoyou; Wang, Dongsheng

    2009-01-01

    The fractal dimensions in different topological spaces of polyferric chloride-humic acid (PFC-HA) flocs, formed in flocculating different kinds of humic acids (HA) water at different initial pH (9.0, 7.0, 5.0) and PFC dosages, were calculated by effective density-maximum diameter, image analysis, and N2 absorption-desorption methods, respectively. The mass fractal dimensions (Df) of PFC-HA flocs were calculated by bi-logarithm relation of effective density with maximum diameter and Logan empirical equation. The Df value was more than 2.0 at initial pH of 7.0, which was 11% and 13% higher than those at pH 9.0 and 5.0, respectively, indicating the most compact flocs formed in flocculated HA water at initial pH of 7.0. The image analysis for those flocs indicates that after flocculating the HA water at initial pH greater than 7.0 with PFC flocculant, the fractal dimensions of D2 (logA vs. logdL) and D3 (logVsphere VS. logdL) of PFC-HA flocs decreased with the increase of PFC dosages, and PFC-HA flocs showed a gradually looser structure. At the optimum dosage of PFC, the D2 (logA vs. logdL) values of the flocs show 14%-43% difference with their corresponding Df, and they even had different tendency with the change of initial pH values. However, the D2 values of the flocs formed at three different initial pH in HA solution had a same tendency with the corresponding Dr. Based on fractal Frenkel-Halsey-Hill (FHH) adsorption and desorption equations, the pore surface fractal dimensions (Ds) for dried powders of PFC-HA flocs formed in HA water with initial pH 9.0 and 7.0 were all close to 2.9421, and the Ds values of flocs formed at initial pH 5.0 were less than 2.3746. It indicated that the pore surface fractal dimensions of PFC-HA flocs dried powder mainly show the irregularity from the mesopore-size distribution and marcopore-size distribution.

  17. Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection.

    PubMed

    Ipek, M; Ipek, A; Seker, M; Gul, M K

    2015-03-27

    The purpose of this research was to characterize an olive core collection using some agronomic characters and simple sequence repeat (SSR) markers and to determine SSR markers associated with the content of fatty acids in olive oil. SSR marker analysis demonstrated the presence of a high amount of genetic variation between the olive cultivars analyzed. A UPGMA dendrogram demonstrated that olive cultivars did not cluster on the basis of their geographic origin. Fatty acid components of olive oil in these cultivars were determined. The results also showed that there was a great amount of variation between the olive cultivars in terms of fatty acid composition. For example, oleic acid content ranged from 57.76 to 76.9% with standard deviation of 5.10%. Significant correlations between fatty acids of olive oil were observed. For instance, a very high negative correlation (-0.812) between oleic and linoleic acids was detected. A structured association analysis between the content of fatty acids in olive oil and SSR markers was performed. STRUCTURE analysis assigned olive cultivars to two gene pools (K = 2). Assignment of olive cultivars to these gene pools was not based on geographical origin. Association between fatty acid traits and SSR markers was evaluated using the general linear model of TASSEL. Significant associations were determined between five SSR markers and stearic, oleic, linoleic, and linolenic acids of olive oil. Very high associations (P < 0.001) between ssrOeUA-DCA14 and stearic acid and between GAPU71B and oleic acid indicated that these markers could be used for marker-assisted selection in olive.

  18. Comparative proteomic analysis of differentially expressed proteins in β-aminobutyric acid enhanced Arabidopsis thaliana tolerance to simulated acid rain.

    PubMed

    Liu, Tingwu; Jiang, Xinwu; Shi, Wuliang; Chen, Juan; Pei, Zhenming; Zheng, Hailei

    2011-05-01

    Acid rain is a worldwide environmental issue that has seriously destroyed forest ecosystems. As a highly effective and broad-spectrum plant resistance-inducing agent, β-aminobutyric acid could elevate the tolerance of Arabidopsis when subjected to simulated acid rain. Using comparative proteomic strategies, we analyzed 203 significantly varied proteins of which 175 proteins were identified responding to β-aminobutyric acid in the absence and presence of simulated acid rain. They could be divided into ten groups according to their biological functions. Among them, the majority was cell rescue, development and defense-related proteins, followed by transcription, protein synthesis, folding, modification and destination-associated proteins. Our conclusion is β-aminobutyric acid can lead to a large-scale primary metabolism change and simultaneously activate antioxidant system and salicylic acid, jasmonic acid, abscisic acid signaling pathways. In addition, β-aminobutyric acid can reinforce physical barriers to defend simulated acid rain stress.

  19. Public medical shows.

    PubMed

    Walusinski, Olivier

    2014-01-01

    In the second half of the 19th century, Jean-Martin Charcot (1825-1893) became famous for the quality of his teaching and his innovative neurological discoveries, bringing many French and foreign students to Paris. A hunger for recognition, together with progressive and anticlerical ideals, led Charcot to invite writers, journalists, and politicians to his lessons, during which he presented the results of his work on hysteria. These events became public performances, for which physicians and patients were transformed into actors. Major newspapers ran accounts of these consultations, more like theatrical shows in some respects. The resultant enthusiasm prompted other physicians in Paris and throughout France to try and imitate them. We will compare the form and substance of Charcot's lessons with those given by Jules-Bernard Luys (1828-1897), Victor Dumontpallier (1826-1899), Ambroise-Auguste Liébault (1823-1904), Hippolyte Bernheim (1840-1919), Joseph Grasset (1849-1918), and Albert Pitres (1848-1928). We will also note their impact on contemporary cinema and theatre.

  20. Comparative physiological and transcriptional analysis of weak organic acid stress in Bacillus subtilis.

    PubMed

    Ter Beek, Alexander; Wijman, Janneke G E; Zakrzewska, Anna; Orij, Rick; Smits, Gertien J; Brul, Stanley

    2015-02-01

    The advent of 'omics' techniques bears significant potential for the assessment of the microbiological stability of foods. This requires the integration of molecular data with their implication for cellular physiology. Here we performed a comparative physiological and transcriptional analysis of Bacillus subtilis stressed with three different weak organic acids: the commonly used food preservatives sorbic- and acetic-acid, plus the well-known uncoupler carbonyl cyanide-m-chlorophenyl hydrazone (CCCP). The concentration of each compound needed to cause a similar reduction of the growth rate negatively correlated with their membrane solubility, and positively with the concentration of undissociated acid. Intracellular acidification was demonstrated by expressing a pH-sensitive GFP derivative. The largest drop in intracellular pH was observed in CCCP-stressed cells and was accompanied by the transcriptional induction of the general stress response (GSR) and SigM regulon, responses known to be induced by acidification. The GSR was induced by acetate, but not by sorbate in mildly-stressed cells. Microarray analysis further revealed that all three acids activate transcriptional programs normally seen upon nutrient limitation and cause diverse responses indicative of an adaptation of the cell envelope. Based on the responses observed and the utilized pH measurements, the inhibitory effect of sorbic acid seems to be more focused on the cell membrane than that of acetic acid or CCCP.

  1. The Great Cometary Show

    NASA Astrophysics Data System (ADS)

    2007-01-01

    its high spatial and spectral resolution, it was possible to zoom into the very heart of this very massive star. In this innermost region, the observations are dominated by the extremely dense stellar wind that totally obscures the underlying central star. The AMBER observations show that this dense stellar wind is not spherically symmetric, but exhibits a clearly elongated structure. Overall, the AMBER observations confirm that the extremely high mass loss of Eta Carinae's massive central star is non-spherical and much stronger along the poles than in the equatorial plane. This is in agreement with theoretical models that predict such an enhanced polar mass-loss in the case of rapidly rotating stars. ESO PR Photo 06c/07 ESO PR Photo 06c/07 RS Ophiuchi in Outburst Several papers from this special feature focus on the later stages in a star's life. One looks at the binary system Gamma 2 Velorum, which contains the closest example of a star known as a Wolf-Rayet. A single AMBER observation allowed the astronomers to separate the spectra of the two components, offering new insights in the modeling of Wolf-Rayet stars, but made it also possible to measure the separation between the two stars. This led to a new determination of the distance of the system, showing that previous estimates were incorrect. The observations also revealed information on the region where the winds from the two stars collide. The famous binary system RS Ophiuchi, an example of a recurrent nova, was observed just 5 days after it was discovered to be in outburst on 12 February 2006, an event that has been expected for 21 years. AMBER was able to detect the extension of the expanding nova emission. These observations show a complex geometry and kinematics, far from the simple interpretation of a spherical fireball in extension. AMBER has detected a high velocity jet probably perpendicular to the orbital plane of the binary system, and allowed a precise and careful study of the wind and the shockwave

  2. Molecular analysis of a bifunctional fatty acid conjugase/desaturase from tung. Implications for the evolution of plant fatty acid diversity.

    PubMed

    Dyer, John M; Chapital, Dorselyn C; Kuan, Jui-Chang W; Mullen, Robert T; Turner, Charlotta; McKeon, Thomas A; Pepperman, Armand B

    2002-12-01

    The seed oil derived from the tung (Aleurites fordii Hemsl.) tree contains approximately 80% alpha-eleostearic acid (18:3delta(9cis,11trans,13trans)), an unusual conjugated fatty acid that imparts industrially important drying qualities to tung oil. Here, we describe the cloning and functional analysis of two closely related Delta(12) oleate desaturase-like enzymes that constitute consecutive steps in the biosynthetic pathway of eleostearic acid. Polymerase chain reaction screening of a tung seed cDNA library using degenerate oligonucleotide primers resulted in identification of two desaturases, FAD2 and FADX, that shared 73% amino acid identity. Both enzymes were localized to the endoplasmic reticulum of tobacco (Nicotiana tabacum cv Bright-Yellow 2) cells, and reverse transcriptase-polymerase chain reaction revealed that FADX was expressed exclusively within developing tung seeds. Expression of the cDNAs encoding these enzymes in yeast (Saccharomyces cerevisiae) revealed that FAD2 converted oleic acid (18:1delta(9cis)) into linoleic acid (18:2delta(9cis,12cis)) and that FADX converted linoleic acid into alpha-eleostearic acid. Additional characterization revealed that FADX exhibited remarkable enzymatic plasticity, capable of generating a variety of alternative conjugated and delta(12)-desaturated fatty acid products in yeast cells cultured in the presence of exogenously supplied fatty acid substrates. Unlike other desaturases reported to date, the double bond introduced by FADX during fatty acid desaturation was in the trans, rather than cis, configuration. Phylogenetic analysis revealed that tung FADX is grouped with delta(12) fatty acid desaturases and hydroxylases rather than conjugases, which is consistent with its desaturase activity. Comparison of FADX and other lipid-modifying enzymes (desaturase, hydroxylase, epoxygenase, acetylenase, and conjugase) revealed several amino acid positions near the active site that may be important determinants of enzymatic

  3. Dietary total fat and fatty acids intake, serum fatty acids and risk of breast cancer: A meta-analysis of prospective cohort studies.

    PubMed

    Cao, Yi; Hou, Lin; Wang, Weijing

    2016-04-15

    Results from prospective cohort studies on the association between dietary total fat and fatty acids intake and risk of breast cancer remain controversial. Pertinent prospective cohort studies were identified by a search of Embase and PubMed from inception to September 2015. Study-specific relative risks (RRs) with 95% confidence intervals were pooled using a random-effect model. Between-study heterogeneity and publication bias were assessed, and sensitivity analysis was conducted. Twenty-four independent studies on dietary total fat and fatty acids intake and seven studies on serum fatty acids were included. The pooled RR of breast cancer for the highest vs. lowest category of dietary total fat intake was 1.10 (1.02-1.19); however, no association was observed in studies adjusting for traditional risk factors of breast cancer. No association was observed between animal fat, vegetable fat, saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), n-3 PUFA, n-6 PUFA, eicosapentaenoic acid, docosahexaenoic acid, alpha-linolenic acid, oleic acid, linoleic acid and arachidonic acid and risk of breast cancer. The pooled RRs of breast cancer for the highest vs. lowest category of serum SFA, MUFA, PUFA, n-3 PUFA and n-6 PUFA were 1.00 (0.78-1.28), 1.41 (0.99-2.03), 0.59 (0.27-1.30), 0.81 (0.60-1.10) and 0.84 (0.60-1.18), respectively. Results from this meta-analysis suggested that dietary total fat and fatty acids might be not associated with risk of breast cancer.

  4. Efficient Fractionation and Analysis of Fatty Acids and their Salts in Fat, Oil and Grease (FOG) Deposits.

    PubMed

    Benecke, Herman P; Allen, Sara K; Garbark, Daniel B

    2017-02-01

    A fractionation methodology of fat, oil and grease (FOG) deposits was developed based on the insolubility of fatty acid salts in dichloromethane (DCM) and the relatively high solubility of fatty acids and triglycerides in DCM. Using this method, coupled with spectral analysis, it was shown that fatty acids rather than fatty acid salts were the predominant species in FOG deposits obtained from three metropolitan locations in the United States and that fatty acid triglycerides were either not detected or were present in very small concentrations. This solubility-based fractionation approach also revealed the presence of nitrogen-containing compounds that had not been previously detected in FOG deposits including peptides and (or) proteins. The comparison of the ratios of stearic acid salts to stearic acid versus the ratio of palmitic acid salts to palmitic acid in FOG deposits may indicate that the initial step in FOG deposit formation is the preferential precipitation of stearic acid salts.

  5. Biomechanical analysis of a new carbon fiber/flax/epoxy bone fracture plate shows less stress shielding compared to a standard clinical metal plate.

    PubMed

    Bagheri, Zahra S; Tavakkoli Avval, Pouria; Bougherara, Habiba; Aziz, Mina S R; Schemitsch, Emil H; Zdero, Radovan

    2014-09-01

    Femur fracture at the tip of a total hip replacement (THR), commonly known as Vancouver B1 fracture, is mainly treated using rigid metallic bone plates which may result in "stress shielding" leading to bone resorption and implant loosening. To minimize stress shielding, a new carbon fiber (CF)/Flax/Epoxy composite plate has been developed and biomechanically compared to a standard clinical metal plate. For fatigue tests, experiments were done using six artificial femurs cyclically loaded through the femoral head in axial compression for four stages: Stage 1 (intact), stage 2 (after THR insertion), stage 3 (after plate fixation of a simulated Vancouver B1 femoral midshaft fracture gap), and stage 4 (after fracture gap healing). For fracture fixation, one group was fitted with the new CF/Flax/Epoxy plate (n = 3), whereas another group was repaired with a standard clinical metal plate (Zimmer, Warsaw, IN) (n = 3). In addition to axial stiffness measurements, infrared thermography technique was used to capture the femur and plate surface stresses during the testing. Moreover, finite element analysis (FEA) was performed to evaluate the composite plate's axial stiffness and surface stress field. Experimental results showed that the CF/Flax/Epoxy plated femur had comparable axial stiffness (fractured = 645 ± 67 N/mm; healed = 1731 ± 109 N/mm) to the metal-plated femur (fractured = 658 ± 69 N/mm; healed = 1751 ± 39 N/mm) (p = 1.00). However, the bone beneath the CF/Flax/Epoxy plate was the only area that had a significantly higher average surface stress (fractured = 2.10 ± 0.66 MPa; healed = 1.89 ± 0.39 MPa) compared to bone beneath the metal plate (fractured = 1.18 ± 0.93 MPa; healed = 0.71 ± 0.24 MPa) (p < 0.05). FEA bone surface stresses yielded peak of 13 MPa at distal epiphysis (stage 1), 16 MPa at distal epiphysis (stage 2), 85 MPa for composite and 129

  6. Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

    PubMed

    Turan, Başak; Selçuki, Cenk

    2014-09-01

    Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

  7. Stretched View Showing 'Victoria'

    NASA Technical Reports Server (NTRS)

    2006-01-01

    [figure removed for brevity, see original site] Stretched View Showing 'Victoria'

    This pair of images from the panoramic camera on NASA's Mars Exploration Rover Opportunity served as initial confirmation that the two-year-old rover is within sight of 'Victoria Crater,' which it has been approaching for more than a year. Engineers on the rover team were unsure whether Opportunity would make it as far as Victoria, but scientists hoped for the chance to study such a large crater with their roving geologist. Victoria Crater is 800 meters (nearly half a mile) in diameter, about six times wider than 'Endurance Crater,' where Opportunity spent several months in 2004 examining rock layers affected by ancient water.

    When scientists using orbital data calculated that they should be able to detect Victoria's rim in rover images, they scrutinized frames taken in the direction of the crater by the panoramic camera. To positively characterize the subtle horizon profile of the crater and some of the features leading up to it, researchers created a vertically-stretched image (top) from a mosaic of regular frames from the panoramic camera (bottom), taken on Opportunity's 804th Martian day (April 29, 2006).

    The stretched image makes mild nearby dunes look like more threatening peaks, but that is only a result of the exaggerated vertical dimension. This vertical stretch technique was first applied to Viking Lander 2 panoramas by Philip Stooke, of the University of Western Ontario, Canada, to help locate the lander with respect to orbiter images. Vertically stretching the image allows features to be more readily identified by the Mars Exploration Rover science team.

    The bright white dot near the horizon to the right of center (barely visible without labeling or zoom-in) is thought to be a light-toned outcrop on the far wall of the crater, suggesting that the rover can see over the low rim of Victoria. In figure 1, the northeast and southeast rims are labeled

  8. An HPLC method with UV detection, pH control, and reductive ascorbic acid for cyanuric acid analysis in water.

    PubMed

    Cantú, R; Evans, O; Kawahara, F K; Shoemaker, J A; Dufour, A P

    2000-12-01

    Every year over 250 million pounds of cyanuric acid (CA) and chlorinated isocyanurates are produced industrially. These compounds are standard ingredients in formulations for household bleaches, industrial cleansers, dishwasher compounds, general sanitizers, and chlorine stabilizers. The method developed for CA using high-performance liquid chromatography (HPLC) with UV detection simplifies and optimizes certain parameters of previous methodologies by effective pH control of the eluent (95% phosphate buffer: 5% methanol, v/v) to the narrow pH range of 7.2-7.4. UV detection was set at the optimum wavelength of 213 nm where the cyanuric ion absorbs strongly. Analysis at the lower pH range of 6.8-7.1 proved inadequate due to CA keto-enol tautomerism, while at pHs of <6.8 there were substantial losses in analytical sensitivity. In contrast, pHs of >7.4 proved more sensitive but their use was rejected because of CA elution at the chromatographic void volume and due to chemical interferences. The complex equilibria of chlorinated isocyanurates and associated species were suppressed by using reductive ascorbic acid to restrict the products to CA. UV, HPLC-UV, and electrospray ionization mass spectrometry techniques were combined to monitor the reactive chlorinated isocyanurates and to support the use of ascorbic acid. The resulting method is reproducible and measures CA in the 0.5-125 mg/L linear concentration range with a method detection limit of 0.05 mg/L in water.

  9. Quick characterization of uronic acid-containing polysaccharides in 5 shellfishes by oligosaccharide analysis upon acid hydrolysis.

    PubMed

    Liu, Bin; Lu, Jiaojiao; Ai, Chunqing; Zhang, Bao; Guo, Li; Song, Shuang; Zhu, Beiwei

    2016-11-29

    Uronic acid-containing polysaccharides (UACPs) including well-known glycosaminoglycans (GAGs) and some non-GAGs exist widely in animal kingdom. Although numerous methods have been established to analyze GAGs, few methods are available for non-GAG UACPs. In the present study, a protocol to identify all kinds of UACPs with repeating disaccharide units of hexosamine and uronic acid was demonstrated, and UACP components in five shellfishes, namely Turritella fortilirata Sowerby (GTF), Batillaria zonalis (GBZ), Nassarius variciferus (GNV), Monodonta labio Linnaeus (GML), and Argopecten irradians Lamarck (BAI) were primarily revealed. After a simple isolation procedure, crude polysaccharides were depolymerized by controlled acid hydrolysis, and then the resulting oligosaccharides were detected by HPLC coupled with mass spectrometer after 1-phenyl-3-methyl-5-pyrazolone (PMP) labeling. According to chromatograms using the triple quadrupole mass spectrometer in the multiple reaction monitoring (MRM) mode, chondroitin sulfate (CS) was found in GNV and GML, a non-GAG named abalone gonad sulfated polysaccharide (AGSP) with a backbone of →4)-β-GlcA-(1 → 2)-α-Man-(1→ repeating units in GBZ, and both of AGSP and CS in BAI and GTF. Further characterization of tetrasaccharides and sulfated/acetylated disaccharides by HPLC combined with an ion trap mass spectrometer confirmed the structural identification of CS and AGSP, and indicated CS in GTF and BAI was Type C. These results suggest the 5 mollusks as potential resources for CS and AGSP. And the analysis protocol presented in this study was powerful and effective for quick characterization of UACPs including GAGs as well as non-GAGs in complicated matrix.

  10. Valproic Acid Downregulates RBP4 and Elicits Hypervitaminosis A-Teratogenesis—A Kinetic Analysis on Retinol/Retinoic Acid Homeostatic System

    PubMed Central

    Chuang, Chao-Ming; Chang, Chi-Huang; Wang, Hui-Er; Chen, Kuan-Chou; Peng, Chiung-Chi; Hsieh, Chiu-Lan; Peng, Robert Y.

    2012-01-01

    Background Valproic acid (VPA) is an antiepileptic and anti-migraine prophylactic drug. VPA exhibits two severe side effects, namely acute liver toxicity and teratogenicity. These side effects are usually seen at the genetic and somatic levels. The cited action mechanisms involve inhibition of histone deacetylase, hypofolatenemia, hyperhomocysteinemia, and reactive oxidative stress. The proteomic information associated with VPA teratogenicity is still unavailable. We hypothesized that proteomic analysis might help us identify functional proteins that could be relevantly affected by VPA, and this phenomenon could be very sensitive in early embryonic stage, resulting in VPA teratogenicity. Methodology/Principal Findings Proteomic analysis on the chicken embryos at Hamburger and Hamilton (HH) stage 28 showed that there were significant downregulations of ovotransferrins, carbonic anhydrase-2, retinol binding protein-4 (RBP4), NADH cytochrome b5 reductase 2 (CYB5R2), apolipoprotein A1, and protein SET, together with upregulation of 60S ribosomal protein L22. Among these, RBP4 was the most significantly downregulated (−32%). Kinetic analysis suggested that this situation could trigger hypervitaminosis A (+39.3%), a condition that has been well known to induce teratogenesis.. Conclusions/Significance This is the first report showing that VPA dowregulates RBP4. Our finding not only has led to a possible mechanism of VPA teratogenesis, but also has initiated new preventive strategies for avoiding VPA teratogeneis. PMID:23028466

  11. Method for the isolation of citric acid and malic acid in Japanese apricot liqueur for carbon stable isotope analysis.

    PubMed

    Akamatsu, Fumikazu; Hashiguchi, Tomokazu; Hisatsune, Yuri; Oe, Takaaki; Kawao, Takafumi; Fujii, Tsutomu

    2017-02-15

    A method for detecting the undeclared addition of acidic ingredients is required to control the authenticity of Japanese apricot liqueur. We developed an analytical procedure that minimizes carbon isotope discrimination for measurement of the δ(13)C values of citric and malic acid isolated from Japanese apricot liqueur. Our results demonstrated that freeze-drying is preferable to nitrogen spray-drying, because it does not significantly affect the δ(13)C values of citric acid and results in smaller isotope discrimination for malic acid. Both 0.1% formic acid and 0.2% phosphoric acid are acceptable HPLC mobile phases for the isolation of citric and malic acid, although the δ(13)C values of malic acid exhibited relatively large variation compared with citric acid following isolation using either mobile phase. The developed procedure allows precise δ(13)C measurements of citric and malic acid isolated from Japanese apricot liqueur.

  12. Analysis of perfluorinated phosponic acids and perfluorooctane sulfonic acid in water, sludge and sediment by LC-MS/MS.

    PubMed

    Esparza, X; Moyano, E; de Boer, J; Galceran, M T; van Leeuwen, S P J

    2011-10-30

    Residues of perfluorinated phosphonic acids (PFPAs) and perfluorooctane sulfonic acid (PFOS) were investigated in various Dutch surface waters, sludge and sediments. For this purpose, a liquid chromatographic (LC) method was optimized by testing several columns with different mobile phases. Atmospheric pressure chemical ionization (APCI) was chosen for the LC tandem mass spectrometry (MS/MS) analysis. An ion-pair reagent was added to the injection solvent to improve peak shape. Different solvents were studied for the extraction from solid samples. For clean-up and pre-concentration, weak anion-exchange solid-phase extraction cartridges were used. Water samples were extracted using the same cartridges. The method was used for screening PFPAs in the Dutch aquatic environment. PFPAs were not observed in sediment or sludge samples. PFOPA was found at 1 ng L(-1) in one surface water sample. PFOS was found at levels between 0.07 ng g(-1) and 48 ng g(-1) (dry weight) in sediments and sewage sludge samples. PFOS concentrations in surface water ranged from 3.3 ng L(-1) to 25.4 ng L(-1).

  13. Analysis of cloned cDNA and genomic sequences for phytochrome: complete amino acid sequences for two gene products expressed in etiolated Avena.

    PubMed Central

    Hershey, H P; Barker, R F; Idler, K B; Lissemore, J L; Quail, P H

    1985-01-01

    Cloned cDNA and genomic sequences have been analyzed to deduce the amino acid sequence of phytochrome from etiolated Avena. Restriction endonuclease site polymorphism between clones indicates that at least four phytochrome genes are expressed in this tissue. Sequence analysis of two complete and one partial coding region shows approximately 98% homology at both the nucleotide and amino acid levels, with the majority of amino acid changes being conservative. High sequence homology is also found in the 5'-untranslated region but significant divergence occurs in the 3'-untranslated region. The phytochrome polypeptides are 1128 amino acid residues long corresponding to a molecular mass of 125 kdaltons. The known protein sequence at the chromophore attachment site occurs only once in the polypeptide, establishing that phytochrome has a single chromophore per monomer covalently linked to Cys-321. Computer analyses of the amino acid sequences have provided predictions regarding a number of structural features of the phytochrome molecule. PMID:3001642

  14. Multiplexed analysis of genes using nucleic acid-stabilized silver-nanocluster quantum dots.

    PubMed

    Enkin, Natalie; Wang, Fuan; Sharon, Etery; Albada, H Bauke; Willner, Itamar

    2014-11-25

    Luminescent nucleic acid-stabilized Ag nanoclusters (Ag NCs) are applied for the optical detection of DNA and for the multiplexed analysis of genes. Two different sensing modules including Ag NCs as luminescence labels are described. One sensing module involves the assembly of a three-component sensing module composed of a nucleic acid-stabilized Ag NC and a quencher-modified nucleic acid hybridized with a nucleic acid scaffold that is complementary to the target DNA. The luminescence of the Ag NCs is quenched in the sensing module nanostructure. The strand displacement of the scaffold by the target DNA separates the nucleic acid-functionalized Ag NCs, leading to the turned-on luminescence of the NCs and to the optical readout of the sensing process. By implementing two different-sized Ag NC-modified sensing modules, the parallel multiplexed analysis of two genes (the Werner Syndrome gene and the HIV, human immunodeficiency, gene), using 615 and 560 nm luminescent Ag NCs, is demonstrated. The second sensing module includes the nucleic acid functionalized Ag NCs and the quencher-modified nucleic acid hybridized with a hairpin DNA scaffold. The luminescence of the Ag NCs is quenched in the sensing module. Opening of the hairpin by the target DNA triggers the luminescence of the Ag NCs, due to the spatial separation of the Ag NCs/quencher units. The system is applied for the optical detection of the BRAC1 gene. In addition, by implementing two-sized Ag NCs, the multiplexed analysis of two genes by the hairpin sensing module approach is demonstrated.

  15. Restriction enzyme analysis of ribosomal DNA shows that Candida inconspicua clinical isolates can be misidentified as Candida norvegensis with traditional diagnostic procedures.

    PubMed

    Majoros, L; Kardos, G; Belák, A; Maráz, A; Asztalos, L; Csánky, E; Barta, Z; Szabó, B

    2003-11-01

    We identified 29 yeast isolates from 22 patients using the API ID32C panel. Twenty-eight of these isolates were Candida norvegensis and one was C. inconspicua. Although C. norvegensis is considered a pseudohypha-producing species, only one isolate produced pseudohyphae. Restriction enzyme analysis of PCR-amplified ribosomal DNA with four different enzymes proved that all isolates were C. inconspicua.

  16. Chemometric analysis of the interactions among different parameters describing health conditions, breast cancer risk and fatty acids profile in serum of rats supplemented with conjugated linoleic acids.

    PubMed

    Białek, Agnieszka; Zagrodzki, Paweł; Tokarz, Andrzej

    2016-03-01

    We investigated how different doses of conjugated linoleic acids applied for various periods of time influence breast cancer risk and fatty acids profile in serum of rats treated or not with 7,12-dimethylbenz[a]anthracene (DMBA). We also search for interactions among parameters describing health conditions and cancer risk. Animals were divided into 18 groups with different diet modifications (vegetable oil, 1.0%, 2.0% additions of CLA) and different periods of supplementation. In groups treated with DMBA mammary adenocarcinomas appeared. Due to the complexity of experiment apart from statistical analysis a chemometric tool-Partial Least Square method was applied. Analysis of pairs of correlated parameters allowed to identify some regularities concerning the relationships between fatty acid profiles and clinical features of animals. Fatty acids profile was the result of prolonged exposure to high dose of CLA and DMBA administration. These two factors underlined the differences in fatty acids profiles among clusters of animals.

  17. Immunochemical analysis of 3-phenoxybenzoic acid, a biomarker of forestry worker exposure to pyrethroid insecticides.

    PubMed

    Ahn, Ki Chang; Gee, Shirley J; Kim, Hee-Joo; Aronov, Pavel A; Vega, Helen; Krieger, Robert I; Hammock, Bruce D

    2011-09-01

    Pyrethroid insecticides widely used in forestry, agricultural, industrial, and residential applications have potential for human exposure. Short sample preparation time and sensitive, economical high-throughput assays are needed for biomonitoring studies that analyze a large number of samples. An enzyme-linked immunosorbent assay (ELISA) was used for determining 3-phenoxybenzoic acid (3-PBA), a general urinary biomarker of exposure to some pyrethroid insecticides. A mixed-mode solid-phase extraction reduced interferences from acid hydrolyzed urine and gave 110 ± 6% recoveries from spiked samples. The method limit of quantification was 2 μg/L. Urine samples were collected from forestry workers that harvest pine cone seeds where pyrethroid insecticides were applied at ten different orchards. At least four samples for each worker were collected in a 1-week period. The 3-PBA in workers classified as high, low, or no exposure based on job analysis over all sampling days was 6.40 ± 9.60 (n = 200), 5.27 ± 5.39 (n = 52), and 3.56 ± 2.64 ng/mL (n = 34), respectively. Pair-wise comparison of the differences in least squares means of 3-PBA concentrations among groups only showed a significant difference between high and no exposure. Although this difference was not significant when 3-PBA excretion was normalized by creatinine excretion, the general trend was still apparent. No significant differences were observed among days or orchards. This ELISA method using a 96-well plate was performed as a high-throughput tool for analyzing around 300 urine samples measured in triplicate to provide data for workers exposure assessment.

  18. Immunochemical analysis of 3-phenoxybenzoic acid, a biomarker of forestry worker exposure to pyrethroid insecticides

    PubMed Central

    Ahn, Ki Chang; Gee, Shirley J.; Kim, Hee-Joo; Aronov, Pavel A.; Vega, Helen; Krieger, Robert I.

    2013-01-01

    Pyrethroid insecticides widely used in forestry, agricultural, industrial, and residential applications have potential for human exposure. Short sample preparation time and sensitive, economical high-throughput assays are needed for biomonitoring studies that analyze a large number of samples. An enzyme-linked immunosorbent assay (ELISA) was used for determining 3-phenoxybenzoic acid (3-PBA), a general urinary biomarker of exposure to some pyrethroid insecticides. A mixed-mode solid-phase extraction reduced interferences from acid hydrolyzed urine and gave 110±6% recoveries from spiked samples. The method limit of quantification was 2 μg/L. Urine samples were collected from forestry workers that harvest pine cone seeds where pyrethroid insecticides were applied at ten different orchards. At least four samples for each worker were collected in a 1-week period. The 3-PBA in workers classified as high, low, or no exposure based on job analysis over all sampling days was 6.40± 9.60 (n=200), 5.27±5.39 (n=52), and 3.56±2.64 ng/mL (n=34), respectively. Pair-wise comparison of the differences in least squares means of 3-PBA concentrations among groups only showed a significant difference between high and no exposure. Although this difference was not significant when 3-PBA excretion was normalized by creatinine excretion, the general trend was still apparent. No significant differences were observed among days or orchards. This ELISA method using a 96-well plate was performed as a high-throughput tool for analyzing around 300 urine samples measured in triplicate to provide data for workers exposure assessment. PMID:21717113

  19. Phylogenetic analysis of beta-papillomaviruses as inferred from nucleotide and amino acid sequence data.

    PubMed

    Gottschling, Marc; Köhler, Anja; Stockfleth, Eggert; Nindl, Ingo

    2007-01-01

    Human papillomaviruses (HPV) of the beta-group seem to be involved in the pathogenesis of non-melanoma skin cancer. Papillomaviruses are host specific and are considered closely co-evolving with their hosts. Evolutionary incongruence between early genes and late genes has been reported among oncogenic genital alpha-papillomaviruses and considerably challenge phylogenetic reconstructions. We investigated the relationships of 29 beta-HPV (25 types plus four putative new types, subtypes, or variants) as inferred from codon aligned and amino acid sequence data of the genes E1, E2, E6, E7, L1, and L2 using likelihood, distance, and parsimony approaches. An analysis of a L1 fragment included additional nucleotide and amino acid sequences from seven non-human beta-papillomaviruses. Early genes and late genes evolution did not conflict significantly in beta-papillomaviruses based on partition homogeneity tests (p > or = 0.001). As inferred from the complete genome analyses, beta-papillomaviruses were monophyletic and segregated into four highly supported monophyletic assemblages corresponding to the species 1, 2, 3, and fused 4/5. They basically split into the species 1 and the remainder of beta-papillomaviruses, whose species 3, 4, and 5 constituted the sistergroup of species 2. beta-Papillomaviruses have been isolated from humans, apes, and monkeys, and phylogenetic analyses of the L1 fragment showed non-human papillomaviruses highly polyphyletic nesting within the HPV species. Thus, host and virus phylogenies were not congruent in beta-papillomaviruses, and multiple invasions across species borders may contribute (additionally to host-linked evolution) to their diversification.

  20. Potential of the compound specific isotope analysis of individual amino acid for studying past nitrogen cycle

    NASA Astrophysics Data System (ADS)

    Choi, Bohyung; Shin, Kyung-Hoon

    2016-04-01

    The nitrogen isotope ratio of bulk sediment has been widely used for studying nitrogen cycle in the marine environment. However, since organic nitrogen in sediment is regarded as a mixture of organic matter, it is challenging to identify its exact sources. Recently, compound specific nitrogen isotope analysis of amino acid (CSIA AAs) has been introduced as a potential tool for complement of bulk nitrogen isotope since amino acid more directly reflects information on primary producer and trophic position. However, studies on CSIA of amino acid in sediments are scarce due to the complexities of the analytical method and relatively high analytica costl. In this study, we established a method of the CSIA AAs which is more suitable for the analysis of sediments and accessed if the CSIA AAs can be used for the study of past nitrogen cycle.

  1. Classification of illicit heroin by UPLC-Q-TOF analysis of acidic and neutral manufacturing impurities.

    PubMed

    Liu, Cuimei; Hua, Zhendong; Bai, Yanping

    2015-12-01

    The illicit manufacture of heroin results in the formation of trace levels of acidic and neutral manufacturing impurities that provide valuable information about the manufacturing process used. In this work, a new ultra performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC-Q-TOF) method; that features high resolution, mass accuracy and sensitivity for profiling neutral and acidic heroin manufacturing impurities was developed. After the UPLC-Q-TOF analysis, the retention times and m/z data pairs of acidic and neutral manufacturing impurities were detected, and 19 peaks were found to be evidently different between heroin samples from "Golden Triangle" and "Golden Crescent". Based on the data set of these 19 impurities in 150 authentic heroin samples, classification of heroin geographic origins was successfully achieved utilizing partial least squares discriminant analysis (PLS-DA). By analyzing another data set of 267 authentic heroin samples, the developed discrimiant model was validated and proved to be accurate and reliable.

  2. Lab-on-a-chip nucleic-acid analysis towards point-of-care applications

    NASA Astrophysics Data System (ADS)

    Kopparthy, Varun Lingaiah

    Recent infectious disease outbreaks, such as Ebola in 2013, highlight the need for fast and accurate diagnostic tools to combat the global spread of the disease. Detection and identification of the disease-causing viruses and bacteria at the genetic level is required for accurate diagnosis of the disease. Nucleic acid analysis systems have shown promise in identifying diseases such as HIV, anthrax, and Ebola in the past. Conventional nucleic acid analysis systems are still time consuming, and are not suitable for point-ofcare applications. Miniaturized nucleic acid systems has shown great promise for rapid analysis, but they have not been commercialized due to several factors such as footprint, complexity, portability, and power consumption. This dissertation presents the development of technologies and methods for a labon-a-chip nucleic acid analysis towards point-of-care applications. An oscillatory-flow PCR methodology in a thermal gradient is developed which provides real-time analysis of nucleic-acid samples. Oscillating flow PCR was performed in the microfluidic device under thermal gradient in 40 minutes. Reverse transcription PCR (RT-PCR) was achieved in the system without an additional heating element for incubation to perform reverse transcription step. A novel method is developed for the simultaneous pattering and bonding of all-glass microfluidic devices in a microwave oven. Glass microfluidic devices were fabricated in less than 4 minutes. Towards an integrated system for the detection of amplified products, a thermal sensing method is studied for the optimization of the sensor output. Calorimetric sensing method is characterized to identify design considerations and optimal parameters such as placement of the sensor, steady state response, and flow velocity for improved performance. An understanding of these developed technologies and methods will facilitate the development of lab-on-a-chip systems for point-of-care analysis.

  3. The mRNA expression of amino acid transporters, aminopeptidase N, and the di- and tri- peptide transporter PepT1 in the embryo of the domesticated chicken (Gallus gallus) shows developmental regulation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mRNA expression profile for ten amino acid transporters (AAT), the di-and tri- peptide transporter (Pept1), and aminopeptidase N (APN) during chick embryogenesis was determined. Fertilized eggs were sampled at days 9, 11, 15, 17, 19, and 20, post fertilization. Three to four embryos were sampl...

  4. Serum Uric Acid Levels in Patients with Alzheimer's Disease: A Meta-Analysis

    PubMed Central

    Chen, Xueping; Guo, Xiaoyan; Huang, Rui; Chen, Yongping; Zheng, Zhenzhen; Shang, Huifang

    2014-01-01

    Background Serum uric acid (UA) could exert neuro-protective effects against Alzheimer's disease (AD) via its antioxidant capacities. Many studies investigated serum UA levels in AD patients, but to date, results from these observational studies are conflicting. Methods We conducted a meta-analysis to compare serum UA levels between AD patients and healthy controls by the random-effects model. Studies were identified by searching PubMed, ISI Web of Science, EMBASE, and the Cochrane library databases from 1966 through July 2013 using the Medical Subject Headings and keywords without restriction in languages. Only case-control studies were included if they had data on serum UA levels in AD patients and healthy controls. Begg's funnel plot and Egger's regression test were applied to assess the potential publication bias. Sensitivity analyses and meta-regression were conducted to explore possible explanations for heterogeneity. Results A total of 11 studies met the inclusion criteria including 2708 participants were abstracted. Serum UA levels were not significantly different in AD patients compared to healthy controls (standardized mean difference (SMD) = −0.50; 95% confidence interval (CI): −1.23 to 0.22). Little evidence of publication bias was observed. Sensitivity analyses showed that the combined SMD was consistent every time omitting any one study, except only one study which greatly influenced the overall results. Meta-regression showed that year of publication, race, sample size, and mean age were not significant sources of heterogeneity. Conclusion Our meta-analysis of case-control studies suggests that serum UA levels do not differ significantly in AD patients, but there may be a trend toward decreased UA in AD after an appropriate interpretation. More well-designed investigations are needed to demonstrate the potential change of serum UA levels in AD patients. PMID:24714617

  5. Poly(lactic-co-glycolic acid) conduit for repair of injured sciatic nerve: A mechanical analysis

    PubMed Central

    Yu, Tao; Zhao, Changfu; Li, Peng; Liu, Guangyao; Luo, Min

    2013-01-01

    Tensile stress and tensile strain directly affect the quality of nerve regeneration after bridging nerve defects by poly(lactic-co-glycolic acid) conduit transplantation and autogenous nerve grafting for sciatic nerve injury. This study collected the sciatic nerve from the gluteus maximus muscle from fresh human cadaver, and established 10-mm-long sciatic nerve injury models by removing the ischium, following which poly(lactic-co-glycolic acid) conduits or autogenous nerve grafts were transplanted. Scanning electron microscopy revealed that the axon and myelin sheath were torn, and the vessels of basilar membrane were obstructed in the poly(lactic-co-glycolic acid) conduit-repaired sciatic nerve following tensile testing. There were no significant differences in tensile tests with autogenous nerve graft-repaired sciatic nerve. Following poly(lactic-co-glycolic acid) conduit transplantation for sciatic nerve repair, tensile test results suggest that maximum tensile load, maximum stress, elastic limit load and elastic limit stress increased compared with autogenous nerve grafts, but elastic limit strain and maximum strain decreased. Moreover, the tendencies of stress-strain curves of sciatic nerves were similar after transplantation of poly(lactic-co-glycolic acid) conduits or autogenous nerve grafts. Results showed that after transplantation in vitro for sciatic nerve injury, poly(lactic-co-glycolic acid) conduits exhibited good intensity, elasticity and plasticity, indicating that poly(lactic-co-glycolic acid) conduits are suitable for sciatic nerve injury repair. PMID:25206505

  6. Poly(lactic-co-glycolic acid) conduit for repair of injured sciatic nerve: A mechanical analysis.

    PubMed

    Yu, Tao; Zhao, Changfu; Li, Peng; Liu, Guangyao; Luo, Min

    2013-07-25

    Tensile stress and tensile strain directly affect the quality of nerve regeneration after bridging nerve defects by poly(lactic-co-glycolic acid) conduit transplantation and autogenous nerve grafting for sciatic nerve injury. This study collected the sciatic nerve from the gluteus maximus muscle from fresh human cadaver, and established 10-mm-long sciatic nerve injury models by removing the ischium, following which poly(lactic-co-glycolic acid) conduits or autogenous nerve grafts were transplanted. Scanning electron microscopy revealed that the axon and myelin sheath were torn, and the vessels of basilar membrane were obstructed in the poly(lactic-co-glycolic acid) conduit-repaired sciatic nerve following tensile testing. There were no significant differences in tensile tests with autogenous nerve graft-repaired sciatic nerve. Following poly(lactic-co-glycolic acid) conduit transplantation for sciatic nerve repair, tensile test results suggest that maximum tensile load, maximum stress, elastic limit load and elastic limit stress increased compared with autogenous nerve grafts, but elastic limit strain and maximum strain decreased. Moreover, the tendencies of stress-strain curves of sciatic nerves were similar after transplantation of poly(lactic-co-glycolic acid) conduits or autogenous nerve grafts. Results showed that after transplantation in vitro for sciatic nerve injury, poly(lactic-co-glycolic acid) conduits exhibited good intensity, elasticity and plasticity, indicating that poly(lactic-co-glycolic acid) conduits are suitable for sciatic nerve injury repair.

  7. Analysis and Identification of Acid-Base Indicator Dyes by Thin-Layer Chromatography

    ERIC Educational Resources Information Center

    Clark, Daniel D.

    2007-01-01

    Thin-layer chromatography (TLC) is a very simple and effective technique that is used by chemists by different purposes, including the monitoring of the progress of a reaction. TLC can also be easily used for the analysis and identification of various acid-base indicator dyes.

  8. Genome-Wide Analysis of Branched-Chain Amino Acid Levels in Arabidopsis Seeds[W

    PubMed Central

    Angelovici, Ruthie; Lipka, Alexander E.; Deason, Nicholas; Gonzalez-Jorge, Sabrina; Lin, Haining; Cepela, Jason; Buell, Robin; Gore, Michael A.; DellaPenna, Dean

    2013-01-01

    Branched-chain amino acids (BCAAs) are three of the nine essential amino acids in human and animal diets and are important for numerous processes in development and growth. However, seed BCAA levels in major crops are insufficient to meet dietary requirements, making genetic improvement for increased and balanced seed BCAAs an important nutritional target. Addressing this issue requires a better understanding of the genetics underlying seed BCAA content and composition. Here, a genome-wide association study and haplotype analysis for seed BCAA traits in Arabidopsis thaliana revealed a strong association with a chromosomal interval containing two BRANCHED-CHAIN AMINO ACID TRANSFERASES, BCAT1 and BCAT2. Linkage analysis, reverse genetic approaches, and molecular complementation analysis demonstrated that allelic variation at BCAT2 is responsible for the natural variation of seed BCAAs in this interval. Complementation analysis of a bcat2 null mutant with two significantly different alleles from accessions Bayreuth-0 and Shahdara is consistent with BCAT2 contributing to natural variation in BCAA levels, glutamate recycling, and free amino acid homeostasis in seeds in an allele-dependent manner. The seed-specific phenotype of bcat2 null alleles, its strong transcription induction during late seed development, and its subcellular localization to the mitochondria are consistent with a unique, catabolic role for BCAT2 in BCAA metabolism in seeds. PMID:24368787

  9. Cellular fatty acid analysis as a potential tool for predicting mosquitocidal activity of Bacillus sphaericus strains.

    PubMed Central

    Frachon, E; Hamon, S; Nicolas, L; de Barjac, H

    1991-01-01

    Gas-liquid chromatography of fatty acid methyl esters and numerical analysis were carried out with 114 Bacillus sphaericus strains. Since only two clusters harbored mosquitocidal strains, this technique could be developed in screening programs to limit bioassays on mosquito larvae. It also allows differentiation of highly homologous strains. PMID:1781697

  10. A Multicomponent UV Analysis of ["alpha"]- and ["beta"]-Acids in Hops

    ERIC Educational Resources Information Center

    Egts, Haley; Durben, Dan J.; Dixson, John A.; Zehfus, Micheal H.

    2012-01-01

    A method is presented for the determination of ["alpha"]- and ["beta"]-acids (humulones and lupulones) in a hops sample using a multicomponent UV spectroscopic analysis of a methanolic hop extract. When compared with standard methods, this lab can be considered "greener" because it uses smaller volumes of safer solvents (methanol instead of…

  11. Grazing food web view from compound-specific stable isotope analysis of amino acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowledge of the trophic position (TP) of organisms in food webs allows ecologists to track energy flow and trophic linkages among organisms in complex networks of ecosystems. Compound-specific stable isotope analysis (CSIA) of amino acids has been employed as a relatively new method with the high p...

  12. [Analysis of cis-9, trans-11-conjugated linoleic acid in milk fat by capillary gas chromatography].

    PubMed

    Wang, Xiaojing; Shen, Xiangzhen; Han, Hangru; Zhao, Ruqian; Chen, Jie

    2006-11-01

    Conjugated linoleic acid (CLA) is a term representing a mixture of positional and geometric isomers of octadecadienoic acid with a conjugated double bond system. Conjugated linoleic acid has attracted a great deal of interest among nutritionists because it is a natural fat component that appears to have a number of health improvement properties. The cis-9, trans-11-CLA is the major CLA isomer found in dairy products accounting for 75% to 90% of the total CLA in milk fat. A capillary gas chromatographic method equipped with a flame ionization detector for the analysis of the cis-9, trans-11-CLA in milk fat was developed. The cis-9, trans-11-CLA was extracted with hexane-isopropanol, methylated with methanol-sodium methylate and cis-9, trans-11-CLA was separated and quantified using gas chromatography. Retention time of the peaks was used for qualitative analysis, while external standard method was used for quantitative analysis. The recovery of the cis-9, trans-11-CLA was 100.26%. The relative standard deviation was 1.9% (n = 6). This method presented is advantageous for high precision, high sensitivity analysis with smaller sample size and simpler pretreatment. It would be of significance for analyzing the contents of other fatty acids in the milk and milk products.

  13. Computer programs for analysis of nucleic acid hybridization, thermal denaturation, and gel electrophoresis data.

    PubMed Central

    Murphy, R F; Pearson, W R; Bonner, J

    1979-01-01

    Computer programs for the analysis of data from techniques frequently used in nucleic acids research are described. In addition to calculating non-linear, least-squares solutions to equations describing these systems, the programs allow for data editing, normalization, plotting and storage, and are flexible and simple to use. Typical applications of the programs are described. PMID:493129

  14. Concurrent and supercritical fluid chromatographic analysis of Terpene Lactones and ginkolic acids in Ginko biloba

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Supercritical fluid chromatography was used to resolve and determine ginkgolic acids (GAs) and terpene lactones concurrently in ginkgo plant materials and commercial dietary supplements. Analysis of GAs (C13:0, C15:0, C15:1 and C17:1) was carried out by ESI (-) mass detection. The ESI (-) spectra of...

  15. A comparative analysis of fatty acid composition of root and shoot lipids in Zea mays under copper and cadmium stress.

    PubMed

    Chaffai, R; Seybou, T N; Marzouk, B; El Ferjani, E

    2009-03-01

    A comparative analysis of fatty acid composition was conducted in maize (Zea mays L.) under copper and cadmium stress. The unsaturation level (double-bond index) of phosphatidylethanolamine (PE) and digalactosyldiacylglycerol (DGDG) was increased in response to both metal treatments, whereas the phosphatidylinositol (PI), the phosphatidylcholine (PC) showed no significant changes. The Cu-treated roots showed a marked increase (about 2-fold) in the phospholipid (PL) content, while the Cd-treated roots showed a slight but insignificant increase. The steryl lipid SL/PL ratio was markedly decreased in response to Cu stress, and therefore, may indicate an activated phospholipid biosynthesis and turnover, in response to damage caused by Cu stress. The double bond indices of chloroplastic lipids: phosphatidylglycerol (PG), monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG) and sulfoquinovosyldiacylglycerol (SQDG) revealed a similar but not identical pattern of change. The PG and MGDG contents in shoots were markedly decreased under Cu (by 53 and 48%) and Cd (by 78 and 65%) stress. The increase in the malondialdehyde (MDA) content in roots induced by both metals indicates lipid peroxidation. Generally, in the presence of Cu fatty acid composition was markedly modulated but to lesser extent under Cd stress. These results suggest that changes in the fatty acid composition under Cu and Cd stress conditions are metal-specific and may therefore result in differential metal tolerance.

  16. Single-Cell Analysis and Next-Generation Immuno-Sequencing Show That Multiple Clones Persist in Patients with Chronic Lymphocytic Leukemia.

    PubMed

    Kriangkum, Jitra; Motz, Sarah N; Mack, Tanner; Beiggi, Sara; Baigorri, Eva; Kuppusamy, Hemalatha; Belch, Andrew R; Johnston, James B; Pilarski, Linda M

    2015-01-01

    The immunoglobulin heavy chain (IGH) gene rearrangement in chronic lymphocytic leukemia (CLL) provides a unique molecular signature; however, we demonstrate that 26/198 CLL patients (13%) had more than one IGH rearrangement, indicating the power of molecular technology over phenotypic analysis. Single-cell PCR analysis and next-generation immuno-sequencing identified IGH-defined clones. In 23% (18/79) of cases whose clones carried unmutated immunoglobulin heavy chain variable (IGHV) genes (U-CLL), IGH rearrangements were bialleic with one productive (P) and one non-productive (NP) allele. Two U-CLL were biclonal, each clone being monoallelic (P). In 119 IGHV-mutated (M-CLL) cases, one had biallelic rearrangements in their CLL (P/NP) and five had 2-4 distinct clones. Allelic exclusion was maintained in all B-clones analyzed. Based on single-cell PCR analysis, 5/11 partner clones (45%) reached levels of >5x10(9) cells/L, suggesting second CLL clones. Partner clones persisted over years. Conventional IGH characterization and next-generation sequencing of 13 CLL, 3 multiple myeloma, 2 Waldenstrom's macroglobulinemia and 3 age-matched healthy donors consistently identified the same rearranged IGH sequences. Most multiple clones occurred in M-CLL, perhaps indicative of weak clonal dominance, thereby associating with a good prognosis. In contrast, biallelic CLL occurred primarily in U-CLL thus being associated with poor prognosis. Extending beyond intra-clonal diversity, molecular analysis of clonal evolution and apparent subclones in CLL may also reflect inter-clonal diversity.

  17. Restriction Enzyme Analysis of Ribosomal DNA Shows that Candida inconspicua Clinical Isolates Can Be Misidentified as Candida norvegensis with Traditional Diagnostic Procedures

    PubMed Central

    Majoros, L.; Kardos, G.; Belák, Á.; Maráz, A.; Asztalos, L.; Csánky, E.; Barta, Z.; Szabó, B.

    2003-01-01

    We identified 29 yeast isolates from 22 patients using the API ID32C panel. Twenty-eight of these isolates were Candida norvegensis and one was C. inconspicua. Although C. norvegensis is considered a pseudohypha-producing species, only one isolate produced pseudohyphae. Restriction enzyme analysis of PCR-amplified ribosomal DNA with four different enzymes proved that all isolates were C. inconspicua. PMID:14605175

  18. Fast simultaneous analysis of caffeine, trigonelline, nicotinic acid and sucrose in coffee by liquid chromatography-mass spectrometry.

    PubMed

    Perrone, Daniel; Donangelo, Carmen Marino; Farah, Adriana

    2008-10-15

    A rapid liquid chromatography-mass spectrometry method for the simultaneous quantification of caffeine, trigonelline, nicotinic acid and sucrose in coffee was developed and validated. The method involved extraction with hot water, clarification with basic lead acetate and membrane filtration, followed by chromatographic separation using a Spherisorb(®) S5 ODS2, 5μm chromatographic column and gradient elution with 0.3% aqueous formic acid/methanol at a flow rate of 0.2mL/min. The electrospray ionization source was operated in the negative mode to generate sucrose ions and in the positive mode to generate caffeine, trigonelline and nicotinic acid ions. Ionization suppression of all analytes was found due to matrix effect. Calibrations curves prepared in green and roasted coffee extracts were linear with r(2)>0.999. Roasted coffee was spiked and recoveries ranged from 93.0% to 105.1% for caffeine, from 85.2% to 116.2% for trigonelline, from 89.6% to 113.5% for nicotinic acid and from 94.1% to 109.7% for sucrose. Good repeatibilities (RSD<5%) were found for all analytes in the matrix. The limit of detection (LOD), calculated on the basis of signal-to-noise ratios of 3:1, was 11.9, 36.4, 18.5 and 5.0ng/mL for caffeine, trigonelline, nicotinic acid and sucrose, respectively. Analysis of 11 coffee samples (regular or decaffeinated green, ground roasted and instant) gave results in agreement with the literature. The method showed to be suitable for different types of coffee available in the market thus appearing as a fast and reliable alternative method to be used for routine coffee analysis.

  19. Waardenburg syndrome (WS): the analysis of a single family with a WS1 mutation showing linkage to RFLP markers on human chromosome 2q.

    PubMed Central

    Asher, J H; Morell, R; Friedman, T B

    1991-01-01

    Waardenburg syndrome type I (WS1; MIM 19350) is caused by a pleiotropic, autosomal dominant mutation with variable penetrance and expressivity. Of individuals with this mutation, 20%-25% are hearing impaired. A multilocus linkage analysis of RFLP data from a single WS1 family with 11 affected individuals indicates that the WS1 mutation in this family is linked to the following four marker loci located on the long arm of chromosome 2: ALPP (alkaline phosphatase, placental), FN1 (fibronectin 1), D2S3 (a unique-copy DNA segment), and COL6A3 (collagen VI, alpha 3). For the RFLP marker loci, a multilocus linkage analysis using MLINK produced a peak lod (Z) of 3.23 for the following linkage relationships and recombination fractions (theta i): (ALPP----.000----FN1)----.122----D2S3----.267----CO L6A3. A similar analysis produced a Z of 6.67 for the following linkage relationships and theta i values among the markers and WS1: (FN1----.000----WS1----.000----ALPP)----.123----D2S 3----.246----COL6A3. The data confirm the conclusion of Foy et al. that at least some WS1 mutations map to chromosome 2q. Images Figure 2 PMID:1670751

  20. Australian Acid Playa Lake as a Mars Analog: Results from Sediment Lipid Analysis

    NASA Astrophysics Data System (ADS)

    Graham, H.; Baldridge, A. M.; Stern, J. C.

    2015-12-01

    The ephemeral saline acidic lakes on the Yilgarn Craton of Western Australia have been suggested as geochemical analogues to martian terrains. Both are characterized by interbedded phyllosilicates and hydrated sulfates. On Mars, these areas indicate shifting environmental conditions, from the neutral/alkaline and wet conditions that dominated during the Noachian era to the more familiar dry, acidic conditions that began in the Hesperian. The habitability of such a dynamic environment can be informed by investigation of the Yilgarn Lake system. Previous work has found phospholipid fatty acids (PLFA) evidence of microbial communities in sections of sediment cores taken from Lake Gilmore. These communities include both Gram-positive and -negative bacteria, Actinomycetes, and even methanotrophs. Given recurring detection of methane on the martian surface, evidence of a methane cycling community in an analogous environment is of particular interest. In this study we analyze the carbon isotope composition of bulk organic material as well as extracted lipids from the Lake Gilmore sediment cores at both a near-shore and mid-lake location. These analyses reveal very low accumulations of organic carbon, concentrated primarily in the gypsum-rich near-shore core. The near-shore sediments show a down-core decrease in abundance of organic carbon as well as depletion in the carbon isotope composition (δ13C) with depth. Bulk carbon did not exhibit the unique, highly depleted, diagnostic signature associated with methanotrophic biomass. Compound-specific isotope analysis (CSIA) of carbon in extracted methanotroph PFLAs can confirm the presence of a methane cycling metabolism at depth. Also, additional extractions have isolated lipids associated with lake-edge grasses. These analyses consider both the chain-length distribution and carbon CSIA of these lipids in order to understand the effect of terrestrial detritus on any preserved methanotroph carbon signal, given the very low

  1. ANALYSIS OF RICIN TOXIN PREPARATIONS FOR CARBOHYDRATE AND FATTY ACID ABUNDANCE AND ISOTOPE RATIO INFORMATION

    SciTech Connect

    Wunschel, David S.; Kreuzer-Martin, Helen W.; Antolick, Kathryn C.; Colburn, Heather A.; Moran, James J.; Melville, Angela M.

    2009-12-01

    This report describes method development and preliminary evaluation for analyzing castor samples for signatures of purifying ricin. Ricin purification from the source castor seeds is essentially a problem of protein purification using common biochemical methods. Indications of protein purification will likely manifest themselves as removal of the non-protein fractions of the seed. Two major, non-protein, types of biochemical constituents in the seed are the castor oil and various carbohydrates. The oil comprises roughly half the seed weight while the carbohydrate component comprises roughly half of the remaining “mash” left after oil and hull removal. Different castor oil and carbohydrate components can serve as indicators of specific toxin processing steps. Ricinoleic acid is a relatively unique fatty acid in nature and is the most abundant component of castor oil. The loss of ricinoleic acid indicates a step to remove oil from the seeds. The relative amounts of carbohydrates and carbohydrate-like compounds, including arabinose, xylose, myo-inositol fucose, rhamnose, glucosamine and mannose detected in the sample can also indicate specific processing steps. For instance, the differential loss of arabinose relative to mannose and N-acetyl glucosamine indicates enrichment for the protein fraction of the seed using protein precipitation. The methods developed in this project center on fatty acid and carbohydrate extraction from castor samples followed by derivatization to permit analysis by gas chromatography-mass spectrometry (GC-MS). Method descriptions herein include: the source and preparation of castor materials used for method evaluation, the equipment and description of procedure required for chemical derivatization, and the instrument parameters used in the analysis. Two types of derivatization methods describe analysis of carbohydrates and one procedure for analysis of fatty acids. Two types of GC-MS analysis is included in the method development, one

  2. Mutational analysis of amino acid residues involved in catalytic activity of a family 18 chitinase from tulip bulbs.

    PubMed

    Suzukawa, Keisuke; Yamagami, Takeshi; Ohnuma, Takayuki; Hirakawa, Hideki; Kuhara, Satoru; Aso, Yoichi; Ishiguro, Masatsune

    2003-02-01

    We expressed chitinase-1 (TBC-1) from tulip bulbs (Tulipa bakeri) in E. coli cells and used site-directed mutagenesis to identify amino acid residues essential for catalytic activity. Mutations at Glu-125 and Trp-251 completely abolished enzyme activity, and activity decreased with mutations at Asp-123 and Trp-172 when glycolchitin was the substrate. Activity changed with the mutations of Trp-251 to one of several amino acids with side-chains of little hydrophobicity, suggesting that hydrophobic interaction of Trp-251 is important for the activity. Molecular dynamics (MD) simulation analysis with hevamine as the model compound showed that the distance between Asp-123 and Glu-125 was extended by mutation of Trp-251. Kinetic studies of Trp-251-mutated chitinases confirmed these various phenomena. The results suggested that Glu-125 and Trp-251 are essential for enzyme activity and that Trp-251 had a direct role in ligand binding.

  3. Campylobacter jejuni fatty acid synthase II: Structural and functional analysis of [beta]-hydroxyacyl-ACP dehydratase (FabZ)

    SciTech Connect

    Kirkpatrick, Andrew S.; Yokoyama, Takeshi; Choi, Kyoung-Jae; Yeo, Hye-Jeong

    2009-08-14

    Fatty acid biosynthesis is crucial for all living cells. In contrast to higher organisms, bacteria use a type II fatty acid synthase (FAS II) composed of a series of individual proteins, making FAS II enzymes excellent targets for antibiotics discovery. The {beta}-hydroxyacyl-ACP dehydratase (FabZ) catalyzes an essential step in the FAS II pathway. Here, we report the structure of Campylobacter jejuni FabZ (CjFabZ), showing a hexamer both in crystals and solution, with each protomer adopting the characteristic hot dog fold. Together with biochemical analysis of CjFabZ, we define the first functional FAS II enzyme from this pathogen, and provide a framework for investigation on roles of FAS II in C. jejuni virulence

  4. X-Ray Crystallographic Analysis, EPR Studies, and Computational Calculations of a Cu(II) Tetramic Acid Complex

    PubMed Central

    Matiadis, Dimitrios; Tsironis, Dimitrios; Stefanou, Valentina; Igglessi–Markopoulou, Olga; McKee, Vickie; Sanakis, Yiannis; Lazarou, Katerina N.

    2017-01-01

    In this work we present a structural and spectroscopic analysis of a copper(II) N-acetyl-5-arylidene