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Sample records for aldrich research biochemicals

  1. 78 FR 12102 - Manufacturer of Controlled Substances; Notice of Application; Sigma Aldrich Research Biochemicals...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-21

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Manufacturer of Controlled Substances; Notice of Application; Sigma Aldrich Research Biochemicals, Inc. Pursuant to Sec. 1301.33(a), Title 21 of the Code of Federal Regulations (CFR), this is notice that on November 21,...

  2. 78 FR 32458 - Manufacturer of Controlled Substances; Notice of Registration; Sigma Aldrich Research...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-30

    ... February 21, 2013, 78 FR 12102, Sigma ] Aldrich Research Biochemicals, Inc., 1-3 Strathmore Road, Natick...-Methylenedioxymethamphetamine (MDMA) I (7405). Psilocybin (7437) I 5-Methoxy-N,N-diisopropyltryptamine (7439). I 1-...

  3. 77 FR 31390 - Manufacturer of Controlled Substances; Notice of Registration; Sigma Aldrich Research...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-25

    ... February 6, 2012, 77 FR 5847, Sigma Aldrich Research Biochemicals, Inc., 1-3 Strathmore Road, Natick...-diisopropyltryptamine (7439)....... I 1- piperidine (7470)..... I N-Benzylpiperazine (7493) I Heroin (9200)...

  4. Biochemical Activities of the Wiskott-Aldrich Syndrome Homology Region 2 Domains of Sarcomere Length Short (SALS) Protein.

    PubMed

    Tóth, Mónika Ágnes; Majoros, Andrea Kinga; Vig, Andrea Teréz; Migh, Ede; Nyitrai, Miklós; Mihály, József; Bugyi, Beáta

    2016-01-01

    Drosophila melanogaster sarcomere length short (SALS) is a recently identified Wiskott-Aldrich syndrome protein homology 2 (WH2) domain protein involved in skeletal muscle thin filament regulation. SALS was shown to be important for the establishment of the proper length and organization of sarcomeric actin filaments. Here, we present the first detailed characterization of the biochemical activities of the tandem WH2 domains of SALS (SALS-WH2). Our results revealed that SALS-WH2 binds both monomeric and filamentous actin and shifts the monomer-filament equilibrium toward the monomeric actin. In addition, SALS-WH2 can bind to but fails to depolymerize phalloidin- or jasplakinolide-bound actin filaments. These interactions endow SALS-WH2 with the following two major activities in the regulation of actin dynamics: SALS-WH2 sequesters actin monomers into non-polymerizable complexes and enhances actin filament disassembly by severing, which is modulated by tropomyosin. We also show that profilin does not influence the activities of the WH2 domains of SALS in actin dynamics. In conclusion, the tandem WH2 domains of SALS are multifunctional regulators of actin dynamics. Our findings suggest that the activities of the WH2 domains do not reconstitute the presumed biological function of the full-length protein. Consequently, the interactions of the WH2 domains of SALS with actin must be tuned in the cellular context by other modules of the protein and/or sarcomeric components for its proper functioning.

  5. The Wiskott-Aldrich Syndrome

    PubMed Central

    Spitler, Lynn E.; Levin, Alan S.; Stites, Daniel P.; Fudenberg, H. Hugh; Pirofsky, Bernard; August, Charles S.; Stiehm, E. Richard; Hitzig, Walter H.; Gatti, Richard A.

    1972-01-01

    12 patients with Wiskott-Aldrich syndrome were treated with therapeutic doses of transfer factor in an attempt to induce cellular immunity. Clinical improvement was noted after transfer factor therapy in 7 of the 12 patients treated. Because this disease has a variable course and temporary spontaneous improvement can occur, the observed improvement cannot necessarily be attributed to the transfer factor. However, in two patients repeated remissions consistently followed transfer factor administration on repeated occasions. This included freedom from infections, regression of splenomegaly, and clearing of eczema. An unexpected finding was a decrease in bleeding in 3 of the 10 patients who had bleeding. Conversion of skin reactivity was obtained in all seven patients who clinically seemed to respond to transfer factor. In vitro studies performed after the administration of transfer factor demonstrated that the lymphocytes of the patients now produced migration inhibitory factor in response to appropriate test antigens, but did not undergo increased radioactive thymidine incorporation in response to the same antigens. A defect in the monocyte IgG receptors has been found in certain patients with the disease, and the current study shows that all patients with defective monocyte IgG receptors responded to transfer factor, whereas only one patient with normal receptors showed any response. This test may thus prove to be useful in predicting the results of transfer factor therapy in patients with Wiskott-Aldrich syndrome, although evaluation of a larger series of patients will be necessary to confirm this point. We conclude that cellular immunity can be induced, that there appears to be clinical benefit in certain patients with Wiskott-Aldrich syndrome by the use of transfer factor, and that this mode of therapy warrents trial in these patients and others with defects of cellular immunity. PMID:4640955

  6. Q & A with Ed Tech Leaders: Interview with Clark Aldrich

    ERIC Educational Resources Information Center

    Shaughnessy, Michael F.; Fulgham, Susan M.

    2016-01-01

    Clark Aldrich is the founder and Managing Partner of Clark Aldrich Designs, and is known as a global education visionary, industry analyst, and speaker. In this interview, he responds to questions about his ideas, his work, and his theories.

  7. [Wiskott-Aldrich Syndrome: An updated review].

    PubMed

    Blancas-Galicia, Lizbeth; Escamilla-Quiroz, Cecilia; Yamazaki-Nakashimada, Marco Antonio

    2011-01-01

    The Wiskott-Aldrich syndrome (WAS) is a primary immunodeficiency and is inherited in an X-linked pattern. Affected patients have mutations in the gene encoding Wiskott-Aldrich syndrome protein (WASP), a key regulator of signaling and reorganization of the cytoskeleton in hematopoietic cells. Mutations in WASP gene lead to a wide clinical spectrum ranging from thrombocytopenia, immunodeficiency, eczema and high susceptibility to tumor development and manifestations such as skin infections, suppurative otitis and pneumonia. Clinical symptoms start around the age of 6 months. Incidence of this disease is 1-10/millions of births. The laboratory tests show low platelet count and small size, but definitive diagnosis can only be confirmed by the demonstration of mutations in WASP gene. Treatment of WAS is based on antimicrobial therapy, prophylactic use of intravenous gamma globulin and bone marrow transplantation. Life expectancy in treated individuals is around 20 years but without treatment is 3.5 years.

  8. [Wiskott-Aldrich syndrome. A report of a new mutation].

    PubMed

    Guillén-Rocha, Nelva; López-Rocha, Eunice; Danielian, Silvia; Segura-Méndez, Nora; López-González, Lucina; Lugo-Reyes, Saúl Oswaldo

    2014-01-01

    Wiskott-Aldrich syndrome was first reported clinically in 1937, and in 1954 the classic triad was identified: eccema, recurrent infections and thrombocytopenia with an X-linked transmission. Its incidence is estimated at 1 to 10 in one million live births per year. Wiskott Aldrich syndrome is caused by mutations in a gene in the short arm of chromosome X that encodes the Wiskott-Aldrich syndrome protein (WASp), which identification and sequencing was first performed in 1994, and since then about 300 mutations have been reported. This paper describes the case of a boy with Wiskott-Aldrich syndrome, with clinical and genetic diagnosis, with a considerable diagnostic delay attributable to an atypical presentation misdiagnosed as immune thrombocytopenia.

  9. Setbacks in blood substitutes research and development: a biochemical perspective.

    PubMed

    Alayash, Abdu I

    2010-06-01

    Recent setbacks in using Hb-based technology to develop oxygen carriers or blood substitutes may spur new and fundamentally different approaches for the development of a new generation of hemoglobin-based oxygen carriers (HBOCs). This article briefly details some underlying mechanisms that may have been responsible for the adverse-event profile associated with HBOCs, with a focus on the contribution of the author's laboratory toward identifying some of these biochemical pathways and some ways and means to control them. It is hoped that this will aid in the development of a safe and effective second generation of HBOCs.

  10. Present status of biochemical research on the insecticide resistance problem*

    PubMed Central

    Agosin, Moises

    1963-01-01

    In order to provide a rational basis for the development of new insecticides, a thorough understanding of resistance mechanisms is necessary and this presupposes a detailed knowledge of the normal biochemical pathways in insects. The author reviews recent progress in this field, particularly the work on enzymatic detoxication of insecticides which appears to be the most important single factor in the production of resistance. The mechanisms include dehydrochlorination and α-methylenic oxidation (DDT), hydrolysis by phosphatases or carboxyesterases (organophosphorus compounds), and oxidation by microsomal enzyme systems (various classes of insecticides). Much work still needs to be done on the enzyme systems involved, especially in relation to substrate specificity and the effect of enzyme inhibitors that might act as synergists of insecticides. PMID:20604178

  11. Autoimmunity in Wiskott–Aldrich Syndrome: An Unsolved Enigma

    PubMed Central

    Catucci, Marco; Castiello, Maria Carmina; Pala, Francesca; Bosticardo, Marita; Villa, Anna

    2012-01-01

    Wiskott–Aldrich Syndrome (WAS) is a severe X-linked Primary Immunodeficiency that affects 1–10 out of 1 million male individuals. WAS is caused by mutations in the WAS Protein (WASP) expressing gene that leads to the absent or reduced expression of the protein. WASP is a cytoplasmic protein that regulates the formation of actin filaments in hematopoietic cells. WASP deficiency causes many immune cell defects both in humans and in the WAS murine model, the Was−/− mouse. Both cellular and humoral immune defects in WAS patients contribute to the onset of severe clinical manifestations, in particular microthrombocytopenia, eczema, recurrent infections, and a high susceptibility to develop autoimmunity and malignancies. Autoimmune diseases affect from 22 to 72% of WAS patients and the most common manifestation is autoimmune hemolytic anemia, followed by vasculitis, arthritis, neutropenia, inflammatory bowel disease, and IgA nephropathy. Many groups have widely explored immune cell functionality in WAS partially explaining how cellular defects may lead to pathology. However, the mechanisms underlying the occurrence of autoimmune manifestations have not been clearly described yet. In the present review, we report the most recent progresses in the study of immune cell function in WAS that have started to unveil the mechanisms contributing to autoimmune complications in WAS patients. PMID:22826711

  12. Spontaneous thrombosis of hepatic aneurysms in an infant with Wiskott-Aldrich syndrome.

    PubMed

    Merlini, Laura; Hanquinet, Sylviane; Gungor, Tayfun; Ozsahin, Hulya

    2009-06-01

    Vasculitides and aneurysm formation are well-known complications in Wiskott-Aldrich syndrome (WAS), most often appearing later in life, usually in second decade. The authors report the case of a 5-month-old boy with a genetically and phenotypically severe Wiskott-Aldrich syndrome and sequential formation and spontaneous thrombosis of hepatic aneurysms. This case demonstrates that aneurysm formation may develop early in the course of severe WAS phenotypes. Because of the progressive nature of these manifestations, surgical or interventional procedures are not advisable. Early allogeneic hematopoietic stem cell transplantation (HSCT) should be considered before the manifestation of irreversible organ damage.

  13. 78 FR 39339 - Importer of Controlled Substances; Notice of Registration; SA INTL GMBH C/O., Sigma Aldrich Co., LLC

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-01

    ..., 78 FR 19015, SA INTL GMBH C/O., Sigma Aldrich Co. LLC., 3500 Dekalb Street, St. Louis, Missouri 63118... (7402). 3,4-Methylenedioxy-N-ethylamphetamine I (7404). 3,4-Methylenedioxymethamphetamine (MDMA) I...

  14. 77 FR 67675 - Importer of Controlled Substances, Notice of Registration, SA INTL GMBH C/O., Sigma Aldrich Co...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-13

    ..., 2012, 77 FR 50162, SA INTL GMBH C/O., Sigma Aldrich Co., LLC., 3500 Dekalb Street, St. Louis, Missouri...-Methoxyamphetamine (7411) I Bufotenine (7433) I Diethyltryptamine (7434) I Dimethyltryptamine (7435) I...

  15. Glycan Arrays: From Basic Biochemical Research to Bioanalytical and Biomedical Applications.

    PubMed

    Geissner, Andreas; Seeberger, Peter H

    2016-06-12

    A major branch of glycobiology and glycan-focused biomedicine studies the interaction between carbohydrates and other biopolymers, most importantly, glycan-binding proteins. Today, this research into glycan-biopolymer interaction is unthinkable without glycan arrays, tools that enable high-throughput analysis of carbohydrate interaction partners. Glycan arrays offer many applications in basic biochemical research, for example, defining the specificity of glycosyltransferases and lectins such as immune receptors. Biomedical applications include the characterization and surveillance of influenza strains, identification of biomarkers for cancer and infection, and profiling of immune responses to vaccines. Here, we review major applications of glycan arrays both in basic and applied research. Given the dynamic nature of this rapidly developing field, we focus on recent findings. PMID:27306309

  16. Glycan Arrays: From Basic Biochemical Research to Bioanalytical and Biomedical Applications

    NASA Astrophysics Data System (ADS)

    Geissner, Andreas; Seeberger, Peter H.

    2016-06-01

    A major branch of glycobiology and glycan-focused biomedicine studies the interaction between carbohydrates and other biopolymers, most importantly, glycan-binding proteins. Today, this research into glycan-biopolymer interaction is unthinkable without glycan arrays, tools that enable high-throughput analysis of carbohydrate interaction partners. Glycan arrays offer many applications in basic biochemical research, for example, defining the specificity of glycosyltransferases and lectins such as immune receptors. Biomedical applications include the characterization and surveillance of influenza strains, identification of biomarkers for cancer and infection, and profiling of immune responses to vaccines. Here, we review major applications of glycan arrays both in basic and applied research. Given the dynamic nature of this rapidly developing field, we focus on recent findings.

  17. Molecular characterization of two Malaysian patients with Wiskott-Aldrich syndrome.

    PubMed

    Baharin, Mohd Farid; Kader Ibrahim, Sabeera Begum; Yap, Song Hong; Abdul Manaf, Aina Mariana; Mat Ripen, Adiratna; Dhaliwal, Jasbir Singh

    2015-08-01

    The Wiskott-Aldrich Syndrome (WAS) is an X-linked immunodeficiency condition characterized by microthrombocytopenia, eczema and recurrent infections. It is caused by mutations in the Wiskott-Aldrich Syndrome protein (WASP) gene. We investigated two Malay boys who presented with congenital thrombocytopenia, eczema and recurrent infections. Here we report two cases of WASP mutation in Malaysia from two unrelated families. One had a novel missense mutation in exon 1 while the other had a nonsense mutation in exon 2. Both patients succumbed to diseaserelated complications. A differential diagnosis of WAS should be considered in any male child who present with early onset thrombocytopenia, especially when this is associated with eczema and recurrent infections. PMID:26277674

  18. Systemic vasculitis and aneurysm formation in the Wiskott-Aldrich syndrome.

    PubMed

    McCluggage, W G; Armstrong, D J; Maxwell, R J; Ellis, P K; McCluskey, D R

    1999-05-01

    A 24 year old male who suffered from the Wiskott-Aldrich syndrome developed intra-abdominal bleeding on two occasions. Radiological investigations showed aneurysmal dilatation of branches of the hepatic and superior mesenteric arteries. The second abdominal bleed necessitated laparotomy and the bleeding was localised to the kidneys. Right nephrectomy was performed and histological examination showed a necrotising vasculitis, mainly involving medium and small sized renal blood vessels. Steroids, immunosuppressive treatment, and control of blood pressure resulted in resolution of the vasculitic process and prevented further haemorrhage. Vasculitis and aneurysm formation are rarely described complications of Wiskott-Aldrich syndrome and may account for the life threatening haemorrhage which occurs in this condition.

  19. Wiskott-Aldrich Syndrome Presenting with JMML-Like Blood Picture and Normal Sized Platelets

    PubMed Central

    Patil, Rajesh B.; Shanmukhaiah, Chandrakala; Bamborde, Shailesh; Wasekar, Nilesh; Toshniwal, Manoj; Mohite, Aniket; Patil, Vinod

    2016-01-01

    Objective. The aim of this paper is to report the case of Wiskott-Aldrich syndrome (WAS) that presented with unusual laboratory features. Clinical Presentation and Intervention. Male neonate admitted with symptoms related to thrombocytopenia, whose initial diagnosis was considered as neonatal alloimmune thrombocytopenia and JMML (juvenile myelomonocytic leukemia) but subsequently diagnosis was confirmed as WAS. Conclusion. This case shows that a suspicion of WAS is warranted in the setting of neonatal thrombocytopenia with JMML-like blood picture and normal sized platelets. PMID:27340577

  20. Biochemical and Hematologic Reference Intervals for Aged Xenopus laevis in a Research Colony

    PubMed Central

    Chang, Angela G; Hu, Jing; Lake, Elizabeth; Bouley, Donna M; Johns, Jennifer L

    2015-01-01

    Xenopus laevis, the African clawed frog, is commonly used in developmental and toxicology research studies. Little information is available on aged X. laevis; however, with the complete mapping of the genome and the availability of transgenic animal models, the number of aged animals in research colonies is increasing. The goals of this study were to obtain biochemical and hematologic parameters to establish reference intervals for aged X. laevis and to compare results with those from young adult X. laevis. Blood samples were collected from laboratory reared, female frogs (n = 52) between the ages of 10 and 14 y. Reference intervals were generated for 30 biochemistry analytes and full hematologic analysis; these data were compared with prior results for young X. laevis from the same vendor. Parameters that were significantly higher in aged compared with young frogs included calcium, calcium:phosphorus ratio, total protein, albumin, HDL, amylase, potassium, CO2, and uric acid. Parameters found to be significantly lower in aged frogs included glucose, AST, ALT, cholesterol, BUN, BUN:creatinine ratio, phosphorus, triglycerides, LDL, lipase, sodium, chloride, sodium:potassium ratio, and anion gap. Hematology data did not differ between young and old frogs. These findings indicate that chemistry reference intervals for young X. laevis may be inappropriate for use with aged frogs. PMID:26424243

  1. N-WASP is required for B-cell-mediated autoimmunity in Wiskott-Aldrich syndrome.

    PubMed

    Volpi, Stefano; Santori, Elettra; Abernethy, Katrina; Mizui, Masayuki; Dahlberg, Carin I M; Recher, Mike; Capuder, Kelly; Csizmadia, Eva; Ryan, Douglas; Mathew, Divij; Tsokos, George C; Snapper, Scott; Westerberg, Lisa S; Thrasher, Adrian J; Candotti, Fabio; Notarangelo, Luigi D

    2016-01-14

    Mutations of the Wiskott-Aldrich syndrome gene (WAS) are responsible for Wiskott-Aldrich syndrome (WAS), a disease characterized by thrombocytopenia, eczema, immunodeficiency, and autoimmunity. Mice with conditional deficiency of Was in B lymphocytes (B/WcKO) have revealed a critical role for WAS protein (WASP) expression in B lymphocytes in the maintenance of immune homeostasis. Neural WASP (N-WASP) is a broadly expressed homolog of WASP, and regulates B-cell signaling by modulating B-cell receptor (BCR) clustering and internalization. We have generated a double conditional mouse lacking both WASP and N-WASP selectively in B lymphocytes (B/DcKO). Compared with B/WcKO mice, B/DcKO mice showed defective B-lymphocyte proliferation and impaired antibody responses to T-cell-dependent antigens, associated with decreased autoantibody production and lack of autoimmune kidney disease. These results demonstrate that N-WASP expression in B lymphocytes is required for the development of autoimmunity of WAS and may represent a novel therapeutic target in WAS. PMID:26468226

  2. N-WASP is required for B-cell-mediated autoimmunity in Wiskott-Aldrich syndrome.

    PubMed

    Volpi, Stefano; Santori, Elettra; Abernethy, Katrina; Mizui, Masayuki; Dahlberg, Carin I M; Recher, Mike; Capuder, Kelly; Csizmadia, Eva; Ryan, Douglas; Mathew, Divij; Tsokos, George C; Snapper, Scott; Westerberg, Lisa S; Thrasher, Adrian J; Candotti, Fabio; Notarangelo, Luigi D

    2016-01-14

    Mutations of the Wiskott-Aldrich syndrome gene (WAS) are responsible for Wiskott-Aldrich syndrome (WAS), a disease characterized by thrombocytopenia, eczema, immunodeficiency, and autoimmunity. Mice with conditional deficiency of Was in B lymphocytes (B/WcKO) have revealed a critical role for WAS protein (WASP) expression in B lymphocytes in the maintenance of immune homeostasis. Neural WASP (N-WASP) is a broadly expressed homolog of WASP, and regulates B-cell signaling by modulating B-cell receptor (BCR) clustering and internalization. We have generated a double conditional mouse lacking both WASP and N-WASP selectively in B lymphocytes (B/DcKO). Compared with B/WcKO mice, B/DcKO mice showed defective B-lymphocyte proliferation and impaired antibody responses to T-cell-dependent antigens, associated with decreased autoantibody production and lack of autoimmune kidney disease. These results demonstrate that N-WASP expression in B lymphocytes is required for the development of autoimmunity of WAS and may represent a novel therapeutic target in WAS.

  3. Thermodynamic analysis of lignocellulosic biofuel production via a biochemical process: guiding technology selection and research focus.

    PubMed

    Sohel, M Imroz; Jack, Michael W

    2011-02-01

    The aim of this paper is to present an exergy analysis of bioethanol production process from lignocellulosic feedstock via a biochemical process to asses the overall thermodynamic efficiency and identify the main loss processes. The thermodynamic efficiency of the biochemical process was found to be 35% and the major inefficiencies of this process were identified as: the combustion of lignin for process heat and power production and the simultaneous scarification and co-fermentation process accounting for 67% and 27% of the lost exergy, respectively. These results were also compared with a previous analysis of a thermochemical process for producing biofuel. Despite fundamental differences, the biochemical and thermochemical processes considered here had similar levels of thermodynamic efficiency. Process heat and power production was the major contributor to exergy loss in both of the processes. Unlike the thermochemical process, the overall efficiency of the biochemical process largely depends on how the lignin is utilized. PMID:21036607

  4. Thermodynamic analysis of lignocellulosic biofuel production via a biochemical process: guiding technology selection and research focus.

    PubMed

    Sohel, M Imroz; Jack, Michael W

    2011-02-01

    The aim of this paper is to present an exergy analysis of bioethanol production process from lignocellulosic feedstock via a biochemical process to asses the overall thermodynamic efficiency and identify the main loss processes. The thermodynamic efficiency of the biochemical process was found to be 35% and the major inefficiencies of this process were identified as: the combustion of lignin for process heat and power production and the simultaneous scarification and co-fermentation process accounting for 67% and 27% of the lost exergy, respectively. These results were also compared with a previous analysis of a thermochemical process for producing biofuel. Despite fundamental differences, the biochemical and thermochemical processes considered here had similar levels of thermodynamic efficiency. Process heat and power production was the major contributor to exergy loss in both of the processes. Unlike the thermochemical process, the overall efficiency of the biochemical process largely depends on how the lignin is utilized.

  5. 77 FR 50162 - Importer of Controlled Substances; Notice of Application; SA INTL GMBH C/O., Sigma Aldrich Co., LLC

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-20

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Importer of Controlled Substances; Notice of Application; SA INTL GMBH C/O., Sigma Aldrich Co., LLC Correction In notice document 2012-19191 appearing on pages 47106-47108 in the issue...

  6. A Hydrophobic Pocket in the Active Site of Glycolytic Aldolase Mediates Interactions with Wiskott-Aldrich Syndrome Protein

    SciTech Connect

    St-Jean,M.; Izard, T.; Sygusch, J.

    2007-01-01

    Aldolase plays essential catalytic roles in glycolysis and gluconeogenesis. However, aldolase is a highly abundant protein that is remarkably promiscuous in its interactions with other cellular proteins. In particular, aldolase binds to highly acidic amino acid sequences, including the C-terminus of the Wiskott-Aldrich syndrome protein, an actin nucleation promoting factor. Here we report the crystal structure of tetrameric rabbit muscle aldolase in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein. Aldolase recognizes a short, 4-residue DEWD motif (residues 498-501), which adopts a loose hairpin turn that folds about the central aromatic residue, enabling its tryptophan side chain to fit into a hydrophobic pocket in the active site of aldolase. The flanking acidic residues in this binding motif provide further interactions with conserved aldolase active site residues, Arg-42 and Arg-303, aligning their side chains and forming the sides of the hydrophobic pocket. The binding of Wiskott-Aldrich syndrome protein to aldolase precludes intramolecular interactions of its C-terminus with its active site, and is competitive with substrate as well as with binding by actin and cortactin. Finally, based on this structure a novel naphthol phosphate-based inhibitor of aldolase was identified and its structure in complex with aldolase demonstrated mimicry of the Wiskott-Aldrich syndrome protein-aldolase interaction. The data support a model whereby aldolase exists in distinct forms that regulate glycolysis or actin dynamics.

  7. Characterization of a human lymphocyte surface sialoglycoprotein that is defective in Wiskott-Aldrich syndrome

    PubMed Central

    1984-01-01

    gpL115 is a lymphocyte surface component that is deficient in patients with the X-chromosome-linked immune deficiency Wiskott-Aldrich syndrome (6). The glycoprotein nature of gpL115 is demonstrated through labeling in carbohydrate moieties by [3H]NaBH4 and its synthesis by lymphocytes through labeling with [35S]methionine. Native gpL115 adheres to wheat germ lectin-Sepharose and sialidase-treated gpL115 does not adhere, indicating that native gpL115 adheres via clusters of sialic acid residues. When tested on peanut lectin, which shows specificity for the disaccharide Gal beta 1-3GalNAc, gpL115 is nonadherent and sialidase- treated gpL115 is adherent, indicating the presence of the sequence sialic acid-Gal beta 1-3GalNAc, which is characteristic for O-linked (mucin-type, acidic-type) carbohydrates. A surface glycoprotein with all the above characteristics was found on the lymphoblastoid cell line CEM. CEM cells were used as immunogen to generate the monoclonal antibody L10, an IgG1, which binds native and sialidase-treated gpL115 . Sialidase-treatment of gpL115 significantly alters its physical properties, reducing its electrophoretic mobility and changing its behavior on isoelectrofocusing. Cumulatively, these findings indicate that gpL115 , like glycophorin of erythrocytes and GPIb of platelets, is a sialoglyco protein with significant quantities of O-linked carbohydrate. On treatment with limiting sialidase concentrations, gpL115 of normal lymphocytes is transformed into a series of partially desialylated species of decreasing electrophoretic mobility. This finding resembles the situation with lymphocytes of some Wiskott- Aldrich syndrome patients. Lymphocytes of eight Wiskott-Aldrich syndrome patients were found to be deficient in 125I-labeled gpL115 . Lymphocytes from three of these patients displayed an abnormal 125I- component of apparent mol wt 135,000. PMID:6547160

  8. Wiskott-Aldrich syndrome proteins in the nucleus: aWASH with possibilities.

    PubMed

    Verboon, Jeffrey M; Sugumar, Bina; Parkhurst, Susan M

    2015-01-01

    Actin and proteins that regulate its dynamics or interactions have well-established roles in the cytoplasm where they function as key components of the cytoskeleton to control diverse processes, including cellular infrastructure, cellular motility, cell signaling, and vesicle transport. Recent work has also uncovered roles for actin and its regulatory proteins in the nucleus, primarily in mechanisms governing gene expression. The Wiskott Aldrich Syndrome (WAS) family of proteins, comprising the WASP/N-WASP, SCAR/WAVE, WHAMM/JMY/WHAMY, and WASH subfamilies, function in the cytoplasm where they activate the Arp2/3 complex to form branched actin filaments. WAS proteins are present in the nucleus and have been implicated as transcriptional regulators. We found that Drosophila Wash, in addition to transcriptional effects, is involved in global nuclear architecture. Here we summarize the regulation and function of nuclear WAS proteins, and highlight how our work with Wash expands the possibilities for the functions of these proteins in the nucleus.

  9. Generation of a lentiviral vector producer cell clone for human Wiskott-Aldrich syndrome gene therapy.

    PubMed

    Wielgosz, Matthew M; Kim, Yoon-Sang; Carney, Gael G; Zhan, Jun; Reddivari, Muralidhar; Coop, Terry; Heath, Richard J; Brown, Scott A; Nienhuis, Arthur W

    2015-01-01

    We have developed a producer cell line that generates lentiviral vector particles of high titer. The vector encodes the Wiskott-Aldrich syndrome (WAS) protein. An insulator element has been added to the long terminal repeats of the integrated vector to limit proto-oncogene activation. The vector provides high-level, stable expression of WAS protein in transduced murine and human hematopoietic cells. We have also developed a monoclonal antibody specific for intracellular WAS protein. This antibody has been used to monitor expression in blood and bone marrow cells after transfer into lineage negative bone marrow cells from WAS mice and in a WAS negative human B-cell line. Persistent expression of the transgene has been observed in transduced murine cells 12-20 weeks following transplantation. The producer cell line and the specific monoclonal antibody will facilitate the development of a clinical protocol for gene transfer into WAS protein deficient stem cells. PMID:26052531

  10. Generation of a lentiviral vector producer cell clone for human Wiskott-Aldrich syndrome gene therapy.

    PubMed

    Wielgosz, Matthew M; Kim, Yoon-Sang; Carney, Gael G; Zhan, Jun; Reddivari, Muralidhar; Coop, Terry; Heath, Richard J; Brown, Scott A; Nienhuis, Arthur W

    2015-01-01

    We have developed a producer cell line that generates lentiviral vector particles of high titer. The vector encodes the Wiskott-Aldrich syndrome (WAS) protein. An insulator element has been added to the long terminal repeats of the integrated vector to limit proto-oncogene activation. The vector provides high-level, stable expression of WAS protein in transduced murine and human hematopoietic cells. We have also developed a monoclonal antibody specific for intracellular WAS protein. This antibody has been used to monitor expression in blood and bone marrow cells after transfer into lineage negative bone marrow cells from WAS mice and in a WAS negative human B-cell line. Persistent expression of the transgene has been observed in transduced murine cells 12-20 weeks following transplantation. The producer cell line and the specific monoclonal antibody will facilitate the development of a clinical protocol for gene transfer into WAS protein deficient stem cells.

  11. Successful Long-term Graft Survival of a Renal Transplantation Patient with Wiskott-Aldrich Syndrome.

    PubMed

    Kai, Kotaro; Sumida, Maki; Motoyoshi, Yaeko; Ogawa, Yuichi; Miki, Katsuyuki; Iwadoh, Kazuhiro; Sannomiya, Akihito; Murakami, Toru; Koyama, Ichiro; Kitajima, Kumiko; Nakajima, Ichiro; Morio, Tomohiro; Fuchinoue, Shohei

    2016-01-01

    Wiskott-Aldrich syndrome, a rare X-linked hereditary syndrome, is characterized by immunodeficiency, thrombocytopenia, and eczema. The underlying T-cell defect renders renal transplantation and immunosuppressive treatments uncertain. The present case exhibited the mild clinical manifestation, regarded as X-linked thrombocytopenia. He successfully underwent a living-donor ABO-compatible renal transplantation and splenectomy in 2002, and thereafter experiencing no severe rejection, serious infection, or malignancy for more than 10 years. Though IgA nephropathy was detected 8 months after transplantation, the patient's renal function and proteinuria were stable without any treatment. The present case showed a successful long-term graft survival and the importance of splenectomy added to renal transplantation. PMID:27374679

  12. Research on: A. Reclamation of borrow pits and denuded lands; B. Biochemical aspects of mycorrhizae of forest trees

    SciTech Connect

    Marx, D.H.

    1990-12-01

    This report furnishes a list of compiled and ongoing studies and a list of publications which resulted from the research accomplished by Institute scientists and other collaborators. The research accomplished can be placed in four categories: I. Research on borrow pit rehabilitation with 12 publications; II. Research on artificial regeneration of southern pines with 34 publications; III. Research on artificial regeneration of eastern hardwoods with 16 publications; and IV. Cooperative research with the University of Georgia on biochemical aspects of mycorrhizae with 5 publications. Major accomplishments of this research are: 1. Procedures to successfully reclaim borrow pits with sludge, subsoiling and seedlings with specific mycorrhizae. 2. Protocols to successfully artificially regenerate southern pines (particularly ling leaf pine) and certain eastern hardwoods. 3. Basic understanding of the biochemistry of mycorrhizae and the discovery of a new pathway for sucrose utilization in plants. 67 refs.

  13. Abnormalities of follicular helper T-cell number and function in Wiskott-Aldrich syndrome

    PubMed Central

    Zhang, Xuan; Dai, Rongxin; Li, Wenyan; Zhao, Hongyi; Zhang, Yongjie; Zhou, Lina; Du, Hongqiang; Luo, Guangjin; Wu, Junfeng; Niu, Linlin; An, Yunfei; Zhang, Zhiyong; Ding, Yuan; Song, Wenxia; Liu, Chaohong

    2016-01-01

    Wiskott-Aldrich syndrome protein (WASp) is a hematopoietic-specific regulator of actin nucleation. Wiskott-Aldrich syndrome (WAS) patients show immunodeficiencies, most of which have been attributed to defective T-cell functions. T follicular helper (Tfh) cells are the major CD4+ T-cell subset with specialized B-cell helper capabilities. Aberrant Tfh cells activities are involved in immunopathologies such as autoimmunity, immunodeficiencies, and lymphomas. We found that in WAS patients, the number of circulating Tfh cells was significantly reduced due to reduced proliferation and increased apoptosis, and Tfh cells were Th2 and Th17 polarized. The expression of inducible costimulator (ICOS) in circulating Tfh cells was higher in WAS patients than in controls. BCL6 expression was decreased in total CD4+ T and Tfh cells of WAS patients. Mirroring the results in patients, the frequency of Tfh cells in WAS knockout (KO) mice was decreased, as was the frequency of BCL6+ Tfh cells, but the frequency of ICOS+ Tfh cells was increased. Using WAS chimera mice, we found that the number of ICOS+ Tfh cells was decreased in WAS chimera mice, indicating that the increase in ICOS+ Tfh cells in WAS KO mice was cell extrinsic. The data from in vivo CD4+ naive T-cell adoptive transfer mice as well as in vitro coculture of naive B and Tfh cells showed that the defective function of WASp-deficient Tfh cells was T-cell intrinsic. Consistent findings in both WAS patients and WAS KO mice suggested an essential role for WASp in the development and memory response of Tfh cells and that WASp deficiency causes a deficient differentiation defect in Tfh cells by downregulating the transcription level of BCL6. PMID:27170596

  14. Neuronal Wiskott-Aldrich syndrome protein regulates TGF-β1-mediated lung vascular permeability.

    PubMed

    Wagener, Brant M; Hu, Meng; Zheng, Anni; Zhao, Xueke; Che, Pulin; Brandon, Angela; Anjum, Naseem; Snapper, Scott; Creighton, Judy; Guan, Jun-Lin; Han, Qimei; Cai, Guo-Qiang; Han, Xiaosi; Pittet, Jean-Francois; Ding, Qiang

    2016-07-01

    TGF-β1 induces an increase in paracellular permeability and actin stress fiber formation in lung microvascular endothelial and alveolar epithelial cells via small Rho GTPase. The molecular mechanism involved is not fully understood. Neuronal Wiskott-Aldrich syndrome protein (N-WASP) has an essential role in actin structure dynamics. We hypothesized that N-WASP plays a critical role in these TGF-β1-induced responses. In these cell monolayers, we demonstrated that N-WASP down-regulation by short hairpin RNA prevented TGF-β1-mediated disruption of the cortical actin structure, actin stress filament formation, and increased permeability. Furthermore, N-WASP down-regulation blocked TGF-β1 activation mediated by IL-1β in alveolar epithelial cells, which requires actin stress fiber formation. Control short hairpin RNA had no effect on these TGF-β1-induced responses. TGF-β1-induced phosphorylation of Y256 of N-WASP via activation of small Rho GTPase and focal adhesion kinase mediates TGF-β1-induced paracellular permeability and actin cytoskeleton dynamics. In vivo, compared with controls, N-WASP down-regulation increases survival and prevents lung edema in mice induced by bleomycin exposure-a lung injury model in which TGF-β1 plays a critical role. Our data indicate that N-WASP plays a crucial role in the development of TGF-β1-mediated acute lung injury by promoting pulmonary edema via regulation of actin cytoskeleton dynamics.-Wagener, B. M., Hu, M., Zheng, A., Zhao, X., Che, P., Brandon, A., Anjum, N., Snapper, S., Creighton, J., Guan, J.-L., Han, Q., Cai, G.-Q., Han, X., Pittet, J.-F., Ding, Q. Neuronal Wiskott-Aldrich syndrome protein regulates TGF-β1-mediated lung vascular permeability.

  15. Efficiency of hexane extraction of napropamide from Aldrich humic acid and soil solutions

    SciTech Connect

    Williams, C.F.; Letey, J.; Farmer, W.J.; Nelson, S.D.; Anderson, M.; Ben-Hur, M.

    1999-12-01

    Dissolved organic matter (DOM) has been shown to form a stable complex with napropamide [2({alpha}-naphthoxy)-N,N-diethyl propionamide] and to facilitate its transport through soil columns. Liquid-liquid extraction of organics is a common method to transfer napropamide from water into an organic phase for gas chromatography analysis. A study was conducted to determine the effect of Aldrich humic acid, soil-derived dissolved organic matter, electrical conductivity, and hydrogen ion activity on the ability of hexane to extract napropamide from solutions and from soil extracts. The electrical conductivity from solutions and from soil extracts. The electrical conductivity of Aldrich humic acid solutions were adjusted to 0.01, 0.97, and 1.69 dS m{sup {minus}1} by adding NaCl and CaCl{sub 2}, and pH was adjusted using HCl and NaOH. Electrical conductivity had no effect on extraction efficiency. In the absence of DOM pH had no effect on extraction efficiency. In the absence of DOM pH had no effect on extraction efficiency. Extraction efficiency decreased with increasing DOM concentration. Maximum reduction in extraction efficiency occurred in the presence of DOM when solution pH was near neutrality. A maximum extraction efficiency of 100% was observed in the absence of DOM and a minimum of 68% when napropamide was added to DOM solutions at pH 8.2 and then lowered to pH 5.6. Management practices such as liming and allowing napropamide to dry on the soil may increase environmental transport. Also quantification of napropamide in environmental samples can be affected by DOM.

  16. Identification of Catalysts and Materials for a High-Energy Density Biochemical Fuel Cell: Cooperative Research and Development Final Report, CRADA Number CRD-09-345

    SciTech Connect

    Ghirardi, M.; Svedruzic, D.

    2013-07-01

    The proposed research attempted to identify novel biochemical catalysts, catalyst support materials, high-efficiency electron transfer agents between catalyst active sites and electrodes, and solid-phase electrolytes in order to maximize the current density of biochemical fuel cells that utilize various alcohols as substrates.

  17. Unification of some biochemical methods of research in the pre- and post-flight periods

    NASA Technical Reports Server (NTRS)

    Tigranyan, R. A.

    1980-01-01

    The biochemical methods for determination of various parameters and factors during pre- and post-flight periods, as used by American and Soviet teams dealing with space flight medicine are compared. The emphasis is on the exchange of information on the study of the blood and urine content of space travelers before and after space flight. A series of electrolytic, enzymatic, and hormonal factors is discussed.

  18. Research and teaching with the AFTOL SBD: an informatics resource for fungal subcellular and biochemical data.

    PubMed

    Arun Kumar, T K; Blackwell, Meredith; Letcher, Peter M; Roberson, Robert W; McLaughlin, David J

    2013-12-01

    The Structural and Biochemical Database (SBD), developed as part of the US NSF-funded Assembling the Fungal Tree of Life (AFTOL), is a multi-investigator project. It is a major resource to present and manage morphological and biochemical information on Fungi and serves as a phyloinformatics tool for the scientific community. It also is an important resource for teaching mycology. The database, available at http://aftol.umn.edu, includes new and previously published subcellular data on Fungi, supplemented with images and literature links. Datasets automatically combined in NEXUS format from the site permit independent and combined (with molecular data) phylogenetic analyses. Character lists, a major feature of the site, serve as primary reference documents of subcellular and biochemical characters that distinguish taxa across the major fungal lineages. The character lists illustrated with images and drawings are informative for evolutionary and developmental biologists as well as educators, students and the public. Fungal Subcellular Ontology (FSO), developed as part of this effort is a primary initiative to provide a controlled vocabulary describing subcellular structures unique to Fungi. FSO establishes a full complement of terms that provide an operating ontological framework for the database. Examples are provided for using the database for teaching.

  19. Age-dependent changes in cuticular hydrocarbons of larvae in Aldrichina grahami (Aldrich) (Diptera: Calliphoridae).

    PubMed

    Xu, Hong; Ye, Gong-Yin; Xu, Ying; Hu, Cui; Zhu, Guang-Hui

    2014-09-01

    Necrophagous flies, comprising the first wave of insects present in a cadaver, provide a great potential for more accurate determination of the late postmortem interval (PMI) based on their age. Cuticular hydrocarbons (CHs) are a promising age indicator in some insect species, especially for the larvae of necrophagous flies. Gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) were used to characterize the age-dependent, quantitative changes in CHs of larval Aldrichina grahami (Aldrich) (Diptera: Calliphoridae) at 24°C. The majority of low-molecular-weight alkanes (≤C25) and almost all of the alkenes decreased in abundance with larval development. By contrast, the abundance of high-molecular-weight alkanes of chain length greater than C25 gradually increased with age. For several peaks, including peak 28 (pentacosene a), peak 31 (n-C25), peak 43 (n-C27) and peak 68 (n-C31), a highly significant correlation was found between peak ratio (n-C29 divided by each chromatographic peak) and chronological age of the larvae. A mathematical model, derived from multivariate linear regression analysis, was developed for determining age of the larvae based on age-dependent changes in CHs. The estimated larval age based on the CHs had a good linear correlation with the chronological age (R(2)>0.9). These results indicate that CHs has a great potential for determining the age of fly larvae, and concomitantly for the PMI in forensic investigation.

  20. Effect of Aldrich humic acid on water-atmosphere transfer of decamethylcyclopentasiloxane.

    PubMed

    Whelan, M J; Sanders, D; van Egmond, R

    2009-02-01

    The behaviour of the cyclic volatile methyl siloxane (cVMS) decamethylcyclopentasiloxane (D5) in surface waters is explored using a combination of laboratory experimentation and mathematical modelling. In the laboratory experiment, changes were observed in the concentration of radiolabelled D5 in open stirred beakers containing mineral medium with different concentrations of added Aldrich humic acid over 120 h. Although D5 is very volatile, its strong affinity for dissolved organic carbon (DOC) reduced the rate of water to air transfer significantly. The data were well described using a simple partitioning model which accounted for hydrolysis and for depth and DOC changes resulting from sampling and evaporation, although there was some evidence for the formation of a hypothetical bound residue with increasing time. The model was used to derive effective values for the partition coefficient between DOC and water [log(K(DOC))]. These values were relatively consistent across five treatments and varied between 5.04 and 5.40 log(L kg(-1)), with no systematic treatment bias. These values are significantly higher than previously published experimental estimates of K(OC) for D5 but more than two orders of magnitude lower than some K(OC) estimates based on the octanol:water partition coefficient (K(OW)). The data confirm that volatilisation will be an important loss mechanism from surface waters for D5, although the rate of loss will decrease with increasing DOC concentration. PMID:19042003

  1. Lentiviral-mediated gene therapy restores B cell tolerance in Wiskott-Aldrich syndrome patients.

    PubMed

    Pala, Francesca; Morbach, Henner; Castiello, Maria Carmina; Schickel, Jean-Nicolas; Scaramuzza, Samantha; Chamberlain, Nicolas; Cassani, Barbara; Glauzy, Salome; Romberg, Neil; Candotti, Fabio; Aiuti, Alessandro; Bosticardo, Marita; Villa, Anna; Meffre, Eric

    2015-10-01

    Wiskott-Aldrich syndrome (WAS) is an X-linked immunodeficiency characterized by microthrombocytopenia, eczema, and high susceptibility to developing tumors and autoimmunity. Recent evidence suggests that B cells may be key players in the pathogenesis of autoimmunity in WAS. Here, we assessed whether WAS protein deficiency (WASp deficiency) affects the establishment of B cell tolerance by testing the reactivity of recombinant antibodies isolated from single B cells from 4 WAS patients before and after gene therapy (GT). We found that pre-GT WASp-deficient B cells were hyperreactive to B cell receptor stimulation (BCR stimulation). This hyperreactivity correlated with decreased frequency of autoreactive new emigrant/transitional B cells exiting the BM, indicating that the BCR signaling threshold plays a major role in the regulation of central B cell tolerance. In contrast, mature naive B cells from WAS patients were enriched in self-reactive clones, revealing that peripheral B cell tolerance checkpoint dysfunction is associated with impaired suppressive function of WAS regulatory T cells. The introduction of functional WASp by GT corrected the alterations of both central and peripheral B cell tolerance checkpoints. We conclude that WASp plays an important role in the establishment and maintenance of B cell tolerance in humans and that restoration of WASp by GT is able to restore B cell tolerance in WAS patients. PMID:26368308

  2. Linkage of the Wiskott-Aldrich syndrome with polymorphic DNA sequences from the human X chromosome

    SciTech Connect

    Peacocke, M.; Siminovitch, K.A.

    1987-05-01

    The Wiskott-Aldrich syndrome (WAS) is one of several human immunodeficiency diseases inherited as an X-linked trait. The location of WAS on the X chromosome is unknown. The authors have studied 10 kindreds segregating for WAS for linkage with cloned, polymorphic DNA markers and have demonstrated significant linkage between WAS and two loci, DXS14 and DXS7, that map to the proximal short arm of the X chromosome. Maximal logarithm of odds (lod scores) for WAS-DXS14 and WAS-DWS7 were 4.29 (at 0 = 0.03) and 4.12 (at 0 = 0.00), respectively. Linkage data between WAS and six markers loci indicate the order of the loci to be (DXYS1-DXS1)-WAS-DXS14-DXS7-(DXS84-OTC). These results suggest that the WAS locus lies within the pericentric region of the X chromosome and provide an initial step toward identifying the WAS gene and improving the genetic counselling WAS families.

  3. Wiskott–Aldrich syndrome: review and report of a large family

    PubMed Central

    Stiehm, E. R.; McIntosh, R. M.

    1967-01-01

    Wiskott–Aldrich syndrome is a sex-linked recessive antibody-deficiency syndrome characterized by thrombocytopenia, eczema and increased susceptibility to infection. All forms of therapy are notably unsuccessful and these patients succumb in the first decade. Three cases of this syndrome are presented from a large family in which nine male infants have succumbed with manifestations of this disease. Two of the infants died at ages 10 months and 4 years respectively. A third child is alive at age 2. Serial quantitative immune globulin studies performed in two cases demonstrated markedly elevated γA, decreased γM and normal γG; levels of γM were initially normal but fell progressively as γA levels increased. The low levels of γM are probably a factor in their low or absent isoagglutinins, poor response to injected antigens, and increased susceptibility to infection; elevated γA levels may indicate immunologic unresponsiveness and/or a compensatory mechanism for the defect in γM synthesis. In two of these patients prolonged trials (17 and 23 months) of periodic plasma infusions (15 ml/kg at 6-week intervals), accompanied by γ-globulin injections (0·1 ml/kg) were undertaken. Although no remarkable effects on the platelets or their resistance to infection was noted, we feel that some benefit might have accrued and that further trails are indicated. PMID:4166240

  4. WIP is a chaperone for Wiskott–Aldrich syndrome protein (WASP)

    PubMed Central

    de la Fuente, Miguel A.; Sasahara, Yoji; Calamito, Marco; Antón, Inés M.; Elkhal, Abdallah; Gallego, Maria D.; Suresh, Koduru; Siminovitch, Katherine; Ochs, Hans D.; Anderson, Kenneth C.; Rosen, Fred S.; Geha, Raif S.; Ramesh, Narayanaswamy

    2007-01-01

    Wiskott–Aldrich syndrome protein (WASP) is in a complex with WASP-interacting protein (WIP). WASP levels, but not mRNA levels, were severely diminished in T cells from WIP−/− mice and were increased by introduction of WIP in these cells. The WASP binding domain of WIP was shown to protect WASP from degradation by calpain in vitro. Treatment with the proteasome inhibitors MG132 and bortezomib increased WASP levels in T cells from WIP−/− mice and in T and B lymphocytes from two WAS patients with missense mutations (R86H and T45M) that disrupt WIP binding. The calpain inhibitor calpeptin increased WASP levels in activated T and B cells from the WASP patients, but not in primary T cells from the patients or from WIP−/− mice. Despite its ability to increase WASP levels proteasome inhibition did not correct the impaired IL-2 gene expression and low F-actin content in T cells from the R86H WAS patient. These results demonstrate that WIP stabilizes WASP and suggest that it may also be important for its function. PMID:17213309

  5. The Mitochondrial Genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the Evolutionary Timescale of Tachinid Flies

    PubMed Central

    Zhao, Zhe; Su, Tian-juan; Chesters, Douglas; Wang, Shi-di; Ho, Simon Y. W.; Zhu, Chao-dong; Chen, Xiao-lin; Zhang, Chun-tian

    2013-01-01

    Tachinid flies are natural enemies of many lepidopteran and coleopteran pests of forests, crops, and fruit trees. In order to address the lack of genetic data in this economically important group, we sequenced the complete mitochondrial genome of the Palaearctic tachinid fly Elodia flavipalpis Aldrich, 1933. Usually found in Northern China and Japan, this species is one of the primary natural enemies of the leaf-roller moths (Tortricidae), which are major pests of various fruit trees. The 14,932-bp mitochondrial genome was typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. However, its control region is only 105 bp in length, which is the shortest found so far in flies. In order to estimate dipteran evolutionary relationships, we conducted a phylogenetic analysis of 58 mitochondrial genomes from 23 families. Maximum-likelihood and Bayesian methods supported the monophyly of both Tachinidae and superfamily Oestroidea. Within the subsection Calyptratae, Muscidae was inferred as the sister group to Oestroidea. Within Oestroidea, Calliphoridae and Sarcophagidae formed a sister clade to Oestridae and Tachinidae. Using a Bayesian relaxed clock calibrated with fossil data, we estimated that Tachinidae originated in the middle Eocene. PMID:23626734

  6. Impact on biochemical research of the discovery of stable isotopes: the outcome of the serendipic meeting of a refugee with the discoverer of heavy isotopes at Columbia University

    SciTech Connect

    Shemin, D.

    1987-03-01

    As late as the 1930s, approaches to biochemical research not only were rather primitive, but a certain amount of mysticism still surrounded the biochemical events that occur in the living cell. To a great extent, this was due to the lack of techniques needed to uncover the subtle reactions in the living cell. In the early 1930s, an accidental meeting of two scientists revolutionized approaches in biochemical studies and led to the scientific explosion in molecular biology that has occurred during the last few decades. The dark political storm in Germany deposited Dr. Rudolf Schoenheimer on the New York shore, where he met Professor Urey, who recently had discovered ''heavy'' hydrogen. Schoenheimer suggested that biological compounds tagged with heavy atoms of hydrogen would enable investigators to follow their metabolic pathways. This intellectual leap revolutionized the thinking and design of experiments and made it possible to uncover the myriad reactions that occur in the living cell.

  7. B-cell reconstitution after lentiviral vector–mediated gene therapy in patients with Wiskott-Aldrich syndrome

    PubMed Central

    Castiello, Maria Carmina; Scaramuzza, Samantha; Pala, Francesca; Ferrua, Francesca; Uva, Paolo; Brigida, Immacolata; Sereni, Lucia; van der Burg, Mirjam; Ottaviano, Giorgio; Albert, Michael H.; Grazia Roncarolo, Maria; Naldini, Luigi; Aiuti, Alessandro; Villa, Anna; Bosticardo, Marita

    2015-01-01

    Background Wiskott-Aldrich syndrome (WAS) is a severe X-linked immunodeficiency characterized by microthrombocytopenia, eczema, recurrent infections, and susceptibility to autoimmunity and lymphomas. Hematopoietic stem cell transplantation is the treatment of choice; however, administration of WAS gene–corrected autologous hematopoietic stem cells has been demonstrated as a feasible alternative therapeutic approach. Objective Because B-cell homeostasis is perturbed in patients with WAS and restoration of immune competence is one of the main therapeutic goals, we have evaluated reconstitution of the B-cell compartment in 4 patients who received autologous hematopoietic stem cells transduced with lentiviral vector after a reduced-intensity conditioning regimen combined with anti-CD20 administration. Methods We evaluated B-cell counts, B-cell subset distribution, B cell–activating factor and immunoglobulin levels, and autoantibody production before and after gene therapy (GT). WAS gene transfer in B cells was assessed by measuring vector copy numbers and expression of Wiskott-Aldrich syndrome protein. Results After lentiviral vector-mediated GT, the number of transduced B cells progressively increased in the peripheral blood of all patients. Lentiviral vector-transduced progenitor cells were able to repopulate the B-cell compartment with a normal distribution of B-cell subsets both in bone marrow and the periphery, showing a WAS protein expression profile similar to that of healthy donors. In addition, after GT, we observed a normalized frequency of autoimmune-associated CD19+CD21−CD35− and CD21low B cells and a reduction in B cell–activating factor levels. Immunoglobulin serum levels and autoantibody production improved in all treated patients. Conclusions We provide evidence that lentiviral vector-mediated GT induces transgene expression in the B-cell compartment, resulting in ameliorated B-cell development and functionality and contributing to immunologic

  8. Measures of Biochemical Sociology

    ERIC Educational Resources Information Center

    Snell, Joel; Marsh, Mitchell

    2008-01-01

    In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

  9. Next Generation Sequencing Reveals Skewing of the T and B Cell Receptor Repertoires in Patients with Wiskott–Aldrich Syndrome

    PubMed Central

    O’Connell, Amy E.; Volpi, Stefano; Dobbs, Kerry; Fiorini, Claudia; Tsitsikov, Erdyni; de Boer, Helen; Barlan, Isil B.; Despotovic, Jenny M.; Espinosa-Rosales, Francisco J.; Hanson, I. Celine; Kanariou, Maria G.; Martínez-Beckerat, Roxana; Mayorga-Sirera, Alvaro; Mejia-Carvajal, Carmen; Radwan, Nesrine; Weiss, Aaron R.; Pai, Sung-Yun; Lee, Yu Nee; Notarangelo, Luigi D.

    2014-01-01

    The Wiskott–Aldrich syndrome (WAS) is due to mutations of the WAS gene encoding for the cytoskeletal WAS protein, leading to abnormal downstream signaling from the T cell and B cell antigen receptors (TCR and BCR). We hypothesized that the impaired signaling through the TCR and BCR in WAS would subsequently lead to aberrations in the immune repertoire of WAS patients. Using next generation sequencing (NGS), the T cell receptor β and B cell immunoglobulin heavy chain (IGH) repertoires of eight patients with WAS and six controls were sequenced. Clonal expansions were identified within memory CD4+ cells as well as in total, naïve and memory CD8+ cells from WAS patients. In the B cell compartment, WAS patient IGH repertoires were also clonally expanded and showed skewed usage of IGHV and IGHJ genes, and increased usage of IGHG constant genes, compared with controls. To our knowledge, this is the first study that demonstrates significant abnormalities of the immune repertoire in WAS patients using NGS. PMID:25101082

  10. Altered BCR and TLR signals promote enhanced positive selection of autoreactive transitional B cells in Wiskott-Aldrich syndrome.

    PubMed

    Kolhatkar, Nikita S; Brahmandam, Archana; Thouvenel, Christopher D; Becker-Herman, Shirly; Jacobs, Holly M; Schwartz, Marc A; Allenspach, Eric J; Khim, Socheath; Panigrahi, Anil K; Luning Prak, Eline T; Thrasher, Adrian J; Notarangelo, Luigi D; Candotti, Fabio; Torgerson, Troy R; Sanz, Ignacio; Rawlings, David J

    2015-09-21

    Wiskott-Aldrich syndrome (WAS) is an X-linked immunodeficiency disorder frequently associated with systemic autoimmunity, including autoantibody-mediated cytopenias. WAS protein (WASp)-deficient B cells have increased B cell receptor (BCR) and Toll-like receptor (TLR) signaling, suggesting that these pathways might impact establishment of the mature, naive BCR repertoire. To directly investigate this possibility, we evaluated naive B cell specificity and composition in WASp-deficient mice and WAS subjects (n = 12). High-throughput sequencing and single-cell cloning analysis of the BCR repertoire revealed altered heavy chain usage and enrichment for low-affinity self-reactive specificities in murine marginal zone and human naive B cells. Although negative selection mechanisms including deletion, anergy, and receptor editing were relatively unperturbed, WASp-deficient transitional B cells showed enhanced proliferation in vivo mediated by antigen- and Myd88-dependent signals. Finally, using both BCR sequencing and cell surface analysis with a monoclonal antibody recognizing an intrinsically autoreactive heavy chain, we show enrichment in self-reactive cells specifically at the transitional to naive mature B cell stage in WAS subjects. Our combined data support a model wherein modest alterations in B cell-intrinsic, BCR, and TLR signals in WAS, and likely other autoimmune disorders, are sufficient to alter B cell tolerance via positive selection of self-reactive transitional B cells. PMID:26371186

  11. Deletion of Wiskott–Aldrich syndrome protein triggers Rac2 activity and increased cross-presentation by dendritic cells

    PubMed Central

    Baptista, Marisa A. P.; Keszei, Marton; Oliveira, Mariana; Sunahara, Karen K. S.; Andersson, John; Dahlberg, Carin I. M.; Worth, Austen J.; Liedén, Agne; Kuo, I-Chun; Wallin, Robert P. A.; Snapper, Scott B.; Eidsmo, Liv; Scheynius, Annika; Karlsson, Mikael C. I.; Bouma, Gerben; Burns, Siobhan O.; Forsell, Mattias N. E.; Thrasher, Adrian J.; Nylén, Susanne; Westerberg, Lisa S.

    2016-01-01

    Wiskott–Aldrich syndrome (WAS) is caused by loss-of-function mutations in the WASp gene. Decreased cellular responses in WASp-deficient cells have been interpreted to mean that WASp directly regulates these responses in WASp-sufficient cells. Here, we identify an exception to this concept and show that WASp-deficient dendritic cells have increased activation of Rac2 that support cross-presentation to CD8+ T cells. Using two different skin pathology models, WASp-deficient mice show an accumulation of dendritic cells in the skin and increased expansion of IFNγ-producing CD8+ T cells in the draining lymph node and spleen. Specific deletion of WASp in dendritic cells leads to marked expansion of CD8+ T cells at the expense of CD4+ T cells. WASp-deficient dendritic cells induce increased cross-presentation to CD8+ T cells by activating Rac2 that maintains a near neutral pH of phagosomes. Our data reveals an intricate balance between activation of WASp and Rac2 signalling pathways in dendritic cells. PMID:27425374

  12. Deletion of Wiskott-Aldrich syndrome protein triggers Rac2 activity and increased cross-presentation by dendritic cells.

    PubMed

    Baptista, Marisa A P; Keszei, Marton; Oliveira, Mariana; Sunahara, Karen K S; Andersson, John; Dahlberg, Carin I M; Worth, Austen J; Liedén, Agne; Kuo, I-Chun; Wallin, Robert P A; Snapper, Scott B; Eidsmo, Liv; Scheynius, Annika; Karlsson, Mikael C I; Bouma, Gerben; Burns, Siobhan O; Forsell, Mattias N E; Thrasher, Adrian J; Nylén, Susanne; Westerberg, Lisa S

    2016-07-18

    Wiskott-Aldrich syndrome (WAS) is caused by loss-of-function mutations in the WASp gene. Decreased cellular responses in WASp-deficient cells have been interpreted to mean that WASp directly regulates these responses in WASp-sufficient cells. Here, we identify an exception to this concept and show that WASp-deficient dendritic cells have increased activation of Rac2 that support cross-presentation to CD8(+) T cells. Using two different skin pathology models, WASp-deficient mice show an accumulation of dendritic cells in the skin and increased expansion of IFNγ-producing CD8(+) T cells in the draining lymph node and spleen. Specific deletion of WASp in dendritic cells leads to marked expansion of CD8(+) T cells at the expense of CD4(+) T cells. WASp-deficient dendritic cells induce increased cross-presentation to CD8(+) T cells by activating Rac2 that maintains a near neutral pH of phagosomes. Our data reveals an intricate balance between activation of WASp and Rac2 signalling pathways in dendritic cells.

  13. Altered BCR and TLR signals promote enhanced positive selection of autoreactive transitional B cells in Wiskott-Aldrich syndrome

    PubMed Central

    Kolhatkar, Nikita S.; Brahmandam, Archana; Thouvenel, Christopher D.; Becker-Herman, Shirly; Jacobs, Holly M.; Schwartz, Marc A.; Allenspach, Eric J.; Khim, Socheath; Panigrahi, Anil K.; Luning Prak, Eline T.; Thrasher, Adrian J.; Notarangelo, Luigi D.; Candotti, Fabio; Torgerson, Troy R.; Sanz, Ignacio

    2015-01-01

    Wiskott-Aldrich syndrome (WAS) is an X-linked immunodeficiency disorder frequently associated with systemic autoimmunity, including autoantibody-mediated cytopenias. WAS protein (WASp)–deficient B cells have increased B cell receptor (BCR) and Toll-like receptor (TLR) signaling, suggesting that these pathways might impact establishment of the mature, naive BCR repertoire. To directly investigate this possibility, we evaluated naive B cell specificity and composition in WASp-deficient mice and WAS subjects (n = 12). High-throughput sequencing and single-cell cloning analysis of the BCR repertoire revealed altered heavy chain usage and enrichment for low-affinity self-reactive specificities in murine marginal zone and human naive B cells. Although negative selection mechanisms including deletion, anergy, and receptor editing were relatively unperturbed, WASp-deficient transitional B cells showed enhanced proliferation in vivo mediated by antigen- and Myd88-dependent signals. Finally, using both BCR sequencing and cell surface analysis with a monoclonal antibody recognizing an intrinsically autoreactive heavy chain, we show enrichment in self-reactive cells specifically at the transitional to naive mature B cell stage in WAS subjects. Our combined data support a model wherein modest alterations in B cell–intrinsic, BCR, and TLR signals in WAS, and likely other autoimmune disorders, are sufficient to alter B cell tolerance via positive selection of self-reactive transitional B cells. PMID:26371186

  14. Second-site mutation in the Wiskott-Aldrich syndrome (WAS) protein gene causes somatic mosaicism in two WAS siblings

    PubMed Central

    Wada, Taizo; Konno, Akihiro; Schurman, Shepherd H.; Garabedian, Elizabeth K.; Anderson, Stacie M.; Kirby, Martha; Nelson, David L.; Candotti, Fabio

    2003-01-01

    Revertant mosaicism due to true back mutations or second-site mutations has been identified in several inherited disorders. The occurrence of revertants is considered rare, and the underlying genetic mechanisms remain mostly unknown. Here we describe somatic mosaicism in two brothers affected with Wiskott-Aldrich syndrome (WAS). The original mutation causing disease in this family is a single base insertion (1305insG) in the WAS protein (WASP) gene, which results in frameshift and abrogates protein expression. Both patients, however, showed expression of WASP in a fraction of their T cells that were demonstrated to carry a second-site mutation causing the deletion of 19 nucleotides from nucleotide 1299 to 1316. This deletion abrogated the effects of the original mutation and restored the WASP reading frame. In vitro expression studies indicated that mutant protein encoded by the second-site mutation was expressed and functional, since it was able to bind to cellular partners and mediate T cell receptor/CD3 downregulation. These observations were consistent with evidence of in vivo selective advantage of WASP-expressing lymphocytes. Molecular analysis revealed that the sequence surrounding the deletion contained two 4-bp direct repeats and that a hairpin structure could be formed by five GC pairs within the deleted fragment. These findings strongly suggest that slipped mispairing was the cause of this second-site mutation and that selective accumulation of WASP-expressing T lymphocytes led to revertant mosaicism in these patients. PMID:12727931

  15. Deletion of Wiskott-Aldrich syndrome protein triggers Rac2 activity and increased cross-presentation by dendritic cells.

    PubMed

    Baptista, Marisa A P; Keszei, Marton; Oliveira, Mariana; Sunahara, Karen K S; Andersson, John; Dahlberg, Carin I M; Worth, Austen J; Liedén, Agne; Kuo, I-Chun; Wallin, Robert P A; Snapper, Scott B; Eidsmo, Liv; Scheynius, Annika; Karlsson, Mikael C I; Bouma, Gerben; Burns, Siobhan O; Forsell, Mattias N E; Thrasher, Adrian J; Nylén, Susanne; Westerberg, Lisa S

    2016-01-01

    Wiskott-Aldrich syndrome (WAS) is caused by loss-of-function mutations in the WASp gene. Decreased cellular responses in WASp-deficient cells have been interpreted to mean that WASp directly regulates these responses in WASp-sufficient cells. Here, we identify an exception to this concept and show that WASp-deficient dendritic cells have increased activation of Rac2 that support cross-presentation to CD8(+) T cells. Using two different skin pathology models, WASp-deficient mice show an accumulation of dendritic cells in the skin and increased expansion of IFNγ-producing CD8(+) T cells in the draining lymph node and spleen. Specific deletion of WASp in dendritic cells leads to marked expansion of CD8(+) T cells at the expense of CD4(+) T cells. WASp-deficient dendritic cells induce increased cross-presentation to CD8(+) T cells by activating Rac2 that maintains a near neutral pH of phagosomes. Our data reveals an intricate balance between activation of WASp and Rac2 signalling pathways in dendritic cells. PMID:27425374

  16. Two sisters with clinical diagnosis of Wiskott-Aldrich Syndrome: Is the condition in the family autosomal recessive?

    SciTech Connect

    Kondoh, T.; Hayashi, K.; Matsumoto, T.

    1995-10-09

    We report two sisters in a family representing manifestations of Wiskott-Aldrich syndrome (WAS), an X-linked immunodeficiency disorder. An elder sister had suffered from recurrent infections, small thrombocytopenic petechiae, purpura, and eczema for 7 years. The younger sister had the same manifestations as the elder sister`s for a 2-year period, and died of intracranial bleeding at age 2 years. All the laboratory data of the two patients were compatible with WAS, although they were females. Sialophorin analysis with the selective radioactive labeling method of this protein revealed that in the elder sister a 115-KD band that should be specific for sialophorin was reduced in quantity, and instead an additional 135-KD fragment was present as a main band. Polymerase chain reaction (PCR) analysis of the sialophorin gene and single-strand conformation polymorphism (SSCP) analysis of the PCR product demonstrated that there were no detectable size-change nor electrophoretic mobility change in the DNA from both patients. The results indicated that their sialophorin gene structure might be normal. Studies on the mother-daughter transmission of X chromosome using a pERT84-MaeIII polymorphic marker mapped at Xp21 and HPRT gene polymorphism at Xq26 suggested that each sister had inherited a different X chromosome from the mother. Two explanations are plausible for the occurrence of the WAS in our patients: the WAS in the patients is attributable to an autosomal gene mutation which may regulate the sialophorin gene expression through the WAS gene, or, alternatively, the condition in this family is an autosomal recessive disorder separated etiologically from the X-linked WAS. 17 refs., 6 figs., 1 tab.

  17. Wiskott-Aldrich Syndrome Protein (WASp) Controls the Delivery of Platelet Transforming Growth Factor-β1*

    PubMed Central

    Kim, Hugh; Falet, Hervé; Hoffmeister, Karin M.; Hartwig, John H.

    2013-01-01

    Platelets are immunologically competent cells containing cytokines such as TGF-β1 that regulate cell-mediated immunity. However, the mechanisms underlying cytokine secretion from platelets are undefined. The Wiskott-Aldrich syndrome protein (WASp) regulates actin polymerization in nucleated hematopoietic cells but has other role(s) in platelets. WASp-null (WASp−/−) platelets stimulated with a PAR-4 receptor agonist had increased TGF-β1 release compared with WT platelets; inhibiting WASp function with wiskostatin augmented TRAP-induced TGF-β1 release in human platelets. TGF-β1 release is dissociated from α-granule secretion (P-selectin up-regulation) and occurs more gradually, with ∼10–15% released after 30–60 min. Blockade of Src family kinase-mediated WASp Tyr-291/Tyr-293 phosphorylation increased TGF-β1 release, with no additive effect in WASp−/− platelets, signifying that phosphorylation is critical for WASp-limited TGF-β1 secretion. Inhibiting F-actin assembly with cytochalasin D enhanced secretion in WT platelets and further increased TGF-β1 release in WASp−/− platelets, indicating that WASp and actin assembly independently regulate TGF-β1 release. A permeabilized platelet model was used to test the role of upstream small GTPases in TGF-β1 release. N17Cdc42, but not Rac1 mutants, increased TGF-β1 secretion and abrogated WASp phosphorylation. We conclude that WASp function restricts TGF-β1 secretion in a Cdc42- and Src family kinase-dependent manner and independently of actin assembly. PMID:24133214

  18. Researchers Hooked on Teaching. Noted Scholars Discuss the Synergies of Teaching and Research. Foundations for Organizational Science Series.

    ERIC Educational Resources Information Center

    Andre, Rae, Ed.; Frost, Peter J., Ed.

    This collection of 19 essays is organized into a narrative of the teaching-research dilemma. The essays include: (1) "Struggling With Balance" (Cynthia V. Fukami); (2) "My Career as a Teacher: Promise, Failure, Redemption" (Howard E. Aldrich); (3) "Teaching and Research: A Puzzling Dichotomy" (Barbara A. Gutek); (4) "If It's Not Teaching and…

  19. Research on biochemical spectrum denoising based on a novel wavelet threshold function and an improved translation-invariance method

    NASA Astrophysics Data System (ADS)

    Ren, Zhong; Liu, Guodong; Zeng, Lvming; Huang, Zhen; Huang, Shuanggen

    2008-12-01

    In this paper, an improved wavelet threshold denoising with combined translation invariance(TI)method is adopted to remove noises existed in the bio-chemical spectrum. Meanwhile, a novel wavelet threshold function and an optimal threshold determination algorithm are proposed. The new function is continuous and high-order derivable, it can overcome the vibration phenomena generated by the classical threshold function and decrease the error of reconstructed spectrum. So, it is superior to the frequency-domain filtering methods, the soft- and hard-threshold function proposed by D.L. Donoho and the semisoft-threshold function proposed by Gao, etc. The experimental results show that the improved TI wavelet threshold(TI-WT) denoising method can availably eliminate the Pseudo-Gibbs phenomena generated by the traditional wavelet thresholding method. At the same time, the improved wavelet threshold function and the TI-WT method present lower root mean-square-error (RMSE) and higher signal-to-noise ratio(SNR) than the frequency-domain filtering, classical soft and hard-threshold denoising The SNR increasing from 17.3200 to 32.5609, the RMSE decreasing from 4.0244 to 0.6257. Otherwise, The improved denoising method not only makes the spectrum smooth, but also effectively preserves the edge characteristics of the original spectrum.

  20. Postnatal cytomegalovirus infection in an infant with congenital thrombocytopenia: how it can support or mislead the diagnosis of Wiskott-Aldrich syndrome.

    PubMed

    Poddighe, Dimitri; Virginia, Elena; Nedbal, Marco; Soresina, Annarosa; Bruni, Paola

    2016-09-01

    A male newborn developed a post-natal cytomegalovirus (CMV) infection, arising in the clinical setting of congenital thrombocytopenia, which was diagnosed as being alloimmune. The evidence of active CMV infection in an infant showing slow-resolution lower airways infection, persistent neonatal and low platelet volume thrombocytopenia, and diffuse eczema (associated to very high levels of serum immunoglobulin E) led to the diagnosis of Wiskott-Aldrich syndrome (WAS) before the third month of life, despite the presence of several confounding clinical factors. The correct interpretation of all clinical features supported the precocious diagnosis of WAS. PMID:27668906

  1. Platelet actin nodules are podosome-like structures dependent on Wiskott–Aldrich syndrome protein and ARP2/3 complex

    PubMed Central

    Poulter, Natalie S.; Pollitt, Alice Y.; Davies, Amy; Malinova, Dessislava; Nash, Gerard B.; Hannon, Mike J.; Pikramenou, Zoe; Rappoport, Joshua Z.; Hartwig, John H.; Owen, Dylan M.; Thrasher, Adrian J.; Watson, Stephen P.; Thomas, Steven G.

    2015-01-01

    The actin nodule is a novel F-actin structure present in platelets during early spreading. However, only limited detail is known regarding nodule organization and function. Here we use electron microscopy, SIM and dSTORM super-resolution, and live-cell TIRF microscopy to characterize the structural organization and signalling pathways associated with nodule formation. Nodules are composed of up to four actin-rich structures linked together by actin bundles. They are enriched in the adhesion-related proteins talin and vinculin, have a central core of tyrosine phosphorylated proteins and are depleted of integrins at the plasma membrane. Nodule formation is dependent on Wiskott–Aldrich syndrome protein (WASp) and the ARP2/3 complex. WASp−/− mouse blood displays impaired platelet aggregate formation at arteriolar shear rates. We propose actin nodules are platelet podosome-related structures required for platelet–platelet interaction and their absence contributes to the bleeding diathesis of Wiskott–Aldrich syndrome. PMID:26028144

  2. Wiskott-Aldrich syndrome in a girl caused by heterozygous WASP mutation and extremely skewed X-chromosome inactivation: a novel association with maternal uniparental isodisomy 6.

    PubMed

    Takimoto, Tomohito; Takada, Hidetoshi; Ishimura, Masataka; Kirino, Makiko; Hata, Kenichiro; Ohara, Osamu; Morio, Tomohiro; Hara, Toshiro

    2015-01-01

    Wiskott-Aldrich syndrome (WAS) is an X-linked disease characterized by microthrombocytopenia, eczema and immune deficiency, caused primarily by mutations in the WASP (Wiskott-Aldrich syndrome protein) gene. Female carriers are usually asymptomatic because of the preferential activation of the normal, nonmutated X-chromosome in their hematopoietic cells. We report our observations of a female child with WAS, who displayed symptoms of congenital thrombocytopenia. DNA sequencing analysis of the WASP gene revealed a heterozygous nonsense mutation in exon 10. The expressions of WASP and normal WASP mRNA were defective. We found preferential inactivation of the X-chromosome on which wild-type WASP was located. Single-nucleotide polymorphism microarray testing and the analysis of the polymorphic variable number of tandem repeat regions revealed maternal uniparental isodisomy of chromosome 6 (UPD6). Our results underscore the importance of WASP evaluation in females with congenital thrombocytopenia and suggest that UPD6 might be related to the pathophysiology of nonrandom X-chromosome inactivation. PMID:25633059

  3. A Program on Biochemical and Biomedical Engineering.

    ERIC Educational Resources Information Center

    San, Ka-Yiu; McIntire, Larry V.

    1989-01-01

    Presents an introduction to the Biochemical and Biomedical Engineering program at Rice University. Describes the development of the academic and enhancement programs, including organizational structure and research project titles. (YP)

  4. Biochemical transformation of coals

    DOEpatents

    Lin, Mow S.; Premuzic, Eugene T.

    1999-03-23

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed.

  5. Biochemical transformation of coals

    DOEpatents

    Lin, M.S.; Premuzic, E.T.

    1999-03-23

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed. 7 figs.

  6. Epstein-Barr serology in immunodeficiencies: an attempt to correlate with immune abnormalities in Wiskott-Aldrich and Chediak-Higashi syndromes and ataxia telangiectasia.

    PubMed Central

    Vilmer, E; Lenoir, G M; Virelizier, J L; Griscelli, C

    1984-01-01

    Epstein-Barr (EB) virus serology was correlated with the results of immunological investigations of three inherited immunodeficiency diseases, in an attempt to understand the immune mechanisms controlling EB virus infection. In nine patients with Wiskott-Aldrich syndrome (WAS), the constant lack of anti-EB virus associated nuclear antigen (EBNA) was accompanied by a consistent impairment of allogeneic cytotoxicity. We confirmed a frequent absence of anti-EBNA antibody in ataxia telangiectasia (AT), and we showed a correlation between the level of anti-EBNA response and the mixed leucocyte response (MLR), i.e., an absence of anti-EBNA antibody correlated with a decreased MLR. In two of three untreated patients with Chediak-Higashi syndrome (CHS), high persistent titres of anti-EA antibodies were observed, which were possibly related to a defective natural killer (NK) cell activity. In spite of previous infection with EB virus, none of the 41 patients exhibited clinical signs attributable to the virus, suggesting that residual or compensatory mechanisms must have limited activation of the virus. In patients with AT and WAS these mechanisms may include NK cell activity, which is not depressed in these syndromes, whereas in patients with CHS, they may involve T cell cytotoxicity. PMID:6321070

  7. IL-2 in the tumor microenvironment is necessary for Wiskott-Aldrich syndrome protein deficient NK cells to respond to tumors in vivo

    PubMed Central

    Kritikou, Joanna S.; Dahlberg, Carin I. M.; Baptista, Marisa A. P.; Wagner, Arnika K.; Banerjee, Pinaki P.; Gwalani, Lavesh Amar; Poli, Cecilia; Panda, Sudeepta K.; Kärre, Klas; Kaech, Susan M.; Wermeling, Fredrik; Andersson, John; Orange, Jordan S.; Brauner, Hanna; Westerberg, Lisa S.

    2016-01-01

    To kill target cells, natural killer (NK) cells organize signaling from activating and inhibitory receptors to form a lytic synapse. Wiskott-Aldrich syndrome (WAS) patients have loss-of-function mutations in the actin regulator WASp and suffer from immunodeficiency with increased risk to develop lymphoreticular malignancies. NK cells from WAS patients fail to form lytic synapses, however, the functional outcome in vivo remains unknown. Here, we show that WASp KO NK cells had decreased capacity to degranulate and produce IFNγ upon NKp46 stimulation and this was associated with reduced capacity to kill MHC class I-deficient hematopoietic grafts. Pre-treatment of WASp KO NK cells with IL-2 ex vivo restored degranulation, IFNγ production, and killing of MHC class I negative hematopoietic grafts. Moreover, WASp KO mice controlled growth of A20 lymphoma cells that naturally produced IL-2. WASp KO NK cells showed increased expression of DNAM-1, LAG-3, and KLRG1, all receptors associated with cellular exhaustion and NK cell memory. NK cells isolated from WAS patient spleen cells showed increased expression of DNAM-1 and had low to negative expression of CD56, a phenotype associated with NK cells exhaustion. Finally, in a cohort of neuroblastoma patients we identified a strong correlation between WASp, IL-2, and patient survival. PMID:27477778

  8. IL-2 in the tumor microenvironment is necessary for Wiskott-Aldrich syndrome protein deficient NK cells to respond to tumors in vivo.

    PubMed

    Kritikou, Joanna S; Dahlberg, Carin I M; Baptista, Marisa A P; Wagner, Arnika K; Banerjee, Pinaki P; Gwalani, Lavesh Amar; Poli, Cecilia; Panda, Sudeepta K; Kärre, Klas; Kaech, Susan M; Wermeling, Fredrik; Andersson, John; Orange, Jordan S; Brauner, Hanna; Westerberg, Lisa S

    2016-01-01

    To kill target cells, natural killer (NK) cells organize signaling from activating and inhibitory receptors to form a lytic synapse. Wiskott-Aldrich syndrome (WAS) patients have loss-of-function mutations in the actin regulator WASp and suffer from immunodeficiency with increased risk to develop lymphoreticular malignancies. NK cells from WAS patients fail to form lytic synapses, however, the functional outcome in vivo remains unknown. Here, we show that WASp KO NK cells had decreased capacity to degranulate and produce IFNγ upon NKp46 stimulation and this was associated with reduced capacity to kill MHC class I-deficient hematopoietic grafts. Pre-treatment of WASp KO NK cells with IL-2 ex vivo restored degranulation, IFNγ production, and killing of MHC class I negative hematopoietic grafts. Moreover, WASp KO mice controlled growth of A20 lymphoma cells that naturally produced IL-2. WASp KO NK cells showed increased expression of DNAM-1, LAG-3, and KLRG1, all receptors associated with cellular exhaustion and NK cell memory. NK cells isolated from WAS patient spleen cells showed increased expression of DNAM-1 and had low to negative expression of CD56, a phenotype associated with NK cells exhaustion. Finally, in a cohort of neuroblastoma patients we identified a strong correlation between WASp, IL-2, and patient survival. PMID:27477778

  9. A Novel Neural Wiskott-Aldrich Syndrome Protein (N-Wasp) Binding Protein, Wish, Induces Arp2/3 Complex Activation Independent of Cdc42

    PubMed Central

    Fukuoka, Maiko; Suetsugu, Shiro; Miki, Hiroaki; Fukami, Kiyoko; Endo, Takeshi; Takenawa, Tadaomi

    2001-01-01

    We identified a novel adaptor protein that contains a Src homology (SH)3 domain, SH3 binding proline-rich sequences, and a leucine zipper-like motif and termed this protein WASP interacting SH3 protein (WISH). WISH is expressed predominantly in neural tissues and testis. It bound Ash/Grb2 through its proline-rich regions and neural Wiskott-Aldrich syndrome protein (N-WASP) through its SH3 domain. WISH strongly enhanced N-WASP–induced Arp2/3 complex activation independent of Cdc42 in vitro, resulting in rapid actin polymerization. Furthermore, coexpression of WISH and N-WASP induced marked formation of microspikes in Cos7 cells, even in the absence of stimuli. An N-WASP mutant (H208D) that cannot bind Cdc42 still induced microspike formation when coexpressed with WISH. We also examined the contribution of WISH to a rapid actin polymerization induced by brain extract in vitro. Arp2/3 complex was essential for brain extract–induced rapid actin polymerization. Addition of WISH to extracts increased actin polymerization as Cdc42 did. However, WISH unexpectedly could activate actin polymerization even in N-WASP–depleted extracts. These findings suggest that WISH activates Arp2/3 complex through N-WASP–dependent and –independent pathways without Cdc42, resulting in the rapid actin polymerization required for microspike formation. PMID:11157975

  10. Signalling to actin assembly via the WASP (Wiskott-Aldrich syndrome protein)-family proteins and the Arp2/3 complex.

    PubMed Central

    Millard, Thomas H; Sharp, Stewart J; Machesky, Laura M

    2004-01-01

    The assembly of a branched network of actin filaments provides the mechanical propulsion that drives a range of dynamic cellular processes, including cell motility. The Arp2/3 complex is a crucial component of such filament networks. Arp2/3 nucleates new actin filaments while bound to existing filaments, thus creating a branched network. In recent years, a number of proteins that activate the filament nucleation activity of Arp2/3 have been identified, most notably the WASP (Wiskott-Aldrich syndrome protein) family. WASP-family proteins activate the Arp2/3 complex, and consequently stimulate actin assembly, in response to extracellular signals. Structural studies have provided a significant refinement in our understanding of the molecular detail of how the Arp2/3 complex nucleates actin filaments. There has also been much progress towards an understanding of the complicated signalling processes that regulate WASP-family proteins. In addition, the use of gene disruption in a number of organisms has led to new insights into the specific functions of individual WASP-family members. The present review will discuss the Arp2/3 complex and its regulators, in particular the WASP-family proteins. Emphasis will be placed on recent developments in the field that have furthered our understanding of actin dynamics and cell motility. PMID:15040784

  11. A LARGE KINDRED WITH X-LINKED NEUTROPENIA WITH AN I294T MUTATION OF THE WISKOTT-ALDRICH SYNDROME GENE

    PubMed Central

    Beel, Karolien; Cotter, Melanie M.; Blatny, Jan; Bond, Jonathan; Lucas, Geoff; Greene, Frances; Vanduppen, Vik; Leung, Daisy W.; Rooney, Sean; Smith, Owen P.; Rosen, Michael K.; Vandenberghe, Peter

    2011-01-01

    X-linked neutropenia (XLN, OMIM #300299) is a rare form of severe congenital neutropenia. It was originally described in a three-generation family with 5 affected members and with an L270P mutation in the GTP-ase binding domain (GBD) of the Wiskott-Aldrich-syndrome protein (WASP) (Devriendt, et al 2001). Here, we report and describe a large three-generation family with XLN, with 10 affected males and 8 female carriers. A c.882T>C WAS gene mutation was identified, resulting in an I294T mutation. The infectious course is variable and mild in view of the deep neutropenia. In addition to the original description, low-normal IgA levels, low to low-normal platelet counts and reduced NK-cell counts also appear as consistent XLN features. However, inverted CD4/CD8 ratios were not found in this family, nor were cases identified with myelodysplastic syndrome or acute myeloid leukaemia. Female carriers exhibited a variable attenuated phenotype. Like L270P WASP, I294T WASP is constitutively active towards actin polymerisation In conclusion, this largest XLN kindred identified to date provides new independent genetic evidence that mutations disrupting the auto-inhibitory GBD of WASP are the cause of XLN. Reduced NK cells, low to low normal platelet counts and low to low-normal IgA levels are also features of XLN. PMID:19006568

  12. B cell–intrinsic deficiency of the Wiskott-Aldrich syndrome protein (WASp) causes severe abnormalities of the peripheral B-cell compartment in mice

    PubMed Central

    Recher, Mike; Burns, Siobhan O.; de la Fuente, Miguel A.; Volpi, Stefano; Dahlberg, Carin; Walter, Jolan E.; Moffitt, Kristin; Mathew, Divij; Honke, Nadine; Lang, Philipp A.; Patrizi, Laura; Falet, Hervé; Keszei, Marton; Mizui, Masayuki; Csizmadia, Eva; Candotti, Fabio; Nadeau, Kari; Bouma, Gerben; Delmonte, Ottavia M.; Frugoni, Francesco; Fomin, Angela B. Ferraz; Buchbinder, David; Lundequist, Emma Maria; Massaad, Michel J.; Tsokos, George C.; Hartwig, John; Manis, John; Terhorst, Cox; Geha, Raif S.; Snapper, Scott; Lang, Karl S.; Malley, Richard; Westerberg, Lisa

    2012-01-01

    Wiskott Aldrich syndrome (WAS) is caused by mutations in the WAS gene that encodes for a protein (WASp) involved in cytoskeleton organization in hematopoietic cells. Several distinctive abnormalities of T, B, and natural killer lymphocytes; dendritic cells; and phagocytes have been found in WASp-deficient patients and mice; however, the in vivo consequence of WASp deficiency within individual blood cell lineages has not been definitively evaluated. By conditional gene deletion we have generated mice with selective deficiency of WASp in the B-cell lineage (B/WcKO mice). We show that this is sufficient to cause a severe reduction of marginal zone B cells and inability to respond to type II T-independent Ags, thereby recapitulating phenotypic features of complete WASp deficiency. In addition, B/WcKO mice showed prominent signs of B-cell dysregulation, as indicated by an increase in serum IgM levels, expansion of germinal center B cells and plasma cells, and elevated autoantibody production. These findings are accompanied by hyperproliferation of WASp-deficient follicular and germinal center B cells in heterozygous B/WcKO mice in vivo and excessive differentiation of WASp-deficient B cells into class-switched plasmablasts in vitro, suggesting that WASp-dependent B cell–intrinsic mechanisms critically contribute to WAS-associated autoimmunity. PMID:22302739

  13. c-Src and neural Wiskott-Aldrich syndrome protein (N-WASP) promote low oxygen-induced accelerated brain invasion by gliomas.

    PubMed

    Tang, Zhuo; Araysi, Lita M; Fathallah-Shaykh, Hassan M

    2013-01-01

    Malignant gliomas remain associated with poor prognosis and high morbidity because of their ability to invade the brain; furthermore, human gliomas exhibit a phenotype of accelerated brain invasion in response to anti-angiogenic drugs. Here, we study 8 human glioblastoma cell lines; U251, U87, D54 and LN229 show accelerated motility in low ambient oxygen. Src inhibition by Dasatinib abrogates this phenotype. Molecular discovery and validation studies evaluate 46 molecules related to motility or the src pathway in U251 cells. Demanding that the molecular changes induced by low ambient oxygen are reversed by Dasatinib in U251 cells, identifies neural Wiskott-Aldrich syndrome protein (NWASP), Focal adhesion Kinase (FAK), [Formula: see text]-Catenin, and Cofilin. However, only Src-mediated NWASP phosphorylation distinguishes the four cell lines that exhibit enhanced motility in low ambient oxygen. Downregulating c-Src or NWASP by RNA interference abrogates the low-oxygen-induced enhancement in motility by in vitro assays and in organotypic brain slice cultures. The findings support the idea that c-Src and NWASP play key roles in mediating the molecular pathogenesis of low oxygen-induced accelerated brain invasion by gliomas.

  14. Biochemical Engineering Fundamentals

    ERIC Educational Resources Information Center

    Bailey, J. E.; Ollis, D. F.

    1976-01-01

    Discusses a biochemical engineering course that is offered as part of a chemical engineering curriculum and includes topics that influence the behavior of man-made or natural microbial or enzyme reactors. (MLH)

  15. Biochemical Education in Leisure.

    ERIC Educational Resources Information Center

    Tayyab, Saad

    1994-01-01

    Presents two alternative teaching approaches to ensure that students become active participants of learning in the biochemistry classroom. Diagrams and rules are provided for using educational playing cards and creating a biochemical comic book. (ZWH)

  16. Disruption of hSWI/SNF complexes in T cells by WAS mutations distinguishes X-linked thrombocytopenia from Wiskott-Aldrich syndrome.

    PubMed

    Sarkar, Koustav; Sadhukhan, Sanjoy; Han, Seong-Su; Vyas, Yatin M

    2014-11-27

    Wiskott-Aldrich syndrome (WAS), an immunodeficiency disorder, and X-linked thrombocytopenia (XLT), a bleeding disorder, both arise from nonsynonymous mutations in WAS, which encodes a hematopoietic-specific WASp. Intriguingly, XLT evolves into WAS in some patients but not in others; yet the biological basis for this cross-phenotype (CP) effect remains unclear. Using human T-helper (TH) cells expressing different disease-causing WAS mutations, we demonstrated that hSWI/SNF-like complexes require nuclear-WASp to execute their chromatin-remodeling activity at promoters of WASp-target, immune function genes during TH1 differentiation. Hot-spot WAS mutations Thr45Met and Arg86Cys, which result in XLT-to-WAS disease progression, impair recruitment of hBRM- but not BRG1-enriched BAF complexes to IFNG and TBX21 promoters. Moreover, promoter enrichment of histone H2A.Z and its catalyzing enzyme EP400 are both impaired. Consequently, activation of Notch signaling, a hBRM-regulated event, and its downstream effector NF-κB are both compromised, along with decreased accessibility of nucleosomal DNA and inefficient transcription-elongation of WASp-target TH1 genes. In contrast, patient mutations Ala236Gly and Arg477Lys that manifest in XLT without progressing to WAS do not disrupt chromatin remodeling or transcriptional reprogramming of TH1 genes. Our study defines an indispensable relationship between nuclear-WASp- and hSWI/SNF-complexes in gene activation and reveals molecular distinctions in TH cells that might contribute to disease severity in the XLT/WAS clinical spectrum.

  17. Biochemical Markers of Myocardial Damage

    PubMed Central

    2016-01-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  18. Biochemical Markers of Myocardial Damage.

    PubMed

    Bodor, Geza S

    2016-04-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  19. Biochemical Education in Brazil.

    ERIC Educational Resources Information Center

    Vella, F.

    1988-01-01

    Described are discussions held concerning the problems of biochemical education in Brazil at a meeting of the Sociedade Brazileira de Bioquimica in April 1988. Also discussed are other visits that were made to universities in Brazil. Three major recommendations to improve the state of biochemistry education in Brazil are presented. (CW)

  20. Biochemical upgrading of oils

    DOEpatents

    Premuzic, E.T.; Lin, M.S.

    1999-01-12

    A process for biochemical conversion of heavy crude oils is provided. The process includes contacting heavy crude oils with adapted biocatalysts. The resulting upgraded oil shows, a relative increase in saturated hydrocarbons, emulsions and oxygenates and a decrease in compounds containing organic sulfur, organic nitrogen and trace metals. Adapted microorganisms which have been modified under challenged growth processes are also disclosed. 121 figs.

  1. Nanoparticles as biochemical sensors

    PubMed Central

    El-Ansary, Afaf; Faddah, Layla M

    2010-01-01

    There is little doubt that nanoparticles offer real and new opportunities in many fields, such as biomedicine and materials science. Such particles are small enough to enter almost all areas of the body, including cells and organelles, potentially leading to new approaches in nanomedicine. Sensors for small molecules of biochemical interest are of critical importance. This review is an attempt to trace the use of nanomaterials in biochemical sensor design. The possibility of using nanoparticles functionalized with antibodies as markers for proteins will be elucidated. Moreover, capabilities and applications for nanoparticles based on gold, silver, magnetic, and semiconductor materials (quantum dots), used in optical (absorbance, luminescence, surface enhanced Raman spectroscopy, surface plasmon resonance), electrochemical, and mass-sensitive sensors will be highlighted. The unique ability of nanosensors to improve the analysis of biochemical fluids is discussed either through considering the use of nanoparticles for in vitro molecular diagnosis, or in the biological/biochemical analysis for in vivo interaction with the human body. PMID:24198472

  2. Research on Effects and Compatibility Taking of Different Sports Supplements on the Biochemical Indicators and Body Functions of Elite Walking Athletes.

    PubMed

    Jia, Jia

    2015-01-01

    Scientific training, elimination of fatigue, and reasonable nutrition is the three important parts of successful training. Especially in the fatigue recovery and reasonable nutrition of track and field endurance project, which is more important than other project significance? This paper is to more scientific nutritional intervention on the walking athletes to improve athletic performance and provide experimental evidence 12 male and 12 female athletes were selected from the Chinese national walking team were given the nutrition intervention of a variety of sports supplements for 9 weeks. The serum testosterone (T), blood urea (BU), and serum creative phosphokinase (CK) and other indicators were tested in several weekends. The results showed that the different exercise taking supplements can increase the T levels of male and female walking athletes, and promote the body protein synthesis and the function of rapid recovery, reduce the levels of serum CK and BU abnormalities after the intensity training, and ensure the smooth completion of the training and a normal competitive level. The different exercise taking supplements can improve the biochemical indicators and improve the level of physical function.

  3. Progress in biochemical engineering.

    PubMed

    Böing, J T

    1976-07-01

    Biochemical engineering is one of the answers to some of the challenges of the present age: hunger, shortage in raw material and energy supply and contamination of environment. Its contribution to the solution of these problems is the industrial production of protein, the use of raw materials (incl. waste products) not used up to now, the accomplishment of chemical reactions at ambient temperatures as well as the degradation or utilization of widely different waste materials.

  4. Wiskott-Aldrich Syndrome Interacting Protein Deficiency Uncovers the Role of the Co-receptor CD19 as a Generic Hub for PI3 Kinase Signaling in B Cells.

    PubMed

    Keppler, Selina Jessica; Gasparrini, Francesca; Burbage, Marianne; Aggarwal, Shweta; Frederico, Bruno; Geha, Raif S; Way, Michael; Bruckbauer, Andreas; Batista, Facundo D

    2015-10-20

    Humans with Wiskott-Aldrich syndrome display a progressive immunological disorder associated with compromised Wiskott-Aldrich Syndrome Interacting Protein (WIP) function. Mice deficient in WIP recapitulate such an immunodeficiency that has been attributed to T cell dysfunction; however, any contribution of B cells is as yet undefined. Here we have shown that WIP deficiency resulted in defects in B cell homing, chemotaxis, survival, and differentiation, ultimately leading to diminished germinal center formation and antibody production. Furthermore, in the absence of WIP, several receptors, namely the BCR, BAFFR, CXCR4, CXCR5, CD40, and TLR4, were impaired in promoting CD19 co-receptor activation and subsequent PI3 kinase (PI3K) signaling. The underlying mechanism was due to a distortion in the actin and tetraspanin networks that lead to altered CD19 cell surface dynamics. In conclusion, our findings suggest that, by regulating the cortical actin cytoskeleton, WIP influences the function of CD19 as a general hub for PI3K signaling. PMID:26453379

  5. Wiskott-Aldrich Syndrome Interacting Protein Deficiency Uncovers the Role of the Co-receptor CD19 as a Generic Hub for PI3 Kinase Signaling in B Cells.

    PubMed

    Keppler, Selina Jessica; Gasparrini, Francesca; Burbage, Marianne; Aggarwal, Shweta; Frederico, Bruno; Geha, Raif S; Way, Michael; Bruckbauer, Andreas; Batista, Facundo D

    2015-10-20

    Humans with Wiskott-Aldrich syndrome display a progressive immunological disorder associated with compromised Wiskott-Aldrich Syndrome Interacting Protein (WIP) function. Mice deficient in WIP recapitulate such an immunodeficiency that has been attributed to T cell dysfunction; however, any contribution of B cells is as yet undefined. Here we have shown that WIP deficiency resulted in defects in B cell homing, chemotaxis, survival, and differentiation, ultimately leading to diminished germinal center formation and antibody production. Furthermore, in the absence of WIP, several receptors, namely the BCR, BAFFR, CXCR4, CXCR5, CD40, and TLR4, were impaired in promoting CD19 co-receptor activation and subsequent PI3 kinase (PI3K) signaling. The underlying mechanism was due to a distortion in the actin and tetraspanin networks that lead to altered CD19 cell surface dynamics. In conclusion, our findings suggest that, by regulating the cortical actin cytoskeleton, WIP influences the function of CD19 as a general hub for PI3K signaling.

  6. Vector Encoding in Biochemical Networks

    NASA Astrophysics Data System (ADS)

    Potter, Garrett; Sun, Bo

    Encoding of environmental cues via biochemical signaling pathways is of vital importance in the transmission of information for cells in a network. The current literature assumes a single cell state is used to encode information, however, recent research suggests the optimal strategy utilizes a vector of cell states sampled at various time points. To elucidate the optimal sampling strategy for vector encoding, we take an information theoretic approach and determine the mutual information of the calcium signaling dynamics obtained from fibroblast cells perturbed with different concentrations of ATP. Specifically, we analyze the sampling strategies under the cases of fixed and non-fixed vector dimension as well as the efficiency of these strategies. Our results show that sampling with greater frequency is optimal in the case of non-fixed vector dimension but that, in general, a lower sampling frequency is best from both a fixed vector dimension and efficiency standpoint. Further, we find the use of a simple modified Ornstein-Uhlenbeck process as a model qualitatively captures many of our experimental results suggesting that sampling in biochemical networks is based on a few basic components.

  7. Biochemical Screening for in utero Drug Exposure.

    PubMed

    Wright, Tricia E

    2015-01-01

    Licit and illicit drug use is a common complication of pregnancy. Accurate information on drug use is difficult to obtain for many reasons as women fear self-disclosure or consenting for drug testing due to stigma, guilt, and fear of social and legal harm. As information about drug use is clinically very important, biochemical testing is an important adjunct to careful maternal history. In addition, research studies depend on accurate measures of exposure when reporting risks of a substance. This paper delineates available matrices for and methods of biochemical drug testing in pregnant women and neonates.

  8. Biochemical Education in Thailand: Past, Present, and Future.

    ERIC Educational Resources Information Center

    Svasti, Jisnuson; Surarit, Rudee

    1991-01-01

    Traces the history of Thailand's biochemical education from its initial evolution from medicine to modern day. Discusses the following aspects of Thailand's modern biochemical education: biochemistry teaching at Thai schools, university departments and biochemistry courses, textbooks, degree programs, interplay between research and teaching, and…

  9. Biochemical indices associated with meditation practice: a literature review.

    PubMed

    Delmonte, M M

    1985-01-01

    Research findings on biochemical responsivity to meditation are reviewed. Although there are some contradictory and inconclusive outcomes, there is nevertheless sufficient evidence of interest to warrant further investigation of this area. However, in the meantime, there is no compelling basis to conclude that meditation practice is associated with special state or trait effects at the biochemical level.

  10. Wiskott-Aldrich Syndrome (WAS)

    MedlinePlus

    ... Patients Procedure for Accessing Lab Services Data Package Requirements AIDS Therapies Resource Guide In Vitro Efficacy Evaluations ... Assurances to Users Application and Approval Process User Requirements Malaria Vaccine Production Services Data Sharing and Release ...

  11. Biochemical Reversal of Aging

    NASA Astrophysics Data System (ADS)

    Ely, John T. A.

    2006-03-01

    We cite our progress on biochemical reversal of aging. However, it may be circa 2 years before we have necessary substances at low cost. Meanwhile, without them, a number of measures can be adopted providing marked improvement for the problems of aging in modern societies. For example, enzymes are needed to excrete toxins that accelerate aging; Hg is the ultimate toxin that disables all enzymes (including those needed to excrete Hg itself). Low Hg level in the urine, due to loss of excretory ability, causes the diagnosis of Hg toxicity to almost always be missed. Hg sources must be removed from the body! Another example is excess sugar; hyperglycemia decreases intracellular ascorbic acid (AA) by competitively inhibiting the insulin- mediated active transport of AA into cells. Thus, immunity is impaired by low leucocyte AA. AA is needed for new proteins in aging tissues. Humans must supplement AA; their need same as in AA-synthesizing mammals.

  12. A randomized controlled trial investigating the effect of Pycnogenol and Bacopa CDRI08 herbal medicines on cognitive, cardiovascular, and biochemical functioning in cognitively healthy elderly people: the Australian Research Council Longevity Intervention (ARCLI) study protocol (ANZCTR12611000487910)

    PubMed Central

    2012-01-01

    Background One of the major challenges associated with our ageing population is the increasing incidence of age-associated cognitive decline, which has significant implications for an individual's ability to lead a productive and fulfilling life. In pure economic terms the costs of ageing reflects decreased productivity and engagement with the workforce. The maintenance of brain health underpinning intact cognition is a key factor to maintaining a positive, engaged, and productive lifestyle. In light of this, the role of diet, including supplementation with nutritional and even pharmacological interventions capable of ameliorating the neurocognitive changes that occur with age constitute vital areas of research. Methods In order to reduce cognitive ageing, the ARC longevity intervention (ARCLI) was developed to examine the effects of two promising natural pharmacologically active supplements on cognitive performance. ARCLI is a randomized, placebo-controlled, double-blind, 3-arm clinical trial in which 465 participants will be randomized to receive an extract of Bacopa monnieri (CDRI08 300 mg/day), Pycnogenol (150 mg/day), or placebo daily for 12 months. Participants will be tested at baseline and then at 3, 6 and 12 months post-randomization on a wide battery of cognitive, neuropsychological and mood measures, cardiovascular (brachial and aortic systolic and diastolic blood pressures as well as arterial stiffness), biochemical (assays to measure inflammation, oxidative stress and safety) as well as genetic assessments (telomere length and several Single Nucleotide Polymorphisms). The primary aim is to investigate the effects of these supplements on cognitive performance. The secondary aims are to explore the time-course of cognitive enhancement as well as potential cardiovascular and biochemical mechanisms underpinning cognitive enhancement over the 12 months of administration. ARCLI will represent one of the largest and most comprehensive experimental clinical

  13. Alcoholic myopathy: biochemical mechanisms.

    PubMed

    Preedy, V R; Paice, A; Mantle, D; Dhillon, A S; Palmer, T N; Peters, T J

    2001-08-01

    Between one- and two-thirds of all alcohol abusers have impairment of muscle function that may be accompanied by biochemical lesions and/or the presence of a defined myopathy characterised by selective atrophy of Type II fibres. Perturbations in protein metabolism are central to the effects on muscle and account for the reductions in muscle mass and fibre diameter. Ethanol abuse is also associated with abnormalities in carbohydrate (as well as lipid) metabolism in skeletal muscle. Ethanol-mediated insulin resistance is allied with the inhibitory effects of ethanol on insulin-stimulated carbohydrate metabolism. It acutely impairs insulin-stimulated glucose and lipid metabolism, although it is not known whether it has an analogous effect on insulin-stimulated protein synthesis. In alcoholic cirrhosis, insulin resistance occurs with respect to carbohydrate metabolism, although the actions of insulin to suppress protein degradation and stimulate amino acid uptake are unimpaired. In acute alcohol-dosing studies defective rates of protein synthesis occur, particularly in Type II fibre-predominant muscles. The relative amounts of mRNA-encoding contractile proteins do not appear to be adversely affected by chronic alcohol feeding, although subtle changes in muscle protein isoforms may occur. There are also rapid and sustained reductions in total (largely ribosomal) RNA in chronic studies. Loss of RNA appears to be related to increases in the activities of specific muscle RNases in these long-term studies. However, in acute dosing studies (less than 1 day), the reductions in muscle protein synthesis are not due to overt loss of total RNA. These data implicate a role for translational modifications in the initial stages of the myopathy, although changes in transcription and/or protein degradation may also be superimposed. These events have important implications for whole-body metabolism.

  14. A Course in... Biochemical Engineering.

    ERIC Educational Resources Information Center

    Ng, Terry K-L.; And Others

    1988-01-01

    Describes a chemical engineering course for senior undergraduates and first year graduate students in biochemical engineering. Discusses five experiments used in the course: aseptic techniques, dissolved oxygen measurement, oxygen uptake by yeast, continuous sterilization, and cultivation of microorganisms. (MVL)

  15. [Biochemical antenatal screening for fetal anomalies.].

    PubMed

    Torfadóttir, G; Jónsson, J J

    2001-05-01

    Biochemical antenatal screening started 30 years ago. Initially, the goal was to detect neural tube defects by measuring a-fetoprotein in maternal serum (MS-AFP) and amniotic fluid (AF-AFP). The serendipitous discovery of an association between low AFP maternal serum concentration and chromosomal anomalies resulted in increased research interest in biochemical screening in pregnancy. Subsequently double, triple or quadruple tests in 2nd trimester of pregnancy became widely used in combination with fetal chromosome determination in at risk individuals. In Iceland, antenatal screening for chromosomal anomalies has essentially been based on fetal chromosome studies offered to pregnant women 35 years or older. This strategy needs to be revised. Recently first trimester biochemical screening based on maternal serum pregnancy associated plasma protein A (MS-PAPP-A) and free b-human chorionic gonadotropin (MS-free b-hCG) and multivariate risk assessment has been developed. This screening test can be improved if done in conjunction with nuchal translucency measurements in an early sonography scan. PMID:17018982

  16. Rethinking glycolysis: on the biochemical logic of metabolic pathways.

    PubMed

    Bar-Even, Arren; Flamholz, Avi; Noor, Elad; Milo, Ron

    2012-05-17

    Metabolic pathways may seem arbitrary and unnecessarily complex. In many cases, a chemist might devise a simpler route for the biochemical transformation, so why has nature chosen such complex solutions? In this review, we distill lessons from a century of metabolic research and introduce new observations suggesting that the intricate structure of metabolic pathways can be explained by a small set of biochemical principles. Using glycolysis as an example, we demonstrate how three key biochemical constraints--thermodynamic favorability, availability of enzymatic mechanisms and the physicochemical properties of pathway intermediates--eliminate otherwise plausible metabolic strategies. Considering these constraints, glycolysis contains no unnecessary steps and represents one of the very few pathway structures that meet cellular demands. The analysis presented here can be applied to metabolic engineering efforts for the rational design of pathways that produce a desired product while satisfying biochemical constraints.

  17. Biotechnology for a renewable resources chemicals and fuels industry, biochemical engineering R and D

    SciTech Connect

    Villet, R.H.

    1980-04-01

    To establish an effective biotechnology of biomass processing for the production of fuels and chemicals, an integration of research in biochemical engineering, microbial genetics, and biochemistry is required. Reduction of the costs of producing chemicals and fuels from renewable resources will hinge on extensive research in biochemical engineering.

  18. BEST: Biochemical Engineering Simulation Technology

    SciTech Connect

    Not Available

    1996-01-01

    The idea of developing a process simulator that can describe biochemical engineering (a relatively new technology area) was formulated at the National Renewable Energy Laboratory (NREL) during the late 1980s. The initial plan was to build a consortium of industrial and U.S. Department of Energy (DOE) partners to enhance a commercial simulator with biochemical unit operations. DOE supported this effort; however, before the consortium was established, the process simulator industry changed considerably. Work on the first phase of implementing various fermentation reactors into the chemical process simulator, ASPEN/SP-BEST, is complete. This report will focus on those developments. Simulation Sciences, Inc. (SimSci) no longer supports ASPEN/SP, and Aspen Technology, Inc. (AspenTech) has developed an add-on to its ASPEN PLUS (also called BioProcess Simulator [BPS]). This report will also explain the similarities and differences between BEST and BPS. ASPEN, developed by the Massachusetts Institute of Technology for DOE in the late 1970s, is still the state-of-the-art chemical process simulator. It was selected as the only simulator with the potential to be easily expanded into the biochemical area. ASPEN/SP, commercially sold by SimSci, was selected for the BEST work. SimSci completed work on batch, fed-batch, and continuous fermentation reactors in 1993, just as it announced it would no longer commercially support the complete ASPEN/SP product. BEST was left without a basic support program. Luckily, during this same time frame, AspenTech was developing a biochemical simulator with its version of ASPEN (ASPEN PLUS), which incorporates most BEST concepts. The future of BEST will involve developing physical property data and models appropriate to biochemical systems that are necessary for good biochemical process design.

  19. Long-term outcome and lineage-specific chimerism in 194 patients with Wiskott-Aldrich syndrome treated by hematopoietic cell transplantation in the period 1980-2009: an international collaborative study

    PubMed Central

    Moratto, Daniele; Giliani, Silvia; Bonfim, Carmem; Mazzolari, Evelina; Fischer, Alain; Ochs, Hans D.; Cant, Andrew J.; Thrasher, Adrian J.; Cowan, Morton J.; Albert, Michael H.; Small, Trudy; Pai, Sung-Yun; Haddad, Elie; Lisa, Antonella; Hambleton, Sophie; Slatter, Mary; Cavazzana-Calvo, Marina; Mahlaoui, Nizar; Picard, Capucine; Torgerson, Troy R.; Burroughs, Lauri; Koliski, Adriana; Neto, Jose Zanis; Porta, Fulvio; Qasim, Waseem; Veys, Paul; Kavanau, Kristina; Hönig, Manfred; Schulz, Ansgar; Friedrich, Wilhelm

    2011-01-01

    In this retrospective collaborative study, we have analyzed long-term outcome and donor cell engraftment in 194 patients with Wiskott-Aldrich syndrome (WAS) who have been treated by hematopoietic cell transplantation (HCT) in the period 1980- 2009. Overall survival was 84.0% and was even higher (89.1% 5-year survival) for those who received HCT since the year 2000, reflecting recent improvement of outcome after transplantation from mismatched family donors and for patients who received HCT from an unrelated donor at older than 5 years. Patients who went to transplantation in better clinical conditions had a lower rate of post-HCT complications. Retrospective analysis of lineage-specific donor cell engraftment showed that stable full donor chimerism was attained by 72.3% of the patients who survived for at least 1 year after HCT. Mixed chimerism was associated with an increased risk of incomplete reconstitution of lymphocyte count and post-HCT autoimmunity, and myeloid donor cell chimerism < 50% was associated with persistent thrombocytopenia. These observations indicate continuous improvement of outcome after HCT for WAS and may have important implications for the development of novel protocols aiming to obtain full correction of the disease and reduce post-HCT complications. PMID:21659547

  20. Long-term outcome and lineage-specific chimerism in 194 patients with Wiskott-Aldrich syndrome treated by hematopoietic cell transplantation in the period 1980-2009: an international collaborative study.

    PubMed

    Moratto, Daniele; Giliani, Silvia; Bonfim, Carmem; Mazzolari, Evelina; Fischer, Alain; Ochs, Hans D; Cant, Andrew J; Thrasher, Adrian J; Cowan, Morton J; Albert, Michael H; Small, Trudy; Pai, Sung-Yun; Haddad, Elie; Lisa, Antonella; Hambleton, Sophie; Slatter, Mary; Cavazzana-Calvo, Marina; Mahlaoui, Nizar; Picard, Capucine; Torgerson, Troy R; Burroughs, Lauri; Koliski, Adriana; Neto, Jose Zanis; Porta, Fulvio; Qasim, Waseem; Veys, Paul; Kavanau, Kristina; Hönig, Manfred; Schulz, Ansgar; Friedrich, Wilhelm; Notarangelo, Luigi D

    2011-08-11

    In this retrospective collaborative study, we have analyzed long-term outcome and donor cell engraftment in 194 patients with Wiskott-Aldrich syndrome (WAS) who have been treated by hematopoietic cell transplantation (HCT) in the period 1980- 2009. Overall survival was 84.0% and was even higher (89.1% 5-year survival) for those who received HCT since the year 2000, reflecting recent improvement of outcome after transplantation from mismatched family donors and for patients who received HCT from an unrelated donor at older than 5 years. Patients who went to transplantation in better clinical conditions had a lower rate of post-HCT complications. Retrospective analysis of lineage-specific donor cell engraftment showed that stable full donor chimerism was attained by 72.3% of the patients who survived for at least 1 year after HCT. Mixed chimerism was associated with an increased risk of incomplete reconstitution of lymphocyte count and post-HCT autoimmunity, and myeloid donor cell chimerism < 50% was associated with persistent thrombocytopenia. These observations indicate continuous improvement of outcome after HCT for WAS and may have important implications for the development of novel protocols aiming to obtain full correction of the disease and reduce post-HCT complications. PMID:21659547

  1. Bone marrow transplantation in a child with Wiskott-Aldrich syndrome latently infected with acyclovir-resistant (ACV(r)) herpes simplex virus type 1: emergence of foscarnet-resistant virus originating from the ACV(r) virus.

    PubMed

    Saijo, Masayuki; Yasuda, Yukiharu; Yabe, Hiromasa; Kato, Shunichi; Suzutani, Tatsuo; De Clercq, Erik; Niikura, Masahiro; Maeda, Akihiko; Kurane, Ichiro; Morikawa, Shigeru

    2002-09-01

    A human leukocyte antigen (HLA)-matched unrelated bone marrow transplantation (BMT) was performed in a 13-year-old patient with the congenital immunodeficiency syndrome, Wiskott-Aldrich syndrome. The patient had a history of acyclovir (ACV)-resistant (ACV(r)) herpes simplex virus type 1 (HSV-1) infections prior to BMT. After BMT, the skin lesions caused by HSV-1 relapsed on the face and genito-anal areas. Ganciclovir (GCV) therapy was initiated, but the mucocutaneous lesions worsened. An HSV-1 isolate recovered from the lesions during this episode was resistant to both ACV and GCV. The ACV(r) isolate was confirmed to have the same mutation in the viral thymidine kinase (TK) gene as that of the previously isolated ACV(r) isolates from the patient. After treatment switch to foscarnet (PFA), there was a satisfactory remission but not a complete recovery. Although the mucocutaneous lesions improved, a PFA-resistant (PFA(r)) HSV-1 was isolated 1 month after the start of PFA therapy. The PFA(r) HSV-1 isolate coded for the same mutation in the viral TK gene as the ACV(r) HSV-1 isolates. Furthermore, the PFA(r) isolate also expressed a mutated viral DNA polymerase (DNA pol) with an amino acid (Gly) substitution for Val at position 715. This is the first report on the clinical course of a BMT-associated ACV(r) HSV-1 infection that subsequently developed resistance to foscarnet as well.

  2. Overview of the DOE/SERI Biochemical Conversion Program

    SciTech Connect

    Wright, J D

    1986-09-01

    The Solar Energy Research Institute manages a program of research and development on the biochemical conversion of renewable lignocellulosic materials to liquid fuels for the Department of Energy's Biofuels and Municipal Waste Technology Division. The Biochemical Conversion Program is mission oriented so effort is concentrated on technologies which appear to have the greatest potential for being adopted by the private sector to economically convert lignocellulosic materials into high value liquid transportation fuels such as ethanol. The program is structured to supply the technology for such fuels to compete economically first as an octane booster or fuel additive, and, with additional improvements, as a neat fuel. 18 refs., 3 figs., 1 tab.

  3. Circadian Clocks: Unexpected Biochemical Cogs

    PubMed Central

    Mori, Tetsuya; Mchaourab, Hassane; Johnson, Carl Hirschie

    2015-01-01

    A circadian oscillation can be reconstituted in vitro from three proteins that cycles with a period of ~24 h. Two recent studies provide surprising biochemical answers to why this remarkable oscillator has such a long time constant and how it can switch effortlessly between alternating enzymatic modes. PMID:26439342

  4. Biochemical Engineering. Part II: Process Design

    ERIC Educational Resources Information Center

    Atkinson, B.

    1972-01-01

    Describes types of industrial techniques involving biochemical products, specifying the advantages and disadvantages of batch and continuous processes, and contrasting biochemical and chemical engineering. See SE 506 318 for Part I. (AL)

  5. Actin dynamics regulated by the balance of neuronal Wiskott-Aldrich syndrome protein (N-WASP) and cofilin activities determines the biphasic response of glucose-induced insulin secretion.

    PubMed

    Uenishi, Eita; Shibasaki, Tadao; Takahashi, Harumi; Seki, Chihiro; Hamaguchi, Hitomi; Yasuda, Takao; Tatebe, Masao; Oiso, Yutaka; Takenawa, Tadaomi; Seino, Susumu

    2013-09-01

    Actin dynamics in pancreatic β-cells is involved in insulin secretion. However, the molecular mechanisms of the regulation of actin dynamics by intracellular signals in pancreatic β-cells and its role in phasic insulin secretion are largely unknown. In this study, we elucidate the regulation of actin dynamics by neuronal Wiskott-Aldrich syndrome protein (N-WASP) and cofilin in pancreatic β-cells and demonstrate its role in glucose-induced insulin secretion (GIIS). N-WASP, which promotes actin polymerization through activation of the actin nucleation factor Arp2/3 complex, was found to be activated by glucose stimulation in insulin-secreting clonal pancreatic β-cells (MIN6-K8 β-cells). Introduction of a dominant-negative mutant of N-WASP, which lacks G-actin and Arp2/3 complex-binding region VCA, into MIN6-K8 β-cells or knockdown of N-WASP suppressed GIIS, especially the second phase. We also found that cofilin, which severs F-actin in its dephosphorylated (active) form, is converted to the phosphorylated (inactive) form by glucose stimulation in MIN6-K8 β-cells, thereby promoting F-actin remodeling. In addition, the dominant-negative mutant of cofilin, which inhibits activation of endogenous cofilin, or knockdown of cofilin reduced the second phase of GIIS. However, the first phase of GIIS occurs in the G-actin predominant state, in which cofilin activity predominates over N-WASP activity. Thus, actin dynamics regulated by the balance of N-WASP and cofilin activities determines the biphasic response of GIIS.

  6. Biochemical Disincentives to Fertilizing Cellulosic Ethanol Crops

    NASA Astrophysics Data System (ADS)

    Gallagher, M. E.; Hockaday, W. C.; Snapp, S.; McSwiney, C.; Baldock, J.

    2010-12-01

    Corn grain biofuel crops produce the highest yields when the cropping ecosystem is not nitrogen (N)-limited, achieved by application of fertilizer. There are environmental consequences for excessive fertilizer application to crops, including greenhouse gas emissions, hypoxic “dead zones,” and health problems from N runoff into groundwater. The increase in corn acreage in response to demand for alternative fuels (i.e. ethanol) could exacerbate these problems, and divert food supplies to fuel production. A potential substitute for grain ethanol that could reduce some of these impacts is cellulosic ethanol. Cellulosic ethanol feedstocks include grasses (switchgrass), hardwoods, and crop residues (e.g. corn stover, wheat straw). It has been assumed that these feedstocks will require similar N fertilization rates to grain biofuel crops to maximize yields, but carbohydrate yield versus N application has not previously been monitored. We report the biochemical stocks (carbohydrate, protein, and lignin in Mg ha-1) of a corn ecosystem grown under varying N levels. We measured biochemical yield in Mg ha-1 within the grain, leaf and stem, and reproductive parts of corn plants grown at seven N fertilization rates (0-202 kg N ha-1), to evaluate the quantity and quality of these feedstocks across a N fertilization gradient. The N fertilization rate study was performed at the Kellogg Biological Station-Long Term Ecological Research Site (KBS-LTER) in Michigan. Biochemical stocks were measured using 13C nuclear magnetic resonance spectroscopy (NMR), combined with a molecular mixing model (Baldock et al. 2004). Carbohydrate and lignin are the main biochemicals of interest in ethanol production since carbohydrate is the ethanol feedstock, and lignin hinders the carbohydrate to ethanol conversion process. We show that corn residue carbohydrate yields respond only weakly to N fertilization compared to grain. Grain carbohydrate yields plateau in response to fertilization at

  7. Biochemical enzyme analysis in acute leukaemia.

    PubMed Central

    Drexler, H G; Gaedicke, G; Minowada, J

    1985-01-01

    This report summarises the current knowledge regarding the clinical utility of biochemical enzyme markers for both diagnostic and therapeutic purposes in acute leukaemia. The enzymes studied most extensively in this field are terminal deoxynucleotidyl transferase, adenosine deaminase, 5'-nucleotidase, purine nucleoside phosphorylase, and acid phosphatase, esterase, hexosaminidase isoenzymes. For each enzyme, the quantitative and qualitative characteristics in various immunologically defined subclasses of acute leukaemia are described. The quantitative evaluation of enzyme activities represents an adjunctive classification technique which should be incorporated into the multivariate analysis, the "multiple marker analysis." By qualitative characterisation pronounced heterogeneity of leukaemia subsets is uncovered. The application of 2'-deoxycoformycin, a specific inhibitor of adenosine deaminase, and the potential usefulness of two other enzymes as targets for treatment with selective agents is discussed. The concept that gene products expressed at certain developmental stages of normal cells can similarly be detected in leukaemic cells (which therefore seem to be "frozen" or "arrested" at this particular maturation/differentiation stage) is supported by the results obtained in enzyme studies. Besides their practical clinical importance for classification and treatment of acute leukaemias, biochemical enzyme markers constitute a valuable research tool to disclose biological properties of leukaemic cells. PMID:2981904

  8. Biochemical responses of the Skylab crewman

    NASA Technical Reports Server (NTRS)

    Leach, C. S.; Rambaut, P. C.

    1974-01-01

    The biochemical investigations of the Skylab crewmen were designed to study the physiological changes that were observed on flight crews returning from previous space flight missions as well as to study those changes expected to result from prolonged weightless exposure. These studies can be divided into two broad categories. One category included routine blood studies similar to those used in clinical medical practice. The second included research-type endocrine analyses used to investigate more thoroughly the metabolic/endocrine responses to the space flight environment. The premission control values indicated that all Skylab crewmen were healthy and were free from biochemical abnormalities. The routine results during and after flight showed slight but significant changes in electrolytes, glucose, total protein, osmolality, uric acid, cholesterol, and creatinine. Plasma hormal changes included adrenocorticotrophic hormone, cortisol, angiotensin I, aldosterone, insulin, and thyroxine. The 24-hour urine analyses results revealed increased excretion of cortisol, catecholamines, antidiuretic hormone, and aldosterone as well as excretion of significant electrolyte and uric acid during the Skylab flights.

  9. Biochemical adaptation to ocean acidification.

    PubMed

    Stillman, Jonathon H; Paganini, Adam W

    2015-06-01

    The change in oceanic carbonate chemistry due to increased atmospheric PCO2  has caused pH to decline in marine surface waters, a phenomenon known as ocean acidification (OA). The effects of OA on organisms have been shown to be widespread among diverse taxa from a wide range of habitats. The majority of studies of organismal response to OA are in short-term exposures to future levels of PCO2 . From such studies, much information has been gathered on plastic responses organisms may make in the future that are beneficial or harmful to fitness. Relatively few studies have examined whether organisms can adapt to negative-fitness consequences of plastic responses to OA. We outline major approaches that have been used to study the adaptive potential for organisms to OA, which include comparative studies and experimental evolution. Organisms that inhabit a range of pH environments (e.g. pH gradients at volcanic CO2 seeps or in upwelling zones) have great potential for studies that identify adaptive shifts that have occurred through evolution. Comparative studies have advanced our understanding of adaptation to OA by linking whole-organism responses with cellular mechanisms. Such optimization of function provides a link between genetic variation and adaptive evolution in tuning optimal function of rate-limiting cellular processes in different pH conditions. For example, in experimental evolution studies of organisms with short generation times (e.g. phytoplankton), hundreds of generations of growth under future conditions has resulted in fixed differences in gene expression related to acid-base regulation. However, biochemical mechanisms for adaptive responses to OA have yet to be fully characterized, and are likely to be more complex than simply changes in gene expression or protein modification. Finally, we present a hypothesis regarding an unexplored area for biochemical adaptation to ocean acidification. In this hypothesis, proteins and membranes exposed to the

  10. Ordering events of biochemical evolution.

    PubMed

    Cunchillos, C; Lecointre, G

    2007-05-01

    Metabolic pathways exhibit structures resulting from an evolutionary process. Pathways have been inherited through time with modification, from the earliest periods of life. It is possible to compare the structure of pathways as done in comparative anatomy, i.e. for inferring ancestral pathways or parts of it (ancestral enzymatic functions), using standard phylogenetic reconstruction. Thus a phylogenetic tree of pathways provides a relative ordering of the rise of enzymatic functions. It even becomes possible to order the birth of each complete pathway in time. This particular "DNA-free" conceptual approach to evolutionary biochemistry is reviewed, gathering all the justifications given for it. Then, the method of assigning a given pathway to a time span of biochemical development is revisited. The previous method used an implicit "clock" of metabolic development that is difficult to justify. We develop a new clock-free approach, using functional biochemical arguments. Results of the two methods are not significantly different; our method is just more precise. This suggests that the clock assumed in the first method does not provoke any important artefact in describing the development of biochemical evolution. It is just unnecessary to postulate it. As a result, most of the amino acid metabolic pathways develop forwards, confirming former models of amino acid catabolism evolution, but not those for amino acid anabolism. The order of appearance of sectors of universal cellular metabolism is: (1) amino acid catabolism, (2) amino acid anabolism and closure of the urea cycle, (3) glycolysis and glycogenesis, (4) closure of the pentose-phosphate cycle, (5) closure of the Krebs cycle and fatty acids metabolism, (6) closure of the Calvin cycle.

  11. Biochemical structure of Calendula officinalis.

    PubMed

    Korakhashvili, A; Kacharava, T; Kiknavelidze, N

    2007-01-01

    Calendula officinalis is a well known medicinal herb. It is common knowledge that its medicinal properties are conditioned on biologically active complex substances of Carotin (Provitamin A), Stearin, Triterpiniod, Plavonoid, Kumarin, macro and micro compound elements. Because of constant need in raw material of Calendula officinalis, features of its ontogenetic development agro-biological qualities in various eco regions of Georgia were investigated. The data of biologically active compounds, biochemical structure and the maintenance both in flowers and in others parts of plant is presented; the pharmacological activity and importance in medicine was reviewed. PMID:17921550

  12. Biochemically enhanced methane production from coal

    NASA Astrophysics Data System (ADS)

    Opara, Aleksandra

    For many years, biogas was connected mostly with the organic matter decomposition in shallow sediments (e.g., wetlands, landfill gas, etc.). Recently, it has been realized that biogenic methane production is ongoing in many hydrocarbon reservoirs. This research examined microbial methane and carbon dioxide generation from coal. As original contributions methane production from various coal materials was examined in classical and electro-biochemical bench-scale reactors using unique, developed facultative microbial consortia that generate methane under anaerobic conditions. Facultative methanogenic populations are important as all known methanogens are strict anaerobes and their application outside laboratory would be problematic. Additional testing examined the influence of environmental conditions, such as pH, salinity, and nutrient amendments on methane and carbon dioxide generation. In 44-day ex-situ bench-scale batch bioreactor tests, up to 300,000 and 250,000 ppm methane was generated from bituminous coal and bituminous coal waste respectively, a significant improvement over 20-40 ppm methane generated from control samples. Chemical degradation of complex hydrocarbons using environmentally benign reagents, prior to microbial biodegradation and methanogenesis, resulted in dissolution of up to 5% bituminous coal and bituminous coal waste and up to 25% lignite in samples tested. Research results confirm that coal waste may be a significant underutilized resource that could be converted to useful fuel. Rapid acidification of lignite samples resulted in low pH (below 4.0), regardless of chemical pretreatment applied, and did not generate significant methane amounts. These results confirmed the importance of monitoring and adjusting in situ and ex situ environmental conditions during methane production. A patented Electro-Biochemical Reactor technology was used to supply electrons and electron acceptor environments, but appeared to influence methane generation in a

  13. 77 FR 5847 - Manufacturer of Controlled Substances; Notice of Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Manufacturer of Controlled Substances; Notice of Application Pursuant to Sec. 1301.33(a), Title 21 of the Code of Federal Regulations (CFR), this is notice that on November 15, 2011, Sigma Aldrich Research Biochemicals,...

  14. 76 FR 5829 - Manufacturer of Controlled Substances; Notice of Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-02

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Manufacturer of Controlled Substances; Notice of Application Pursuant to Sec. 1301.33(a), Title 21 of the Code of Federal Regulations (CFR), this is notice that on November 24, 2010, Sigma Aldrich Research Biochemicals,...

  15. 75 FR 14190 - Manufacturer of Controlled Substances; Notice of Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-24

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Manufacturer of Controlled Substances; Notice of Application Pursuant to Sec. 1301.33(a) of Title 21 of the Code of Federal Regulations (CFR), this is notice that on December 4, 2009, Sigma Aldrich Research Biochemicals,...

  16. Occurrence of bacteria and biochemical markers on public surfaces.

    PubMed

    Reynolds, Kelly A; Watt, Pamela M; Boone, Stephanie A; Gerba, Charles P

    2005-06-01

    From 1999-2003, the hygiene of 1061 environmental surfaces from shopping, daycare, and office environments, personal items, and miscellaneous activities (i.e., gymnasiums, airports, movie theaters, restaurants, etc.), in four US cities, was monitored. Samples were analyzed for fecal and total coliform bacteria, protein, and biochemical markers. Biochemical markers, i.e., hemoglobin (blood marker), amylase (mucus, saliva, sweat, and urine marker), and urea (urine and sweat marker) were detected on 3% (26/801); 15% (120/801), and 6% (48/801) of the surfaces, respectively. Protein (general hygiene marker) levels > or = 200 microg/10 cm2 were present on 26% (200/801) of the surfaces tested. Surfaces from children's playground equipment and daycare centers were the most frequently contaminated (biochemical markers on 36%; 15/42 and 46%; 25/54, respectively). Surfaces from the shopping, miscellaneous activities, and office environments were positive for biochemical markers with a frequency of 21% (69/333), 21% (66/308), and 11% (12/105), respectively). Sixty samples were analyzed for biochemical markers and bacteria. Total and fecal coliforms were detected on 20% (12/60) and 7% (4/ 60) of the surfaces, respectively. Half and one-third of the sites positive for biochemical markers were also positive for total and fecal coliforms, respectively. Artificial contamination of public surfaces with an invisible fluorescent tracer showed that contamination from outside surfaces was transferred to 86% (30/ 35) of exposed individual's hands and 82% (29/35) tracked the tracer to their home or personal belongings hours later. Results provide information on the relative hygiene of commonly encountered public surfaces and aid in the identification of priority environments where contaminant occurrence and risk of exposure may be greatest. Children's playground equipment is identified as a priority surface for additional research on the occurrence of and potential exposure to infectious

  17. Biochemical Conversion: Using Enzymes, Microbes, and Catalysis to Make Fuels and Chemicals

    SciTech Connect

    2013-07-26

    This fact sheet describes the Bioenergy Technologies Office's biochemical conversion work and processes. BETO conducts collaborative research, development, and demonstration projects to improve several processing routes for the conversion of cellulosic biomass.

  18. Assessing phenotypic, biochemical, and molecular diversity in coriander (Coriandrum sativum L.) germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This research was conducted to elucidate phenotypic and biochemical diversity in 60 coriander (Coriandrum sativum L.) accessions maintained at the North Central Regional Plant Introduction Station and examine relationships between amplified fragment length polymorphisms (AFLP) and patterns of phenot...

  19. Biochemical Analysis of Protein SUMOylation

    PubMed Central

    Alontaga, Aileen Y.; Bobkova, Ekaterina; Chen, Yuan

    2012-01-01

    SUMOylation, the covalent attachment of Small Ubiquitin-like MOdifier (SUMO) polypeptides to other proteins, is among the most important post-translational modifications that regulate the functional properties of a large number of proteins. SUMOylation is broadly involved in cellular processes such as gene transcription, hormone response, signal transduction, DNA repair and nuclear transport. SUMO modification has also been implicated in the pathogenesis of human diseases, such as cancer, neurodegenerative disorders and viral infection. Attachment of a SUMO protein to another protein is carried out in multiple steps catalyzed by three enzymes. This unit describes and discusses the in vitro biochemical methods used for investigating each step of the SUMOylation process. In addition, a high throughput screening protocol is included for the identification of inhibitors of SUMOylation. PMID:22870855

  20. Biochemical markers of acute pancreatitis.

    PubMed

    Matull, W R; Pereira, S P; O'Donohue, J W

    2006-04-01

    Serum amylase remains the most commonly used biochemical marker for the diagnosis of acute pancreatitis, but its sensitivity can be reduced by late presentation, hypertriglyceridaemia, and chronic alcoholism. Urinary trypsinogen-2 is convenient, of comparable diagnostic accuracy, and provides greater (99%) negative predictive value. Early prediction of the severity of acute pancreatitis can be made by well validated scoring systems at 48 hours, but the novel serum markers procalcitonin and interleukin 6 allow earlier prediction (12 to 24 hours after admission). Serum alanine transaminase >150 IU/l and jaundice suggest a gallstone aetiology, requiring endoscopic retrograde cholangiopancreatography. For obscure aetiologies, serum calcium and triglycerides should be measured. Genetic polymorphisms may play an important role in "idiopathic" acute recurrent pancreatitis.

  1. Hyponatraemia: biochemical and clinical perspectives.

    PubMed Central

    Gill, G.; Leese, G.

    1998-01-01

    Hyponatraemia is a common bio-chemical abnormality, occurring in about 15% of hospital inpatients. It is often associated with severe illness and relatively poor outcome. Pathophysiologically, hyponatraemia may be spurious, dilutional, depletional or redistributional. Particularly difficult causes and concepts of hyponatraemia are the syndrome of inappropriate antidiuresis and the sick cell syndrome, which are discussed here in detail. Therapy should always be targeted at the underlying disease process. 'Hyponatraemic symptoms' are of doubtful importance, and may be more related to water overload and/or the causative disease, than to hyponatraemia per se. Artificial elevation of plasma sodium by saline infusion carries the risk of induction of osmotic demyelination (central pontine myelinolysis). PMID:10211323

  2. Diagnosis of hyperandrogenism: biochemical criteria.

    PubMed

    Stanczyk, Frank Z

    2006-06-01

    Biochemical derangements in ovarian, adrenal, and peripheral androgen production and metabolism play an important role in underlying causes of hyperandrogenism. Specific diagnostic serum markers such as testosterone (total) and dehydroepiandrosterone sulfate (DHEAS), respectively, may be helpful in the diagnosis of ovarian and adrenal hyperandrogenism, respectively. Validated immunoassays or mass spectrometry assays should be used to quantify testosterone, DHEAS and other principal androgens. Free testosterone measurements, determined by equilibrium dialysis or the calculated method, are advocated for routine evaluation of more subtle forms of hyperandrogenism. The skin, with its pilosebaceous units (PSUs), is an important site of active androgen production. A key regulator in PSUs is 5alpha-reductase, which transforms testosterone or androstenedione to dihydrotestosterone (DHT). DHT in blood is not effective in indicating the presence of hyperandrogenism. However, distal metabolites of DHT have been shown to be good markers of clinical manifestations of hirsutism, acne and alopecia. Assays for these peripheral markers need improvement for routine clinical testing. PMID:16772150

  3. Know-how and know-why in biochemical engineering.

    PubMed

    von Stockar, U; Valentinotti, S; Marison, I; Cannizzaro, C; Herwig, C

    2003-08-01

    This contribution analyzes the position of biochemical engineering in general and bioprocess engineering particularly in the force fields between fundamental science and applications, and between academia and industry. By using culture technology as an example, it can be shown that bioprocess engineering has moved slowly but steadily from an empirical art concerned with mainly know-how to a science elucidating the know-why of culture behavior. Highly powerful monitoring tools enable biochemical engineers to understand and explain quantitatively the activity of cellular culture on a metabolic basis. Among these monitoring tools are not just semi-online analyses of culture broth by HPLC, GC and FIA, but, increasingly, also noninvasive methods such as midrange IR, Raman and capacitance spectroscopy, as well as online calorimetry. The detailed and quantitative insight into the metabolome and the fluxome that bioprocess engineers are establishing offers an unprecedented opportunity for building bridges between molecular biology and engineering biosciences. Thus, one of the major tasks of biochemical engineering sciences is not developing new know-how for industrial applications, but elucidating the know-why in biochemical engineering by conducting research on the underlying scientific fundamentals.

  4. Genetics Home Reference: Wiskott-Aldrich syndrome

    MedlinePlus

    ... Syndrome: a model for defective actin reorganization, cell trafficking and synapse formation. Curr Opin Immunol. 2003 Oct; ... Accessibility FOIA Viewers & Players U.S. Department of Health & Human Services National Institutes of Health National Library of ...

  5. Biochemical transformation of solid carbonaceous material

    DOEpatents

    Lin, Mow S.; Premuzic, Eugene T.

    2001-09-25

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed.

  6. Serum Biochemical Phenotypes in the Domestic Dog.

    PubMed

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A

    2016-01-01

    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  7. Serum Biochemical Phenotypes in the Domestic Dog

    PubMed Central

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A.

    2016-01-01

    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  8. Molecular and biochemical pharmacology of the histamine H4 receptor

    PubMed Central

    Leurs, Rob; Chazot, Paul L; Shenton, Fiona C; Lim, Herman D; de Esch, Iwan JP

    2009-01-01

    The elucidation of the human genome has had a major impact on histamine receptor research. The identification of the human H4 receptor by several groups has been instrumental for a new appreciation of the role of histamine in the modulation of immune function. In this review, we summarize the historical developments and the molecular and biochemical pharmacology of the H4 receptor. PMID:19413568

  9. Accurate atom-mapping computation for biochemical reactions.

    PubMed

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  10. Biochemical Characterization of Indole Prenyltransferases

    PubMed Central

    Yu, Xia; Liu, Yan; Xie, Xiulan; Zheng, Xiao-Dong; Li, Shu-Ming

    2012-01-01

    The putative prenyltransferase gene ACLA_031240 belonging to the dimethylallyltryptophan synthase superfamily was identified in the genome sequence of Aspergillus clavatus and overexpressed in Escherichia coli. The soluble His-tagged protein EAW08391 was purified to near homogeneity and used for biochemical investigation with diverse aromatic substrates in the presence of different prenyl diphosphates. It has shown that in the presence of dimethylallyl diphosphate (DMAPP), the recombinant enzyme accepted very well simple indole derivatives with l-tryptophan as the best substrate. Product formation was also observed for tryptophan-containing cyclic dipeptides but with much lower conversion yields. In contrast, no product formation was detected in the reaction mixtures of l-tryptophan with geranyl or farnesyl diphosphate. Structure elucidation of the enzyme products by NMR and MS analyses proved unequivocally the highly regiospecific regular prenylation at C-5 of the indole nucleus of the simple indole derivatives. EAW08391 was therefore termed 5-dimethylallyltryptophan synthase, and it filled the last gap in the toolbox of indole prenyltransferases regarding their prenylation positions. Km values of 5-dimethylallyltryptophan synthase were determined for l-tryptophan and DMAPP at 34 and 76 μm, respectively. Average turnover number (kcat) at 1.1 s−1 was calculated from kinetic data of l-tryptophan and DMAPP. Catalytic efficiencies of 5-dimethylallyltryptophan synthase for l-tryptophan at 25,588 s−1·m−1 and for other 11 simple indole derivatives up to 1538 s−1·m−1 provided evidence for its potential usage as a catalyst for chemoenzymatic synthesis. PMID:22123822

  11. PHA bioplastics, biochemicals, and energy from crops.

    PubMed

    Somleva, Maria N; Peoples, Oliver P; Snell, Kristi D

    2013-02-01

    Large scale production of polyhydroxyalkanoates (PHAs) in plants can provide a sustainable supply of bioplastics, biochemicals, and energy from sunlight and atmospheric CO(2). PHAs are a class of polymers with various chain lengths that are naturally produced by some microorganisms as storage materials. The properties of these polyesters make them functionally equivalent to many of the petroleum-based plastics that are currently in the market place. However, unlike most petroleum-derived plastics, PHAs can be produced from renewable feedstocks and easily degrade in most biologically active environments. This review highlights research efforts over the last 20 years to engineer the production of PHAs in plants with a focus on polyhydroxybutryrate (PHB) production in bioenergy crops with C(4) photosynthesis. PHB has the potential to be a high volume commercial product with uses not only in the plastics and materials markets, but also in renewable chemicals and feed. The major challenges of improving product yield and plant fitness in high biomass yielding C(4) crops are discussed in detail.

  12. Biochemical studies of the tracheobronchial epithelium

    SciTech Connect

    Mass, M.J.; Kaufman, D.G.

    1984-06-01

    Tracheobronchial epithelium has been a focus of intense investigation in the field of chemical carcinogenesis. We have reviewed some biochemical investigations that have evolved through linkage with carcinogenesis research. These areas of investigation have included kinetics of carcinogen metabolism, identification of carcinogen metabolites, levels of carcinogen binding to DNA, and analysis of carcinogen-DNA adducts. Such studies appear to have provided a reasonable explanation for the susceptibilities of the respiratory tracts of rats and hamsters to carcinogenesis by benzo(a)pyrene. Coinciding with the attempts to understand the initiation of carcinogenesis in the respiratory tract has also been a major thrust aimed at effecting its prevention both in humans and in animal models for human bronchogenic carcinoma. These studies have concerned the effects of derivatives of vitamin A (retinoids) and their influence on normal cell biology and biochemistry of this tissue. Recent investigations have included the effects of retinoid deficiency on the synthesis of RNA and the identification of RNA species associated with this biological state, and also have included the effects of retinoids on the synthesis of mucus-related glycoproteins. Tracheal organ cultures from retinoid-deficient hamsters have been used successfully to indicate the potency of synthetic retinoids by monitoring the reversal of squamous metaplasia. Techniques applied to this tissue have also served to elucidate features of the metabolism of retinoic acid using high pressure liquid chromatography. 94 references, 9 figures, 2 tables.

  13. PHA bioplastics, biochemicals, and energy from crops.

    PubMed

    Somleva, Maria N; Peoples, Oliver P; Snell, Kristi D

    2013-02-01

    Large scale production of polyhydroxyalkanoates (PHAs) in plants can provide a sustainable supply of bioplastics, biochemicals, and energy from sunlight and atmospheric CO(2). PHAs are a class of polymers with various chain lengths that are naturally produced by some microorganisms as storage materials. The properties of these polyesters make them functionally equivalent to many of the petroleum-based plastics that are currently in the market place. However, unlike most petroleum-derived plastics, PHAs can be produced from renewable feedstocks and easily degrade in most biologically active environments. This review highlights research efforts over the last 20 years to engineer the production of PHAs in plants with a focus on polyhydroxybutryrate (PHB) production in bioenergy crops with C(4) photosynthesis. PHB has the potential to be a high volume commercial product with uses not only in the plastics and materials markets, but also in renewable chemicals and feed. The major challenges of improving product yield and plant fitness in high biomass yielding C(4) crops are discussed in detail. PMID:23294864

  14. Exploring the remote sensing of foliar biochemical concentrations with AVIRIS data

    NASA Technical Reports Server (NTRS)

    Smith, Geoffrey M.; Curran, Paul J.

    1992-01-01

    Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data shows promise for the estimation of foliar biochemical concentrations at the scale of the canopy. There are, however, several problems associated with the use of AVIRIS data in this way and these are detailed in recent Plant Biochemical Workshop Report. The research reported was concentrated upon three of these problems: field sampling of forest canopies, wet laboratory assay of foliar chemicals, and the visualization of AVIRIS data.

  15. Biochemical Lab Activity Supports Evolution Theory

    ERIC Educational Resources Information Center

    Dyman, Daniel J.

    1974-01-01

    Described is thin-layer chromatography (TLC), a technique that can be conveniently used in the laboratory to generate evidence supporting the principle that degrees of biochemical similarity reflect degrees of evolutionary relatedness among organisms. (Author/PEB)

  16. [Biochemical diagnostics of fatal opium intoxication].

    PubMed

    Papyshev, I P; Astashkina, O G; Tuchik, E S; Nikolaev, B S; Cherniaev, A L

    2013-01-01

    Biochemical diagnostics of fatal opium intoxication remains a topical problem in forensic medical science and practice. We investigated materials obtained in the course of forensic medical expertise of the cases of fatal opium intoxication. The study revealed significant differences between myoglobin levels in blood, urine, myocardium, and skeletal muscles. The proposed approach to biochemical diagnostics of fatal opium intoxication enhances the accuracy and the level of evidence of expert conclusions.

  17. Causal correlation of foliar biochemical concentrations with AVIRIS spectra using forced entry linear regression

    NASA Technical Reports Server (NTRS)

    Dawson, Terence P.; Curran, Paul J.; Kupiec, John A.

    1995-01-01

    A major goal of airborne imaging spectrometry is to estimate the biochemical composition of vegetation canopies from reflectance spectra. Remotely-sensed estimates of foliar biochemical concentrations of forests would provide valuable indicators of ecosystem function at regional and eventually global scales. Empirical research has shown a relationship exists between the amount of radiation reflected from absorption features and the concentration of given biochemicals in leaves and canopies (Matson et al., 1994, Johnson et al., 1994). A technique commonly used to determine which wavelengths have the strongest correlation with the biochemical of interest is unguided (stepwise) multiple regression. Wavelengths are entered into a multivariate regression equation, in their order of importance, each contributing to the reduction of the variance in the measured biochemical concentration. A significant problem with the use of stepwise regression for determining the correlation between biochemical concentration and spectra is that of 'overfitting' as there are significantly more wavebands than biochemical measurements. This could result in the selection of wavebands which may be more accurately attributable to noise or canopy effects. In addition, there is a real problem of collinearity in that the individual biochemical concentrations may covary. A strong correlation between the reflectance at a given wavelength and the concentration of a biochemical of interest, therefore, may be due to the effect of another biochemical which is closely related. Furthermore, it is not always possible to account for potentially suitable waveband omissions in the stepwise selection procedure. This concern about the suitability of stepwise regression has been identified and acknowledged in a number of recent studies (Wessman et al., 1988, Curran, 1989, Curran et al., 1992, Peterson and Hubbard, 1992, Martine and Aber, 1994, Kupiec, 1994). These studies have pointed to the lack of a physical

  18. Biochemical remediation using plant enzymes

    SciTech Connect

    Wolfe, N.L.

    1994-06-01

    The transformation of trinitrotoluene (TNT) to environmentally acceptable compounds is achieved through a lab-developed process that uses common aquatic weeds containing a nitroreductase enzyme. This research breakthrough provides an efficient and inexpensive technology for the cleanup of soils contaminated with munitions waste at military installations and other sites.

  19. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  20. 40 CFR 158.2010 - Biochemical pesticides data requirements.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides... required to support registration of biochemical pesticides. Sections 158.2080 through 158.2084 identify...

  1. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  2. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  3. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  4. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  5. Biochemical Production of Ethanol from Corn Stover: 2007 State of Technology Model

    SciTech Connect

    Aden, Andy

    2008-05-01

    Since 2001, NREL has kept track of technical research progress in the biochemical process through what are known as “State of Technology” (SOT) assessments. The purpose of this report is to update the FY 2005 SOT model with the latest research results from the past two years.

  6. Nonlinear biochemical signal processing via noise propagation

    NASA Astrophysics Data System (ADS)

    Kim, Kyung Hyuk; Qian, Hong; Sauro, Herbert M.

    2013-10-01

    Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance, fluctuations in biochemical activities become significant and such "noise" can propagate through regulatory cascades in terms of biochemical reaction networks. Here we develop an intuitive, yet fully quantitative method for analyzing how noise affects cellular phenotypes based on identifying a system's nonlinearities and noise propagations. We observe that such noise can simultaneously enhance sensitivities in one behavioral region while reducing sensitivities in another. Employing this novel phenomenon we designed three biochemical signal processing modules: (a) A gene regulatory network that acts as a concentration detector with both enhanced amplitude and sensitivity. (b) A non-cooperative positive feedback system, with a graded dose-response in the deterministic case, that serves as a bistable switch due to noise-induced ultra-sensitivity. (c) A noise-induced linear amplifier for gene regulation that requires no feedback. The methods developed in the present work allow one to understand and engineer nonlinear biochemical signal processors based on fluctuation-induced phenotypes.

  7. Nonlinear biochemical signal processing via noise propagation.

    PubMed

    Kim, Kyung Hyuk; Qian, Hong; Sauro, Herbert M

    2013-10-14

    Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance, fluctuations in biochemical activities become significant and such "noise" can propagate through regulatory cascades in terms of biochemical reaction networks. Here we develop an intuitive, yet fully quantitative method for analyzing how noise affects cellular phenotypes based on identifying a system's nonlinearities and noise propagations. We observe that such noise can simultaneously enhance sensitivities in one behavioral region while reducing sensitivities in another. Employing this novel phenomenon we designed three biochemical signal processing modules: (a) A gene regulatory network that acts as a concentration detector with both enhanced amplitude and sensitivity. (b) A non-cooperative positive feedback system, with a graded dose-response in the deterministic case, that serves as a bistable switch due to noise-induced ultra-sensitivity. (c) A noise-induced linear amplifier for gene regulation that requires no feedback. The methods developed in the present work allow one to understand and engineer nonlinear biochemical signal processors based on fluctuation-induced phenotypes.

  8. Parameter inference for biochemical systems that undergo a Hopf bifurcation.

    PubMed

    Kirk, Paul D W; Toni, Tina; Stumpf, Michael P H

    2008-07-01

    The increasingly widespread use of parametric mathematical models to describe biological systems means that the ability to infer model parameters is of great importance. In this study, we consider parameter inferability in nonlinear ordinary differential equation models that undergo a bifurcation, focusing on a simple but generic biochemical reaction model. We systematically investigate the shape of the likelihood function for the model's parameters, analyzing the changes that occur as the model undergoes a Hopf bifurcation. We demonstrate that there exists an intrinsic link between inference and the parameters' impact on the modeled system's dynamical stability, which we hope will motivate further research in this area.

  9. Remote sensing of forest canopy and leaf biochemical contents

    NASA Technical Reports Server (NTRS)

    Peterson, David L.; Matson, Pamela A.; Card, Don H.; Aber, John D.; Wessman, Carol; Swanberg, Nancy; Spanner, Michael

    1988-01-01

    Recent research on the remote sensing of forest leaf and canopy biochemical contents suggests that the shortwave IR region contains this information; laboratory analyses of dry ground leaves have yielded reliable predictive relationships between both leaf nitrogen and lignin with near-IR spectra. Attention is given to the application of these laboratory techniques to a limited set of spectra from fresh, whole leaves of conifer species. The analysis of Airborne Imaging Spectrometer data reveals that total water content variations in deciduous forest canopies appear as overall shifts in the brightness of raw spectra.

  10. Reconfigurable neuromorphic computation in biochemical systems.

    PubMed

    Chiang, Hui-Ju Katherine; Jiang, Jie-Hong R; Fages, Francois

    2015-08-01

    Implementing application-specific computation and control tasks within a biochemical system has been an important pursuit in synthetic biology. Most synthetic designs to date have focused on realizing systems of fixed functions using specifically engineered components, thus lacking flexibility to adapt to uncertain and dynamically-changing environments. To remedy this limitation, an analog and modularized approach to realize reconfigurable neuromorphic computation with biochemical reactions is presented. We propose a biochemical neural network consisting of neuronal modules and interconnects that are both reconfigurable through external or internal control over the concentrations of certain molecular species. Case studies on classification and machine learning applications using the DNA strain displacement technology demonstrate the effectiveness of our design in both reconfiguration and autonomous adaptation. PMID:26736417

  11. Biochemical Removal of HAP Precursors From Coal

    SciTech Connect

    Olson, G.; Tucker, L.; Richards, J.

    1997-07-01

    This project addresses DOE`s interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals.

  12. Testosterone Deficiency - Establishing A Biochemical Diagnosis

    PubMed Central

    Krakowsky, Yonah

    2015-01-01

    Testosterone deficiency is a common and often unrecognized disorder impacting the lives of many men. Symptoms related to low testosterone are relatively non-specific and clinicians must therefore ensure that a patients’ symptomatology is supported by a biochemical profile suggestive of testosterone deficiency. There are many options available to determine a patient’s testosterone level and laboratories will vary in the type of biochemical assessment they provide. In assessing patients with suspected low testosterone, the presence of symptoms and a low total testosterone is usually sufficient to initiate therapy. In equivocal cases, measurement of free or bioavailable testosterone with a reliable assay can further clarify the clinical picture. By understanding the differences between total, free and bioavailable testosterone, and the accuracy and reliability of their measurement, clinicians can better interpret their patients’ biochemical testosterone profile.

  13. SERI Biochemical Conversion Program: FY 1986, annual report

    SciTech Connect

    Not Available

    1987-09-01

    The Biochemical Conversion Program is mission oriented; effort is concentrated on technologies that appear to have the greatest potential for being adopted by the private sector to economically convert lignocellulosic materials into high-value liquid transportation fuels, particularly ethanol. The goal of the program is to develop the technology base for the biochemical conversion of these renewable lignocellulosic resources into fuels. The program is structured to supply the technology for such fuels to compete economically first as an octane booster or fuel additive, and, with additional improvements, as a neat fuel. The objectives of the program are to improve the pretreatment, hydrolysis, and bioconversion processes through research so that ethanol can be produced economically from lignocellulosic biomass; develop technologies to convert the underutilized portions of the lignocellulosic feedstock (xylan and lignin) to high-value liquid transportation fuels; evaluate the performance of the emerging process technologies in the smallest possible scale integrated experiment to assess their readiness for scaleup and to better define research needs; and to transfer the technology to the private sector for rapid commercialization by involving industry in the research process at the earliest possible time.

  14. Biochemical computation for spine structural plasticity

    PubMed Central

    Nishiyama, Jun; Yasuda, Ryohei

    2015-01-01

    The structural plasticity of dendritic spines is considered to be essential for various forms of synaptic plasticity, learning and memory. The process is mediated by a complex signaling network consisting of numerous species of molecules. Furthermore, the spatiotemporal dynamics of the biochemical signaling is regulated in a complicated manner due to geometrical restrictions from the unique morphology of the dendritic branches and spines. Recent advances in optical techniques have enabled the exploration of the spatiotemporal aspects of the signal regulations in spines and dendrites and have provided many insights into the principle of the biochemical computation that underlies spine structural plasticity. PMID:26139370

  15. Simulation of Biochemical Pathway Adaptability Using Evolutionary Algorithms

    SciTech Connect

    Bosl, W J

    2005-01-26

    -driven experimentation. This LDRD will focus on developing prototype software for the evolutionary computation and demonstrating its efficacy on a well-known biochemical pathway in yeast. Expected outcomes from this LDRD project included a demonstration of computational modeling of evolvability in a biochemical pathway, an important collaboration with the Systems Biology department at Harvard University, several proposals to secure external long-term funding from one or more sources and the nucleus of a new, focused research effort at LLNL in computational genomics, focused principally on Genomes to Life goals. All of these goals were achieved.

  16. A Course in Biochemical Engineering Fundamentals (Revisited).

    ERIC Educational Resources Information Center

    Bailey, J. E.; Ollis, D. F.

    1985-01-01

    Provides: (1) a glossary of terms used in biochemical engineering; (2) a list of key developments in the field; and (3) emphases placed in 15 topic areas in a course restructured on the basis of these developments. Topic areas include enzyme kinetics/applications, genetics and microbial control, transport phenomena, and others. (JN)

  17. Predictive biochemical assays for late radiation effects

    SciTech Connect

    Rubin, P.; Finkelstein, J.N.; Siemann, D.W.; Shapiro, D.L.; Van Houtte, P.; Penney, D.P.

    1986-04-01

    Surfactant precursors or other products of Type II pneumocytes have the potential to be the first biochemical marker for late radiation effects. This is particularly clinically important in the combined modality era because of the frequent occurrence of pneumonitis and pulmonary fibrosis secondary to radiation or chemotherapy. Accordingly, correlative studies have been pursued with the Type II pneumocyte as a beginning point to understand the complex pathophysiology of radiation pneumonitis and fibrosis. From our ultrastructural and biochemical studies, it is evident that Type II pneumocytes are an early target of radiation and the release of surfactant into the alveolus shortly after exposure persists for days and weeks. Through the use of lavaging techniques, alveolar surfactant has been elevated after pulmonary irradiation. In three murine strains and in the rabbit, there is a strong correlation with surfactant release at 7 and/or 28 days in vivo with later lethality in months. In vitro studies using cultures of type II pneumocytes also demonstrate dose response and tolerance factors that are comparable to the in vivo small and large animal diagnostic models. New markers are being developed to serve as a predictive index for later lethal pneumonopathies. With the development of these techniques, the search for early biochemical markers in man has been undertaken. Through the use of biochemical, histological, and ultrastructural techniques, a causal relationship between radiation effects on type II pneumocytes, pulmonary cells, endothelial cells of blood vessels, and their roles in the production of pneumonitis and fibrosis will evolve.

  18. Biochemical Applications in the Analytical Chemistry Lab

    ERIC Educational Resources Information Center

    Strong, Cynthia; Ruttencutter, Jeffrey

    2004-01-01

    An HPLC and a UV-visible spectrophotometer are identified as instruments that helps to incorporate more biologically-relevant experiments into the course, in order to increase the students understanding of selected biochemistry topics and enhances their ability to apply an analytical approach to biochemical problems. The experiment teaches…

  19. 2009 Biochemical Conversion Platform Review Report

    SciTech Connect

    Ferrell, John

    2009-12-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program’s Biochemical Conversion platform review meeting, held on April 14-16, 2009, at the Sheraton Denver Downtown, Denver, Colorado.

  20. Biochemical Thermodynamics under near Physiological Conditions

    ERIC Educational Resources Information Center

    Mendez, Eduardo

    2008-01-01

    The recommendations for nomenclature and tables in Biochemical Thermodynamics approved by IUBMB and IUPAC in 1994 can be easily introduced after the chemical thermodynamic formalism. Substitution of the usual standard thermodynamic properties by the transformed ones in the thermodynamic equations, and the use of appropriate thermodynamic tables…

  1. Survey of Biochemical Education in Japanese Universities.

    ERIC Educational Resources Information Center

    Kagawa, Yasuo

    1995-01-01

    Reports findings of questionnaires sent to faculty in charge of biochemical education in medical schools and other programs from dentistry to agriculture. Total class hours have declined since 1984. New trends include bioethics and computer-assisted learning. Tables show trends in lecture hours, lecture content, laboratory hours, core subject…

  2. Biochemical Approaches to Improved Nitrogen Fixation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improving symbiotic nitrogen fixation by legumes has emerged again as an important topic on the world scene due to the energy crisis and lack of access to nitrogen fertilizer in developing countries. We have taken a biochemical genomics approach to improving symbiotic nitrogen fixation in legumes. L...

  3. Characterizing autism spectrum disorders by key biochemical pathways

    PubMed Central

    Subramanian, Megha; Timmerman, Christina K.; Schwartz, Joshua L.; Pham, Daniel L.; Meffert, Mollie K.

    2015-01-01

    The genetic and phenotypic heterogeneity of autism spectrum disorders (ASD) presents a substantial challenge for diagnosis, classification, research, and treatment. Investigations into the underlying molecular etiology of ASD have often yielded mixed and at times opposing findings. Defining the molecular and biochemical underpinnings of heterogeneity in ASD is crucial to our understanding of the pathophysiological development of the disorder, and has the potential to assist in diagnosis and the rational design of clinical trials. In this review, we propose that genetically diverse forms of ASD may be usefully parsed into entities resulting from converse patterns of growth regulation at the molecular level, which lead to the correlates of general synaptic and neural overgrowth or undergrowth. Abnormal brain growth during development is a characteristic feature that has been observed both in children with autism and in mouse models of autism. We review evidence from syndromic and non-syndromic ASD to suggest that entities currently classified as autism may fundamentally differ by underlying pro- or anti-growth abnormalities in key biochemical pathways, giving rise to either excessive or reduced synaptic connectivity in affected brain regions. We posit that this classification strategy has the potential not only to aid research efforts, but also to ultimately facilitate early diagnosis and direct appropriate therapeutic interventions. PMID:26483618

  4. Research.

    ERIC Educational Resources Information Center

    Raudenbush, Stephen

    In May of 1999, the American Academy of Arts and Sciences hosted a conference on ways to improve the scientific quality of educational research. In medicine, thanks to work 40 years ago by 2 researchers, Howard Hyatt and Frederick Mosteller, the commitment of medical professionals to base their diagnoses and prescriptions on clinical trials in…

  5. A general method for modeling biochemical and biomedical response

    NASA Astrophysics Data System (ADS)

    Ortiz, Roberto; Lerd Ng, Jia; Hughes, Tyler; Abou Ghantous, Michel; Bouhali, Othmane; Arredouani, Abdelilah; Allen, Roland

    2012-10-01

    The impressive achievements of biomedical science have come mostly from experimental research with human subjects, animal models, and sophisticated laboratory techniques. Additionally, theoretical chemistry has been a major aid in designing new drugs. Here we introduce a method which is similar to others already well known in theoretical systems biology, but which specifically addresses biochemical changes as the human body responds to medical interventions. It is common in systems biology to use first-order differential equations to model the time evolution of various chemical concentrations, and we as physicists can make a significant impact through designing realistic models and then solving the resulting equations. Biomedical research is rapidly advancing, and the technique presented in this talk can be applied in arbitrarily large models containing tens, hundreds, or even thousands of interacting species, to determine what beneficial effects and side effects may result from pharmaceuticals or other medical interventions.

  6. Biochemical Genetic Pathways that Modulate Aging in Multiple Species

    PubMed Central

    Bitto, Alessandro; Wang, Adrienne M.; Bennett, Christopher F.; Kaeberlein, Matt

    2016-01-01

    The mechanisms underlying biological aging have been extensively studied in the past 20 years with the avail of mainly four model organisms: the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, the fruitfly Drosophila melanogaster, and the domestic mouse Mus musculus. Extensive research in these four model organisms has identified a few conserved genetic pathways that affect longevity as well as metabolism and development. Here, we review how the mechanistic target of rapamycin (mTOR), sirtuins, adenosine monophosphate-activated protein kinase (AMPK), growth hormone/insulin-like growth factor 1 (IGF-1), and mitochondrial stress-signaling pathways influence aging and life span in the aforementioned models and their possible implications for delaying aging in humans. We also draw some connections between these biochemical pathways and comment on what new developments aging research will likely bring in the near future. PMID:26525455

  7. Kombucha tea fermentation: Microbial and biochemical dynamics.

    PubMed

    Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

    2016-03-01

    Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

  8. Kombucha tea fermentation: Microbial and biochemical dynamics.

    PubMed

    Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

    2016-03-01

    Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

  9. Research

    ERIC Educational Resources Information Center

    Mathematics Teaching, 1973

    1973-01-01

    Implications for teachers from Piagetian-oriented piagetian-oriented research on problem solving reported in an article by Eleanor Duckworth are presented. Edward de Bono's Children Solve Problems,'' a collection of examples, is also discussed. (MS)

  10. Enabling intelligent readout of luminescent signals from nanoscale biochemical sensors

    NASA Astrophysics Data System (ADS)

    Yao, Lei; Yung, Ka Yi; Tripathi, Vijay; Chodavarapu, Vamsy; Cartwright, Alexander; Bright, Frank

    2009-02-01

    The development of intelligent miniaturized biochemical sensors has been an area of active research over the past several years. These microsensors and sensor microarrays are finding niche applications in point-of-care diagnostics, personal care, food safety, and environmental monitoring. Among these sensors, optical (luminescence) sensing holds a great promise towards implementing simple, specific, and highly sensitive biochemical sensors. It is generally understood that biochemical recognition elements that respond specifically to the target analytes play a critical role in the overall sensor operation. Aside from the recognition elements, signal detection and processing components are important to collect the information provided by recognition elements and output an easily understandable response. The signal processing component provides the best opportunity to incorporate intelligence to achieve low-power, adaptive, accurate, and reliable sensors. We deal with sensors that use sol-gel derived xerogels as recognition materials and Complementary Metal-Oxide Semiconductor (CMOS) integrated circuits for signal detection and processing. Xerogels are nano/microporous glasses that can be used to encapsulate luminophores, enzymes, and nanoparticles in their pores. In this Article, we will describe some of the emerging integrated sensor platforms that are based on monitoring the excited-state luminescence intensity and lifetimes of the luminophores housed in the xerogels. Specifically, we describe a CMOS imaging system for simultaneously monitoring xerogels sensor arrays. Next, we describe a non-linear phase luminometric system with enhanced and dynamically tunable sensitivity and improved signal-to-noise performance. Finally, we will describe time-based signal processing that could enable the direct measurement of excited state fluorescence lifetimes. This time-to-digital converter requires simple circuit implementation and can be used to measure lifetimes that are on

  11. Structural and biochemical characterization of DSL ribozyme.

    PubMed

    Horie, Souta; Ikawa, Yoshiya; Inoue, Tan

    2006-01-01

    We recently reported on the molecular design and synthesis of a new RNA ligase ribozyme (DSL), whose active site was selected from a sequence library consisting of 30 random nucleotides set on a defined 3D structure of a designed RNA scaffold. In this study, we report on the structural and biochemical analyses of DSL. Structural analysis indicates that the active site, which consists of the selected sequence, attaches to the folded scaffold as designed. To see whether DSL resembles known ribozymes, a biochemical assay was performed. Metal-dependent kinetic studies suggest that the ligase requires Mg2+ ions. The replacement of Mg2+ with Co(NH3)6(3+) prohibits the reaction, indicating that DSL requires innersphere coordination of Mg2+ for a ligation reaction. The results show that DSL has requirements similar to those of previously reported catalytic RNAs.

  12. Thermodynamics of biochemical networks and duality theorems

    NASA Astrophysics Data System (ADS)

    De Martino, Daniele

    2013-05-01

    One interesting yet difficult computational issue has recently been posed in biophysics in regard to the implementation of thermodynamic constraints to complex networks. Biochemical networks of enzymes inside cells are among the most efficient, robust, differentiated, and flexible free-energy transducers in nature. How is the second law of thermodynamics encoded for these complex networks? In this article it is demonstrated that for chemical reaction networks in the steady state the exclusion (presence) of closed reaction cycles makes possible (impossible) the definition of a chemical potential vector. Interestingly, this statement is encoded in one of the key results in combinatorial optimization, i.e., the Gordan theorem of the alternatives. From a computational viewpoint, the theorem reveals that calculating a reaction's free energy and identifying infeasible loops in flux states are dual problems whose solutions are mutually exclusive, and this opens the way for efficient and scalable methods to perform the energy balance analysis of large-scale biochemical networks.

  13. Least squares estimation in stochastic biochemical networks.

    PubMed

    Rempala, Grzegorz A

    2012-08-01

    The paper presents results on the asymptotic properties of the least-squares estimates (LSEs) of the reaction constants in mass-action, stochastic, biochemical network models. LSEs are assumed to be based on the longitudinal data from partially observed trajectories of a stochastic dynamical system, modeled as a continuous-time, pure jump Markov process. Under certain regularity conditions on such a process, it is shown that the vector of LSEs is jointly consistent and asymptotically normal, with the asymptotic covariance structure given in terms of a system of ordinary differential equations (ODE). The derived asymptotic properties hold true as the biochemical network size (the total species number) increases, in which case the stochastic dynamical system converges to the deterministic mass-action ODE. An example is provided, based on synthetic as well as RT-PCR data from the retro-transcription network of the LINE1 gene.

  14. Construction and analysis of biochemical networks

    NASA Astrophysics Data System (ADS)

    Binns, Michael; Theodoropoulos, Constantinos

    2012-09-01

    Bioprocesses are being implemented for a range of different applications including the production of fuels, chemicals and drugs. Hence, it is becoming increasingly important to understand and model how they function and how they can be modified or designed to give the optimal performance. Here we discuss the construction and analysis of biochemical networks which are the first logical steps towards this goal. The construction of a reaction network is possible through reconstruction: extracting information from literature and from databases. This can be supplemented by reaction prediction methods which can identify steps which are missing from the current knowledge base. Analysis of biochemical systems generally requires some experimental input but can be used to identify important reactions and targets for enhancing the performance of the organism involved. Metabolic flux, pathway and metabolic control analysis can be used to determine the limits, capabilities and potential targets for enhancement respectively.

  15. Biochemical alterations during swimming induced stress.

    PubMed

    Aruj, N; Sharafatullah, T; Najam, R; Ahmed, S P; Ahmad, S I

    1994-07-01

    Stress can be defined as any stimulus that creates an imbalance in the internal environment. Hypothalamus has sensors that detect changes produced in the body. Stress can cause diseases by altering immune system, cardiovascular System neurotransmitter and neuroendocrine functions. Present study is designed to evaluate the effect of stress on few biochemical parameters during swimming induced stress. Significant changes have been observed especially in lipid profile. Corticosterone was also evaluated as reliable stress marker.

  16. Biochemical correlates of neurosensory changes in weightlessness

    NASA Technical Reports Server (NTRS)

    Leach, Carolyn S.; Reschke, Millard F.

    1989-01-01

    The possible existence of a relationship between space motion sickness and chemical and biochemical variables measured in body fluids is studied. Clinical chemistry and endocrine measurements from blood and urine samples taken before and after Space Shuttle flights were analyzed along with the occurrence of SMS during flight and provocative testing before flight. Significant positive correlations were observed with serum chloride and significant negative correlations with serum phosphate, serum uric acid, and plasma thyroid stimulating hormone.

  17. Biochemical Activities of 320 ToxCast Chemicals Evaluated Across 239 Functional Targets

    EPA Science Inventory

    EPA’s ToxCast research program is profiling chemical bioactivity in order to generate predictive signatures of toxicity. The present study evaluated 320 chemicals across 239 biochemical assays. ToxCast phase I chemicals include 309 unique structures, most of which are pesticide ...

  18. Electronic modulation of biochemical signal generation

    NASA Astrophysics Data System (ADS)

    Gordonov, Tanya; Kim, Eunkyoung; Cheng, Yi; Ben-Yoav, Hadar; Ghodssi, Reza; Rubloff, Gary; Yin, Jun-Jie; Payne, Gregory F.; Bentley, William E.

    2014-08-01

    Microelectronic devices that contain biological components are typically used to interrogate biology rather than control biological function. Patterned assemblies of proteins and cells have, however, been used for in vitro metabolic engineering, where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. Such devices form part of technologies that attempt to recreate animal and human physiological functions on a chip and could be used to revolutionize drug development. These ambitious goals will, however, require new biofabrication methodologies that help connect microelectronics and biological systems and yield new approaches to device assembly and communication. Here, we report the electrically mediated assembly, interrogation and control of a multi-domain fusion protein that produces a bacterial signalling molecule. The biological system can be electrically tuned using a natural redox molecule, and its biochemical response is shown to provide the signalling cues to drive bacterial population behaviour. We show that the biochemical output of the system correlates with the electrical input charge, which suggests that electrical inputs could be used to control complex on-chip biological processes.

  19. Electronic modulation of biochemical signal generation.

    PubMed

    Gordonov, Tanya; Kim, Eunkyoung; Cheng, Yi; Ben-Yoav, Hadar; Ghodssi, Reza; Rubloff, Gary; Yin, Jun-Jie; Payne, Gregory F; Bentley, William E

    2014-08-01

    Microelectronic devices that contain biological components are typically used to interrogate biology rather than control biological function. Patterned assemblies of proteins and cells have, however, been used for in vitro metabolic engineering, where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. Such devices form part of technologies that attempt to recreate animal and human physiological functions on a chip and could be used to revolutionize drug development. These ambitious goals will, however, require new biofabrication methodologies that help connect microelectronics and biological systems and yield new approaches to device assembly and communication. Here, we report the electrically mediated assembly, interrogation and control of a multi-domain fusion protein that produces a bacterial signalling molecule. The biological system can be electrically tuned using a natural redox molecule, and its biochemical response is shown to provide the signalling cues to drive bacterial population behaviour. We show that the biochemical output of the system correlates with the electrical input charge, which suggests that electrical inputs could be used to control complex on-chip biological processes.

  20. Stoichiometric network theory for nonequilibrium biochemical systems.

    PubMed

    Qian, Hong; Beard, Daniel A; Liang, Shou-dan

    2003-02-01

    We introduce the basic concepts and develop a theory for nonequilibrium steady-state biochemical systems applicable to analyzing large-scale complex isothermal reaction networks. In terms of the stoichiometric matrix, we demonstrate both Kirchhoff's flux law sigma(l)J(l)=0 over a biochemical species, and potential law sigma(l) mu(l)=0 over a reaction loop. They reflect mass and energy conservation, respectively. For each reaction, its steady-state flux J can be decomposed into forward and backward one-way fluxes J = J+ - J-, with chemical potential difference deltamu = RT ln(J-/J+). The product -Jdeltamu gives the isothermal heat dissipation rate, which is necessarily non-negative according to the second law of thermodynamics. The stoichiometric network theory (SNT) embodies all of the relevant fundamental physics. Knowing J and deltamu of a biochemical reaction, a conductance can be computed which directly reflects the level of gene expression for the particular enzyme. For sufficiently small flux a linear relationship between J and deltamu can be established as the linear flux-force relation in irreversible thermodynamics, analogous to Ohm's law in electrical circuits.

  1. Hydrogel-based piezoresistive biochemical microsensors

    NASA Astrophysics Data System (ADS)

    Guenther, Margarita; Schulz, Volker; Gerlach, Gerald; Wallmersperger, Thomas; Solzbacher, Florian; Magda, Jules J.; Tathireddy, Prashant; Lin, Genyao; Orthner, Michael P.

    2010-04-01

    This work is motivated by a demand for inexpensive, robust and reliable biochemical sensors with high signal reproducibility and long-term-stable sensitivity, especially for medical applications. Micro-fabricated sensors can provide continuous monitoring and on-line control of analyte concentrations in ambient aqueous solutions. The piezoresistive biochemical sensor containing a special biocompatible polymer (hydrogel) with a sharp volume phase transition in the neutral physiological pH range near 7.4 can detect a specific analyte, for example glucose. Thereby the hydrogel-based biochemical sensors are useful for the diagnosis and monitoring of diabetes. The response of the glucosesensitive hydrogel was studied at different regimes of the glucose concentration change and of the solution supply. Sensor response time and accuracy with which a sensor can track gradual changes in glucose was estimated. Additionally, the influence of various recommended sterilization methods on the gel swelling properties and on the mechano-electrical transducer of the pH-sensors has been evaluated in order to choose the most optimal sterilization method for the implantable sensors. It has been shown that there is no negative effect of gamma irradiation with a dose of 25.7 kGy on the hydrogel sensitivity. In order to achieve an optimum between sensor signal amplitude and sensor response time, corresponding calibration and measurement procedures have been proposed and evaluated for the chemical sensors.

  2. Biochemical reaction engineering for redox reactions.

    PubMed

    Wandrey, Christian

    2004-01-01

    Redox reactions are still a challenge for biochemical engineers. A personal view for the development of this field is given. Cofactor regeneration was an obstacle for quite some time. The first technical breakthrough was achieved with the system formate/formate dehydrogenase for the regeneration of NADH2. In cases where the same enzyme could be used for chiral reduction as well as for cofactor regeneration, isopropanol as a hydrogen source proved to be beneficial. The coproduct (acetone) can be removed by pervaporation. Whole-cell reductions (often yeast reductions) can also be used. By proper biochemical reaction engineering, it is possible to apply these systems in a continuous way. By cloning a formate dehydrogenase and an oxidoreductase "designer bug" can be obtained where formate is used instead of glucose as the hydrogen source. Complex sequences of redox reactions can be established by pathway engineering with a focus on gene overexpression or with a focus on establishing non-natural pathways. The success of pathway engineering can be controlled by measuring cytosolic metabolite concentrations. The optimal exploitation of such systems calls for the integrated cooperation of classical and molecular biochemical engineering.

  3. [INVITED] Tilted fiber grating mechanical and biochemical sensors

    NASA Astrophysics Data System (ADS)

    Guo, Tuan; Liu, Fu; Guan, Bai-Ou; Albert, Jacques

    2016-04-01

    The tilted fiber Bragg grating (TFBG) is a new kind of fiber-optic sensor that possesses all the advantages of well-established Bragg grating technology in addition to being able to excite cladding modes resonantly. This device opens up a multitude of opportunities for single-point sensing in hard-to-reach spaces with very controllable cross-sensitivities, absolute and relative measurements of various parameters, and an extreme sensitivity to materials external to the fiber without requiring the fiber to be etched or tapered. Over the past five years, our research group has been developing multimodal fiber-optic sensors based on TFBG in various shapes and forms, always keeping the device itself simple to fabricate and compatible with low-cost manufacturing. This paper presents a brief review of the principle, fabrication, characterization, and implementation of TFBGs, followed by our progress in TFBG sensors for mechanical and biochemical applications, including one-dimensional TFBG vibroscopes, accelerometers and micro-displacement sensors; two-dimensional TFBG vector vibroscopes and vector rotation sensors; reflective TFBG refractometers with in-fiber and fiber-to-fiber configurations; polarimetric and plasmonic TFBG biochemical sensors for in-situ detection of cell, protein and glucose.

  4. Influence of low-frequency vibration on changes of biochemical parameters of living rats

    NASA Astrophysics Data System (ADS)

    Kasprzak, Cezary; Damijan, Zbigniew; Panuszka, Ryszard

    2001-05-01

    The aim of the research was to investigate how some selected biochemical parameters of living rats depend on exposure of low-frequency vibrations. Experiments were run on 30 Wistar rats randomly segregated into three groups: (I) 20 days old (before puberty), (II) 70th day after; (III) control group. The exposure was repeated seven times, for 3 h, at the same time of day. Vibrations applied during the first tests of the experiment had acceleration 1.22 m/s2 and frequency 20 Hz. At the 135th day the rats' bones were a subject of morphometric/biochemical examination. The results of biochemical tests proved decrease in LDL and HDL cholesterol levels for exposed rats as well as the Ca contents in blood plasma. There was evident increasing of Ca in blood plasma in exposed rats for frequency of exposition.

  5. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

    PubMed

    Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

    2014-09-01

    Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

  6. River Water Quality Model no. 1 (RWQM1): II. Biochemical process equations.

    PubMed

    Reichert, P; Borchardt, D; Henze, M; Rauch, W; Shanahan, P; Somlyódy, L; Vanrolleghem, P

    2001-01-01

    In this paper, biochemical process equations are presented as a basis for water quality modelling in rivers under aerobic and anoxic conditions. These equations are not new, but they summarise parts of the development over the past 75 years. The primary goals of the presentation are to stimulate communication among modellers and field-oriented researchers of river water quality and of wastewater treatment, to facilitate practical application of river water quality modelling, and to encourage the use of elemental mass balances for the derivation of stoichiometric coefficients of biochemical transformation processes. This paper is part of a series of three papers. In the first paper, the general modelling approach is described; in the present paper, the biochemical process equations of a complex model are presented; and in the third paper, recommendations are given for the selection of a reasonable submodel for a specific application.

  7. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic.

    PubMed

    Privman, Vladimir; Halámek, Jan; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-11-11

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by H(2)O(2) was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.

  8. Autonomous bio-chemical decontaminator (ABCD) against weapons of mass destruction

    NASA Astrophysics Data System (ADS)

    Hyacinthe, Berg P.

    2006-05-01

    The proliferation of weapons of mass destruction (WMD) and the use of such elements pose an eminent asymmetric threat with disastrous consequences to the national security of any nation. In particular, the use of biochemical warfare agents against civilians and unprotected troops in international conflicts or by terrorists against civilians is considered as a very peculiar threat. Accordingly, taking a quarantine-before-inhalation approach to biochemical warfare, the author introduces the notion of autonomous biochemical decontamination against WMD. In the unfortunate event of a biochemical attack, the apparatus proposed herein is intended to automatically detect, identify, and more importantly neutralize a biochemical threat. Along with warnings concerning a cyber-WMD nexus, various sections cover discussions on human senses and computer sensors, corroborating evidence related to detection and neutralization of chemical toxins, and cyber-assisted olfaction in stand alone, peer-to-peer, and network settings. In essence, the apparatus can be used in aviation and mass transit security to initiate mass decontamination by dispersing a decontaminant aerosol or to protect the public water supply against a potential bioterrorist attack. Future effort may involve a system-on-chip (SoC) embodiment of this apparatus that allows a safer environment for the emerging phenomenon of cyber-assisted olfaction and morph cell phones into ubiquitous sensors/decontaminators. Although this paper covers mechanisms and protocols to avail a neutralizing substance, further research will need to explore the substance's various pharmacological profiles and potential side effects.

  9. Biochemical, endocrine, and hematological factors in human oxygen tolerance extension: Predictive studies 6

    NASA Technical Reports Server (NTRS)

    Lambertsen, C. J.; Clark, J. M.

    1992-01-01

    The Predictive Studies VI (Biochemical, endocrine, and hematological factors in human oxygen tolerance extension) Program consisted of two related areas of research activity, integrated in design and performance, that were each based on an ongoing analysis of human organ oxygen tolerance data obtained for the continuous oxygen exposures of the prior Predictive Studies V Program. The two research areas effectively blended broad investigation of systematically varied intermittent exposure patterns in animals with very selective evaluation of specific exposure patterns in man.

  10. Genetic and Biochemical Mechanisms of Pollen Wall Development.

    PubMed

    Shi, Jianxin; Cui, Meihua; Yang, Li; Kim, Yu-Jin; Zhang, Dabing

    2015-11-01

    The pollen wall is a specialized extracellular cell wall matrix that surrounds male gametophytes and plays an essential role in plant reproduction. Uncovering the mechanisms that control the synthesis and polymerization of the precursors of pollen wall components has been a major research focus in plant biology. We review current knowledge on the genetic and biochemical mechanisms underlying pollen wall development in eudicot model Arabidopsis thaliana and monocot model rice (Oryza sativa), focusing on the genes involved in the biosynthesis, transport, and assembly of various precursors of pollen wall components. The conserved and divergent aspects of the genes involved as well as their regulation are addressed. Current challenges and future perspectives are also highlighted.

  11. Biochemical paths in humans and cells: Frontiers of AMS bioanalysis

    NASA Astrophysics Data System (ADS)

    Vogel, J. S.; Palmblad, N. M.; Ognibene, T.; Kabir, M. M.; Buchholz, B. A.; Bench, G.

    2007-06-01

    The publication rate of 3H and 14C use in biomedical research decreased by a factor of three since 1990 when the first applications of AMS in biomedicine were published. Against this decrease, the high sensitivity of AMS for these isotopes in small isolated samples has made significant contributions. New smaller spectrometers and increased commercial availability of AMS have solved some of the issues surrounding availability and cost, but improved quantitation in non-isotopic methods now compete with some early uses of AMS. We review the strength of AMS for quantifying rare biochemical events and chemical passages through individual people or cells and consider these as the frontiers of quantitation leading to profitable science unavailable to other techniques.

  12. [Metabolic correction: a biochemical option against diseases].

    PubMed

    Miranda-Massari, Jorge R; González, Michael J; Rodriguez-Gomez, José R; Duconge, Jorge; Allende-Vigo, Myriam Z; Jiménez Ramirez, Francisco J; Cintrón, Kenneth; Ricart, Carlos; Zaragoza-Urdaz, Rafael; Berdiel, Miguel Jabbar; Vázquez, Alex

    2015-01-01

    Human development and its physiology depends on a number of complex biochemical body processes, many of which are interactive and codependent. The speed and the degree in which many physiological reactions are completed depend on enzyme activity, which in turn depends on the bioavailability of co-factors and micronutrients such as vitamins and minerals. To achieve a healthy physiological state, organism need that biochemical reactions occur in a controlled and specific way at a particular speed and level or grade fully completed. To achieve this, is required an optimal metabolic balance. Factors such as, a particular genetic composition, inadequate dietary consumption patterns, traumas, diseases, toxins and environmental stress all of these factors rising demands for nutrients in order to obtain optimal metabolic balance. Metabolic correction is a biochemical and physiological concept that explains how improvements in cellular biochemistry of an organism can help the body achieve metabolic and physiological optimization. We summarize the contribution of several pioneers in understanding the role of micronutrients in health management. The concept of metabolic correction is becoming a significant term due to the presence of genetic variants that affect the speed of reactions of enzymes, causing metabolic alterations that enhance or promote the state/development of multiple diseases. Decline in the nutritional value of the food we eat, the increase in demand for certain nutrients caused by normal development, diseases and medications induce, usually, nutrients consumption. These nutritional deficiencies and insufficiencies are causing massive economic costs due to increased morbidity and mortality in our society. In summary, metabolic correction improves the enzymatic function, which favors the physiological normal functions, thus, contributing to improving health and the welfare of the human being. The purpose of this paper is to describe and introduce the concept

  13. Biochemical processing of heavy oils and residuum

    SciTech Connect

    Lin, M.S.; Premuzic, T.; Yablon, J.H.; Zhou, Wei-Min

    1995-05-01

    During the past several decades, the petroleum industry has adjusted gradually to accommodate the changes in market product demands, government regulations, and the quality and cost of feedstock crude oils. For example, the trends show that the demand for distillate fuels, such as diesel, as compared to gasoline are increasing. Air-quality standards have put additional demand on the processing of heavier and higher sulfur feed stocks. Thus, the 1990 Clean Air Act amendments require the industry to produce greater quantities of oxygenated gasoline, and lower sulfur diesel and reformulated gasoline. Biochemical technology may play an important role in responding to these demands on the petroleum industry.

  14. Noise-induced metastability in biochemical networks.

    PubMed

    Biancalani, Tommaso; Rogers, Tim; McKane, Alan J

    2012-07-01

    Intracellular biochemical reactions exhibit a rich dynamical phenomenology which cannot be explained within the framework of mean-field rate equations and additive noise. Here, we show that the presence of metastable states and radically different time scales are general features of a broad class of autocatalytic reaction networks, and that this fact may be exploited to gain analytical results. The latter point is demonstrated by a treatment of the paradigmatic Togashi-Kaneko reaction, which has resisted theoretical analysis for the last decade.

  15. Thermal lens spectrometry in biochemical analysis.

    PubMed

    Martín-Biosca, Y; García-Alvarez-Coque, M C; Ramis-Ramos, G

    1994-07-01

    The photothermal spectroscopic techniques, with special emphasis on the thermal lens spectrometry (TLS), are introduced to the non-specialist in laser spectroscopy. The following topics are treated on an elementary basis: fundamentals and analytical characteristics, instrumentation, selectivity and multi-wavelength capability, the models describing the signal-concentration relationship, the sensitivity, background noise and limits of detection, the influence of light scattering and flow. Applications related to the fields of clinical and biochemical analysis and organic pollution are given. The thermal lens circular dichroism and the infrared TLS are also briefly outlined.

  16. Biochemical Manifestation of HIV Lipodystrophy Syndrome

    PubMed Central

    Ihenetu, Kenneth; Mason, Darius

    2012-01-01

    Objectives Highly active anti-retroviral therapy (HAART), including protease inhibitors (PI) have led to dramatic improvements in the quality and quantity of life in patients with acquired immunodeficiency syndrome (AIDS). However, a significant number of AIDS patients on HAART develop characteristic changes in body fat redistribution referred to as lipodystrophy syndrome (LDS). Features of LDS include hypertrophy in the neck fat pad (buffalo hump), increased fat in the abdominal region (protease paunch), gynecomastia and loss of fat in the mid-face and extremities. Methods The aim of this paper is to review the current knowledge regarding this syndrome. This article reviews the published investigations on biochemical manifestation of HIV lipodystrophy syndrome. Results It is estimated that approximately 64% of patients treated with PI will experience this syndrome. Biochemically, these patients have increased triglycerides (Trig), total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-C) and extremely low high-density lipoprotein-cholesterol (HDL-C). Conclusions and Public Health Implications It is hoped that awareness of this syndrome would aid in early diagnosis and better patient management, possibly leading to a lower incidence of cardiovascular complications among these patients.

  17. Biochemical basis for the biological clock

    NASA Technical Reports Server (NTRS)

    Morre, D. James; Chueh, Pin-Ju; Pletcher, Jake; Tang, Xiaoyu; Wu, Lian-Ying; Morre, Dorothy M.

    2002-01-01

    NADH oxidases at the external surface of plant and animal cells (ECTO-NOX proteins) exhibit stable and recurring patterns of oscillations with potentially clock-related, entrainable, and temperature-compensated period lengths of 24 min. To determine if ECTO-NOX proteins might represent the ultradian time keepers (pacemakers) of the biological clock, COS cells were transfected with cDNAs encoding tNOX proteins having a period length of 22 min or with C575A or C558A cysteine to alanine replacements having period lengths of 36 or 42 min. Here we demonstrate that such transfectants exhibited 22, 36, or 40 to 42 h circadian patterns in the activity of glyceraldehyde-3-phosphate dehydrogenase, a common clock-regulated protein, in addition to the endogenous 24 h circadian period length. The fact that the expression of a single oscillatory ECTO-NOX protein determines the period length of a circadian biochemical marker (60 X the ECTO-NOX period length) provides compelling evidence that ECTO-NOX proteins are the biochemical ultradian drivers of the cellular biological clock.

  18. Transient absolute robustness in stochastic biochemical networks.

    PubMed

    Enciso, German A

    2016-08-01

    Absolute robustness allows biochemical networks to sustain a consistent steady-state output in the face of protein concentration variability from cell to cell. This property is structural and can be determined from the topology of the network alone regardless of rate parameters. An important question regarding these systems is the effect of discrete biochemical noise in the dynamical behaviour. In this paper, a variable freezing technique is developed to show that under mild hypotheses the corresponding stochastic system has a transiently robust behaviour. Specifically, after finite time the distribution of the output approximates a Poisson distribution, centred around the deterministic mean. The approximation becomes increasingly accurate, and it holds for increasingly long finite times, as the total protein concentrations grow to infinity. In particular, the stochastic system retains a transient, absolutely robust behaviour corresponding to the deterministic case. This result contrasts with the long-term dynamics of the stochastic system, which eventually must undergo an extinction event that eliminates robustness and is completely different from the deterministic dynamics. The transiently robust behaviour may be sufficient to carry out many forms of robust signal transduction and cellular decision-making in cellular organisms. PMID:27581485

  19. Biochemical properties and cellular localisation of STIM proteins.

    PubMed

    Dziadek, Marie A; Johnstone, Lorna S

    2007-08-01

    Human and murine STIM1 were originally discovered as candidate growth regulators in tumours and in the bone marrow stroma, and the structurally related vertebrate family members, STIM2 and the Drosophila homologue D-Stim, were subsequently identified. STIM proteins are ubiquitously expressed type I single-pass transmembrane proteins which have a unique combination of structural motifs within their polypeptide sequences. The extracellular regions contain an N-terminal unpaired EF-hand Ca(2+) binding motif adjacent to an unconventional glycosylated SAM domain, while the cytoplasmic regions contain alpha-helical coiled-coil domains within a region having homology to ERM domains adjacent to the transmembrane region, and phosphorylated proline-rich domains near the C-terminus. STIM1, STIM2 and D-Stim diverge significantly only in their structure C-terminal to the coiled-coil/ERM domains. The STIM structural domains were predicted to function in Ca(2+) binding as well as in mediating interactions between STIM proteins and other proteins, and homotypic STIM1-STIM1 and heterotypic STIM1-STIM2 interactions were demonstrated biochemically. However, the functional significance of the cellular localisation of STIM1 and its domain structure only became evident after recent breakthrough research identified STIM1 as a key regulator of store-operated calcium (SOC) entry into cells. It is now clear that STIM1 is both a sensor of Ca(2+) depletion in the endoplasmic reticulum (ER) lumen and an activator of Orai1-containing SOC channels in the plasma membrane. On the basis of recent functional studies a model can be proposed to explain how the biochemical properties of STIM1 contribute to its precise membrane localisation and its function in regulating SOC entry. PMID:17382385

  20. Photoinduced biochemical activity of fullerene carboxylic acid

    SciTech Connect

    Tokuyama, Hidetoshi; Yamago, Shigeru; Nakamura, Eiichi; Shiraki, Takashi; Sugiura, Yukio

    1993-08-25

    Here we report the preparation of a water-miscible fullerene carboxylic acid (2) and its biological activity-cytotoxicity and G-selective DNA cleaving ability. What is truly remarkable is that the biological activity of C{sub 60} was observed only under irradiation with visible light and not in the dark, suggesting that fullerenes may serve as useful photosensitive biochemical probes. We have found, for the first time, that even low-energy visible light is surfficient to induce biological activity in fullerene derivatives. Among the numerous implications of the present findings, the most exciting prospect includes the use of fullerene derivatives for photodynamic therapy. 18 refs., 2 figs., 1 tab.

  1. Thin membrane sensor with biochemical switch

    NASA Technical Reports Server (NTRS)

    Case, George D. (Inventor); Worley, III, Jennings F. (Inventor)

    1994-01-01

    A modular biosensor system for chemical or biological agent detection utilizes electrochemical measurement of an ion current across a gate membrane triggered by the reaction of the target agent with a recognition protein conjugated to a channel blocker. The sensor system includes a bioresponse simulator or biochemical switch module which contains the recognition protein-channel blocker conjugate, and in which the detection reactions occur, and a transducer module which contains a gate membrane and a measuring electrode, and in which the presence of agent is sensed electrically. In the poised state, ion channels in the gate membrane are blocked by the recognition protein-channel blocker conjugate. Detection reactions remove the recognition protein-channel blocker conjugate from the ion channels, thus eliciting an ion current surge in the gate membrane which subsequently triggers an output alarm. Sufficiently large currents are generated that simple direct current electronics are adequate for the measurements. The biosensor has applications for environmental, medical, and industrial use.

  2. The biochemical basis of hereditary fructose intolerance.

    PubMed

    Bouteldja, Nadia; Timson, David J

    2010-04-01

    Hereditary fructose intolerance is a rare, but potentially lethal, inherited disorder of fructose metabolism, caused by mutation of the aldolase B gene. Treatment currently relies solely on dietary restriction of problematic sugars. Biochemical study of defective aldolase B enzymes is key to revealing the molecular basis of the disease and providing a stronger basis for improved treatment and diagnosis. Such studies have revealed changes in enzyme activity, stability and oligomerisation. However, linking these changes to disease phenotypes has not always been straightforward. This review gives a general overview of the features of hereditary fructose intolerance, then concentrates on the biochemistry of the AP variant (Ala149Pro variant of aldolase B) and molecular pathological consequences of mutation of the aldolase B gene.

  3. Peter Hochachka: adventures in biochemical adaptation.

    PubMed

    Somero, George N; Suarez, Raul K

    2005-01-01

    Peter Hochachka was one of the most creative forces in the field of comparative physiology during the past half-century. His career was truly an exploratory adventure, in both intellectual and geographic senses. His broad comparative studies of metabolism in organisms as diverse as trout, tunas, oysters, squid, turtles, locusts, hummingbirds, seals, and humans revealed the adaptable features of enzymes and metabolic pathways that provide the biochemical bases for diverse lifestyles and environments. In its combined breadth and depth, no other corpus of work better illustrates the principle of "unity in diversity" that marks comparative physiology. Through his publications, his stimulating mentorship, his broad editorial services, and his continuous-and highly infectious-enthusiasm for his field, Peter Hochachka served as one of the most influential leaders in the transformation of comparative physiology.

  4. Biochemical pathways in seed oil synthesis.

    PubMed

    Bates, Philip D; Stymne, Sten; Ohlrogge, John

    2013-06-01

    Oil produced in plant seeds is utilized as a major source of calories for human nutrition, as feedstocks for non-food uses such as soaps and polymers, and can serve as a high-energy biofuel. The biochemical pathways leading to oil (triacylglycerol) synthesis in seeds involve multiple subcellular organelles, requiring extensive lipid trafficking. Phosphatidylcholine plays a central role in these pathways as a substrate for acyl modifications and likely as a carrier for the trafficking of acyl groups between organelles and membrane subdomains. Although much has been clarified regarding the enzymes and pathways responsible for acyl-group flux, there are still major gaps in our understanding. These include the identity of several key enzymes, how flux between alternative pathways is controlled and the specialized cell biology leading to biogenesis of oil bodies that store up to 80% of carbon in seeds.

  5. [Biochemical complications of experimental vesico-sigmoidostomy].

    PubMed

    Nuñez, R; Blesa, E; Ramos, S; Morillo, M; Ortega, L; Requena, F; Cardesa, J J

    1987-03-01

    Three experimental models of vesico-sigmoidostomy are studied (model-1, end to side V-S plus urethral ligation, model-2, end to end V-S, in "Y of Rous" plus urethral ligation and model-3, vesico-sigmoidoplasty), with aim of reproducing chemical imbalance observed in human subjects with ureterosigmoidostomy. Authors have evaluated clinical biochemical (serum acido-base balance, Cl, Na+, K+, BUN, creatinine, ammonia and albumin), and histologic variables in the first, third and fifth month after operation in 225 rats. Animal of model-1 presented more frequently than model-2 and model-3, alterations (hyperchloraemic acidosis, uraemia, hyperammonemia and hypoalbumin) as well as affectation of upper urinary system for acute or chronic pyelonephritis.

  6. Droplet microfluidics in (bio)chemical analysis.

    PubMed

    Basova, Evgenia Yu; Foret, Frantisek

    2015-01-01

    Droplet microfluidics may soon change the paradigm of performing chemical analyses and related instrumentation. It can improve not only the analysis scale, possibility for sensitivity improvement, and reduced consumption of chemical and biological reagents, but also the speed of performing a variety of unit operations. At present, microfluidic platforms can reproducibly generate monodisperse droplet populations at kHz or higher rates with droplet sizes suitable for high-throughput experiments, single-cell detection or even single molecule analysis. In addition to being used as microreactors with volume in the micro- to femtoliter range, droplet based systems have also been used to directly synthesize particles and encapsulate biological entities for biomedicine and biotechnology applications. This minireview summarizes various droplet microfluidics operations and applications for (bio)chemical assays described in the literature during the past few years.

  7. Hemoglobin Variants: Biochemical Properties and Clinical Correlates

    PubMed Central

    Thom, Christopher S.; Dickson, Claire F.; Gell, David A.; Weiss, Mitchell J.

    2013-01-01

    Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples. PMID:23388674

  8. Hemoglobin variants: biochemical properties and clinical correlates.

    PubMed

    Thom, Christopher S; Dickson, Claire F; Gell, David A; Weiss, Mitchell J

    2013-03-01

    Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples.

  9. [Biochemical and immunological markers of autoimmune thyroiditis].

    PubMed

    Biktagirova, E M; Sattarova, L I; Vagapova, G R; Skibo, Y V; Chuhlovina, E N; Kravtsova, O A; Abramova, Z I

    2016-05-01

    Correlations between biochemical and immunological markers of programmed cell death (apoptosis), and the functional state of the thyroid gland (hyperthyroidism, euthyroidism, hypothyroidism) have been investigated in autoimmune thyroiditis (AT) (also known as chronic autoimmune thyroiditis). Annexin V, TRAIL and TNF-a, as well as DNA-hydrolyzing antibodies were used as the main markers. Increased levels of TRAIL were found in the serum of AT patients (hyperthyroidism>hypothyroidism>euthyroidism) compared with healthy individuals. The highest frequency of antibodies to denatured DNA (Abs-dDNA) had the highest frequency in AT patients (97%) compared with healthy controls. Among these patients, 75% had hyperthyroidism, 85% had hypothyroidism, and 84.7% had euthyroidism. Abs hydrolyzing activity demonstrated correlation dependence with symptoms of the thyroid dysfunction. PMID:27563001

  10. Biochemical Pharmacology of the Sigma-1 Receptor.

    PubMed

    Chu, Uyen B; Ruoho, Arnold E

    2016-01-01

    The sigma-1 receptor (S1R) is a 223 amino acid two transmembrane (TM) pass protein. It is a non-ATP-binding nonglycosylated ligand-regulated molecular chaperone of unknown three-dimensional structure. The S1R is resident to eukaryotic mitochondrial-associated endoplasmic reticulum and plasma membranes with broad functions that regulate cellular calcium homeostasis and reduce oxidative stress. Several multitasking functions of the S1R are underwritten by chaperone-mediated direct (and indirect) interactions with ion channels, G-protein coupled receptors and cell-signaling molecules involved in the regulation of cell growth. The S1R is a promising drug target for the treatment of several neurodegenerative diseases related to cellular stress. In vitro and in vivo functional and molecular characteristics of the S1R and its interactions with endogenous and synthetic small molecules have been discovered by the use of pharmacologic, biochemical, biophysical, and molecular biology approaches. The S1R exists in monomer, dimer, tetramer, hexamer/octamer, and higher oligomeric forms that may be important determinants in defining the pharmacology and mechanism(s) of action of the S1R. A canonical GXXXG in putative TM2 is important for S1R oligomerization. The ligand-binding regions of S1R have been identified and include portions of TM2 and the TM proximal regions of the C terminus. Some client protein chaperone functions and interactions with the cochaperone 78-kDa glucose-regulated protein (binding immunoglobulin protein) involve the C terminus. Based on its biochemical features and mechanisms of chaperone action the possibility that the S1R is a member of the small heat shock protein family is discussed.

  11. Biochemical diagnosis of neuroendocrine GEP tumor.

    PubMed Central

    Oberg, K.

    1997-01-01

    Neuroendocrine gut and pancreatic tumors are known to contain and secret different peptide hormones and amines. During the last two decades, many radioimmunoassays and Elizas have been developed to analyze these substances in blood and urine, which has enabled clinicians to improve the diagnosis and monitoring of patients with various neuroendocrine tumors. Due to cost constraints in medical care, it is important to try to define the most useful biochemical markers from the clinical point of view. The glycoprotein chromogranin A has been shown to be a useful marker for diagnosing various neuroendocrine tumors, both by histopathology and circulating tumor markers. In patients with demonstrable endocrine tumors, about 90 percent of the patients present high circulating levels of chromogranin A. A hundred-fold increase of plasma chromogranin is seen in patients with midgut carcinoid tumors and liver metastases. The plasma levels of chromogranin A reflect the tumor mass and can be used for monitoring the patient during treatment and follow-up, although the day-to-day variation might be 30-40 percent. High circulating levels of the chromogranin A might be an indicator of bad prognosis in patients with malignant carcinoid tumors. Besides analyzing plasma chromogranin A, specific analyses such as urinary 5-HIAA in midgut carcinoid patients, serum gastrin in patients with Zollinger-Ellison syndrome and insulin/proinsulin in patients with hypoglycemia should be performed. In patients with small tumor masses or intermittent symptoms, provocative tests such as a meal stimulation test, secretin test or pentagastrin stimulation of tachykinin release can supplement the basal measurements of peptides and amines. To fully evaluate the growth potential in neuroendocrine tumors, traditional biochemical markers should be supplemented with indicators of growth proliferation (Ki-67, PCNA) and immunohistochemical staining for the adhesion molecule CD44 and the PDGF-alpha receptor

  12. Transcription fluctuation effects on biochemical oscillations.

    PubMed

    Nishino, Ryota; Sakaue, Takahiro; Nakanishi, Hiizu

    2013-01-01

    Some biochemical systems show oscillation. They often consist of feedback loops with repressive transcription regulation. Such biochemical systems have distinctive characteristics in comparison with ordinary chemical systems: i) numbers of molecules involved are small, ii) there are typically only a couple of genes in a cell with a finite regulation time. Due to the fluctuations caused by these features, the system behavior can be quite different from the one by deterministic rate equations, because the rate equations ignore molecular fluctuations and thus are exact only in the infinite molecular number limit. The molecular fluctuations on a free-running circadian system have been studied by Gonze et al. (2002) by introducing a scale parameter [Formula: see text] for the system size. They consider, however, only the first effect, assuming that the gene process is fast enough for the second effect to be ignored, but this has not been examined systematically yet. Here we study fluctuation effects due to the finite gene regulation time by introducing a new scale parameter [Formula: see text], which we take as the unbinding time of a nuclear protein from the gene. We focus on the case where the fluctuations due to small molecular numbers are negligible. In simulations on the same system studied by Gonze et al., we find the system is unexpectedly sensitive to the fluctuation in the transcription regulation; the period of oscillation fluctuates about 30 min even when the regulation time scale [Formula: see text] is around 30 s, that is even smaller than 1/1000 of its circadian period. We also demonstrate that the distribution width for the oscillation period and amplitude scales with [Formula: see text], and the correlation time scales with [Formula: see text] in the small [Formula: see text] regime. The relative fluctuations for the period are about half of that for the amplitude, namely, the periodicity is more stable than the amplitude.

  13. Pattern Selection by Dynamical Biochemical Signals

    PubMed Central

    Palau-Ortin, David; Formosa-Jordan, Pau; Sancho, José M.; Ibañes, Marta

    2015-01-01

    The development of multicellular organisms involves cells to decide their fate upon the action of biochemical signals. This decision is often spatiotemporally coordinated such that a spatial pattern arises. The dynamics that drive pattern formation usually involve genetic nonlinear interactions and positive feedback loops. These complex dynamics may enable multiple stable patterns for the same conditions. Under these circumstances, pattern formation in a developing tissue involves a selection process: why is a certain pattern formed and not another stable one? Herein we computationally address this issue in the context of the Notch signaling pathway. We characterize a dynamical mechanism for developmental selection of a specific pattern through spatiotemporal changes of the control parameters of the dynamics, in contrast to commonly studied situations in which initial conditions and noise determine which pattern is selected among multiple stable ones. This mechanism can be understood as a path along the parameter space driven by a sequence of biochemical signals. We characterize the selection process for three different scenarios of this dynamical mechanism that can take place during development: the signal either 1) acts in all the cells at the same time, 2) acts only within a cluster of cells, or 3) propagates along the tissue. We found that key elements for pattern selection are the destabilization of the initial pattern, the subsequent exploration of other patterns determined by the spatiotemporal symmetry of the parameter changes, and the speeds of the path compared to the timescales of the pattern formation process itself. Each scenario enables the selection of different types of patterns and creates these elements in distinct ways, resulting in different features. Our approach extends the concept of selection involved in cellular decision-making, usually applied to cell-autonomous decisions, to systems that collectively make decisions through cell

  14. Scaling up Semi-Arid Grassland Biochemical Content from the Leaf to the Canopy Level: Challenges and Opportunities

    PubMed Central

    He, Yuhong; Mui, Amy

    2010-01-01

    Remote sensing imagery is being used intensively to estimate the biochemical content of vegetation (e.g., chlorophyll, nitrogen, and lignin) at the leaf level. As a result of our need for vegetation biochemical information and our increasing ability to obtain canopy spectral data, a few techniques have been explored to scale leaf-level biochemical content to the canopy level for forests and crops. However, due to the contribution of non-green materials (i.e., standing dead litter, rock, and bare soil) from canopy spectra in semi-arid grasslands, it is difficult to obtain information about grassland biochemical content from remote sensing data at the canopy level. This paper summarizes available methods used to scale biochemical information from the leaf level to the canopy level and groups these methods into three categories: direct extrapolation, canopy-integrated approach, and inversion of physical models. As for semi-arid heterogeneous grasslands, we conclude that all methods are useful, but none are ideal. It is recommended that future research should explore a systematic upscaling framework which combines spatial pattern analysis, canopy-integrated approach, and modeling methods to retrieve vegetation biochemical content at the canopy level. PMID:22163513

  15. Optical tweezers and multiphoton microscopies integrated photonic tool for mechanical and biochemical cell processes studies

    NASA Astrophysics Data System (ADS)

    de Thomaz, A. A.; Faustino, W. M.; Fontes, A.; Fernandes, H. P.; Barjas-Castro, M. d. L.; Metze, K.; Giorgio, S.; Barbosa, L. C.; Cesar, C. L.

    2007-09-01

    The research in biomedical photonics is clearly evolving in the direction of the understanding of biological processes at the cell level. The spatial resolution to accomplish this task practically requires photonics tools. However, an integration of different photonic tools and a multimodal and functional approach will be necessary to access the mechanical and biochemical cell processes. This way we can observe mechanicaly triggered biochemical events or biochemicaly triggered mechanical events, or even observe simultaneously mechanical and biochemical events triggered by other means, e.g. electricaly. One great advantage of the photonic tools is its easiness for integration. Therefore, we developed such integrated tool by incorporating single and double Optical Tweezers with Confocal Single and Multiphoton Microscopies. This system can perform 2-photon excited fluorescence and Second Harmonic Generation microscopies together with optical manipulations. It also can acquire Fluorescence and SHG spectra of specific spots. Force, elasticity and viscosity measurements of stretched membranes can be followed by real time confocal microscopies. Also opticaly trapped living protozoas, such as leishmania amazonensis. Integration with CARS microscopy is under way. We will show several examples of the use of such integrated instrument and its potential to observe mechanical and biochemical processes at cell level.

  16. Physiological, biochemical, and molecular mechanisms of heat stress tolerance in plants.

    PubMed

    Hasanuzzaman, Mirza; Nahar, Kamrun; Alam, Md Mahabub; Roychowdhury, Rajib; Fujita, Masayuki

    2013-05-03

    High temperature (HT) stress is a major environmental stress that limits plant growth, metabolism, and productivity worldwide. Plant growth and development involve numerous biochemical reactions that are sensitive to temperature. Plant responses to HT vary with the degree and duration of HT and the plant type. HT is now a major concern for crop production and approaches for sustaining high yields of crop plants under HT stress are important agricultural goals. Plants possess a number of adaptive, avoidance, or acclimation mechanisms to cope with HT situations. In addition, major tolerance mechanisms that employ ion transporters, proteins, osmoprotectants, antioxidants, and other factors involved in signaling cascades and transcriptional control are activated to offset stress-induced biochemical and physiological alterations. Plant survival under HT stress depends on the ability to perceive the HT stimulus, generate and transmit the signal, and initiate appropriate physiological and biochemical changes. HT-induced gene expression and metabolite synthesis also substantially improve tolerance. The physiological and biochemical responses to heat stress are active research areas, and the molecular approaches are being adopted for developing HT tolerance in plants. This article reviews the recent findings on responses, adaptation, and tolerance to HT at the cellular, organellar, and whole plant levels and describes various approaches being taken to enhance thermotolerance in plants.

  17. Biochemical reaction engineering and process development in anaerobic wastewater treatment.

    PubMed

    Aivasidis, Alexander; Diamantis, Vasileios

    2005-01-01

    Developments in production technology have frequently resulted in the concentrated local accumulation of highly organic-laden wastewaters. Anaerobic wastewater treatment, in industrial applications, constitutes an advanced method of synthesis by which inexpensive substrates are converted into valuable disproportionate products. A critical discussion of certain fundamental principles of biochemical reaction engineering relevant to the anaerobic mode of operation is made here, with special emphasis on the roles of thermodynamics, kinetics, mass and heat transfer, reactor design, biomass retention and recycling. The applications of the anaerobic processes are discussed, introducing the principles of an upflow anaerobic sludge bed reactor and a fixed-bed loop reactor. The merits of staging reactor systems are presented using selected examples based on two decades of research in the field of anaerobic fermentation and wastewater treatment at the Forschungszentrum Julich (Julich Research Center, Germany). Wastewater treatment is an industrial process associated with one of the largest levels of mass throughput known, and for this reason it provides a major impetus to further developments in bioprocess technology in general.

  18. A Biochemical Approach to the Problem of Dyslexia.

    ERIC Educational Resources Information Center

    Baker, Sidney McDonald

    1985-01-01

    The paper presents the case of a sixth-grade boy, labeled dyslexic, who responded positively to a biochemical approach. Remedy of iron, zinc, and Vitamin B-6 deficiencies as well as an imbalance of fatty acids resulted in improvements in hair and skin and also in reading. A biochemical approach to behavior problems is proposed. (Author/CL)

  19. Simulation studies in biochemical signaling and enzyme reactions

    NASA Astrophysics Data System (ADS)

    Nelatury, Sudarshan R.; Vagula, Mary C.

    2014-06-01

    Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

  20. Alternative aircraft anti-icing formulations with reduced aquatic toxicity and biochemical oxygen demand

    USGS Publications Warehouse

    Gold, Harris; Joback, Kevin; Geis, Steven; Bowman, George; Mericas, Dean; Corsi, Steven R.; Ferguson, Lee

    2010-01-01

    The current research was conducted to identify alternative aircraft and pavement deicer and anti-icer formulations with improved environmental characteristics compared to currently used commercial products (2007). The environmental characteristics of primary concern are the biochemical oxygen demand (BOD) and aquatic toxicity of the fully formulated products. Except when the distinction among products is necessary for clarity, “deicer” will refer to aircraft-deicing fluids (ADFs), aircraft anti-icing fluids (AAFs), and pavementdeicing materials (PDMs).

  1. Model-Based Design of Biochemical Microreactors

    PubMed Central

    Elbinger, Tobias; Gahn, Markus; Neuss-Radu, Maria; Hante, Falk M.; Voll, Lars M.; Leugering, Günter; Knabner, Peter

    2016-01-01

    Mathematical modeling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation, and optimization of metabolic processes in biochemical microreactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first microreactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments of the reactor multienzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions. The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multienzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the microreactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P) was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns, which differ for different experimental arrangements. Furthermore, the total output of G6P

  2. Model-Based Design of Biochemical Microreactors.

    PubMed

    Elbinger, Tobias; Gahn, Markus; Neuss-Radu, Maria; Hante, Falk M; Voll, Lars M; Leugering, Günter; Knabner, Peter

    2016-01-01

    Mathematical modeling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation, and optimization of metabolic processes in biochemical microreactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first microreactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments of the reactor multienzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions. The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multienzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the microreactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P) was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns, which differ for different experimental arrangements. Furthermore, the total output of G6P

  3. Biochemical analysis of Phytolacca DOPA dioxygenase.

    PubMed

    Takahashi, Kana; Yoshida, Kazuko; Yura, Kei; Ashihara, Hiroshi; Sakuta, Masaaki

    2015-05-01

    The biochemical analysis of Phytolacca americana DOPA dioxygenases (PaDOD1 and PaDOD2) was carried out. The recombinant protein of PaDOD1 catalyzed the conversion of DOPA to betalamic acid, whereas DOD activity was not detected in PaDOD2 in vitro. While the reported motif conserved in DODs from betalain-producing plants was found in PaDOD1, a single amino acid residue alteration was detected in PaDOD2. A mutated PaDOD1 protein with a change of 177 Asn to Gly showed reduced specific activity compared with PaDOD1, while DOPA dioxygenase activity was not observed for a mutated PaDOD2 protein which had its conserved motif replaced with that of PaDOD. A three-dimensional (3D) structural model of PaDOD1 and PaDOD2 showed that the conserved motif in DODs was located in the N-terminal side of a loop, which was found close to the putative active site. The difference in stability of the loop may affect the enzymatic activity of PaDOD2. PMID:26058142

  4. Applied spectrophotometry: analysis of a biochemical mixture.

    PubMed

    Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software. PMID:23625877

  5. Biochemical analysis of Phytolacca DOPA dioxygenase.

    PubMed

    Takahashi, Kana; Yoshida, Kazuko; Yura, Kei; Ashihara, Hiroshi; Sakuta, Masaaki

    2015-05-01

    The biochemical analysis of Phytolacca americana DOPA dioxygenases (PaDOD1 and PaDOD2) was carried out. The recombinant protein of PaDOD1 catalyzed the conversion of DOPA to betalamic acid, whereas DOD activity was not detected in PaDOD2 in vitro. While the reported motif conserved in DODs from betalain-producing plants was found in PaDOD1, a single amino acid residue alteration was detected in PaDOD2. A mutated PaDOD1 protein with a change of 177 Asn to Gly showed reduced specific activity compared with PaDOD1, while DOPA dioxygenase activity was not observed for a mutated PaDOD2 protein which had its conserved motif replaced with that of PaDOD. A three-dimensional (3D) structural model of PaDOD1 and PaDOD2 showed that the conserved motif in DODs was located in the N-terminal side of a loop, which was found close to the putative active site. The difference in stability of the loop may affect the enzymatic activity of PaDOD2.

  6. Biochemical and Proteomic Characterization of Alkaptonuric Chondrocytes

    PubMed Central

    Braconi, Daniela; Bernardini, Giulia; Bianchini, Claretta; Laschi, Marcella; Millucci, Lia; Amato, Loredana; Tinti, Laura; Serchi, Tommaso; Chellini, Federico; Spreafico, Adriano; Santucci, Annalisa

    2012-01-01

    Alkaptonuria (AKU) is a rare genetic disease associated with the accumulation of homogentisic acid (HGA) and its oxidized/polymerized products which leads to the deposition of melanin-like pigments (ochronosis) in connective tissues. Although numerous case reports have described ochronosis in joints, little is known on the molecular mechanisms leading to such a phenomenon. For this reason, we characterized biochemically chondrocytes isolated from the ochronotic cartilage of AKU patients. Based on the macroscopic appearance of the ochronotic cartilage, two sub-populations were identified: cells coming from the black portion of the cartilage were referred to as “black” AKU chondrocytes, while those coming from the white portion were referred to as “white” AKU chondrocytes. Notably, both AKU chondrocytic types were characterized by increased apoptosis, NO release, and levels of pro-inflammatory cytokines. Transmission electron microscopy also revealed that intracellular ochronotic pigment deposition was common to both “white” and “black” AKU cells. We then undertook a proteomic and redox-proteomic analysis of AKU chondrocytes which revealed profound alterations in the levels of proteins involved in cell defence, protein folding, and cell organization. An increased post-translational oxidation of proteins, which also involved high molecular weight protein aggregates, was found to be particularly relevant in “black” AKU chondrocytes. J. Cell. Physiol. 227: 3333–3343, 2012. © 2011 Wiley Periodicals, Inc. PMID:22213341

  7. Biochemical markers in butadiene-exposed workers

    SciTech Connect

    Bechtold, W.E.; Hayes, R.B.; Thornton-Manning, J.R.; Henderson, R.F.

    1994-11-01

    1,3-Butadiene (BD) is used to manufacture a wide range of polymers and copolymers including styrene-butadiene rubber, polybutadiene, and acrylonitrile-butadiene-syrene resins. The carcinogenicity of BD has been determined in life-span inhalation studies in both Sprague-Dawley rats and B6C3F{sub 1} mice. Results suggest a marked species difference in the carcinogenic effects of BD. For example, female mice exposed to as low as 6.25 ppm BD exhibited increased alveolar/bronchiolar neoplasms. In contrast, BD was only a weak carcinogen in Sprague-Dawley rats. Rats were observed to have an increase only in mammary tumors after exposure to 1000 ppm. A biochemical study of highly exposed BD workers and unexposed controls is providing valuable information on BD metabolism in humans, and how this relates to the development of intermediate biologic effects. A group of heavily exposed workers were identified in a BD production facility in China. The purpose of this paper is to report the initial results from the sampling trip in the first quarter of 1994.

  8. Control analysis for autonomously oscillating biochemical networks.

    PubMed

    Reijenga, Karin A; Westerhoff, Hans V; Kholodenko, Boris N; Snoep, Jacky L

    2002-01-01

    It has hitherto not been possible to analyze the control of oscillatory dynamic cellular processes in other than qualitative ways. The control coefficients, used in metabolic control analyses of steady states, cannot be applied directly to dynamic systems. We here illustrate a way out of this limitation that uses Fourier transforms to convert the time domain into the stationary frequency domain, and then analyses the control of limit cycle oscillations. In addition to the already known summation theorems for frequency and amplitude, we reveal summation theorems that apply to the control of average value, waveform, and phase differences of the oscillations. The approach is made fully operational in an analysis of yeast glycolytic oscillations. It follows an experimental approach, sampling from the model output and using discrete Fourier transforms of this data set. It quantifies the control of various aspects of the oscillations by the external glucose concentration and by various internal molecular processes. We show that the control of various oscillatory properties is distributed over the system enzymes in ways that differ among those properties. The models that are described in this paper can be accessed on http://jjj.biochem.sun.ac.za.

  9. Biochemical Plant Responses to Ozone 1

    PubMed Central

    Rosemann, Detlef; Heller, Werner; Sandermann, Heinrich

    1991-01-01

    Formation of the stilbenes pinosylvin and pinosylvin 3-methyl ether, as well as the activity of the biosynthetic enzyme stilbene synthase (pinosylvin-forming), were induced several hundred- to thousandfold in primary needles of 6-week-old pine (Pinus sylvestris L.) seedlings upon exposure to a single pulse of ozone of at least 0.15 microliters per liter. The seedlings required 4 hours of exposure as a minimum for the induction of stilbene biosynthesis when exposed to 0.2 microliters per liter ozone. Both stilbene synthase activity and stilbene accumulation increased with the duration of ozone treatment. The activity of phenylalanine ammonia-lyase and the activity of chalcone synthase, a key enzyme of the flavonoid pathway that uses the same substrates as stilbene synthase, were also stimulated about twofold by ozone. Stilbene biosynthesis appears to represent the first example of a dose-dependent biochemical response to ozone in a conifer species and may serve as a useful biomarker to study stress impacts on pine trees. PMID:16668544

  10. Multiple capillary biochemical analyzer with barrier member

    DOEpatents

    Dovichi, Norman J.; Zhang, Jian Z.

    1996-01-01

    A multiple capillary biochemical analyzer for sequencing DNA and performing other analyses, in which a set of capillaries extends from wells in a microtiter plate into a cuvette. In the cuvette the capillaries are held on fixed closely spaced centers by passing through a sandwich construction having a pair of metal shims which squeeze between them a rubber gasket, forming a leak proof seal for an interior chamber in which the capillary ends are positioned. Sheath fluid enters the chamber and entrains filament sample streams from the capillaries. The filament sample streams, and sheath fluid, flow through aligned holes in a barrier member spaced close to the capillary ends, into a collection chamber having a lower glass window. The filament streams are illuminated above the barrier member by a laser, causing them to fluoresce. The fluorescence is viewed end-on by a CCD camera chip located below the glass window. The arrangement ensures an equal optical path length from all fluorescing spots to the CCD chip and also blocks scattered fluorescence illumination, providing more uniform results and an improved signal to noise ratio.

  11. Multiple capillary biochemical analyzer with barrier member

    DOEpatents

    Dovichi, N.J.; Zhang, J.Z.

    1996-10-22

    A multiple capillary biochemical analyzer is disclosed for sequencing DNA and performing other analyses, in which a set of capillaries extends from wells in a microtiter plate into a cuvette. In the cuvette the capillaries are held on fixed closely spaced centers by passing through a sandwich construction having a pair of metal shims which squeeze between them a rubber gasket, forming a leak proof seal for an interior chamber in which the capillary ends are positioned. Sheath fluid enters the chamber and entrains filament sample streams from the capillaries. The filament sample streams, and sheath fluid, flow through aligned holes in a barrier member spaced close to the capillary ends, into a collection chamber having a lower glass window. The filament streams are illuminated above the barrier member by a laser, causing them to fluoresce. The fluorescence is viewed end-on by a CCD camera chip located below the glass window. The arrangement ensures an equal optical path length from all fluorescing spots to the CCD chip and also blocks scattered fluorescence illumination, providing more uniform results and an improved signal-to-noise ratio. 12 figs.

  12. Applied spectrophotometry: analysis of a biochemical mixture.

    PubMed

    Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software.

  13. Diagnosis of growth retardation by biochemical methods.

    PubMed

    Klopper, A

    1984-08-01

    The substances in the blood or urine of a pregnant woman which may give an indication of the state of fetal growth are examined. The drawback of measuring such substances is that the values are variable, making it difficult to distinguish between normal and abnormal. Variability arises from technical factors in measurements, from short-term changes of no significance and from the large spread of normal values from one individual to the next. Biochemical parameters of fetal growth can be applied in one of two ways: as screening tests or as control measures by serial assays to guide management. The criteria by which any test should be evaluated--sensitivity, specificity and relative risk--are examined. Particular substances whose measurement may be helpful are considered in terms of the steroids or proteins produced by the fetoplacental unit. The oestrogens, notably oestriol, hold pride of place among the steroids. Dynamic tests of steroid synthesis are also considered. The chief placental proteins of interest are chorionic gonadotrophin, placental lactogen and Schwangerschaftsprotein 1. It is concluded that the method to be recommended is to screen a whole obstetric population with assays of placental lactogen and to follow those with values below the normal limit with serial oestriol assays. PMID:6332704

  14. In situ biospectroscopic investigation of rapid ischemic and postmortem induced biochemical alterations in the rat brain.

    PubMed

    Hackett, Mark J; Britz, Carter J; Paterson, Phyllis G; Nichol, Helen; Pickering, Ingrid J; George, Graham N

    2015-02-18

    Rapid advances in imaging technologies have pushed novel spectroscopic modalities such as Fourier transform infrared spectroscopy (FTIR) and X-ray absorption spectroscopy (XAS) at the sulfur K-edge to the forefront of direct in situ investigation of brain biochemistry. However, few studies have examined the extent to which sample preparation artifacts confound results. Previous investigations using traditional analyses, such as tissue dissection, homogenization, and biochemical assay, conducted extensive research to identify biochemical alterations that occur ex vivo during sample preparation. In particular, altered metabolism and oxidative stress may be caused by animal death. These processes were a concern for studies using biochemical assays, and protocols were developed to minimize their occurrence. In this investigation, a similar approach was taken to identify the biochemical alterations that are detectable by two in situ spectroscopic methods (FTIR, XAS) that occur as a consequence of ischemic conditions created during humane animal killing. FTIR and XAS are well suited to study markers of altered metabolism such as lactate and creatine (FTIR) and markers of oxidative stress such as aggregated proteins (FTIR) and altered thiol redox (XAS). The results are in accordance with previous investigations using biochemical assays and demonstrate that the time between animal death and tissue dissection results in ischemic conditions that alter brain metabolism and initiate oxidative stress. Therefore, future in situ biospectroscopic investigations utilizing FTIR and XAS must take into consideration that brain tissue dissected from a healthy animal does not truly reflect the in vivo condition, but rather reflects a state of mild ischemia. If studies require the levels of metabolites (lactate, creatine) and markers of oxidative stress (thiol redox) to be preserved as close as possible to the in vivo condition, then rapid freezing of brain tissue via decapitation into

  15. Mechanical and biochemical mapping of human auricular cartilage for reliable assessment of tissue-engineered constructs.

    PubMed

    Nimeskern, Luc; Pleumeekers, Mieke M; Pawson, Duncan J; Koevoet, Wendy L M; Lehtoviita, Iina; Soyka, Michael B; Röösli, Christof; Holzmann, David; van Osch, Gerjo J V M; Müller, Ralph; Stok, Kathryn S

    2015-07-16

    It is key for successful auricular (AUR) cartilage tissue-engineering (TE) to ensure that the engineered cartilage mimics the mechanics of the native tissue. This study provides a spatial map of the mechanical and biochemical properties of human auricular cartilage, thus establishing a benchmark for the evaluation of functional competency in AUR cartilage TE. Stress-relaxation indentation (instantaneous modulus, Ein; maximum stress, σmax; equilibrium modulus, Eeq; relaxation half-life time, t1/2; thickness, h) and biochemical parameters (content of DNA; sulfated-glycosaminoglycan, sGAG; hydroxyproline, HYP; elastin, ELN) of fresh human AUR cartilage were evaluated. Samples were categorized into age groups and according to their harvesting region in the human auricle (for AUR cartilage only). AUR cartilage displayed significantly lower Ein, σmax, Eeq, sGAG content; and significantly higher t1/2, and DNA content than NAS cartilage. Large amounts of ELN were measured in AUR cartilage (>15% ELN content per sample wet mass). No effect of gender was observed for either auricular or nasoseptal samples. For auricular samples, significant differences between age groups for h, sGAG and HYP, and significant regional variations for Ein, σmax, Eeq, t1/2, h, DNA and sGAG were measured. However, only low correlations between mechanical and biochemical parameters were seen (R<0.44). In conclusion, this study established the first comprehensive mechanical and biochemical map of human auricular cartilage. Regional variations in mechanical and biochemical properties were demonstrated in the auricle. This finding highlights the importance of focusing future research on efforts to produce cartilage grafts with spatially tunable mechanics.

  16. Generation of KCL029 research grade human embryonic stem cell line carrying a mutation in WAS gene

    PubMed Central

    Miere, Cristian; Hewitson, Heema; Wood, Victoria; Kadeva, Neli; Cornwell, Glenda; Codognotto, Stefano; Stephenson, Emma; Ilic, Dusko

    2016-01-01

    The KCL029 human embryonic stem cell line was derived from an embryo donated for research that carried a c.814 T > C mutation in the WAS gene, which is linked to the Wiskott-Aldrich syndrome, a rare, inherited, X-linked, recessive disease characterized by immune dysregulation and microthrombocytopenia. The line is also carrier for a mutation p.N1152H in the gene encoding the cystic fibrosis transmembrane conductance regulator CFTR. The ICM was isolated using laser microsurgery and plated on γ-irradiated human foreskin fibroblasts. Both the derivation and cell line propagation were performed in an animal product-free environment. Pluripotent state and differentiation potential were confirmed by in vitro assays. PMID:27345811

  17. Generation of KCL029 research grade human embryonic stem cell line carrying a mutation in WAS gene.

    PubMed

    Miere, Cristian; Hewitson, Heema; Wood, Victoria; Kadeva, Neli; Cornwell, Glenda; Codognotto, Stefano; Stephenson, Emma; Ilic, Dusko

    2016-01-01

    The KCL029 human embryonic stem cell line was derived from an embryo donated for research that carried a c.814T>C mutation in the WAS gene, which is linked to the Wiskott-Aldrich syndrome, a rare, inherited, X-linked, recessive disease characterized by immune dysregulation and microthrombocytopenia. The line is also carrier for a mutation p.N1152H in the gene encoding the cystic fibrosis transmembrane conductance regulator CFTR. The ICM was isolated using laser microsurgery and plated on γ-irradiated human foreskin fibroblasts. Both the derivation and cell line propagation were performed in an animal product-free environment. Pluripotent state and differentiation potential were confirmed by in vitro assays. PMID:27345811

  18. Biochemical genetics of largemouth bass. Final report

    SciTech Connect

    Phillipp, D.P.; Childers, W.F.; Whitt, G.S.

    1982-10-01

    Distinct biochemical genetic differences exist among largemouth bass (Micropterus salmoides) populations from different geographic regions. The level of genetic variation at 28 enzyme loci was determined for 90 bass populations throughout the United States through the use of vertical starch gel electrophoretic analyses. Allelic polymorphism was observed at 17 of these enzyme loci. Marked differences in allele frequencies at six of these loci exist among populations from the different geographic areas studied. Allele frequencies at two of these loci (isocitrate dehydrogenase-B and aspartate aminotransferase-B) can be used to quantitatively determine the contributions by each of the two recognized subspecies, M. s. salmoides and M. s. floridanus to the total gene pool of any population of largemouth bass. The current range of each subspecies and the extent of the range of intergradation has been redescribed. Furthermore, distinct north-south clinal distributions of the alleles at four of these loci (malate dehydrogenase-B, superoxide dismutase-A, isocitrate dehydrogenase-B and aspartate aminotransferase-B) indicate a possible involvement of these enzymes in the determination of the thermal tolerance/preference limits for this species. In vitro analyses of the different allelic isozymes at the malate dehydrogenase-B locus representing the northern and the southern phenotypes have revealed kinetic differences at temperatures which are encountered routinely in the environment, suggesting a possible mechanism for the genetic determination of thermal requirements. The results of these genetic analyses clearly indicate the need for incorporating sound genetic principles into current and future management programs.

  19. Genetically controlled food preference: biochemical mechanisms.

    PubMed Central

    Guarna, M M; Borowsky, R L

    1993-01-01

    Food choice is known to be correlated with genotype in the crustacean Gammarus palustris. Given a choice of Enteromorpha intestinalis (E) over Ulva lactuca (U), individuals homozygous for the Amy II.52 allele have a greater preference for E than do Amy II.55 homozygotes. To account for this correlation, we hypothesized that the proportions of saccharides released by the enzymatic action of Amy II.52 on E or Amy II.55 on U starches differ from and better stimulate feeding than those released by Amy II.52 on U and Amy II.55 on E starches. To test this, the two forms of amylase were purified by glycogen/ethanol precipitation and preparative PAGE. Their product distributions with each of the starches were determined by HPLC. Each amylase/starch combination gave different distributions of the main products: maltose, maltotriose, and maltotetraose. Feeding preference tests using artificial foods containing these sugars showed that the product distributions from Amy II.52/E starch or Amy II.55/U starch were preferred over those from Amy II.52/U or Amy II.55/E. Patterns of preferences for the artificial foods closely matched those observed in earlier experiments in which different genotypes fed on intact algae. Thus, genetic differences in feeding preferences can be understood in terms of variation in biochemical properties of a digestive enzyme. These results highlight a previously unappreciated role for digestive enzymes: in their capacity to modify the chemical nature of environmental stimuli prior to gustation, digestive enzymes can be viewed as having important chemosensory roles. PMID:7685121

  20. Biochemical and molecular characterisation of cubozoan protein toxins.

    PubMed

    Brinkman, Diane L; Burnell, James N

    2009-12-15

    Class Cubozoa includes several species of box jellyfish that are harmful to humans. The venoms of box jellyfish are stored and discharged by nematocysts and contain a variety of bioactive proteins that are cytolytic, cytotoxic, inflammatory or lethal. Although cubozoan venoms generally share similar biological activities, the diverse range and severity of effects caused by different species indicate that their venoms vary in protein composition, activity and potency. To date, few individual venom proteins have been thoroughly characterised, however, accumulating evidence suggests that cubozoan jellyfish produce at least one group of homologous bioactive proteins that are labile, basic, haemolytic and similar in molecular mass (42-46 kDa). The novel box jellyfish toxins are also potentially lethal and the cause of cutaneous pain, inflammation and necrosis, similar to that observed in envenomed humans. Secondary structure analysis and remote protein homology predictions suggest that the box jellyfish toxins may act as alpha-pore-forming toxins. However, more research is required to elucidate their structures and investigate their mechanism(s) of action. The biological, biochemical and molecular characteristics of cubozoan venoms and their bioactive protein components are reviewed, with particular focus on cubozoan cytolysins and the newly emerging family of box jellyfish toxins. PMID:19232527

  1. Automatising the analysis of stochastic biochemical time-series

    PubMed Central

    2015-01-01

    Background Mathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these frameworks it is possible to analyse complex models under a variety of configurations, eventually selecting the best setting of, e.g., parameters for a target system. Motivation This operational pipeline relies on the ability to interpret the predictions of a model, often represented as simulation time-series. Thus, an efficient data analysis pipeline is crucial to automatise time-series analyses, bearing in mind that errors in this phase might mislead the modeller's conclusions. Results For this reason we have developed an intuitive framework-independent Python tool to automate analyses common to a variety of modelling approaches. These include assessment of useful non-trivial statistics for simulation ensembles, e.g., estimation of master equations. Intuitive and domain-independent batch scripts will allow the researcher to automatically prepare reports, thus speeding up the usual model-definition, testing and refinement pipeline. PMID:26051821

  2. The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase

    SciTech Connect

    Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

    2007-03-22

    Abstract We derived and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method to cytidine deaminase. The environmental effects on the substrate in the active site are examined. The ONIOM-MD simulations show that the product uridine is strongly perturbed by the thermal motion of the environment and dissociates easily from the active site. TM and MA were supported in part by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan. MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.

  3. Fuzzy clustering of physicochemical and biochemical properties of amino acids.

    PubMed

    Saha, Indrajit; Maulik, Ujjwal; Bandyopadhyay, Sanghamitra; Plewczynski, Dariusz

    2012-08-01

    In this article, we categorize presently available experimental and theoretical knowledge of various physicochemical and biochemical features of amino acids, as collected in the AAindex database of known 544 amino acid (AA) indices. Previously reported 402 indices were categorized into six groups using hierarchical clustering technique and 142 were left unclustered. However, due to the increasing diversity of the database these indices are overlapping, therefore crisp clustering method may not provide optimal results. Moreover, in various large-scale bioinformatics analyses of whole proteomes, the proper selection of amino acid indices representing their biological significance is crucial for efficient and error-prone encoding of the short functional sequence motifs. In most cases, researchers perform exhaustive manual selection of the most informative indices. These two facts motivated us to analyse the widely used AA indices. The main goal of this article is twofold. First, we present a novel method of partitioning the bioinformatics data using consensus fuzzy clustering, where the recently proposed fuzzy clustering techniques are exploited. Second, we prepare three high quality subsets of all available indices. Superiority of the consensus fuzzy clustering method is demonstrated quantitatively, visually and statistically by comparing it with the previously proposed hierarchical clustered results. The processed AAindex1 database, supplementary material and the software are available at http://sysbio.icm.edu.pl/aaindex/ .

  4. Methanogenic archaea database containing physiological and biochemical characteristics.

    PubMed

    Jabłoński, Sławomir; Rodowicz, Paweł; Łukaszewicz, Marcin

    2015-04-01

    The methanogenic archaea are a group of micro-organisms that have developed a unique metabolic pathway for obtaining energy. There are 150 characterized species in this group; however, novel species continue to be discovered. Since methanogens are considered a crucial part of the carbon cycle in the anaerobic ecosystem, characterization of these micro-organisms is important for understanding anaerobic ecology. A methanogens database (MDB; http://metanogen.biotech.uni.wroc.pl/), including physiological and biochemical characteristics of methanogens, was constructed based on the descriptions of isolated type strains. Analysis of the data revealed that methanogens are able to grow from 0 to 122 °C. Methanogens growing at the same temperature may have very different growth rates. There is no clear correlation between the optimal growth temperature and the DNA G+C content. The following substrate preferences are observed in the database: 74.5% of archaea species utilize H2+CO2, 33% utilize methyl compounds and 8.5% utilize acetate. Utilization of methyl compounds (mainly micro-organisms belonging to the genera Methanosarcina and Methanolobus ) is seldom accompanied by an ability to utilize H2+CO2. Very often, data for described species are incomplete, especially substrate preferences. Additional research leading to completion of missing information and development of standards, especially for substrate utilization, would be very helpful.

  5. The Yeast Actin Cytoskeleton: from Cellular Function to Biochemical Mechanism

    PubMed Central

    Moseley, James B.; Goode, Bruce L.

    2006-01-01

    All cells undergo rapid remodeling of their actin networks to regulate such critical processes as endocytosis, cytokinesis, cell polarity, and cell morphogenesis. These events are driven by the coordinated activities of a set of 20 to 30 highly conserved actin-associated proteins, in addition to many cell-specific actin-associated proteins and numerous upstream signaling molecules. The combined activities of these factors control with exquisite precision the spatial and temporal assembly of actin structures and ensure dynamic turnover of actin structures such that cells can rapidly alter their cytoskeletons in response to internal and external cues. One of the most exciting principles to emerge from the last decade of research on actin is that the assembly of architecturally diverse actin structures is governed by highly conserved machinery and mechanisms. With this realization, it has become apparent that pioneering efforts in budding yeast have contributed substantially to defining the universal mechanisms regulating actin dynamics in eukaryotes. In this review, we first describe the filamentous actin structures found in Saccharomyces cerevisiae (patches, cables, and rings) and their physiological functions, and then we discuss in detail the specific roles of actin-associated proteins and their biochemical mechanisms of action. PMID:16959963

  6. Label-Free Optical Ring Resonator Bio/Chemical Sensors

    NASA Astrophysics Data System (ADS)

    Zhu, Hongying; Suter, Jonathan D.; Fan, Xudong

    Optical micro-ring resonator sensors are an emerging category of label-free optical sensors for bio/chemical sensing that have recently been under intensive investigation. Researchers of this technology have been motivated by a tremendous breadth of different applications, including medical diagnosis, environmental monitoring, homeland security, and food quality control, which require sensitive analytical tools. Ring resonator sensors use total internal reflection to support circulating optical resonances called whispering gallery modes (WGMs). The WGMs have an evanescent field of several hundred nanometers into the surrounding medium, and can therefore detect the refractive index change induced when the analyte binds to the resonator surface. Despite the small physical size of a resonator, the circulating nature of the WGM creates extremely long effective lengths, greatly increasing light-matter interaction and improving its sensing performance. Moreover, only small sample volume is needed for detection because the sensors can be fabricated in sizes well below 100 μm. The small footprint allows integration of those ring resonator sensors onto lab-on-a-chip types of devices for multiplexed detection.

  7. Biochemical and molecular characterisation of cubozoan protein toxins.

    PubMed

    Brinkman, Diane L; Burnell, James N

    2009-12-15

    Class Cubozoa includes several species of box jellyfish that are harmful to humans. The venoms of box jellyfish are stored and discharged by nematocysts and contain a variety of bioactive proteins that are cytolytic, cytotoxic, inflammatory or lethal. Although cubozoan venoms generally share similar biological activities, the diverse range and severity of effects caused by different species indicate that their venoms vary in protein composition, activity and potency. To date, few individual venom proteins have been thoroughly characterised, however, accumulating evidence suggests that cubozoan jellyfish produce at least one group of homologous bioactive proteins that are labile, basic, haemolytic and similar in molecular mass (42-46 kDa). The novel box jellyfish toxins are also potentially lethal and the cause of cutaneous pain, inflammation and necrosis, similar to that observed in envenomed humans. Secondary structure analysis and remote protein homology predictions suggest that the box jellyfish toxins may act as alpha-pore-forming toxins. However, more research is required to elucidate their structures and investigate their mechanism(s) of action. The biological, biochemical and molecular characteristics of cubozoan venoms and their bioactive protein components are reviewed, with particular focus on cubozoan cytolysins and the newly emerging family of box jellyfish toxins.

  8. Are There Any Promising Biochemical Correlates of Achievement Behavior and Motivation? The Evidence for Serum Uric Acid and Serum Cholesterol

    ERIC Educational Resources Information Center

    Kasl, Stanislav V.

    1974-01-01

    This review examines the available evidence in support of the argument that serum uric acid (SUA) possesses considerable promise as an indicator of one type of biochemical influence on achievement behavior. The evidence arguing for further research into the role of serum cholesterol in achievement behavior is also examined. (Author/JR)

  9. [INVESTIGATION OF BLOOD BIOCHEMICAL INDICES DURING BICYCLE ERGOMETRY].

    PubMed

    Davydov, B V; Stepanova, G P; Krivitsyna, Z A; Vorontsov, A L; Voronkov, Yu I

    2015-01-01

    Our investigations showed that physical work (bicycle ergometry) alters the biochemical status of male volunteers. On the 5th minute of bicycle endometry capillary blood looses significantly glucose and increases magnesium, phosphorus and particularly lactic acid. Creatine phosphokinase activity and trygliceride levels did not deviate much from baseline values. All the changes had a similar trend equally in the supine and sitting position. Therefore, biochemical investigations may complement essentially the physiological and neurophysiological tests of human adaptability to physical loads. The investigation utilized the dry chemistry technology of rapid biochemical diagnostics. PMID:26738302

  10. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  11. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  12. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  13. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  14. Myoinositol Attenuates the Cell Loss and Biochemical Changes Induced by Kainic Acid Status Epilepticus

    PubMed Central

    Kikvidze, Marina

    2016-01-01

    Identification of compounds preventing or modifying the biochemical changes that underlie the epileptogenesis process and understanding the mechanism of their action are of great importance. We have previously shown that myoinositol (MI) daily treatment for 28 days prevents certain biochemical changes that are triggered by kainic acid (KA) induced status epilepticus (SE). However in these studies we have not detected any effects of MI on the first day after SE. In the present study we broadened our research and focused on other molecular and morphological changes at the early stages of SE induced by KA and effects of MI treatment on these changes. The increase in the amount of voltage-dependent anionic channel-1 (VDAC-1), cofilin, and caspase-3 activity was observed in the hippocampus of KA treated rats. Administration of MI 4 hours later after KA treatment abolishes these changes, whereas diazepam treatment by the same time schedule has no significant influence. The number of neuronal cells in CA1 and CA3 subfields of hippocampus is decreased after KA induced SE and MI posttreatment significantly attenuates this reduction. No significant changes are observed in the neocortex. Obtained results indicate that MI posttreatment after KA induced SE could successfully target the biochemical processes involved in apoptosis, reduces cell loss, and can be successfully used in the future for translational research.

  15. Myoinositol Attenuates the Cell Loss and Biochemical Changes Induced by Kainic Acid Status Epilepticus

    PubMed Central

    Kikvidze, Marina

    2016-01-01

    Identification of compounds preventing or modifying the biochemical changes that underlie the epileptogenesis process and understanding the mechanism of their action are of great importance. We have previously shown that myoinositol (MI) daily treatment for 28 days prevents certain biochemical changes that are triggered by kainic acid (KA) induced status epilepticus (SE). However in these studies we have not detected any effects of MI on the first day after SE. In the present study we broadened our research and focused on other molecular and morphological changes at the early stages of SE induced by KA and effects of MI treatment on these changes. The increase in the amount of voltage-dependent anionic channel-1 (VDAC-1), cofilin, and caspase-3 activity was observed in the hippocampus of KA treated rats. Administration of MI 4 hours later after KA treatment abolishes these changes, whereas diazepam treatment by the same time schedule has no significant influence. The number of neuronal cells in CA1 and CA3 subfields of hippocampus is decreased after KA induced SE and MI posttreatment significantly attenuates this reduction. No significant changes are observed in the neocortex. Obtained results indicate that MI posttreatment after KA induced SE could successfully target the biochemical processes involved in apoptosis, reduces cell loss, and can be successfully used in the future for translational research. PMID:27642592

  16. Myoinositol Attenuates the Cell Loss and Biochemical Changes Induced by Kainic Acid Status Epilepticus.

    PubMed

    Tsverava, Lia; Lordkipanidze, Tamar; Lepsveridze, Eka; Nozadze, Maia; Kikvidze, Marina; Solomonia, Revaz

    2016-01-01

    Identification of compounds preventing or modifying the biochemical changes that underlie the epileptogenesis process and understanding the mechanism of their action are of great importance. We have previously shown that myoinositol (MI) daily treatment for 28 days prevents certain biochemical changes that are triggered by kainic acid (KA) induced status epilepticus (SE). However in these studies we have not detected any effects of MI on the first day after SE. In the present study we broadened our research and focused on other molecular and morphological changes at the early stages of SE induced by KA and effects of MI treatment on these changes. The increase in the amount of voltage-dependent anionic channel-1 (VDAC-1), cofilin, and caspase-3 activity was observed in the hippocampus of KA treated rats. Administration of MI 4 hours later after KA treatment abolishes these changes, whereas diazepam treatment by the same time schedule has no significant influence. The number of neuronal cells in CA1 and CA3 subfields of hippocampus is decreased after KA induced SE and MI posttreatment significantly attenuates this reduction. No significant changes are observed in the neocortex. Obtained results indicate that MI posttreatment after KA induced SE could successfully target the biochemical processes involved in apoptosis, reduces cell loss, and can be successfully used in the future for translational research. PMID:27642592

  17. Genetic, Biochemical and Clinical Insights into Primary Congenital Glaucoma

    PubMed Central

    Faiq, Muneeb; Sharma, Reetika; Dada, Rima; Mohanty, Kuldeep; Saluja, Daman

    2013-01-01

    ABSTRACT Glaucoma is an irreversible form of optic neuropathy in which the optic nerve suffers damage in a characteristic manner with optic nerve cupping and retinal ganglion cell death. Primary congenital glaucoma (PCG) is an idiopathic irreversible childhood blinding disorder which manifests at birth or within the first year of life. PCG presents with a classical triad of symptoms (viz epiphora, photophobia and blepharospasm) though there are many additional symptoms, including large eye ball and hazy cornea. The only anatomical anomaly found in PCG is trabecular meshwork (TM) dysgenesis. PCG is an inheritable disease with established genetic etiology. It transmits through autosomal recessive mode. A number of cases are sporadic also. Mutations in many genes have been found to be causative in PCG and many are yet to be found. Mutations in cytochrome P4501B1 (CYP1B1) gene have been found to be the predominant cause of PCG. Other genes that have been implicated in PCG etiology are myocilin, Forkhead-related transcription factor C1 (FOXC1) and latent transforming growth factor beta-binding protein 2 (LTBP2). Mutations in these genes have been reported from many parts of the world. In addition to this, mitochondrial genome mutations are also thought to be involved in its pathogenesis. There appears to be some mechanism involving more than one genetic factor. In this review, we will discuss the various clinical, biochemical and genetic aspects of PCG. We emphasize that etiology of PCG does not lie in a single gene or genetic factor. Research needs to be oriented into a direction where gene-gene interactions, ocular embryology, ophthalmic metabolism and systemic oxidative status need to be studied in order to understand this disorder. We also accentuate the need for ophthalmic genetic facilities in all ophthalmology setups. How to cite this article: Faiq M, Sharma R, Dada R, Mohanty K, Saluja D, Dada T. Genetic, Biochemical and Clinical Insights into Primary Congenital

  18. Comparison of cold resistance physiological and biochemical features of four Herba Rhodiola seedlings under low temperature

    PubMed Central

    He, Shuling; Zhao, Kentian; Ma, Lingfa; Yang, Jingjun; Chang, Yuwei; Ashraf, Muhammad Aqeel

    2015-01-01

    To discuss the cold resistance performance of different Herba Rhodiolae and successfully transplant Herba Rhodiolae to the Gansu plateau area for nursing, domestication and planting, this paper systematically studies six physiological and biochemical features of Rhodiola kirilowii, Rhodiola algida, Rhodiola crenulata and Herba Rhodiolae that are closely associated with cold resistance features and concludes with the cold resistance capability of Rhodiola kirilowii. In the selected six main indexes of the Herba Rhodiolae, the POD, SOD and CAT activity and MDA and Pro content in the leaf are the main physiological and biochemical indexes to indicate the cold resistance performance of four Herba Rhodiolae seedlings and can be regarded as the preliminary indexes to assess the winter performance of Herba Rhodiolae. The research work will provide the theoretical basis for the wild variants of Herba Rhodiolae and GAPJ base construction. PMID:26981000

  19. [Odor Emission Characteristics from Biochemical Treatment Facilities of Kichen Waste in China].

    PubMed

    Zhang, Yan; Wang, Yuan-gang; Lu, Zhi-qiang; Han, Meng; Shang, Xi-bin; Cao, Yan; Zhang, Jun

    2015-10-01

    Xining, Ningbo and Beijing were closen as the representative cities about biochemical treatment of kichen waste. The treatment facilities of these cities were investigated and set as the sampling points. The main compositions and the material contents were analyzed by GC/MS, the odor concertration was obtained by the Triangle odor bag method. The results showed that oxygenated hydrocarbons including alcohol, aldehyde, ketone, ester were higher than others in the odor gases, however, the largest contribution to odor pollution were sulfocompounds and the 2nd materials were terpenes; According to the research of the three enterprises, ethyl alcohol, limonene, sulfuretted hydrogen, methyl mercaptan, dimethyl sulfide, dimethyl disulfide, acetaldehyde and ethyl acetate were likely to be considered as the typical odorants from the biochemical treatment facilities of kichen waste. PMID:26841591

  20. [Mitochondrial diseases in children including Leigh syndrome--biochemical and molecular background].

    PubMed

    Pronicka, Ewa; Piekutowska-Abramczuk, Dorota; Pronicki, Maciej

    2008-01-01

    Mitochondrial diseases in children are more frequently caused by mutations in nuclear DNA then in mtDNA. Special clinical phenotypes are associated with the mutations in SURF1 gene, in SCO2 gene and with mtDNA depletion syndromes. Leigh syndrome is the most common clinical presentation of various mitochondrial disorders during childhood. Elevation of lactate in blood, cerebrospinal fluid and urine is a simple biochemical marker of mitochondrial disorders but its specificity and sensitivity are low. Biochemical investigation of muscle biopsy and search for mitochondrial mutations remain a gold standard in the diagnosis. The standarized diagnostic criteria to establish level of diagnostic certainty (possible, probable, definite) are proposed to be used in practice; these include clinical features, neuroimaging and muscle biopsy investigations. Further research directions to improve our understanding of mitochondrial pathologies in children are suggested.

  1. Design and implementation of multi-campus, modular master classes in biochemical engineering

    NASA Astrophysics Data System (ADS)

    Wuyts, Niek; Bruneel, Dorine; Meyers, Myriam; Van Hoof, Etienne; De Vos, Leander; Langie, Greet; Rediers, Hans

    2015-07-01

    The Master of Science in engineering technology: biochemical engineering is organised in KU Leuven at four geographically dispersed campuses. To sustain the Master's programmes at all campuses, it is clear that a unique education profile at each campus is crucial. In addition, a rationalisation is required by increased cooperation, increased exchange of lecturers, and increased student mobility. To achieve this, a multicampus education system for the M.Sc. in engineering technology: biochemical engineering was developed by offering modules that are also available for students of other campuses. Such a module is primarily based on the research expertise present at the campus. In the development, special attention has been given to the optimal organisation of the modules, evaluation, required modifications of the current curricula, and the practical consequences for students following the module at another campus. Even in the first year of implementation, around 30% of the students followed a multicampus module, which indicates the potential success of the multicampus concept described here.

  2. [Odor Emission Characteristics from Biochemical Treatment Facilities of Kichen Waste in China].

    PubMed

    Zhang, Yan; Wang, Yuan-gang; Lu, Zhi-qiang; Han, Meng; Shang, Xi-bin; Cao, Yan; Zhang, Jun

    2015-10-01

    Xining, Ningbo and Beijing were closen as the representative cities about biochemical treatment of kichen waste. The treatment facilities of these cities were investigated and set as the sampling points. The main compositions and the material contents were analyzed by GC/MS, the odor concertration was obtained by the Triangle odor bag method. The results showed that oxygenated hydrocarbons including alcohol, aldehyde, ketone, ester were higher than others in the odor gases, however, the largest contribution to odor pollution were sulfocompounds and the 2nd materials were terpenes; According to the research of the three enterprises, ethyl alcohol, limonene, sulfuretted hydrogen, methyl mercaptan, dimethyl sulfide, dimethyl disulfide, acetaldehyde and ethyl acetate were likely to be considered as the typical odorants from the biochemical treatment facilities of kichen waste.

  3. SEROLOGICAL AND BIOCHEMICAL GENETIC MARKERS AND THEIR ASSOCIATIONS WITH PSYCHIATRIC DISORDERS : A REVIEW

    PubMed Central

    Balgir, R.S.

    1983-01-01

    SUMMARY The studies pertaining to associations of serological and biochemical genetic markers (blood groups in particular and scrum proteins and enzymes in general) with the psychiatric disorders such as psychoses in general, Schizophrenia, manic-depressive psychosis including unipolar and bipolar affective disorders and neuroses have been critically examined. The reasons for inconsistent findings of various investigators have been pointed out to assist the future researchers to overcome the previous drawbacks. Implications of associations of genetic markers with the psychiatric disorders have been discussed and future areas of research suggested. PMID:21847304

  4. Serological and biochemical genetic markers and their associations with psychiatric disorders : a review.

    PubMed

    Balgir, R S

    1983-10-01

    The studies pertaining to associations of serological and biochemical genetic markers (blood groups in particular and scrum proteins and enzymes in general) with the psychiatric disorders such as psychoses in general, Schizophrenia, manic-depressive psychosis including unipolar and bipolar affective disorders and neuroses have been critically examined. The reasons for inconsistent findings of various investigators have been pointed out to assist the future researchers to overcome the previous drawbacks. Implications of associations of genetic markers with the psychiatric disorders have been discussed and future areas of research suggested. PMID:21847304

  5. Biochemical observation during 28 days of space flight

    NASA Technical Reports Server (NTRS)

    Leach, C. S.; Kambaut, P. C.

    1975-01-01

    With the completion of the 28-day flight of Skylab 2, the sum of biochemical data on human reaction to the weightless environment was significantly extended both quantitatively and qualitatively. The biochemical studies were divided into two broad categories. One group included the more routine blood studies similar to those used in everyday medical practice. The second category encompassed those analyses used to investigate more thoroughly the endocrinological and fluid changes first seen in the crewmembers following the Gemini, Apollo, and Soviet missions. Significant biochemical changes were observed that varied in magnitude and direction, but all disappeared shortly after return to earth. Most of changes indicate successful adaptation by the body to the combined stresses of weightlessness. Results of the biochemical observation are presented in the form of data tables and graphs.

  6. Pleural, peritoneal and pericardial effusions – a biochemical approach

    PubMed Central

    Kopcinovic, Lara Milevoj; Culej, Jelena

    2014-01-01

    The pathological accumulation of serous fluids in the pleural, peritoneal and pericardial space occurs in a variety of conditions. Since patient management depends on right and timely diagnosis, biochemical analysis of extravascular body fluids is considered a valuable tool in the patient management process. The biochemical evaluation of serous fluids includes the determination of gross appearance, differentiation of transudative from exudative effusions and additional specific biochemical testing to assess the effusion etiology. This article summarized data from the most relevant literature concerning practice with special emphasis on usefulness of biochemical tests used for the investigation of pleural, peritoneal and pericardial effusions. Additionally, preanalytical issues concerning serous fluid analysis were addressed and recommendations concerning acceptable analytical practice in serous fluid analysis were presented. PMID:24627721

  7. 2011 Biomass Program Platform Peer Review: Biochemical Conversion

    SciTech Connect

    Pezzullo, Leslie

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Biochemical Conversion Platform Review meeting.

  8. CELLULAR, BIOCHEMICAL, AND MOLECULAR TECHNIQUES IN DEVELOPMENTAL TOXICOLOGY

    EPA Science Inventory

    Cellular, molecular and biochemical approaches vastly expand the possibilities for revealing the underlying mechanisms of developmental toxicity. The increasing interest in embryonic development as a model system for the study of gene expression has resulted in a cornucopia of i...

  9. Between biochemists and embryologists -- the biochemical study of embryonic induction in the 1930s.

    PubMed

    Armon, Rony

    2012-01-01

    The discovery by Hans Spemann of the "organizer" tissue and its ability to induce the formation of the amphibian embryo's neural tube inspired leading embryologists to attempt to elucidate embryonic inductions' underlying mechanism. Joseph Needham, who during the 1930s conducted research in biochemical embryology, proposed that embryonic induction is mediated by a specific chemical entity embedded in the inducing tissue, surmising that chemical to be a hormone of sterol-like structure. Along with embryologist Conrad H. Waddington, they conducted research aimed at the isolation and functional characterization of the underlying agent. As historians clearly pointed out, embryologists came to question Needham's biochemical approach; he failed to locate the hormone he sought and eventually abandoned his quest. Yet, this study finds that the difficulties he ran into resulted primarily from the limited conditions for conducting his experiments at his institute. In addition, Needham's research reflected the interests of leading biochemists in hormone and cancer research, because it offered novel theoretical models and experimental methods for engaging with the function of the hormones and carcinogens they isolated. Needham and Waddington were deterred neither by the mounting challenges nor by the limited experimental infrastructure. Like their colleagues in hormone and cancer research, they anticipated difficulties in attempting to establish causal links between complex biological phenomena and simple chemical triggering.

  10. Energy-based analysis of biochemical cycles using bond graphs

    PubMed Central

    Gawthrop, Peter J.; Crampin, Edmund J.

    2014-01-01

    Thermodynamic aspects of chemical reactions have a long history in the physical chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems, where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on the early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks. PMID:25383030

  11. [Fifty years of cooperation--FEBS and Polish Biochemical Society].

    PubMed

    Barańska, Jolanta

    2014-01-01

    This year, the Federation of European Biochemical Societies (FEBS) celebrates its 50th anniversary. The Polish Biochemical Society, represented by the Society's President, Kazimierz Zakrzewski, was a founding member of the organization. The text presents a history of collaboration between FEBS and Polish Biochemical Society, the participation of Polish Biochemical Society members in different FEBS activities, as well as the role they played in running the Federation. Author describes FEBS Congresses which taken place in Warsaw, the first 3rd FEBS Meeting in 1966 and then 29th Congress in 2004. The profiles of Jakub Karol Parnas, the founding father of the Polish biochemistry and some crucial Presidents of the Society, are also presented. The text describes Parnas Conferences, organized jointly by Polish and Ukrainian Biochemical Societies from 1996, and growing from 2011 into three-nation event with participation of Ukrainian, Israeli and Polish scientists, largely due to significant help from FEBS. Summarizing the last few years, author judge the cooperation between the Federation and the Polish Biochemical Society as optimal.

  12. Energy-based analysis of biochemical cycles using bond graphs.

    PubMed

    Gawthrop, Peter J; Crampin, Edmund J

    2014-11-01

    Thermodynamic aspects of chemical reactions have a long history in the physical chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems, where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on the early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks. PMID:25383030

  13. The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy.

    PubMed

    Yamamoto, Hayashi; Shima, Takayuki; Yamaguchi, Masaya; Mochizuki, Yuh; Hoshida, Hisashi; Kakuta, Soichiro; Kondo-Kakuta, Chika; Noda, Nobuo N; Inagaki, Fuyuhiko; Itoh, Takehiko; Akada, Rinji; Ohsumi, Yoshinori

    2015-12-01

    Autophagy is a conserved degradation process in which autophagosomes are generated by cooperative actions of multiple autophagy-related (Atg) proteins. Previous studies using the model yeast Saccharomyces cerevisiae have provided various insights into the molecular basis of autophagy; however, because of the modest stability of several Atg proteins, structural and biochemical studies have been limited to a subset of Atg proteins, preventing us from understanding how multiple Atg proteins function cooperatively in autophagosome formation. With the goal of expanding the scope of autophagy research, we sought to identify a novel organism with stable Atg proteins that would be advantageous for in vitro analyses. Thus, we focused on a newly isolated thermotolerant yeast strain, Kluyveromyces marxianus DMKU3-1042, to utilize as a novel system elucidating autophagy. We developed experimental methods to monitor autophagy in K. marxianus cells, identified the complete set of K. marxianus Atg homologs, and confirmed that each Atg homolog is engaged in autophagosome formation. Biochemical and bioinformatic analyses revealed that recombinant K. marxianus Atg proteins have superior thermostability and solubility as compared with S. cerevisiae Atg proteins, probably due to the shorter primary sequences of KmAtg proteins. Furthermore, bioinformatic analyses showed that more than half of K. marxianus open reading frames are relatively short in length. These features make K. marxianus proteins broadly applicable as tools for structural and biochemical studies, not only in the autophagy field but also in other fields. PMID:26442587

  14. Estimating Biochemical Parameters of Tea (camellia Sinensis (L.)) Using Hyperspectral Techniques

    NASA Astrophysics Data System (ADS)

    Bian, M.; Skidmore, A. K.; Schlerf, M.; Liu, Y.; Wang, T.

    2012-07-01

    Tea (Camellia Sinensis (L.)) is an important economic crop and the market price of tea depends largely on its quality. This research aims to explore the potential of hyperspectral remote sensing on predicting the concentration of biochemical components, namely total tea polyphenols, as indicators of tea quality at canopy scale. Experiments were carried out for tea plants growing in the field and greenhouse. Partial least squares regression (PLSR), which has proven to be the one of the most successful empirical approach, was performed to establish the relationship between reflectance and biochemical concentration across six tea varieties in the field. Moreover, a novel integrated approach involving successive projections algorithms as band selection method and neural networks was developed and applied to detect the concentration of total tea polyphenols for one tea variety, in order to explore and model complex nonlinearity relationships between independent (wavebands) and dependent (biochemicals) variables. The good prediction accuracies (r2 > 0.8 and relative RMSEP < 10 %) achieved for tea plants using both linear (partial lease squares regress) and nonlinear (artificial neural networks) modelling approaches in this study demonstrates the feasibility of using airborne and spaceborne sensors to cover wide areas of tea plantation for in situ monitoring of tea quality cheaply and rapidly.

  15. The Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy.

    PubMed

    Yamamoto, Hayashi; Shima, Takayuki; Yamaguchi, Masaya; Mochizuki, Yuh; Hoshida, Hisashi; Kakuta, Soichiro; Kondo-Kakuta, Chika; Noda, Nobuo N; Inagaki, Fuyuhiko; Itoh, Takehiko; Akada, Rinji; Ohsumi, Yoshinori

    2015-12-01

    Autophagy is a conserved degradation process in which autophagosomes are generated by cooperative actions of multiple autophagy-related (Atg) proteins. Previous studies using the model yeast Saccharomyces cerevisiae have provided various insights into the molecular basis of autophagy; however, because of the modest stability of several Atg proteins, structural and biochemical studies have been limited to a subset of Atg proteins, preventing us from understanding how multiple Atg proteins function cooperatively in autophagosome formation. With the goal of expanding the scope of autophagy research, we sought to identify a novel organism with stable Atg proteins that would be advantageous for in vitro analyses. Thus, we focused on a newly isolated thermotolerant yeast strain, Kluyveromyces marxianus DMKU3-1042, to utilize as a novel system elucidating autophagy. We developed experimental methods to monitor autophagy in K. marxianus cells, identified the complete set of K. marxianus Atg homologs, and confirmed that each Atg homolog is engaged in autophagosome formation. Biochemical and bioinformatic analyses revealed that recombinant K. marxianus Atg proteins have superior thermostability and solubility as compared with S. cerevisiae Atg proteins, probably due to the shorter primary sequences of KmAtg proteins. Furthermore, bioinformatic analyses showed that more than half of K. marxianus open reading frames are relatively short in length. These features make K. marxianus proteins broadly applicable as tools for structural and biochemical studies, not only in the autophagy field but also in other fields.

  16. A proposed biochemical mechanism involving hemoglobin for blast overpressure-induced injury.

    PubMed

    Elsayed, N M; Gorbunov, N V; Kagan, V E

    1997-07-25

    Blast overpressure (BOP) is the abrupt, rapid, rise in atmospheric pressure resulting from explosive detonation, firing of large-caliber weapons, and accidental occupational explosions. Exposure to incident BOP waves causes internal injuries, mostly to the hollow organs, particularly the ears, lungs and gastrointestinal tract. BOP-induced injury used to be considered of military concern because it occurred mostly in military environments during military actions or training, and to a lesser extent during civilian occupational accidents. However, in recent years with the proliferation of indiscriminate terrorist bombings worldwide involving civilians, blast injury has become a societal concern, and the need to understand the biochemical and molecular mechanism(s) of injury, and to find new and effective methods for treatment gained importance. In general, past BOP research has focused on the physiological and pathological manifestations of incapacitation, thresholds of safety, and on predictive modeling. However, we have been studying the molecular mechanism of BOP-induced injury, and recently began to have an insight into that mechanism, and recognize the role of hemoglobin released during hemorrhage in catalyzing free radical reactions leading to oxidative stress. In this report we discuss the biochemical changes observed after BOP exposure in rat blood and lung tissue, and propose a biochemical mechanism for free radical-induced oxidative stress that can potentially complicate the injury. Moreover, we observed that some antioxidants can interact with Hb oxidation products (oxy-, met- and oxoferrylHb) and act as prooxidants that can increase the damage rather than decrease it.

  17. [Design of high-efficiency double compound parabolic concentrator system in near infrared noninvasive biochemical analysis].

    PubMed

    Gao, Jing; Lu, Qi-Peng; Peng, Zhong-Qi; Ding, Hai-Quan; Gao, Hong-Zhi

    2013-05-01

    High signal-to-noise ratio (SNR) of system is necessary to obtain accurate blood components in near infrared noninvasive biochemical analysis. In order to improve SNR of analytical system, high-efficiency double compound parabolic concentrator (DCPC) system was researched, which was aimed at increasing light utilization efficiency. Firstly, with the request of collection efficiency in near infrared noninvasive biochemical analysis, the characteristic of emergent rays through compound parabolic concentrator (CPC) was analyzed. Then the maximum focusing angle range of the first stage CPC was determined. Secondly, the light utilization efficiency of truncated type was compared with standard DCPC, thus the best structure parameters of DCPC system were optimized. Lastly, combined with optical parameters of skin tissue, calculations were operated when incident wavelength is 1 000 nm. The light utilization efficiency of DCPC system, CPC-focusing mirror system, and non-optical collecting system was calculated. The results show that the light utilization efficiency of the three optical systems is 1.46%, 0.84% and 0.26% respectively. So DCPC system enhances collecting ability for human diffuse reflection light, and helps improve SNR of noninvasive biochemical analysis system and overall analysis accuracy effectively.

  18. A proposed biochemical mechanism involving hemoglobin for blast overpressure-induced injury.

    PubMed

    Elsayed, N M; Gorbunov, N V; Kagan, V E

    1997-07-25

    Blast overpressure (BOP) is the abrupt, rapid, rise in atmospheric pressure resulting from explosive detonation, firing of large-caliber weapons, and accidental occupational explosions. Exposure to incident BOP waves causes internal injuries, mostly to the hollow organs, particularly the ears, lungs and gastrointestinal tract. BOP-induced injury used to be considered of military concern because it occurred mostly in military environments during military actions or training, and to a lesser extent during civilian occupational accidents. However, in recent years with the proliferation of indiscriminate terrorist bombings worldwide involving civilians, blast injury has become a societal concern, and the need to understand the biochemical and molecular mechanism(s) of injury, and to find new and effective methods for treatment gained importance. In general, past BOP research has focused on the physiological and pathological manifestations of incapacitation, thresholds of safety, and on predictive modeling. However, we have been studying the molecular mechanism of BOP-induced injury, and recently began to have an insight into that mechanism, and recognize the role of hemoglobin released during hemorrhage in catalyzing free radical reactions leading to oxidative stress. In this report we discuss the biochemical changes observed after BOP exposure in rat blood and lung tissue, and propose a biochemical mechanism for free radical-induced oxidative stress that can potentially complicate the injury. Moreover, we observed that some antioxidants can interact with Hb oxidation products (oxy-, met- and oxoferrylHb) and act as prooxidants that can increase the damage rather than decrease it. PMID:9217317

  19. The equation for prediction of blood viscosity from biochemical laboratory data

    NASA Astrophysics Data System (ADS)

    Sahin, B.; Yigitarslan, S.

    2015-03-01

    In most cases, the viscosity of blood is measured after adulteration with heparin or EDTA. The aim of the present research was to derive an equation that can be used for determination of viscosity from biochemical data. Blood samples taken from seven healthy people were analyzed in biochemical laboratory and their viscosities were measured by adding EDTA as anticoagulant. Ten parameters of biochemical laboratory including blood cells (erythrocytes, leukocytes, thrombocytes) and their functional products that directly affect the blood viscosity were chosen. Several equations relating viscosity to those parameters were derived by using a computer program. According to the regression analysis of the functions derived, the viscosity equation was obtained. This equation can be used for determination of blood viscosity from classical laboratory analysis. The advantages of using the derived equation are elimination of anticoagulant addition and elimination of Fahraeus_Lindquist effect. After proving that the equation is acceptable for numerous people, apparent viscosity changes can be followed during any disease and successfulness of anticoagulant drugs can be investigated.

  20. A method for zooming of nonlinear models of biochemical systems

    PubMed Central

    2011-01-01

    Background Models of biochemical systems are typically complex, which may complicate the discovery of cardinal biochemical principles. It is therefore important to single out the parts of a model that are essential for the function of the system, so that the remaining non-essential parts can be eliminated. However, each component of a mechanistic model has a clear biochemical interpretation, and it is desirable to conserve as much of this interpretability as possible in the reduction process. Furthermore, it is of great advantage if we can translate predictions from the reduced model to the original model. Results In this paper we present a novel method for model reduction that generates reduced models with a clear biochemical interpretation. Unlike conventional methods for model reduction our method enables the mapping of predictions by the reduced model to the corresponding detailed predictions by the original model. The method is based on proper lumping of state variables interacting on short time scales and on the computation of fraction parameters, which serve as the link between the reduced model and the original model. We illustrate the advantages of the proposed method by applying it to two biochemical models. The first model is of modest size and is commonly occurring as a part of larger models. The second model describes glucose transport across the cell membrane in baker's yeast. Both models can be significantly reduced with the proposed method, at the same time as the interpretability is conserved. Conclusions We introduce a novel method for reduction of biochemical models that is compatible with the concept of zooming. Zooming allows the modeler to work on different levels of model granularity, and enables a direct interpretation of how modifications to the model on one level affect the model on other levels in the hierarchy. The method extends the applicability of the method that was previously developed for zooming of linear biochemical models to

  1. SIM-GC-MS analysis of biochemical evolution in Amanita genus

    NASA Astrophysics Data System (ADS)

    Ristoiu, Dumitru; Kovacs, Emoke Dalma; Cobzac, Codruta; Parvu, Marcel; Ristoiu, Tania; Kovacs, Melinda Haydee

    2010-11-01

    Amanita is one of the most well known basidiomycetes genus throughout the world because some of its species that are acknowledged due to their toxic and/or hallucinogenic properties. Considering these properties in the last decades become more important for scientist to dignify exactly the chemical content of these mushroom species. Latter researches shown that A. phalloides contain two main groups of toxins: the amatoxins and the phallotoxins. As regards A. rubescens there are not so much studies referring to its biochemical "fingerprint". Two species (A. rubescens and A. phalloides) of Amanita genus were studied in order to determine the biochemical hall-mark at nanoscale for these basidiomycete's species. Parts as caps, gills, flesh and stem of these mushrooms were analyzed on quadrupole mass spectrometer engaged with a gas chromatograph (GC-qMS) using selective ion monitoring mode (SIM). The biochemical profiles of these species had shown the presence of compounds like fatty acid methyl esters (FAMEs), alkaloids, and volatile compounds (including alcohol compounds, carbonyl compounds, terpenes). The levels of biochemical compounds from these species were compared between the two types of species and also between young, mature and old samples for the same species as well as between the parts of mushroom. After this comparison were between the two species it was observed that in case of A. phalloides the alkaloid content were higher usually with almost 50 %. As regards presence of volatile compounds they have almost similar level in both mushroom species. Considering the levels of fatty acid methyl esters, their levels were higher with 30 - 40 % in case of A. rubescens.

  2. Microfluidics meets metabolomics to reveal the impact of Campylobacter jejuni infection on biochemical pathways.

    PubMed

    Mortensen, Ninell P; Mercier, Kelly A; McRitchie, Susan; Cavallo, Tammy B; Pathmasiri, Wimal; Stewart, Delisha; Sumner, Susan J

    2016-06-01

    Microfluidic devices that are currently being used in pharmaceutical research also have a significant potential for utilization in investigating exposure to infectious agents. We have established a microfluidic device cultured with Caco-2 cells, and utilized metabolomics to investigate the biochemical responses to the bacterial pathogen Campylobacter jejuni. In the microfluidic devices, Caco-2 cells polarize at day 5, are uniform, have defined brush borders and tight junctions, and form a mucus layer. Metabolomics analysis of cell culture media collected from both Caco-2 cell culture systems demonstrated a more metabolic homogenous biochemical profile in the media collected from microfluidic devices, compared with media collected from transwells. GeneGo pathway mapping indicated that aminoacyl-tRNA biosynthesis was perturbed by fluid flow, suggesting that fluid dynamics and shear stress impacts the cells translational quality control. Both microfluidic device and transwell culturing systems were used to investigate the impact of Campylobacter jejuni infection on biochemical processes. Caco-2 cells cultured in either system were infected at day 5 with C. jejuni 81-176 for 48 h. Metabolomics analysis clearly differentiated C. jejuni 81-176 infected and non-infected medias collected from the microfluidic devices, and demonstrated that C. jejuni 81-176 infection in microfluidic devices impacts branched-chain amino acid metabolism, glycolysis, and gluconeogenesis. In contrast, no distinction was seen in the biochemical profiles of infected versus non-infected media collected from cells cultured in transwells. Microfluidic culturing conditions demonstrated a more metabolically homogenous cell population, and present the opportunity for studying host-pathogen interactions for extended periods of time. PMID:27231016

  3. Impact of Delayed Analysis in Avian Blood Biochemical Values Measured With the Abaxis VetScan VS2.

    PubMed

    Hoppes, Sharman M; Boyd, Janice D; Brightsmith, Donald J

    2015-09-01

    For biochemical analysis with a point-of-care biochemical analyzer, standard procedure is to analyze the sample as rapidly as possible (<1 hour) after venipuncture to minimize any changes in analyte concentrations that might occur over time. However, under some circumstances, such as when collecting blood at remote field sites, a longer delay may be unavoidable. This study evaluates the effect of delayed analysis time under unrefrigerated conditions on avian (psittacine) biochemical analyte concentrations obtained with the VetScan VS2 using Avian/Reptilian Profile Plus rotors. Venipuncture was performed on a group of 36 psittacine birds as part of routine health checks in a research aviary (Texas A&M University, College of Veterinary Medicine, College Station, TX, USA). Whole blood was kept at room temperature and analyzed at 4 time intervals: <1, 3, 6, and 24 hours after venipuncture. At 3 hours or less after collection, most biochemical parameters changed by <2%, with the exception of phosphorus (decrease of about -9%). Major increases by 24 hours after collection were observed in phosphorus (+67%) and potassium (+103%) concentrations, whereas aspartate aminotransferase (AST), uric acid, glucose, and sodium concentrations also showed statistically significant changes. Our results suggest that accurate information from analyses using the VetScan VS2 may be obtained for up to 3 hours after venipuncture without refrigeration, but researchers and clinicians do need to exercise care when interpreting blood chemistry analyte concentrations obtained after multihour delays between venipuncture and sample analysis. PMID:26378666

  4. Biochemical characterisation during seed development of oil palm (Elaeis guineensis).

    PubMed

    Kok, Sau-Yee; Namasivayam, Parameswari; Ee, Gwendoline Cheng-Lian; Ong-Abdullah, Meilina

    2013-07-01

    Developmental biochemical information is a vital base for the elucidation of seed physiology and metabolism. However, no data regarding the biochemical profile of oil palm (Elaeis guineensis Jacq.) seed development has been reported thus far. In this study, the biochemical changes in the developing oil palm seed were investigated to study their developmental pattern. The biochemical composition found in the seed differed significantly among the developmental stages. During early seed development, the water, hexose (glucose and fructose), calcium and manganese contents were present in significantly high levels compared to the late developmental stage. Remarkable changes in the biochemical composition were observed at 10 weeks after anthesis (WAA): the dry weight and sucrose content increased significantly, whereas the water content and hexose content declined. The switch from a high to low hexose/sucrose ratio could be used to identify the onset of the maturation phase. At the late stage, dramatic water loss occurred, whereas the content of storage reserves increased progressively. Lauric acid was the most abundant fatty acid found in oil palm seed starting from 10 WAA. PMID:23575803

  5. Maximizing the biochemical resolving power of fluorescence microscopy.

    PubMed

    Esposito, Alessandro; Popleteeva, Marina; Venkitaraman, Ashok R

    2013-01-01

    Most recent advances in fluorescence microscopy have focused on achieving spatial resolutions below the diffraction limit. However, the inherent capability of fluorescence microscopy to non-invasively resolve different biochemical or physical environments in biological samples has not yet been formally described, because an adequate and general theoretical framework is lacking. Here, we develop a mathematical characterization of the biochemical resolution in fluorescence detection with Fisher information analysis. To improve the precision and the resolution of quantitative imaging methods, we demonstrate strategies for the optimization of fluorescence lifetime, fluorescence anisotropy and hyperspectral detection, as well as different multi-dimensional techniques. We describe optimized imaging protocols, provide optimization algorithms and describe precision and resolving power in biochemical imaging thanks to the analysis of the general properties of Fisher information in fluorescence detection. These strategies enable the optimal use of the information content available within the limited photon-budget typically available in fluorescence microscopy. This theoretical foundation leads to a generalized strategy for the optimization of multi-dimensional optical detection, and demonstrates how the parallel detection of all properties of fluorescence can maximize the biochemical resolving power of fluorescence microscopy, an approach we term Hyper Dimensional Imaging Microscopy (HDIM). Our work provides a theoretical framework for the description of the biochemical resolution in fluorescence microscopy, irrespective of spatial resolution, and for the development of a new class of microscopes that exploit multi-parametric detection systems. PMID:24204821

  6. Maximizing the Biochemical Resolving Power of Fluorescence Microscopy

    PubMed Central

    Esposito, Alessandro; Popleteeva, Marina; Venkitaraman, Ashok R.

    2013-01-01

    Most recent advances in fluorescence microscopy have focused on achieving spatial resolutions below the diffraction limit. However, the inherent capability of fluorescence microscopy to non-invasively resolve different biochemical or physical environments in biological samples has not yet been formally described, because an adequate and general theoretical framework is lacking. Here, we develop a mathematical characterization of the biochemical resolution in fluorescence detection with Fisher information analysis. To improve the precision and the resolution of quantitative imaging methods, we demonstrate strategies for the optimization of fluorescence lifetime, fluorescence anisotropy and hyperspectral detection, as well as different multi-dimensional techniques. We describe optimized imaging protocols, provide optimization algorithms and describe precision and resolving power in biochemical imaging thanks to the analysis of the general properties of Fisher information in fluorescence detection. These strategies enable the optimal use of the information content available within the limited photon-budget typically available in fluorescence microscopy. This theoretical foundation leads to a generalized strategy for the optimization of multi-dimensional optical detection, and demonstrates how the parallel detection of all properties of fluorescence can maximize the biochemical resolving power of fluorescence microscopy, an approach we term Hyper Dimensional Imaging Microscopy (HDIM). Our work provides a theoretical framework for the description of the biochemical resolution in fluorescence microscopy, irrespective of spatial resolution, and for the development of a new class of microscopes that exploit multi-parametric detection systems. PMID:24204821

  7. Biochemical diagnosis in 3040 kidney stone formers in Argentina.

    PubMed

    Spivacow, Francisco Rodolfo; del Valle, Elisa Elena; Negri, Armando Luis; Fradinger, Erich; Abib, Anabella; Rey, Paula

    2015-08-01

    Nephrolithiasis is a frequent condition in urology that has an important recurrence and high impact in health economy. Knowing the biochemical abnormalities implicated in its pathogenesis is mandatory to establish therapeutic aims. Our objectives are to present the results in 3040 kidney stone formers in Argentina. All patients were selected after completing an ambulatory metabolic protocol with diagnostic purposes. There were 1717 men, (56.48%), with a mean age of 45±12 years, and 1323 women, (43.52%), mean age 44±12 years. 2781 patients had biochemical abnormalities, (91.49%), and were arbitrarily divided in two groups: those who had only one (single) biochemical abnormality (n=2156) and those who had associated abnormalities (n=625). No biochemical abnormalities were found in 259 patients (8.51%). The abnormalities present, single and associated, in order of frequency, were idiopathic hypercalciuria, (56.88%), hyperuricosuria (21.08%), unduly acidic urine (10.95%), hypocitraturia (10.55%), hypomagnesuria (7.9%), primary hyperparathyroidism (3.01%), hyperoxaluria (2.6%), and cystinuria (0.32%). We performed in 484 patient's stone composition and found calcium oxalate stones related to idiopathic hypercalciuria predominantly while uric acid stones to unduly acidic urine. In conclusion, the biochemical abnormalities described are similar to those found in a previous series of our own and to those reported in the literature. Its diagnosis is important to therapeutic purposes to avoid eventual recurrence.

  8. Microstereolithography and its application to biochemical IC chip

    NASA Astrophysics Data System (ADS)

    Ikuta, Koji; Maruo, Shoji; Hasegawa, Tadahiro; Adachi, Takao

    2001-06-01

    The world's first micro stereo lithography, named IH process, was proposed and developed by the speaker in 1992. By now, several types of micro stereo lithography systems have been developed. Three-dimensional resolution of solidification has reached to 0.2 micron at present. These 3D micro fabrication processes using UV curable polymer gave a big impact on not only MEMS but also optics. The latest version of IH process enables us to make a movable micro mechanism without assemble process or sacrificial layer technique often used in silicon process. It is well known that the IH process is the mother of two-photon micro stereo lithography and its applications. Recently new micro chemical device named Biochemical IC Chip was proposed and developed by the speaker. This chip is based on the module IC chip-set like today's TTL family. IH process enable to make the biochemical IC including real three-dimensional micro fluid channels. Various kinds of Biochemical IC chips such as micro pump, switching valve, reactor, concentrator and detector have already been fabricated successfully. Basic performance of micro chemical devices constructed by the biochemical IC chips were demonstrated. The biochemical IC chips will open new bioscience and medicine based on innovative technology.

  9. Biochemical characterisation during seed development of oil palm (Elaeis guineensis).

    PubMed

    Kok, Sau-Yee; Namasivayam, Parameswari; Ee, Gwendoline Cheng-Lian; Ong-Abdullah, Meilina

    2013-07-01

    Developmental biochemical information is a vital base for the elucidation of seed physiology and metabolism. However, no data regarding the biochemical profile of oil palm (Elaeis guineensis Jacq.) seed development has been reported thus far. In this study, the biochemical changes in the developing oil palm seed were investigated to study their developmental pattern. The biochemical composition found in the seed differed significantly among the developmental stages. During early seed development, the water, hexose (glucose and fructose), calcium and manganese contents were present in significantly high levels compared to the late developmental stage. Remarkable changes in the biochemical composition were observed at 10 weeks after anthesis (WAA): the dry weight and sucrose content increased significantly, whereas the water content and hexose content declined. The switch from a high to low hexose/sucrose ratio could be used to identify the onset of the maturation phase. At the late stage, dramatic water loss occurred, whereas the content of storage reserves increased progressively. Lauric acid was the most abundant fatty acid found in oil palm seed starting from 10 WAA.

  10. Biochemical changes and treatment in glaucoma.

    PubMed

    Ciotu, I M; Stoian, I; Gaman, L; Popescu, M V; Atanasiu, V

    2015-01-01

    Glaucoma is the second cause of blindness worldwide. This disease is a neurodegenerative disorder characterized by high intraocular pressure, loss of retinal ganglion cells (apoptosis). Even though there is much research done in this field, the results have not yet managed to stop the progression of glaucoma or to heal this pathology. Free oxygen radicals play a major role; they are formed in the aqueous humor and in the vitreous and they produce apoptosis of the neurons in the optic nerve head, degradation of the trabecular meshwork cells. The purpose of the article is to help in trying to understand the physiopathology of glaucoma and the efficacy of its treatments.

  11. Advanced biochemical processes for geothermal brines FY 1998 annual operating plan

    SciTech Connect

    1997-10-01

    As part of the overall Geothermal Energy Research which is aimed at the development of economical geothermal resources production systems, the aim of the Advanced Biochemical Processes for Geothermal Brines (ABPGB) effort is the development of economic and environmentally acceptable methods for disposal of geothermal wastes and conversion of by-products to useful forms. Methods are being developed for dissolution, separation and immobilization of geothermal wastes suitable for disposal, usable in inert construction materials, suitable for reinjection into the reservoir formation, or used for recovery of valuable metals.

  12. Techno-Economic Analysis of Bioconversion of Methane into Biofuel and Biochemical (Poster)

    SciTech Connect

    Fei, Q.; Tao, L.; Pienkos, P .T.; Guarnieri, M.; Palou-Rivera, I.

    2014-10-01

    In light of the relatively low price of natural gas and increasing demands of liquid transportation fuels and high-value chemicals, attention has begun to turn to novel biocatalyst for conversion of methane (CH4) into biofuels and biochemicals [1]. A techno-economic analysis (TEA) was performed for an integrated biorefinery process using biological conversion of methane, such as carbon yield, process efficiency, productivity (both lipid and acid), natural gas and other raw material prices, etc. This analysis is aimed to identify research challenges as well provide guidance for technology development.

  13. Computer simulation of initial events in the biochemical mechanisms of DNA damage

    NASA Technical Reports Server (NTRS)

    Chatterjee, A.; Holley, W. R.

    1993-01-01

    Understanding the systematic and quantitative correlation between the physical events of energy deposition by ionizing radiation and the ensuing chemical and biochemical processes leading to DNA damage is one of the goals in radiation research. Significant progress has been made toward achieving the stated goal by using theoretical modeling techniques. These techniques are strongly dependent on computer simulation procedures. A review of such techniques with details of various stages of simulation development, including a comparison with available experimental data, is presented in this article.

  14. Computer simulation of initial events in the biochemical mechanisms of DNA damage.

    PubMed

    Chatterjee, A; Holley, W R

    1993-01-01

    Understanding the systematic and quantitative correlation between the physical events of energy deposition by ionizing radiation and the ensuing chemical and biochemical processes leading to DNA damage is one of the goals in radiation research. Significant progress has been made toward achieving the stated goal by using theoretical modeling techniques. These techniques are strongly dependent on computer simulation procedures. A review of such techniques with details of various stages of simulation development, including a comparison with available experimental data, is presented in this article. PMID:11537895

  15. Platform biochemicals for a biorenewable chemical industry.

    PubMed

    Nikolau, Basil J; Perera, M Ann D N; Brachova, Libuse; Shanks, Brent

    2008-05-01

    The chemical industry is currently reliant on a historically inexpensive, petroleum-based carbon feedstock that generates a small collection of platform chemicals from which highly efficient chemical conversions lead to the manufacture of a large variety of chemical products. Recently, a number of factors have coalesced to provide the impetus to explore alternative renewable sources of carbon. Here we discuss the potential impact on the chemical industry of shifting from non-renewable carbon sources to renewable carbon sources. This change to the manufacture of chemicals from biological carbon sources will provide an opportunity for the biological research community to contribute fundamental knowledge concerning carbon metabolism and its regulation. We discuss whether fundamental biological research into metabolic processes at a holistic level, made possible by completed genome sequences and integrated with detailed structural understanding of biocatalysts, can change the chemical industry from being dependent on fossil-carbon feedstocks to using biorenewable feedstocks. We illustrate this potential by discussing the prospect of building a platform technology based upon a concept of combinatorial biosynthesis, which would explore the enzymological flexibilities of polyketide biosynthesis. PMID:18476861

  16. Platform biochemicals for a biorenewable chemical industry.

    PubMed

    Nikolau, Basil J; Perera, M Ann D N; Brachova, Libuse; Shanks, Brent

    2008-05-01

    The chemical industry is currently reliant on a historically inexpensive, petroleum-based carbon feedstock that generates a small collection of platform chemicals from which highly efficient chemical conversions lead to the manufacture of a large variety of chemical products. Recently, a number of factors have coalesced to provide the impetus to explore alternative renewable sources of carbon. Here we discuss the potential impact on the chemical industry of shifting from non-renewable carbon sources to renewable carbon sources. This change to the manufacture of chemicals from biological carbon sources will provide an opportunity for the biological research community to contribute fundamental knowledge concerning carbon metabolism and its regulation. We discuss whether fundamental biological research into metabolic processes at a holistic level, made possible by completed genome sequences and integrated with detailed structural understanding of biocatalysts, can change the chemical industry from being dependent on fossil-carbon feedstocks to using biorenewable feedstocks. We illustrate this potential by discussing the prospect of building a platform technology based upon a concept of combinatorial biosynthesis, which would explore the enzymological flexibilities of polyketide biosynthesis.

  17. Click Chemistry-Mediated Nanosensors for Biochemical Assays

    PubMed Central

    Chen, Yiping; Xianyu, Yunlei; Wu, Jing; Yin, Binfeng; Jiang, Xingyu

    2016-01-01

    Click chemistry combined with functional nanoparticles have drawn increasing attention in biochemical assays because they are promising in developing biosensors with effective signal transformation/amplification and straightforward signal readout for clinical diagnostic assays. In this review, we focus on the latest advances of biochemical assays based on Cu (I)-catalyzed 1, 3-dipolar cycloaddition of azides and alkynes (CuAAC)-mediated nanosensors, as well as the functionalization of nanoprobes based on click chemistry. Nanoprobes including gold nanoparticles, quantum dots, magnetic nanoparticles and carbon nanomaterials are covered. We discuss the advantages of click chemistry-mediated nanosensors for biochemical assays, and give perspectives on the development of click chemistry-mediated approaches for clinical diagnosis and other biomedical applications. PMID:27217831

  18. Combined Biochemical and Serological Typing of Clinical Isolates of Klebsiella

    PubMed Central

    Rennie, R. P.; Duncan, I. B. R.

    1974-01-01

    In a series of 640 strains of Klebsiella isolated from clinical specimens over a 7-month period, there were sufficient biochemical differences between strains to allow a biochemical typing system to be established. Biochemical tests were done in solid media inoculated with a modified Steers inocula replicator. Biotypes were designated by a numerical coding system; 29 distinct biotypes were found among the 640 strains of Klebsiella. Serotyping of 270 of the strains was done by the Quellung reaction, and 40 capsular types were identified. Numerical biotypes and serotypes of strains appeared to vary independently. When used in conjunction, the two methods subdivided the strains into many more distinct types than either used alone. With the combined method over 100 types of Klebsiella were distinguished among the 270 isolates. PMID:4608362

  19. Hematologic and plasma biochemical values of hyacinth macaws (Anodorhynchus hyacinthinus).

    PubMed

    Kolesnikovas, Cristiane K M; Niemeyer, Claudia; Teixeira, Rodrigo H F; Nunes, Adauto L V; Rameh-de-Albuquerque, Luciana C; Sant'Anna, Sávio S; Catão-Dias, José L

    2012-09-01

    The hyacinth macaw (Anodorhyncus hyacinthinus), considered the largest psittacine bird species in the world, is an endangered species, with a remaining population of approximately 6500 birds in the wild. To establish hematologic and plasma biochemical reference ranges and to verify differences related to sex, samples from 29 hyacinth macaws (14 males, 15 females) were obtained from birds apprehended from illegal wildlife trade and subsequently housed at the Sorocaba Zoo, Brazil. No significant differences in hematologic or plasma biochemical values were found between females and males. Compared with published reference values, differences were found in mean concentrations of total red blood cell count, corpuscular volume, corpuscular hemoglobin level, total white blood cell count, aspartate aminotransferase level, creatine kinase concentration, alkaline phosphatase concentration, and phosphorus level. Baseline hematologic and plasma biochemical ranges were established, which may be useful as reference values for clinicians working with this endangered species in captivity or rehabilitation centers.

  20. Biochemical markers in oral submucous fibrosis: A review and update

    PubMed Central

    Kamath, V V; Satelur, K; Komali, Y

    2013-01-01

    Oral submucous fibrosis (OSMF) is a potentially malignant oral condition effectively linked to the causative habit of chewing areca nut. Since its first description in the 1950s, numerous epidemiological, biochemical, histological, and genetic studies have been reported. While most studies point out to the cause and effect of areca nut, co-additive factors are also implicated in the progression and malignant transformation of this condition. Biochemical investigations have concentrated on outlining such changes in the blood, serum or tissues of these patients and have given insights on the possible pathogenesis of OSMF. This article attempts to compile details of biochemical investigations in OSMF and summarize and infer on the findings. PMID:24348612

  1. Use of EPR to Solve Biochemical Problems

    PubMed Central

    Sahu, Indra D.; McCarrick, Robert M.; Lorigan, Gary A.

    2013-01-01

    EPR spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information on a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers on the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems which are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems. PMID:23961941

  2. Susceptibility to antibiotics and biochemical properties of Desulfovibrio desulfuricans strains.

    PubMed

    Dzierzewicz, Z; Cwalina, B; Jaworska-Kik, M; Weglarz, L; Wilczok, T

    2001-01-01

    Susceptibility to several antibiotics and biochemical properties of intestinal and soil strains of Desulfovibrio desulfuricans bacteria were investigated using the tests: ATB ANA, Sceptor Anaerobic MIC/ID and API ZYM. It was demonstrated that the D. desulfuricans strains were resistant to penicillin, cefoxitin, clindamycin, metronidazole, erythromycin, rifampicin and teicoplanin. The strains initially susceptible to imipenem became resistant to this drug following 72 h incubation with it. Of 25 analyzed antibiotics there was none that after 72 h action on the bacteria was effective in relation to all of the investigated strains. The differences in susceptibility of D. desulfuricans strains to antibiotics were not associated with the strains' biochemical properties. PMID:12197616

  3. Fast and simple spectral FLIM for biochemical and medical imaging.

    PubMed

    Popleteeva, Marina; Haas, Kalina T; Stoppa, David; Pancheri, Lucio; Gasparini, Leonardo; Kaminski, Clemens F; Cassidy, Liam D; Venkitaraman, Ashok R; Esposito, Alessandro

    2015-09-01

    Spectrally resolved fluorescence lifetime imaging microscopy (λFLIM) has powerful potential for biochemical and medical imaging applications. However, long acquisition times, low spectral resolution and complexity of λFLIM often narrow its use to specialized laboratories. Therefore, we demonstrate here a simple spectral FLIM based on a solid-state detector array providing in-pixel histrogramming and delivering faster acquisition, larger dynamic range, and higher spectral elements than state-of-the-art λFLIM. We successfully apply this novel microscopy system to biochemical and medical imaging demonstrating that solid-state detectors are a key strategic technology to enable complex assays in biomedical laboratories and the clinic.

  4. Physiological and molecular biochemical mechanisms of bile formation

    PubMed Central

    Reshetnyak, Vasiliy Ivanovich

    2013-01-01

    This review considers the physiological and molecular biochemical mechanisms of bile formation. The composition of bile and structure of a bile canaliculus, biosynthesis and conjugation of bile acids, bile phospholipids, formation of bile micellar structures, and enterohepatic circulation of bile acids are described. In general, the review focuses on the molecular physiology of the transporting systems of the hepatocyte sinusoidal and apical membranes. Knowledge of physiological and biochemical basis of bile formation has implications for understanding the mechanisms of development of pathological processes, associated with diseases of the liver and biliary tract. PMID:24259965

  5. A biochemical strategy for simulation of endochondral and intramembranous ossification.

    PubMed

    Garzón-Alvarado, Diego A

    2014-01-01

    Following the assumption that parathyroid hormone related protein and Indian hedgehog form a biochemical regulatory loop for the endochondral process and bone morphogenetic protein 2 and Noggin in the intramembranous process, this paper implements these regulatory mechanisms. For this purpose, we use a set of reaction-diffusion equations that are widely used in morphogenesis, in which biochemical factors are assumed to be secreted by precursor cells, mesenchymal cells and chondrocytes, in endochondral and intramembranous ossification, respectively. The solution leads to the so-called Turing patterns, which represent these processes of ossification in a very approximate way.

  6. [Biochemical features of gallbladder bile in biliary tract diseases].

    PubMed

    Plotnikova, E Iu; Aleksandrova, A Iu; Beloborodova, E I; Didlovslaia, N A

    2007-06-01

    Sixty-two and 58 patients with hypo- and hypermotor biliary tract dysfunction (BTD), respectively, as well as 59 patients with chronic acalculous cholecystitis (CAC) and 63 with opisthorchiasis-complicated CAC were examined. A control group comprised 33 patients of the same sex and age. All the patients underwent fractional duodenal intubation, followed by clinical, biochemical, and serological bile studies. All the examinees were found to increased gallbladder bile lithogenicity, minor changes being observed in biliary tract dysfunction and more pronounced ones being in opisthorchiasis. A biochemical study of gallbladder bile, followed by its lithogenicity correction, is recommended in the treatment of different forms of BTD. PMID:17682480

  7. The Biochemical Properties of Antibodies and Their Fragments.

    PubMed

    Hnasko, Robert M

    2015-01-01

    Immunoglobulins (Ig) or antibodies are powerful molecular recognition tools that can be used to identify minute quantities of a given target analyte. Their antigen-binding properties define both the sensitivity and selectivity of an immunoassay. Understanding the biochemical properties of this class of protein will provide users with the knowledge necessary to select the appropriate antibody composition to maximize immunoassay results. Here we define the general biochemical properties of antibodies and their similarities and differences, explain how these properties influence their functional relationship to an antigen target, and describe a method for the enzymatic fragmentation of antibodies into smaller functional parts.

  8. The Stereochemistry of Biochemical Molecules: A Subject to Revisit

    NASA Astrophysics Data System (ADS)

    Centelles, Josep J.; Imperial, Santiago

    2005-01-01

    Although Fischer’s convention for stereoisomers is useful for simple molecules, the stereochemistry of complex biochemical molecules is often poorly indicated in textbooks. This article reports on errors in stereochemistry of complex hydrosoluble vitamin B 12 molecule. Twenty-five popular biochemistry textbooks were examined for their treatment of the stereoisomery of vitamin B 12 . Mistakes, discrepancies, and oddities reported in vitamin B 12 are just an example of this problem. Biochemistry textbook authors and teachers should pay more attention to the stereoisomery of biochemical molecules to avoid students’ confusion.

  9. Overall view of chemical and biochemical weapons.

    PubMed

    Pitschmann, Vladimír

    2014-06-04

    This article describes a brief history of chemical warfare, which culminated in the signing of the Chemical Weapons Convention. It describes the current level of chemical weapons and the risk of using them. Furthermore, some traditional technology for the development of chemical weapons, such as increasing toxicity, methods of overcoming chemical protection, research on natural toxins or the introduction of binary technology, has been described. In accordance with many parameters, chemical weapons based on traditional technologies have achieved the limit of their development. There is, however, a big potential of their further development based on the most recent knowledge of modern scientific and technical disciplines, particularly at the boundary of chemistry and biology. The risk is even higher due to the fact that already, today, there is a general acceptance of the development of non-lethal chemical weapons at a technologically higher level. In the future, the chemical arsenal will be based on the accumulation of important information from the fields of chemical, biological and toxin weapons. Data banks obtained in this way will be hardly accessible and the risk of their materialization will persist.

  10. Behavior and biochemical analysis of phencyclidine

    SciTech Connect

    McCann, D.J.

    1988-01-01

    The objectives of this research were: (1) to develop the radial maze as a tool for the study of phencyclidine (PCP) and related drugs; (2) to evaluate verapamil and colonidine, two proposed treatments for PCP intoxication, as potential antagonists of PCP in the radial maze; and (3) to evaluate the functionality of two distinct types of PCP binding sites as receptors by comparing, for a series of drugs, activity in competitive binding experiments with behavioral activity. The radial maze proved to be a useful tool for the study of PCP and related drugs. With training, rats became highly efficient at obtaining the 8 food pellets placed in the maze. However, PCP and related drugs disrupted this performance, causing numerous reentries into previously visited arms. Results of correlation analyses comparing rank-order affinities with rank-order potencies of (+)SKF-10,047 (the prototypical sigma-opioid agonist), PCP, and several PCP analogs support the involvement of ({sup 3}H)-1-(2-thienyl)cyclohexyl piperidine binding sites (TCP sites) in mediating both the discriminative stimulus properties of PCP and disruption of performance in a 4-arm radial maze.

  11. Overall View of Chemical and Biochemical Weapons

    PubMed Central

    Pitschmann, Vladimír

    2014-01-01

    This article describes a brief history of chemical warfare, which culminated in the signing of the Chemical Weapons Convention. It describes the current level of chemical weapons and the risk of using them. Furthermore, some traditional technology for the development of chemical weapons, such as increasing toxicity, methods of overcoming chemical protection, research on natural toxins or the introduction of binary technology, has been described. In accordance with many parameters, chemical weapons based on traditional technologies have achieved the limit of their development. There is, however, a big potential of their further development based on the most recent knowledge of modern scientific and technical disciplines, particularly at the boundary of chemistry and biology. The risk is even higher due to the fact that already, today, there is a general acceptance of the development of non-lethal chemical weapons at a technologically higher level. In the future, the chemical arsenal will be based on the accumulation of important information from the fields of chemical, biological and toxin weapons. Data banks obtained in this way will be hardly accessible and the risk of their materialization will persist. PMID:24902078

  12. Biochemical and medical importance of vanadium compounds.

    PubMed

    Korbecki, Jan; Baranowska-Bosiacka, Irena; Gutowska, Izabela; Chlubek, Dariusz

    2012-01-01

    Vanadium belongs to the group of transition metals and is present in the air and soil contaminants in large urban agglomerations due to combustion of fossil fuels. It forms numerous inorganic compounds (vanadyl sulfate, sodium metavanadate, sodium orthovanadate, vanadium pentoxide) as well as complexes with organic compounds (BMOV, BEOV, METVAN). Depending on the research model, vanadium compounds exhibit antitumor or carcinogenic properties. Vanadium compounds generate ROS as a result of Fenton's reaction or of the reaction with atmospheric oxygen. They inactivate the Cdc25B(2) phosphatase and lead to degradation of Cdc25C, which induces G(2)/M phase arrest. In cells, vanadium compounds activate numerous signaling pathways and transcription factors, including PI3K-PKB/Akt-mTOR, NF-κB, MEK1/2-ERK, that cause cell survival or increased expression and release of VEGF. Vanadium compounds inhibit p53-dependent apoptosis and promote entry into the S phase of cells containing functional p53 protein. In addition, vanadium compounds, in particular organic derivatives, have insulin-mimetic and antidiabetic properties. Vanadium compounds lower blood glucose levels in animals and in clinical trials. They also inhibit the activity of protein tyrosine phosphatase 1B. By activating the PI3K-PKB/Akt pathway, vanadium compaunds increase the cellular uptake of glucose by the GLUT4 transporter. The PKB/Akt pathway is also used to inactivate glycogen synthase kinase-3. The impact of vanadium compounds on inflammatory reactions has not been fully studied. Vanadium pentoxide causes expression of COX-2 and the release of proinflammatory cytokines in a human lung fibroblast model. Other vanadium compounds activate NF-κB in macrophages by activating IKKβ.

  13. Study on color difference estimation method of medicine biochemical analysis

    NASA Astrophysics Data System (ADS)

    Wang, Chunhong; Zhou, Yue; Zhao, Hongxia; Sun, Jiashi; Zhou, Fengkun

    2006-01-01

    The biochemical analysis in medicine is an important inspection and diagnosis method in hospital clinic. The biochemical analysis of urine is one important item. The Urine test paper shows corresponding color with different detection project or different illness degree. The color difference between the standard threshold and the test paper color of urine can be used to judge the illness degree, so that further analysis and diagnosis to urine is gotten. The color is a three-dimensional physical variable concerning psychology, while reflectance is one-dimensional variable; therefore, the estimation method of color difference in urine test can have better precision and facility than the conventional test method with one-dimensional reflectance, it can make an accurate diagnose. The digital camera is easy to take an image of urine test paper and is used to carry out the urine biochemical analysis conveniently. On the experiment, the color image of urine test paper is taken by popular color digital camera and saved in the computer which installs a simple color space conversion (RGB -> XYZ -> L *a *b *)and the calculation software. Test sample is graded according to intelligent detection of quantitative color. The images taken every time were saved in computer, and the whole illness process will be monitored. This method can also use in other medicine biochemical analyses that have relation with color. Experiment result shows that this test method is quick and accurate; it can be used in hospital, calibrating organization and family, so its application prospect is extensive.

  14. MATLAB-Based Teaching Modules in Biochemical Engineering

    ERIC Educational Resources Information Center

    Lee, Kilho; Comolli, Noelle K.; Kelly, William J.; Huang, Zuyi

    2015-01-01

    Mathematical models play an important role in biochemical engineering. For example, the models developed in the field of systems biology have been used to identify drug targets to treat pathogens such as Pseudomonas aeruginosa in biofilms. In addition, competitive binding models for chromatography processes have been developed to predict expanded…

  15. Biochemical and Structural Studies of RNA Modification and Repair

    ERIC Educational Resources Information Center

    Chan, Chio Mui

    2009-01-01

    RNA modification, RNA interference, and RNA repair are important events in the cell. This thesis presents three projects related to these three fields. By using both biochemical and structural methods, we characterized enzymatic activities of pseudouridine synthase TruD, solved the structure of "A. aeolicus" GidA, and reconstituted a novel…

  16. Annelid Aminotransferase Activity--An Exercise in Basic Biochemical Skills.

    ERIC Educational Resources Information Center

    Teal, A. R.; Alcock, R. S.

    1978-01-01

    A practical exercise is described that allows students to investigate a specific problem using a variety of biochemical techniques. The need for a thorough understanding of the theoretical principles underlying these processes is emphasized. A program of private study and assessment is suggested to enable the progress of students to be followed.…

  17. Metstoich--Teaching Quantitative Metabolism and Energetics in Biochemical Engineering

    ERIC Educational Resources Information Center

    Wong, Kelvin W. W.; Barford, John P.

    2010-01-01

    Metstoich, a metabolic calculator developed for teaching, can provide a novel way to teach quantitative metabolism to biochemical engineering students. It can also introduce biochemistry/life science students to the quantitative aspects of life science subjects they have studied. Metstoich links traditional biochemistry-based metabolic approaches…

  18. Biosensors and bioelectronics on smartphone for portable biochemical detection.

    PubMed

    Zhang, Diming; Liu, Qingjun

    2016-01-15

    Smartphone has been widely integrated with sensors, such as test strips, sensor chips, and hand-held detectors, for biochemical detections due to its portability and ubiquitous availability. Utilizing built-in function modules, smartphone is often employed as controller, analyzer, and displayer for rapid, real-time, and point-of-care monitoring, which can significantly simplify design and reduce cost of the detecting systems. This paper presents a review of biosensors and bioelectronics on smartphone for portable biochemical detections. The biosensors and bioelectronics based on smartphone can mainly be classified into biosensors using optics, surface plasmon resonance, electrochemistry, and near-field communication. The developments of these biosensors and bioelectronics on smartphone are reviewed along with typical biochemical detecting cases. Sensor strategies, detector attachments, and coupling methods are highlighted to show designs of the compact, lightweight, and low-cost sensor systems. The performances and advantages of these designs are introduced with their applications in healthcare diagnosis, environment monitoring, and food evaluation. With advances in micro-manufacture, sensor technology, and miniaturized electronics, biosensor and bioelectronic devices on smartphone can be used to perform biochemical detections as common and convenient as electronic tag readout in foreseeable future.

  19. Parameter identifiability of power-law biochemical system models.

    PubMed

    Srinath, Sridharan; Gunawan, Rudiyanto

    2010-09-01

    Mathematical modeling has become an integral component in biotechnology, in which these models are frequently used to design and optimize bioprocesses. Canonical models, like power-laws within the Biochemical Systems Theory, offer numerous mathematical and numerical advantages, including built-in flexibility to simulate general nonlinear behavior. The construction of such models relies on the estimation of unknown case-specific model parameters by way of experimental data fitting, also known as inverse modeling. Despite the large number of publications on this topic, this task remains the bottleneck in canonical modeling of biochemical systems. The focus of this paper concerns with the question of identifiability of power-law models from dynamic data, that is, whether the parameter values can be uniquely and accurately identified from time-series data. Existing and newly developed parameter identifiability methods were applied to two power-law models of biochemical systems, and the results pointed to the lack of parametric identifiability as the root cause of the difficulty faced in the inverse modeling. Despite the focus on power-law models, the analyses and conclusions are extendable to other canonical models, and the issue of parameter identifiability is expected to be a common problem in biochemical system modeling. PMID:20197073

  20. Biochemical aspects of pressure tolerance in marine mammals.

    PubMed

    Castellini, Michael A; Rivera, Patricia M; Castellini, Judith M

    2002-11-01

    Some marine mammals can dive to depths approaching 2000 m. At these hydrostatic pressures (200 atm), some fish species show alterations in enzyme structure and function that make them pressure-tolerant. Do marine mammals also possess biochemical adaptations to withstand such pressures? In theory, biochemical alterations might occur at the control of enzymatic pathways, by impacting cell membrane fluidity changes or at a higher level, such as cellular metabolism. Studies of marine mammal tissues show evidence of all of these changes, but the results are not consistent across species or diving depth. This review discusses whether the elevated body temperature of marine mammals imparts pressure tolerance at the biochemical level, whether there are cell membrane structural differences in marine mammals and whether whole, living cells from marine mammals alter their metabolism when pressure stressed. We conclude that temperature alone is probably not protective against pressure and that cell membrane composition data are not conclusive. Whole cell studies suggest that marine mammals either respond positively to pressure or are not impacted by pressure. However, the range of tissue types and enzyme systems that have been studied is extremely limited and needs to be expanded before more general conclusions about how these mammals tolerate elevated pressures on a biochemical level can be drawn.

  1. A MULTILAYER BIOCHEMICAL DRY DEPOSITION MODEL 2. MODEL EVALUATION

    EPA Science Inventory

    The multilayer biochemical dry deposition model (MLBC) described in the accompanying paper was tested against half-hourly eddy correlation data from six field sites under a wide range of climate conditions with various plant types. Modeled CO2, O3, SO2<...

  2. 40 CFR 158.2010 - Biochemical pesticides data requirements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... can be found in § 158.2000. (b) Each data table includes “use patterns” under which the individual... table and the test notes following the data table must be used to determine whether the data requirement... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Biochemical pesticides...

  3. 40 CFR 158.2010 - Biochemical pesticides data requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... can be found in § 158.2000. (b) Each data table includes “use patterns” under which the individual... table and the test notes following the data table must be used to determine whether the data requirement... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Biochemical pesticides...

  4. 40 CFR 158.2010 - Biochemical pesticides data requirements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... can be found in § 158.2000. (b) Each data table includes “use patterns” under which the individual... table and the test notes following the data table must be used to determine whether the data requirement... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticides...

  5. Biochemical Parameters of Orienteers Competing in a Long Distance Race.

    ERIC Educational Resources Information Center

    Mikan, Vladimir; And Others

    1992-01-01

    Measured important biochemical parameters in a group of orienteers two hours before beginning and immediately after an orienteering marathon. Found levels of dehydration. Suggests a drinking regimen which is designed for orienteering races. Concludes that no runner having kidney or liver abnormalities or changes in the urine should be allowed to…

  6. [Strategies for diagnosis and biochemical control of porphyrias].

    PubMed

    Brock, Axel; Rasmussen, Lars Melholt; Hertz, Jens Michael

    2014-02-17

    Porphyrias are rare, distinct and well characterized diseases due to impairment of one of the eight steps in the biosynthesis of haem, which is the functional group of haemoglobin, myoglobin and cytochromes, including the cytochrome P-450 family. The actual strategies for diagnosis and biochemical control of the five most common porphyrias are described.

  7. Classic and contemporary approaches to modeling biochemical reactions

    PubMed Central

    Chen, William W.; Niepel, Mario; Sorger, Peter K.

    2010-01-01

    Recent interest in modeling biochemical networks raises questions about the relationship between often complex mathematical models and familiar arithmetic concepts from classical enzymology, and also about connections between modeling and experimental data. This review addresses both topics by familiarizing readers with key concepts (and terminology) in the construction, validation, and application of deterministic biochemical models, with particular emphasis on a simple enzyme-catalyzed reaction. Networks of coupled ordinary differential equations (ODEs) are the natural language for describing enzyme kinetics in a mass action approximation. We illustrate this point by showing how the familiar Briggs-Haldane formulation of Michaelis-Menten kinetics derives from the outer (or quasi-steady-state) solution of a dynamical system of ODEs describing a simple reaction under special conditions. We discuss how parameters in the Michaelis-Menten approximation and in the underlying ODE network can be estimated from experimental data, with a special emphasis on the origins of uncertainty. Finally, we extrapolate from a simple reaction to complex models of multiprotein biochemical networks. The concepts described in this review, hitherto of interest primarily to practitioners, are likely to become important for a much broader community of cellular and molecular biologists attempting to understand the promise and challenges of “systems biology” as applied to biochemical mechanisms. PMID:20810646

  8. Physiologic and biochemical aspects of skeletal muscle denervation and reinnervation

    NASA Technical Reports Server (NTRS)

    Max, S. R.; Mayer, R. F.

    1984-01-01

    Some of the physiologic and biochemical changes that occur in mammalian skeletal muscle following denervation and reinnervation are considered and some comparisons are made with changes observed following altered motor function. The nature of the trophic influence by which nerves control muscle properties are discussed, including the effects of choline acetyltransferase and acetylcholinesterase and the role of the acetylcholine receptor.

  9. Biochemical Engineering with Extensive Use of Personal Computers.

    ERIC Educational Resources Information Center

    Bungay, H. R.

    1986-01-01

    Describes a course in biochemical engineering fundamentals which relies heavily on the use of personal computers. The computers are used with interactive tutorials, problems that require computer simulations of differential equations, and homework assignments. A list of computer assignments and student term projects is included. (TW)

  10. Biochemical correlates in an animal model of depression

    SciTech Connect

    Johnson, J.O.

    1986-01-01

    A valid animal model of depression was used to explore specific adrenergic receptor differences between rats exhibiting aberrant behavior and control groups. Preliminary experiments revealed a distinct upregulation of hippocampal beta-receptors (as compared to other brain regions) in those animals acquiring a response deficit as a result of exposure to inescapable footshock. Concurrent studies using standard receptor binding techniques showed no large changes in the density of alpha-adrenergic, serotonergic, or dopaminergic receptor densities. This led to the hypothesis that the hippocampal beta-receptor in responses deficient animals could be correlated with the behavioral changes seen after exposure to the aversive stimulus. Normalization of the behavior through the administration of antidepressants could be expected to reverse the biochemical changes if these are related to the mechanism of action of antidepressant drugs. This study makes three important points: (1) there is a relevant biochemical change in the hippocampus of response deficient rats which occurs in parallel to a well-defined behavior, (2) the biochemical and behavioral changes are normalized by antidepressant treatments exhibiting both serotonergic and adrenergic mechanisms of action, and (3) the mode of action of antidepressants in this model is probably a combination of serotonergic and adrenergic influences modulating the hippocampal beta-receptor. These results are discussed in relation to anatomical and biochemical aspects of antidepressant action.

  11. The Stereochemistry of Biochemical Molecules: A Subject to Revisit

    ERIC Educational Resources Information Center

    Centelles, Josep J.; Imperial, Santiago

    2005-01-01

    Although Fischer's convention for stereoisomers is useful for simple molecules, the stereochemistry of complex biochemical molecules is often poorly indicated in textbooks. This article reports on errors in stereochemistry of complex hydrosoluble vitamin B12 molecule. Twenty-five popular biochemistry textbooks were examined for their treatment of…

  12. Salvage Brachytherapy for Biochemically Recurrent Prostate Cancer following Primary Brachytherapy

    PubMed Central

    Lacy, John M.; Wilson, William A.; Bole, Raevti; Chen, Li; Meigooni, Ali S.; Rowland, Randall G.; Clair, William H. St.

    2016-01-01

    Purpose. In this study, we evaluated our experience with salvage brachytherapy after discovery of biochemical recurrence after a prior brachytherapy procedure. Methods and Materials. From 2001 through 2012 twenty-one patients treated by brachytherapy within University of Kentucky or from outside centers developed biochemical failure and had no evidence of metastases. Computed tomography (CT) scans were evaluated; patients who had an underseeded portion of their prostate were considered for reimplantation. Results. The majority of the patients in this study (61.9%) were low risk and median presalvage PSA was 3.49 (range 17.41–1.68). Mean follow-up was 61 months. At last follow-up after reseeding, 11/21 (52.4%) were free of biochemical recurrence. There was a trend towards decreased freedom from biochemical recurrence in low risk patients (p = 0.12). International Prostate Symptom Scores (IPSS) increased at 3-month follow-up visits but decreased and were equivalent to baseline scores at 18 months. Conclusions. Salvage brachytherapy after primary brachytherapy is possible; however, in our experience the side-effect profile after the second brachytherapy procedure was higher than after the first brachytherapy procedure. In this cohort of patients we demonstrate that approximately 50% oncologic control, low risk patients appear to have better outcomes than others. PMID:27092279

  13. Biochemical and physiological consequences of the Apollo flight diet.

    NASA Technical Reports Server (NTRS)

    Hander, E. W.; Leach, C. S.; Fischer, C. L.; Rummel, J.; Rambaut, P.; Johnson, P. C.

    1971-01-01

    Six male subjects subsisting on a typical Apollo flight diet for five consecutive days were evaluated for changes in biochemical and physiological status. Laboratory examinations failed to demonstrate any significant changes of the kind previously attributed to weightlessness, such as in serum electrolytes, endocrine values, body fluid, or hematologic parameters.

  14. BIOCHEMICAL INDICES OF EXPOSURE TO ENVIRONMENTAL ESTROGENS: A SPECIES COMPARISON

    EPA Science Inventory

    Existence of endocrine active substances in the aquatic environment has been clearly established in several studies. Exposure of organisms to both natural and synthetic xenoestrogens have been found to alter biochemical homeostatis and, in some cases, result in reproductive and d...

  15. A MULTILAYER BIOCHEMICAL DRY DEPOSITION MODEL 1. MODEL FORMULATION

    EPA Science Inventory

    A multilayer biochemical dry deposition model has been developed based on the NOAA Multilayer Model (MLM) to study gaseous exchanges between the soil, plants, and the atmosphere. Most of the parameterizations and submodels have been updated or replaced. The numerical integration ...

  16. Hematologic and biochemical reference intervals for specific pathogen free 6-week-old Hampshire-Yorkshire crossbred pigs

    PubMed Central

    2014-01-01

    Background Hematologic and biochemical reference intervals depend on many factors, including age. A review of the literature highlights the lack of reference intervals for 6-wk-old specific pathogen free (SPF) Hampshire-Yorkshire crossbred pigs. For translational research, 6-wk-old pigs represent an important animal model for both human juvenile colitis and diabetes mellitus type 2 given the similarities between the porcine and human gastrointestinal maturation process. The aim of this study was to determine reference intervals for hematological and biochemical parameters in healthy 6-wk-old crossbred pigs. Blood samples were collected from 66 clinically healthy Hampshire-Yorkshire pigs. The pigs were 6 wks old, represented both sexes, and were housed in a SPF facility. Automated hematological and biochemical analysis were performed using an ADVIA 120 Hematology System and a Cobas 6000 C501 Clinical Chemistry Analyzer. Results Reference intervals were calculated using both parametric and nonparametric methods. The mean, median, minimum, and maximum values were calculated. Conclusion As pigs are used more frequently as medical models of human disease, having reference intervals for commonly measured hematological and biochemical parameters in 6-wk-old pigs will be useful. The reference intervals calculated in this study will aid in the diagnosis and monitoring of both naturally occurring and experimentally induced disease. In comparison to published reference intervals for older non SPF pigs, notable differences in leukocyte populations, and in levels of sodium, potassium, glucose, protein, and alkaline phosphatase were observed. PMID:24410946

  17. What is the biochemical and physiological rationale for using cold-water immersion in sports recovery? A systematic review.

    PubMed

    Bleakley, Chris M; Davison, Gareth W

    2010-02-01

    Cold-water immersion (CWI) is a popular recovery intervention after exercise. The scientific rationale is not clear, and there are no clear guidelines for its use. The aim of this review was to study the physiological and biochemical effect of short periods of CWI. A computer-based literature search, citation tracking and related articles searches were undertaken. Primary research studies using healthy human participants, immersed in cold water (<15 degrees C), for 5 min durations or less were included. Data were extracted on body temperature, cardiovascular, respiratory and biochemical response. 16 studies were included. Sample size was restricted, and there was a large degree of study heterogeneity. CWI was associated with an increase in heart rate, blood pressure, respiratory minute volume and metabolism. Decreases in end tidal carbon dioxide partial pressure and a decrease in cerebral blood flow were also reported. There was evidence of increases in peripheral catecholamine concentration, oxidative stress and a possible increase in free-radical-species formation. The magnitude of these responses may be attenuated with acclimatisation. CWI induces significant physiological and biochemical changes to the body. Much of this evidence is derived from full body immersions using resting healthy participants. The physiological and biochemical rationale for using short periods of CWI in sports recovery still remains unclear.

  18. Clinical, endocrinological and biochemical effects of zinc deficiency.

    PubMed

    Prasad, A S

    1985-08-01

    suggested that this trace element may have a role in the in vivo regulation of prolactin release. Thymopoietin, a hormone needed for T-cell maturation, has also been shown to be zinc dependent. It is clear that zinc may have several roles in biochemical and hormonal functions of various endocrine organs. Future research in this area is very much needed.

  19. Recommendations for terminology and databases for biochemical thermodynamics.

    PubMed

    Alberty, Robert A; Cornish-Bowden, Athel; Goldberg, Robert N; Hammes, Gordon G; Tipton, Keith; Westerhoff, Hans V

    2011-05-01

    Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K' for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ(r)G'°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ(f)G(i)'° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ(f)G(j)° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ(r)G'° of reactions and Δ(f)G(i)'° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature.

  20. Immunological and biochemical effects of 60 Hz electric and magnetic fields in humans

    SciTech Connect

    Fotopoulos, S.S.; Graham, C.

    1985-02-05

    Demand for electric power increased at an annual average rate of 7.5% between 1912 and 1971. In order to meet this demand, utility companies have had to increase both the number and the operating voltages employed in their overhead transmission lines. Public concern has been expressed about possible risks to human health and function arising from exposure to the electric and magnetic fields generated by these lines. The New York State Department of Health (NYSDH) is currently administering a wide-ranging research program to address the above issues. As part of this effort, MRI was funded to perform the first double-blind human study of the effects of exposure to combined 60-Hz electric and magnetic fields. The study focused on measure of human performance physiology and subjective state. The present project into the planned double-blind study. The purpose of Phase 1 was to conduct a comprehensive, screening evaluation of the effects of field exposure on human immunologic hematologic and biochemical parameters. Phase 1 of the current program has now also been completed, and the purpose of this report is to summarize our findings in regard to the effects of field exposure on measures of human immunologic, hematologic and biochemical function. The following sections of this document present the specific aims of the research conducted, the experimental methods and procedures followed, and the statistical analysis performed. The document concludes with a discussion of the findings obtained.

  1. Uroncor consensus statement: Management of biochemical recurrence after radical radiotherapy for prostate cancer: From biochemical failure to castration resistance.

    PubMed

    López Torrecilla, José; Hervás, Asunción; Zapatero, Almudena; Gómez Caamaño, Antonio; Macías, Victor; Herruzo, Ismael; Maldonado, Xavier; Gómez Iturriaga, Alfonso; Casas, Francesc; González San Segundo, Carmen

    2015-01-01

    Management of patients who experience biochemical failure after radical radiotherapy with or without hormonal therapy is highly challenging. The clinician must not only choose the type of treatment, but also the timing and optimal sequence of treatment administration. When biochemical failure occurs, numerous treatment scenarios are possible, thus making it more difficult to select the optimal approach. Moreover, rapid and ongoing advances in treatment options require that physicians make decisions that could impact both survival and quality of life. The aim of the present consensus statement, developed by the Urological Tumour Working Group (URONCOR) of the Spanish Society of Radiation Oncology (SEOR), is to provide cancer specialists with the latest, evidence-based information needed to make the best decisions for the patient under all possible treatment scenarios. The structure of this consensus statement follows the typical development of disease progression after biochemical failure, with the most appropriate treatment recommendations given for each stage. The consensus statement is organized into three separate chapters, as follows: biochemical failure with or without local recurrence and/or metastasis; progression after salvage therapy; and treatment of castration-resistant patients. PMID:26109913

  2. State-of-the-Art of (Bio)Chemical Sensor Developments in Analytical Spanish Groups

    PubMed Central

    Plata, María Reyes; Contento, Ana María; Ríos, Angel

    2010-01-01

    (Bio)chemical sensors are one of the most exciting fields in analytical chemistry today. The development of these analytical devices simplifies and miniaturizes the whole analytical process. Although the initial expectation of the massive incorporation of sensors in routine analytical work has been truncated to some extent, in many other cases analytical methods based on sensor technology have solved important analytical problems. Many research groups are working in this field world-wide, reporting interesting results so far. Modestly, Spanish researchers have contributed to these recent developments. In this review, we summarize the more representative achievements carried out for these groups. They cover a wide variety of sensors, including optical, electrochemical, piezoelectric or electro-mechanical devices, used for laboratory or field analyses. The capabilities to be used in different applied areas are also critically discussed. PMID:22319260

  3. The End of Alzheimer’s disease - from biochemical pharmacology to ecopsychosociology: a personal perspective

    PubMed Central

    Whitehouse, Peter J

    2014-01-01

    The future of the Alzheimer’s disease (AD) field involves a more complete understanding not only the state of current scientific approaches, but also the linguistic and cultural context of preclinical and clinical research and policy activities. The challenges surrounding dementia are large and growing but are only part of broader social and health concerns. In this latter context, the current state of research in the AD area is reviewed together with necessary priorities in moving forward. Creating a more optimistic future will depend less on genetic and reductionist approaches and more on environmental and intergenerative approaches that will aid in recalibrating the study of AD from an almost exclusive focus on biochemical, molecular and genetic aspects to better encompass “real world” ecological and psychosocial models of health PMID:24304687

  4. Biochemical and microbial features of shallow marine sediments along the Terra Nova Bay (Ross Sea, Antarctica)

    NASA Astrophysics Data System (ADS)

    Baldi, Franco; Marchetto, Davide; Pini, Francesco; Fani, Renato; Michaud, Luigi; Lo Giudice, Angelina; Berto, Daniela; Giani, Michele

    2010-09-01

    Shallow marine sediments were collected from seven stations (three of which located at Gerlache Inlet, two at Tethys Bay, one at Adelie Cove and one just beneath the Italian Research Base) along the Terra Nova Bay coast (Ross Sea, Antarctica). Their chemical, biochemical and microbiological properties were studied in order to provide further insights in the knowledge of this Antarctic benthic ecosystem. Overall, the organic carbon (OC) represented the major fraction of total carbon (TC) and displayed concentrations similar to or slightly lower than those previously measured in Antarctic bottom sediments. The biopolymeric carbon within OC ranged from 4.1% to 19.9% and showed a wide trophic range (65-834 μg g -1 d.w.). Proteins (PRT) represented on average the main biochemical class contributing to labile organic carbon, followed by lipids (LIP) and carbohydrates (CHO). The activity of aminopeptidase, β- D-glucosidase, alkaline phosphatase and esterase was checked, giving the highest values at Tethys Bay and at the deepest water sediments. The principal component analysis, which was computed considering physical, chemical (elemental and biochemical sedimentary composition) and microbiological parameters (including bacterial abundance, ectoenzymatic activities, T-RFs richness and diversity indices), allowed to obtain two main clusters ("Tethys Bay" and "other stations"). Based on data obtained, two representative 16S rRNA clone libraries using samples from Tethys Bay and Gerlache Inlet were constructed. The sequences of 171 clones were compared to those available in public databases to determine their approximate phylogenetic affiliations. Both aerobic and anaerobic bacteria were disclosed, with the majority of them affiliated with the Gamma- and Deltaproteobacteria, Bacteroidetes and Acidobacteria. The occurrence of strictly anaerobic bacteria suggests that sediments might also undergo anoxic conditions that, in turn, could favor the accumulation of PRT in respect

  5. Acidic deposition, cation mobilization, and biochemical indicators of stress in healthy red spruce

    SciTech Connect

    Shortle, W.C.; Smith, K.T.; Minocha, R.

    1997-05-01

    Dendrochemical and biochemical markers link stress in apparently healthy red spruce trees (Picea rubens) to acidic deposition. Previous reports related visible damage of trees at high elevations to root and soil processes. In this report, dendrochemical and foliar biochemical markers indicate perturbations in biological processes in healthy red spruce trees across the northeastern USA. Previous research on the dendrochemistry of red spruce stemwood indicated that under uniform environmental conditions, stemwood concentrations of Ca and Mg decreased with increasing radial distance from the pith. For nine forest locations, frequency analysis shows that 28 and 52% of samples of red spruce stemwood formed in the 1960s are enriched in Ca and Mg, respectively, relative to wood formed prior to and after the 1960s. This enrichment in trees throughout the northeastern USA may be interpretable as a signal of increased availability of essential cations in forest soils. Such a temporary increase in the availability of Ca and Mg could be caused by cation mobilization, a consequence of increased acidic deposition. During cation mobilization, essential and Ca and Mg as well as potentially harmful Al become more available for interaction with binding sites in the soil and absorbing roots. As conditions which favor cation mobilization continue, Ca and Mg can be leached or displaced from the soil. A measure of the interaction between Ca and Al is the Al/Ca binding ratio (molar charge ratio of exchangeable Al to exchangeable Ca). As the Al/Ca binding ratio in the root zone increased from 0.3 to 1.9, the foliar concentration of the biochemical stress marker putrescine also increased form 45 to 145 nm g{sup {minus}1}. The correlation of the putrescine concentration to the Al/Ca binding ratio (adj. r{sup 2} = 0.68, P <0.027) suggests that foliar stress may be linked to soil chemistry. 32 refs., 2 figs., 1 tab.

  6. Energy allocation in Daphnia magna exposed to xenobiotics: A biochemical approach

    SciTech Connect

    Coen, W.M. De; Janssen, C.R.; Persoone, G.

    1995-12-31

    A new approach to sublethal aquatic toxicity testing based on a biochemical assessment of the energy budget of Daphnia magna was developed and evaluated. With this method energy consumption (E{sub c}) is estimated by measuring the electron transport activity based on the calorimetric measurement of a tetrazolium salt reduction. Total available energy (E{sub a}) is assessed by measuring the lipid, protein and sugar content of the test organism using calorimetric methods. E{sub a} {minus} E{sup c} can subsequently be calculated and represents the ``surplus`` energy available for growth and reproduction. D. magna neonates were exposed to cadmium and 2,4-dichlorophenoxy acetic acid for 4 days after which the electron transport activity and the total lipid, protein and sugar content of the test organisms were determined. Using the enthalpy of combustion of the different macromolecular groups and converting the oxygen consumption into oxyenthalpic equivalents, an estimation of the total energy budget of the test organisms was made. Additionally, the age specific survival and reproduction and the growth of D. magna populations exposed to the same sublethal concentrations was assessed in 21 day life table experiments. Energy allocation patterns of stressed D. magna obtained with the new biochemical approach were similar to those obtained with the conventional Scope for Growth determinations. Although more research is needed, comparison between the suborganismal (biochemical) and supraorganismal (life table) endpoints indicate that the proposed short-term assay based on energy allocation could be used to predict long-term effects on the survival, growth and reproduction of daphnids.

  7. Acidic deposition, cation mobilization, and biochemical indicators of stress in healthy red spruce

    USGS Publications Warehouse

    Shortle, W.C.; Smith, K.T.; Minocha, R.; Lawrence, G.B.; David, M.B.

    1997-01-01

    Dendrochemical and biochemical markers link stress in apparently healthy red spruce trees (Picea rubens) to acidic deposition. Acidic deposition to spruce forests of the northeastern USA increased sharply during the 1960s. Previous reports related visible damage of trees at high elevations to root and soil processes. In this report, dendrochemical and foliar biochemical markers indicate perturbations in biological processes in healthy red spruce trees across the northeastern USA. Previous research on the dendrochemistry of red spruce stemwood indicated that under uniform environmental conditions, stemwood concentrations of Ca and Mg decreased with increasing radial distance from the pith. For nine forest locations, frequency analysis shows that 28 and 52% of samples of red spruce stemwood formed in the 1960s are enriched in Ca and Mg, respectively, relative to wood formed prior to and after the 1960s. This enrichment in trees throughout the northeastern USA may be interpretable as a signal of increased availability of essential cations in forest soils. Such a temporary increase in the availability of Ca and Mg could be caused by cation mobilization, a consequence of increased acidic deposition. During cation mobilization, essential Ca and Mg as well as potentially harmful Al become more available for interaction with binding sites in the soil and absorbing roots. As conditions which favor cation mobilization continue, Ca and Mg can be leached or displaced from the soil. A measure of the interaction between Ca and Al is the Al/Ca binding ratio (molar charge ratio of exchangeable Al to exchangeable Ca). As the Al/Ca binding ratio in the root zone increased from 0.3 to 1.9, the foliar concentration of the biochemical stress marker putrescine also increased from 45 to 145 nm g-1. The correlation of the putrescine concentration to the Al/Ca binding ratio (adj. r2 = 0.68, P < 0.027) suggests that foliar stress may be linked to soil chemistry.

  8. National Bioenergy Center Biochemical Platform Integration Project: Quarterly Update #26, January - March 2010

    SciTech Connect

    Schell, D.

    2010-04-01

    January-March, 2010 edition of the National Bioenergy Center's Biochemical Platform Integration Project quarterly newsletter. Issue topics: understanding and improving sugar measurements in biomass hydrolysates; expansion of the NREL/DOE Biochemical Pilot Plant.

  9. ESTIMATING GASEOUS EXCHANGES BETWEEN THE ATMOSPHERE AND PLANTS USING A COUPLED BIOCHEMICAL DRY DEPOSITION MODEL

    EPA Science Inventory

    To study gaseous exchanges between the soil, biosphere and atmosphere, a biochemical model was coupled with the latest version of Meyers Multi-Layer Deposition Model. The biochemical model describes photosynthesis and respiration and their coupling with stomatal resistance for...

  10. The free energy cost of accurate biochemical oscillations

    PubMed Central

    Cao, Yuansheng; Wang, Hongli; Ouyang, Qi; Tu, Yuhai

    2015-01-01

    Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how biochemical circuits suppress phase fluctuations and what is the incurred thermodynamic cost. Here, we study three different types of biochemical oscillations representing three basic oscillation motifs shared by all known oscillatory systems. In all the systems studied, we find that the phase diffusion constant depends on the free energy dissipation per period following the same inverse relation parameterized by system specific constants. This relationship and its range of validity are shown analytically in a model of noisy oscillation. Microscopically, we find that the oscillation is driven by multiple irreversible cycles that hydrolyze the fuel molecules such as ATP; the number of phase coherent periods is proportional to the free energy consumed per period. Experimental evidence in support of this general relationship and testable predictions are also presented. PMID:26566392

  11. Biochemical functionalization of peptide nanotubes with phage displayed peptides

    NASA Astrophysics Data System (ADS)

    Swaminathan, Swathi; Cui, Yue

    2016-09-01

    The development of a general approach for the biochemical functionalization of peptide nanotubes (PNTs) could open up existing opportunities in both fundamental studies as well as a variety of applications. PNTs are spontaneously assembled organic nanostructures made from peptides. Phage display has emerged as a powerful approach for identifying selective peptide binding motifs. Here, we demonstrate for the first time the biochemical functionalization of PNTs via peptides identified from a phage display peptide library. The phage-displayed peptides are shown to recognize PNTs. These advances further allow for the development of bifunctional peptides for the capture of bacteria and the self-assembly of silver particles onto PNTs. We anticipate that these results could provide significant opportunities for using PNTs in both fundamental studies and practical applications, including sensors and biosensors nanoelectronics, energy storage devices, drug delivery, and tissue engineering.

  12. The free-energy cost of accurate biochemical oscillations

    NASA Astrophysics Data System (ADS)

    Cao, Yuansheng; Wang, Hongli; Ouyang, Qi; Tu, Yuhai

    2015-09-01

    Oscillations within the cell regulate the timing of many important life cycles. However, in this noisy environment, oscillations can be highly inaccurate owing to phase fluctuations. It remains poorly understood how biochemical circuits suppress these phase fluctuations and what is the incurred thermodynamic cost. Here, we study three different types of biochemical oscillation, representing three basic oscillation motifs shared by all known oscillatory systems. In all the systems studied, we find that the phase diffusion constant depends on the free-energy dissipation per period, following the same inverse relation parameterized by system-specific constants. This relationship and its range of validity are shown analytically in a model of noisy oscillation. Microscopically, we find that the oscillation is driven by multiple irreversible cycles that hydrolyse fuel molecules such as ATP; the number of phase coherent periods is proportional to the free energy consumed per period. Experimental evidence in support of this general relationship and testable predictions are also presented.

  13. Biochemical functionalization of peptide nanotubes with phage displayed peptides.

    PubMed

    Swaminathan, Swathi; Cui, Yue

    2016-09-01

    The development of a general approach for the biochemical functionalization of peptide nanotubes (PNTs) could open up existing opportunities in both fundamental studies as well as a variety of applications. PNTs are spontaneously assembled organic nanostructures made from peptides. Phage display has emerged as a powerful approach for identifying selective peptide binding motifs. Here, we demonstrate for the first time the biochemical functionalization of PNTs via peptides identified from a phage display peptide library. The phage-displayed peptides are shown to recognize PNTs. These advances further allow for the development of bifunctional peptides for the capture of bacteria and the self-assembly of silver particles onto PNTs. We anticipate that these results could provide significant opportunities for using PNTs in both fundamental studies and practical applications, including sensors and biosensors nanoelectronics, energy storage devices, drug delivery, and tissue engineering. PMID:27479451

  14. Biochemical markers in the assessment of bone disease

    NASA Technical Reports Server (NTRS)

    Bikle, D. D.

    1997-01-01

    As the mean age of our population increases, increasing attention has been paid to the diseases associated with aging, including diseases of the skeleton such as osteoporosis. Effective means of treating and possibly preventing such skeletal disorders are emerging, making their early recognition an important goal for the primary care physician. Although bone density measurements and skeletal imaging studies remain of primary diagnostic importance in this regard, a large number of assays for biochemical markers of bone formation and resorption are being developed that promise to complement the densitometry measurements and imaging studies, providing an assessment of the rates of bone turnover and an earlier evaluation of the effects of therapy. In this review, emphasizing the recent literature, the major biochemical markers currently in use or under active investigation are described, and their application in a number of diseases of the skeleton including osteoporosis is evaluated.

  15. Adult amphibian epidermal proteins: biochemical characterization and developmental appearance.

    PubMed

    Reeves, O R

    1975-08-01

    The keratin-like proteins (KLPs) from the epidermis of adult frogs of the species Xenopus laevis have been isolated and biochemically characterized by means of polyacrylamide gel electrophoresis, amino acid analysis, tryptic peptide mapping, amino-terminal end-group analysis and isoelectric focusing. One particular protein fraction of rather unusual amino acid composition found only in epidermal tissue was isolated in quantity by preparative gel electrophoresis and monospecific antibodies prepared against it. Using this anti-KLP antibody preparation it was possible to show that at least one kine of keratin-like protein characteristic of the adult epidermis first appears within the larval epidermis during metamorphosis. This is the first reported biochemical characterization of a tissue-specific protien from adult amphibian skin.

  16. Electrolyte-Gated Graphene Ambipolar Frequency Multipliers for Biochemical Sensing.

    PubMed

    Fu, Wangyang; Feng, Lingyan; Mayer, Dirk; Panaitov, Gregory; Kireev, Dmitry; Offenhäusser, Andreas; Krause, Hans-Joachim

    2016-04-13

    In this Letter, the ambipolar properties of an electrolyte-gated graphene field-effect transistor (GFET) have been explored to fabricate frequency-doubling biochemical sensor devices. By biasing the ambipolar GFETs in a common-source configuration, an input sinusoidal voltage at frequency f applied to the electrolyte gate can be rectified to a sinusoidal wave at frequency 2f at the drain electrode. The extraordinary high carrier mobility of graphene and the strong electrolyte gate coupling provide the graphene ambipolar frequency doubler an unprecedented unity gain, as well as a detection limit of ∼4 pM for 11-mer single strand DNA molecules in 1 mM PBS buffer solution. Combined with an improved drift characteristics and an enhanced low-frequency 1/f noise performance by sampling at doubled frequency, this good detection limit suggests the graphene ambipolar frequency doubler a highly promising biochemical sensing platform. PMID:26928906

  17. SABIO-RK--database for biochemical reaction kinetics.

    PubMed

    Wittig, Ulrike; Kania, Renate; Golebiewski, Martin; Rey, Maja; Shi, Lei; Jong, Lenneke; Algaa, Enkhjargal; Weidemann, Andreas; Sauer-Danzwith, Heidrun; Mir, Saqib; Krebs, Olga; Bittkowski, Meik; Wetsch, Elina; Rojas, Isabel; Müller, Wolfgang

    2012-01-01

    SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually extracted from the literature and data directly submitted from lab experiments. The database content includes kinetic parameters in relation to biochemical reactions and their biological sources with no restriction on any particular set of organisms. Additionally, kinetic rate laws and corresponding equations as well as experimental conditions are represented. All the data are manually curated and annotated by biological experts, supported by automated consistency checks. SABIO-RK can be accessed via web-based user interfaces or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language), e.g. for import in modelling tools.

  18. The application of information theory to biochemical signaling systems.

    PubMed

    Rhee, Alex; Cheong, Raymond; Levchenko, Andre

    2012-08-01

    Cell signaling can be thought of fundamentally as an information transmission problem in which chemical messengers relay information about the external environment to the decision centers within a cell. Due to the biochemical nature of cellular signal transduction networks, molecular noise will inevitably limit the fidelity of any messages received and processed by a cell's signal transduction networks, leaving it with an imperfect impression of its environment. Fortunately, Shannon's information theory provides a mathematical framework independent of network complexity that can quantify the amount of information that can be transmitted despite biochemical noise. In particular, the channel capacity can be used to measure the maximum number of stimuli a cell can distinguish based upon the noisy responses of its signaling systems. Here, we provide a primer for quantitative biologists that covers fundamental concepts of information theory, highlights several key considerations when experimentally measuring channel capacity, and describes successful examples of the application of information theoretic analysis to biological signaling.

  19. Electrolyte-Gated Graphene Ambipolar Frequency Multipliers for Biochemical Sensing.

    PubMed

    Fu, Wangyang; Feng, Lingyan; Mayer, Dirk; Panaitov, Gregory; Kireev, Dmitry; Offenhäusser, Andreas; Krause, Hans-Joachim

    2016-04-13

    In this Letter, the ambipolar properties of an electrolyte-gated graphene field-effect transistor (GFET) have been explored to fabricate frequency-doubling biochemical sensor devices. By biasing the ambipolar GFETs in a common-source configuration, an input sinusoidal voltage at frequency f applied to the electrolyte gate can be rectified to a sinusoidal wave at frequency 2f at the drain electrode. The extraordinary high carrier mobility of graphene and the strong electrolyte gate coupling provide the graphene ambipolar frequency doubler an unprecedented unity gain, as well as a detection limit of ∼4 pM for 11-mer single strand DNA molecules in 1 mM PBS buffer solution. Combined with an improved drift characteristics and an enhanced low-frequency 1/f noise performance by sampling at doubled frequency, this good detection limit suggests the graphene ambipolar frequency doubler a highly promising biochemical sensing platform.

  20. Genetic and biochemical dissection of the eucaryotic flagellum

    PubMed Central

    1984-01-01

    The axoneme is the basic functional unit of the eucaryotic flagellum. Periodic structures appended to its 9+2 microtubule core are responsible for generation of flagellar bending. An account of biochemical and genetic studies of flagellar-defective mutants of Chlamydomonas reinhardtii is presented. These studies provide insights into the complex molecular composition of the appended structures, their mode of assembly, and the way in which they interact to modulate flagellar function. PMID:6230366

  1. Current diagnostic guidelines for biochemical diagnosis of acromegaly.

    PubMed

    Ferone, D; Resmini, E; Bocca, L; Giusti, M; Barreca, A; Minuto, F

    2004-12-01

    Acromegaly is a rare and chronic disease that, in the majority of cases, is due to the presence of a benign growth hormone (GH)-producing tumor of the pituitary. In the past, the diagnosis of acromegaly was established basically on physical changes, and only the patients with a severe clinical picture were brought to medical attention. The development of a radioimmunoassay for detecting GH allowed for the first time to confirm the diagnosis biochemically. Subsequently, methods for measuring insulin-like growth factor 1 (IGF-I) became available and added another important biochemical marker for the diagnosis and follow-up of these patients. Progressive improvements in assay methods have allowed for progressively better definitions of normality and, as a result, have permitted the diagnosis to be biochemically established in patients with only mild forms of the disease. Moreover, new potential markers of disease activity, such as other GH-dependent IGF system parameters, have been investigated and proposed in the diagnostic work-up and for monitoring the therapeutic outcome. Optimal assessment of disease activity, for both diagnostic and follow-up purposes, is mandatory. This subject has been strongly debated regarding proper cut-off values using highly sensitive GH assays as well as the problems linked to IGF system components measurement. Consequently, several consensus reports, as well as original studies, have been issued giving special attention to diagnostic procedures, cut-off revisions and definition of disease activity. The present review discuss principally the biochemical diagnosis of acromegaly based on these articles and on the experience collected in an endocrinological unit considered as reference center for pituitary diseases. PMID:15765030

  2. Examining the Relationship between Gender and Drug-Using Behaviors in Adolescents: The Use of Diagnostic Assessments and Biochemical Analyses of Urine Samples.

    ERIC Educational Resources Information Center

    James, William H.; Moore, David D.

    1999-01-01

    Examines the relationship between gender and drug use among adolescents using diagnostic assessments and biochemical analyses of urine samples. Statistical significance was found in the relationship between gender and marijuana use. The study confirms that more research is needed in this area. (Author/MKA)

  3. The energy costs of insulators in biochemical networks.

    PubMed

    Barton, John P; Sontag, Eduardo D

    2013-03-19

    Complex networks of biochemical reactions, such as intracellular protein signaling pathways and genetic networks, are often conceptualized in terms of modules--semiindependent collections of components that perform a well-defined function and which may be incorporated in multiple pathways. However, due to sequestration of molecular messengers during interactions and other effects, collectively referred to as retroactivity, real biochemical systems do not exhibit perfect modularity. Biochemical signaling pathways can be insulated from impedance and competition effects, which inhibit modularity, through enzymatic futile cycles that consume energy, typically in the form of ATP. We hypothesize that better insulation necessarily requires higher energy consumption. We test this hypothesis through a combined theoretical and computational analysis of a simplified physical model of covalent cycles, using two innovative measures of insulation, as well as a possible new way to characterize optimal insulation through the balancing of these two measures in a Pareto sense. Our results indicate that indeed better insulation requires more energy. While insulation may facilitate evolution by enabling a modular plug-and-play interconnection architecture, allowing for the creation of new behaviors by adding targets to existing pathways, our work suggests that this potential benefit must be balanced against the metabolic costs of insulation necessarily incurred in not affecting the behavior of existing processes. PMID:23528097

  4. Biochemical Markers of Bone Turnover Part I: Biochemistry and Variability

    PubMed Central

    2005-01-01

    With the ageing population in most countries, disorders of bone and mineral metabolism are becoming increasingly relevant to every day clinical practice. Consequently, the interest in, and the need for effective measures to be used in the screening, diagnosis and follow-up of such pathologies has markedly grown. Together with clinical and imaging techniques, biochemical tests play an important role in the assessment and differential diagnosis of metabolic bone disease. In recent years, the isolation and characterisation of cellular and extracellular components of the skeletal matrix have resulted in the development of molecular markers that are considered to reflect either bone formation or bone resorption. These biochemical indices are non-invasive, comparatively inexpensive and, when applied and interpreted correctly, helpful tools in the diagnostic and therapeutic assessment of metabolic bone disease. Part I of this article provides an overview of the basic biochemistry of bone markers, and sources of non-specific variability. Part II (to be published in a subsequent issue of this journal) will review the current evidence regarding the clinical use of biochemical markers of bone remodelling in metabolic and metastatic bone disease. PMID:16648882

  5. Design of a biochemical circuit motif for learning linear functions.

    PubMed

    Lakin, Matthew R; Minnich, Amanda; Lane, Terran; Stefanovic, Darko

    2014-12-01

    Learning and adaptive behaviour are fundamental biological processes. A key goal in the field of bioengineering is to develop biochemical circuit architectures with the ability to adapt to dynamic chemical environments. Here, we present a novel design for a biomolecular circuit capable of supervised learning of linear functions, using a model based on chemical reactions catalysed by DNAzymes. To achieve this, we propose a novel mechanism of maintaining and modifying internal state in biochemical systems, thereby advancing the state of the art in biomolecular circuit architecture. We use simulations to demonstrate that the circuit is capable of learning behaviour and assess its asymptotic learning performance, scalability and robustness to noise. Such circuits show great potential for building autonomous in vivo nanomedical devices. While such a biochemical system can tell us a great deal about the fundamentals of learning in living systems and may have broad applications in biomedicine (e.g. autonomous and adaptive drugs), it also offers some intriguing challenges and surprising behaviours from a machine learning perspective. PMID:25401175

  6. Polyphenol oxidase as a biochemical seed defense mechanism

    PubMed Central

    Fuerst, E. Patrick; Okubara, Patricia A.; Anderson, James V.; Morris, Craig F.

    2014-01-01

    Seed dormancy and resistance to decay are fundamental survival strategies, which allow a population of seeds to germinate over long periods of time. Seeds have physical, chemical, and biological defense mechanisms that protect their food reserves from decay-inducing organisms and herbivores. Here, we hypothesize that seeds also possess enzyme-based biochemical defenses, based on induction of the plant defense enzyme, polyphenol oxidase (PPO), when wild oat (Avena fatua L.) caryopses and seeds were challenged with seed-decaying Fusarium fungi. These studies suggest that dormant seeds are capable of mounting a defense response to pathogens. The pathogen-induced PPO activity from wild oat was attributed to a soluble isoform of the enzyme that appeared to result, at least in part, from proteolytic activation of a latent PPO isoform. PPO activity was also induced in wild oat hulls (lemma and palea), non-living tissues that cover and protect the caryopsis. These results are consistent with the hypothesis that seeds possess inducible enzyme-based biochemical defenses arrayed on the exterior of seeds and these defenses represent a fundamental mechanism of seed survival and longevity in the soil. Enzyme-based biochemical defenses may have broader implications since they may apply to other defense enzymes as well as to a diversity of plant species and ecosystems. PMID:25540647

  7. Inactivation of food-borne viruses using natural biochemical substances.

    PubMed

    Li, Dan; Baert, Leen; Uyttendaele, Mieke

    2013-08-01

    Food-borne viruses such as human Noroviruses (NoVs), hepatitis A virus (HAV), Rotaviruses (RoVs) are a public health concern worldwide. Biochemical substances, which occur naturally in plants, animals or microorganisms, might possess considerable antimicrobial properties. In this study, the reported effects of biochemical substances on food-borne viruses are reviewed. The biochemical substances are grouped into several categories including (i) polyphenols and proanthocyanins, (ii) saponin, (iii) polysaccharides, (iv) organic acids, (v) proteins and polypeptides, (vi) essential oils. Although not fully understood, the mechanism of action for the antiviral activity of the natural compounds is presented. Generally, it is thought to be the prevention of the viral attachment to host cells, either by causing damage on the viral capsids or change of the receptors on the cell membranes. It is recommended that further studies are undertaken not only on the wide-range screening for novel antiviral substances, but also on the mechanism in-depth as well as the exploration for their potential application in controlling virus contamination in foods or food processing. PMID:23628607

  8. How special is the biochemical function of native proteins?

    PubMed

    Skolnick, Jeffrey; Gao, Mu; Zhou, Hongyi

    2016-01-01

    Native proteins perform an amazing variety of biochemical functions, including enzymatic catalysis, and can engage in protein-protein and protein-DNA interactions that are essential for life. A key question is how special are these functional properties of proteins. Are they extremely rare, or are they an intrinsic feature? Comparison to the properties of compact conformations of artificially generated compact protein structures selected for thermodynamic stability but not any type of function, the artificial (ART) protein library, demonstrates that a remarkable number of the properties of native-like proteins are recapitulated. These include the complete set of small molecule ligand-binding pockets and most protein-protein interfaces. ART structures are predicted to be capable of weakly binding metabolites and cover a significant fraction of metabolic pathways, with the most enriched pathways including ancient ones such as glycolysis. Native-like active sites are also found in ART proteins. A small fraction of ART proteins are predicted to have strong protein-protein and protein-DNA interactions. Overall, it appears that biochemical function is an intrinsic feature of proteins which nature has significantly optimized during evolution. These studies raise questions as to the relative roles of specificity and promiscuity in the biochemical function and control of cells that need investigation.

  9. Weighting schemes in metabolic graphs for identifying biochemical routes.

    PubMed

    Ghosh, S; Baloni, P; Vishveshwara, S; Chandra, N

    2014-03-01

    Metabolism forms an integral part of all cells and its study is important to understand the functioning of the system, to understand alterations that occur in disease state and hence for subsequent applications in drug discovery. Reconstruction of genome-scale metabolic graphs from genomics and other molecular or biochemical data is now feasible. Few methods have also been reported for inferring biochemical pathways from these networks. However, given the large scale and complex inter-connections in the networks, the problem of identifying biochemical routes is not trivial and some questions still remain open. In particular, how a given path is altered in perturbed conditions remains a difficult problem, warranting development of improved methods. Here we report a comparison of 6 different weighting schemes to derive node and edge weights for a metabolic graph, weights reflecting various kinetic, thermodynamic parameters as well as abundances inferred from transcriptome data. Using a network of 50 nodes and 107 edges of carbohydrate metabolism, we show that kinetic parameter derived weighting schemes [Formula: see text] fare best. However, these are limited by their extent of availability, highlighting the usefulness of omics data under such conditions. Interestingly, transcriptome derived weights yield paths with best scores, but are inadequate to discriminate the theoretical paths. The method is tested on a system of Escherichia coli stress response. The approach illustrated here is generic in nature and can be used in the analysis for metabolic network from any species and perhaps more importantly for comparing condition-specific networks.

  10. Endothelial cells and cathepsins: Biochemical and biomechanical regulation.

    PubMed

    Platt, Manu O; Shockey, W Andrew

    2016-03-01

    Cathepsins are mechanosensitive proteases that are regulated not only by biochemical factors, but are also responsive to biomechanical forces in the cardiovascular system that regulate their expression and activity to participate in cardiovascular tissue remodeling. Their elastinolytic and collagenolytic activity have been implicated in atherosclerosis, abdominal aortic aneurysms, and in heart valve disease, all of which are lined by endothelial cells that are the mechanosensitive monolayer of cells that sense and respond to fluid shear stress as the blood flows across the surfaces of the arteries and valve leaflets. Inflammatory cytokine signaling is integrated with biomechanical signaling pathways by the endothelial cells to transcribe, translate, and activate either the cysteine cathepsins to remodel the tissue or to express their inhibitors to maintain healthy cardiovascular tissue structure. Other cardiovascular diseases should now be included in the study of the cysteine cathepsin activation because of the additional biochemical cues they provide that merges with the already existing hemodynamics driving cardiovascular disease. Sickle cell disease causes a chronic inflammation including elevated TNFα and increased numbers of circulating monocytes that alter the biochemical stimulation while the more viscous red blood cells due to the sickling of hemoglobin alters the hemodynamics and is associated with accelerated elastin remodeling causing pediatric strokes. HIV-mediated cardiovascular disease also occurs earlier in than the broader population and the influence of HIV-proteins and antiretrovirals on endothelial cells must be considered to understand these accelerated mechanisms in order to identify new therapeutic targets for prevention.

  11. How special is the biochemical function of native proteins?

    PubMed Central

    Skolnick, Jeffrey; Gao, Mu; Zhou, Hongyi

    2016-01-01

    Native proteins perform an amazing variety of biochemical functions, including enzymatic catalysis, and can engage in protein-protein and protein-DNA interactions that are essential for life. A key question is how special are these functional properties of proteins. Are they extremely rare, or are they an intrinsic feature? Comparison to the properties of compact conformations of artificially generated compact protein structures selected for thermodynamic stability but not any type of function, the artificial (ART) protein library, demonstrates that a remarkable number of the properties of native-like proteins are recapitulated. These include the complete set of small molecule ligand-binding pockets and most protein-protein interfaces. ART structures are predicted to be capable of weakly binding metabolites and cover a significant fraction of metabolic pathways, with the most enriched pathways including ancient ones such as glycolysis. Native-like active sites are also found in ART proteins. A small fraction of ART proteins are predicted to have strong protein-protein and protein-DNA interactions. Overall, it appears that biochemical function is an intrinsic feature of proteins which nature has significantly optimized during evolution. These studies raise questions as to the relative roles of specificity and promiscuity in the biochemical function and control of cells that need investigation. PMID:26962440

  12. Basic statistical recipes for the emergence of biochemical discernment.

    PubMed

    Michel, Denis

    2011-09-01

    An essential step towards understanding life would be to identify the very basic mechanisms responsible for the discerning behaviour of living biochemical systems, absent from randomly reacting chemical soups. One intuitively feels that this question goes beyond the particular nature of the biological molecules and should relate to general physical principles. The pre-eminent physicist Ludwig Boltzmann early envisioned life as a struggle for entropy, in concordance with the subsequent principle of self-organization out of equilibrium. Re-examination of elementary steady state biochemical systems from a statistical perspective supports this view and shows that sigmoidal responses arising from microstates elimination, are sufficient to explain innermost characteristics of life, including its capacity to convert random molecular interactions into accurate biological reactions. A primary operating strategy to achieve this goal is the introduction of time-irreversible transitions in molecular state conversion cycles by injection of free energy, which confers decisional capacity to single macromolecules. Selected examples from various fields of molecular biology such as enzymology and gene expression, are provided to show that these non-equilibrium steady state mechanisms remain important in contemporary biochemical systems. But in addition, information archiving allowed the emergence of the time-reversible counterparts of these mechanisms, mediated by evolutionary pre-organized macromolecular complexes capable of generating discernment in a non-dissipative manner.

  13. Modelling biochemical reaction systems by stochastic differential equations with reflection.

    PubMed

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-01

    In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach.

  14. Micro biochemical sensor based on SOI planar optical waveguide

    NASA Astrophysics Data System (ADS)

    Du, Yang; Dong, Ying

    2014-02-01

    A novel biochemical sensor based on planar optical waveguide is presented in this paper. The features of the sensor are as follows, the planar optical waveguide is made of SOI (Silicon-On-Insulator) material, a Mach Zehnder (M-Z) Interferometer structure is adopted as the sensing part, the sensor chip is fabricated using CMOS compatible technology and the size of the sensor chip is on the micron scale. Compared with the traditional biochemical sensors, this new type of sensor has such notable advantages as miniaturization, integration, high sensitivity and strong anti-interference capability, which provide the sensor with potential applications where traditional biochemical sensors cannot be used. At first, the benefits of SOI material comparing to other optical waveguide materials were analyzed in this paper. Then, according to the optical waveguide mode theory, M-Z interferometer waveguide was designed for the single mode behavior. By theoretical analysis of the radiation loss in the Y-junction of the planar waveguide interferometer, the relationship between the branch angle and the radiation loss was obtained. The power transfer function and the parametric equation of sensitivity of the M-Z interferometer were obtained through analysis of the waveguide structure. At last, the resolution of the effective refractive index and the characteristics of sensitivity of the sensor based on SOI M-Z Interferometer waveguide were simulated and analyzed by utilizing MATLAB software. As a result, the sensitivity of SOI M-Z Interferometer sensor can reach the order of 10-7 magnitude.

  15. Design of a biochemical circuit motif for learning linear functions

    PubMed Central

    Lakin, Matthew R.; Minnich, Amanda; Lane, Terran; Stefanovic, Darko

    2014-01-01

    Learning and adaptive behaviour are fundamental biological processes. A key goal in the field of bioengineering is to develop biochemical circuit architectures with the ability to adapt to dynamic chemical environments. Here, we present a novel design for a biomolecular circuit capable of supervised learning of linear functions, using a model based on chemical reactions catalysed by DNAzymes. To achieve this, we propose a novel mechanism of maintaining and modifying internal state in biochemical systems, thereby advancing the state of the art in biomolecular circuit architecture. We use simulations to demonstrate that the circuit is capable of learning behaviour and assess its asymptotic learning performance, scalability and robustness to noise. Such circuits show great potential for building autonomous in vivo nanomedical devices. While such a biochemical system can tell us a great deal about the fundamentals of learning in living systems and may have broad applications in biomedicine (e.g. autonomous and adaptive drugs), it also offers some intriguing challenges and surprising behaviours from a machine learning perspective. PMID:25401175

  16. Effects of colchicine on parotid gland: structural and biochemical studies.

    PubMed

    Malberti, A I; González de Crosa, M

    1998-01-01

    The present study involves the analysis of structural, ultrastructural and biochemical modifications induced by colchicine (Col) in Guinea Pig parotid gland. The biochemical studies showed that the highest concentration of soluble proteins occurred 4 hs after colchicine injection. The curve of a-amylase activity in the gland showed an increase in enzyme activity over control at approximately 4 hs post-injection. At 8 hours the rise was even greater. The structural and ultrastructural analyses of the gland revealed that 4 hs post-injection colchicine exerts its maximum inhibitory effect on secretion. At this treatment time, the cytoplasm contained granules of various sizes and sharp outlines. Large areas of the cytoplasm exhibited material which resembled the granular content and seemed to result from the fusion of granules. No secretion was found in the lumen of the ducts. The inhibitory effect on secretion would be due to the disassembly of microtubules which would in turn impair transport of the granules to the apical surface of the membrane and eventual exocytosis. We herein propose that the effects of colchicine in the experimental conditions of this study would be largely reversible at 24 hours. At this time, structural, ultrastructural and biochemical features were similar to those of controls. PMID:11885456

  17. Effect of Different Psychoactive Substances on Serum Biochemical Parameters

    PubMed Central

    Sanli, Dilek Beker; Bilici, Rabia; Suner, Ozgur; Citak, Serhat; Kartkaya, Kazim; Mutlu, Fezan Sahin

    2015-01-01

    Background: Psychoactive substances affect mainly central nervous system and brain function causing changes in behavior. Objectives: The purpose of this study was to determine the effects of different psychoactive substances on serum biochemical parameters. Patients and Methods: The study included 324 drug dependents, and 69 controls. The patient group was determined according to DSM-IV (The diagnostic and statistical manual of mental disorders, fourth edition) criteria. All patients and control subjects were tested for routine biochemical parameters and urine toxicology parameters for psychoactive substance use. Cases and controls with accompanying diseases like diabetes, cancer, metabolic disorders etc. are excluded from the study. Moreover, an association between urine toxicology results and changes in biochemical parameters was evaluated for statistical significance. Results: There was a statistically significant difference in the Gamma-Glutamyl Transferase (GGT), uric acid, creatinine, urea, albumin, Aspartate Aminotransferase (AST) medians between the dependent and control groups (P < 0.05). We found a statistically significant difference in sodium and albumin levels between the opium-dependent and control groups (P < 0.05). In the benzodiazepin dependent group, we found a significant difference in GGT, urea, glucose, sodium, T protein, and AST levels (P < 0.05). Moreover, a statistically significant difference was observed in triglyceride and GGT levels between the ethyl glucuronide and control groups (P < 0.05). Conclusions: In psychoactive substance dependents, serum routine biochemistry parameters can be used to predict the need for intensive monitoring and treatment programs. PMID:26405680

  18. 40 CFR 180.1127 - Biochemical pesticide plant floral volatile attractant compounds: cinnamaldehyde, cinnamyl...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticide plant floral... From Tolerances § 180.1127 Biochemical pesticide plant floral volatile attractant compounds... biochemical pesticide plant floral volatile attractant compounds: cinnamaldehyde, cinnamyl alcohol,...

  19. 40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070 Biochemical pesticides product performance data requirements. Product performance data must be developed...

  20. Discovering Reliable Sources of Biochemical Thermodynamic Data to Aid Students' Understanding

    ERIC Educational Resources Information Center

    Me´ndez, Eduardo; Cerda´, María F.

    2016-01-01

    Students of physical chemistry in biochemical disciplines need biochemical examples to capture the need, not always understood, of a difficult area in their studies. The use of thermodynamic data in the chemical reference state may lead to incorrect interpretations in the analysis of biochemical examples when the analysis does not include relevant…

  1. 40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070 Biochemical pesticides product performance data requirements. Product performance data must be developed...

  2. 40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides residue data... (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2040 Biochemical pesticides residue data requirements table. (a) General. Sections 158.100 through 158.130 describe how to...

  3. 40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070 Biochemical pesticides product performance data requirements. Product performance data must be developed...

  4. 40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070 Biochemical pesticides product performance data requirements. Product performance data must be developed...

  5. 40 CFR 158.2070 - Biochemical pesticides product performance data requirements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2070 Biochemical pesticides product performance data requirements. Product performance data must be developed...

  6. Short-term effects of different organic amendments on soil chemical, biochemical and biological indicators

    NASA Astrophysics Data System (ADS)

    Mondelli, Donato; Aly, Adel; Yirga Dagnachew, Ababu; Piscitelli, Lea; Dumontet, Stefano; Miano, Teodoro

    2014-05-01

    The limited availability of animal manure and the high cost of good quality compost lead to difficult soil quality management under organic agriculture. Therefore, it is important to find out alternative organic soil amendments and more flexible strategies that are able to sustain crop productivity and maintain and enhance soil quality. A three years study was carried out in the experimental fields of the Mediterranean Agronomic Institute of Bari located in Valenzano, Italy. The main objective of this research is to investigate the effects of different fertility management strategies on soil quality in order to estimate the role of innovative matrices for their use in organic farming. The experiment consists of seven treatments applied to a common crop rotation. The treatments include alternative organic amendments (1- olive mill wastewater OMW, 2- residues of mushroom cultivation MUS, 3- coffee chaff COF), common soil amendments (4- compost COM, 5- faba bean intercropping LEG, 6- cow manure - MAN) and as a reference treatment (7- mineral fertilizer COV). The soil quality was assessed before and after the application of the treatments, through biological (microbial biomass carbon and nitrogen, soil respiration and metabolic quotient), biochemical (soil enzymatic activities: β-glucosidase, alkaline phospatase, urease, fluorescein diacetate (FDA) hydrolysis), and chemical (pH, soil organic carbon, soil organic matter, total nitrogen, available phosphorous, exchangeable potassium, dissolved organic carbon and total dissolved nitrogen) indicators. Based on the results obtained after the second year, all treatments were able to improve various soil chemical parameters as compared to mineral fertilizer. The incorporation of COF and OMW seemed to be more effective in improving soil total N and exchangeable K, while MAN significantly increased available P. All the amendments enhance dissolved organic C, soil respiration, microbial biomass and metabolic quotient as

  7. Biochemical characterization of Arabidopsis APYRASE family reveals their roles in regulating endomembrane NDP/NMP homoeostasis.

    PubMed

    Chiu, Tsan-Yu; Lao, Jeemeng; Manalansan, Bianca; Loqué, Dominique; Roux, Stanley J; Heazlewood, Joshua L

    2015-11-15

    Plant apyrases are nucleoside triphosphate (NTP) diphosphohydrolases (NTPDases) and have been implicated in an array of functions within the plant including the regulation of extracellular ATP. Arabidopsis encodes a family of seven membrane bound apyrases (AtAPY1-7) that comprise three distinct clades, all of which contain the five conserved apyrase domains. With the exception of AtAPY1 and AtAPY2, the biochemical and the sub-cellular characterization of the other members are currently unavailable. In this research, we have shown all seven Arabidopsis apyrases localize to internal membranes comprising the cis-Golgi, endoplasmic reticulum (ER) and endosome, indicating an endo-apyrase classification for the entire family. In addition, all members, with the exception of AtAPY7, can function as endo-apyrases by complementing a yeast double mutant (Δynd1Δgda1) which lacks apyrase activity. Interestingly, complementation of the mutant yeast using well characterized human apyrases could only be accomplished by using a functional ER endo-apyrase (NTPDase6), but not the ecto-apyrase (NTPDase1). Furthermore, the substrate specificity analysis for the Arabidopsis apyrases AtAPY1-6 indicated that each member has a distinct set of preferred substrates covering various NDPs (nucleoside diphosphates) and NTPs. Combining the biochemical analysis and sub-cellular localization of the Arabidopsis apyrases family, the data suggest their possible roles in regulating endomembrane NDP/NMP (nucleoside monophosphate) homoeostasis.

  8. Reverse engineering of biochemical equations from time-course data by means of genetic programming.

    PubMed

    Sugimoto, Masahiro; Kikuchi, Shinichi; Tomita, Masaru

    2005-05-01

    Increased research aimed at simulating biological systems requires sophisticated parameter estimation methods. All current approaches, including genetic algorithms, need pre-existing equations to be functional. A generalized approach to predict not only parameters but also biochemical equations from only observable time-course information must be developed and a computational method to generate arbitrary equations without knowledge of biochemical reaction mechanisms must be developed. We present a technique to predict an equation using genetic programming. Our technique can search topology and numerical parameters of mathematical expression simultaneously. To improve the search ability of numeric constants, we added numeric mutation to the conventional procedure. As case studies, we predicted two equations of enzyme-catalyzed reactions regarding adenylate kinase and phosphofructokinase. Our numerical experimental results showed that our approach could obtain correct topology and parameters that were close to the originals. The mean errors between given and simulation-predicted time-courses were 1.6 x 10(-5)% and 2.0 x 10(-3)%, respectively. Our equation prediction approach can be applied to identify metabolic reactions from observable time-courses.

  9. Official Positions for FRAX® clinical regarding biochemical markers from Joint Official Positions Development Conference of the International Society for Clinical Densitometry and International Osteoporosis Foundation on FRAX®.

    PubMed

    McCloskey, Eugene V; Vasikaran, Samuel; Cooper, Cyrus

    2011-01-01

    The best indirect evidence that increased bone turnover contributes to fracture risk is the fact that most of the proven therapies for osteoporosis are inhibitors of bone turnover. The evidence base that we can use biochemical markers of bone turnover in the assessment of fracture risk is somewhat less convincing. This relates to natural variability in the markers, problems with the assays, disparity in the statistical analyses of relevant studies and the independence of their contribution to fracture risk. More research is clearly required to address these deficiencies before biochemical markers might contribute a useful independent risk factor for inclusion in FRAX(®).

  10. A comparison of variant theories of intact biochemical systems. I. Enzyme-enzyme interactions and biochemical systems theory.

    PubMed

    Sorribas, A; Savageau, M A

    1989-06-01

    The need for a well-structured theory of intact biochemical systems becomes increasingly evident as one attempts to integrate the vast knowledge of individual molecular constituents, which has been expanding for several decades. In recent years, several apparently different approaches to the development of such a theory have been proposed. Unfortunately, the resulting theories have not been distinguished from each other, and this has led to considerable confusion with numerous duplications and rediscoveries. Detailed comparisons and critical tests of alternative theories are badly needed to reverse these unfortunate developments. In this paper we (1) characterize a specific system involving enzyme-enzyme interactions for reference in comparing alternative theories, and (2) analyze the reference system by applying the explicit S-system variant within biochemical systems theory (BST), which represents a fundamental framework based upon the power-law formalism and includes several variants. The results provide the first complete and rigorous numerical analysis within the power-law formalism of a specific biochemical system and further evidence for the accuracy of the explicit S-system variant within BST. This theory is shown to represent enzyme-enzyme interactions in a systematically structured fashion that facilitates analysis of complex biochemical systems in which these interactions play a prominent role. This representation also captures the essential character of the underlying nonlinear processes over a wide range of variation (on average 20-fold) in the independent variables of the system. In the companion paper in this issue the same reference system is analyzed by other variants within BST as well as by two additional theories within the same power-law formalism--flux-oriented and metabolic control theories. The results show how all these theories are related to one another.

  11. [Biochemical markers of bone remodeling: pre-analytical variations and guidelines for their use. SFBC (Société Française de Biologie Clinique) Work Group. Biochemical markers of bone remodeling].

    PubMed

    Garnero, P; Bianchi, F; Carlier, M C; Genty, V; Jacob, N; Kamel, S; Kindermans, C; Plouvier, E; Pressac, M; Souberbielle, J C

    2000-01-01

    Biochemical markers of bone turnover have been developed over the past 20 years that are more specific for bone tissue than conventional ones such as total alkaline phosphatase and urinary hydroxyproline. They have been widely used in clinical research and in clinical trials of new therapies as secondary end points of treatment efficacy. Most of the interest has been devoted to their use in postmenopausal osteoporosis, a condition characterized by subtle modifications of bone metabolism that cannot be detected readily by conventional markers of bone turnover. Although several recent studies have suggested that biochemical markers may be used for the management of the individual patient in routine clinical practice, this has not been clearly defined and is a matter of debate. Because of the crucial importance to clarify this issue, the Société Francaise de Biologie Clinique prompted an expert committee to summarize the available data and to make recommendations. The following paper includes a review on the biochemical and analytical aspects of the markers of bone formation and resorption and on the sources of variability such as sex, age, menstrual cycle, pregnancy and lactation, physical activity, seasonal variation and effects of diseases and treatments. We will also describe the effects of pre-analytical factors on the measurements of the different markers. Finally based on that review, we will make practical recommendations for the use of these markers in order to minimize the variability of the measurements and improve the clinical interpretation of the data.

  12. A new trend to determine biochemical parameters by quantitative FRET assays

    PubMed Central

    Liao, Jia-yu; Song, Yang; Liu, Yan

    2015-01-01

    Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research because it can determine molecule or particle interactions within a range of 1–10 nm. The sensitivity and efficiency of FRET strongly depend on the distance between the FRET donor and acceptor. Historically, FRET assays have been used to quantitatively deduce molecular distances. However, another major potential application of the FRET assay has not been fully exploited, that is, the use of FRET signals to quantitatively describe molecular interactive events. In this review, we discuss the use of quantitative FRET assays for the determination of biochemical parameters, such as the protein interaction dissociation constant (Kd), enzymatic velocity (kcat) and Km. We also describe fluorescent microscopy-based quantitative FRET assays for protein interaction affinity determination in cells as well as fluorimeter-based quantitative FRET assays for protein interaction and enzymatic parameter determination in solution. PMID:26567729

  13. A Computational Model of Cell Migration in Response to Biochemical Diffusion

    SciTech Connect

    Dexter, Nicholas C; Kruse, Kara L; Nutaro, James J; Ward, Richard C

    2009-01-01

    The Computational Sciences and Engineering Division of the Oak Ridge National Laboratory is partnering with the University of Tennessee Graduate School of Medicine to design a computational model describing various factors related to the development of intimal hyperplasia (IH) in response to arterial injury. This research focuses on modeling the chemotactic and haptotactic processes that stimulate vascular smooth muscle cell migration into the intima. A hybrid discrete-continuous mathematical model of cell migration in response to biochemical diffusion was developed in C++. Chemoattractant diffusion is modeled as a continuous partial differential equation, whereas migration of the cells is modeled as a series of discrete events. Results obtained from the discrete state model for cell migration agree with those obtained from Boyden chamber experiments.

  14. Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals

    PubMed Central

    Su, Fei; Xu, Ping

    2014-01-01

    Microbial strains with high substrate efficiency and excellent environmental tolerance are urgently needed for the production of platform bio-chemicals. Bacillus coagulans has these merits; however, little genetic information is available about this species. Here, we determined the genome sequences of five B. coagulans strains, and used a comparative genomic approach to reconstruct the central carbon metabolism of this species to explain their fermentation features. A novel xylose isomerase in the xylose utilization pathway was identified in these strains. Based on a genome-wide positive selection scan, the selection pressure on amino acid metabolism may have played a significant role in the thermal adaptation. We also researched the immune systems of B. coagulans strains, which provide them with acquired resistance to phages and mobile genetic elements. Our genomic analysis provides comprehensive insights into the genetic characteristics of B. coagulans and paves the way for improving and extending the uses of this species. PMID:24473268

  15. Toward better understanding of postharvest deterioration: biochemical changes in stored cassava (Manihot esculenta Crantz) roots.

    PubMed

    Uarrota, Virgílio Gavicho; Nunes, Eduardo da Costa; Peruch, Luiz Augusto Martins; Neubert, Enilto de Oliveira; Coelho, Bianca; Moresco, Rodolfo; Domínguez, Moralba Garcia; Sánchez, Teresa; Meléndez, Jorge Luis Luna; Dufour, Dominique; Ceballos, Hernan; Becerra Lopez-Lavalle, Luis Augusto; Hershey, Clair; Rocha, Miguel; Maraschin, Marcelo

    2016-05-01

    Food losses can occur during production, postharvest, and processing stages in the supply chain. With the onset of worldwide food shortages, interest in reducing postharvest losses in cassava has been increasing. In this research, the main goal was to evaluate biochemical changes and identify the metabolites involved in the deterioration of cassava roots. We found that high levels of ascorbic acid (AsA), polyphenol oxidase (PPO), dry matter, and proteins are correlated with overall lower rates of deterioration. On the other hand, soluble sugars such as glucose and fructose, as well as organic acids, mainly, succinic acid, seem to be upregulated during storage and may play a role in the deterioration of cassava roots. Cultivar Branco (BRA) was most resilient to postharvest physiological deterioration (PPD), while Oriental (ORI) was the most susceptible. Our findings suggest that PPO, AsA, and proteins may play a distinct role in PPD delay.

  16. Toward better understanding of postharvest deterioration: biochemical changes in stored cassava (Manihot esculenta Crantz) roots.

    PubMed

    Uarrota, Virgílio Gavicho; Nunes, Eduardo da Costa; Peruch, Luiz Augusto Martins; Neubert, Enilto de Oliveira; Coelho, Bianca; Moresco, Rodolfo; Domínguez, Moralba Garcia; Sánchez, Teresa; Meléndez, Jorge Luis Luna; Dufour, Dominique; Ceballos, Hernan; Becerra Lopez-Lavalle, Luis Augusto; Hershey, Clair; Rocha, Miguel; Maraschin, Marcelo

    2016-05-01

    Food losses can occur during production, postharvest, and processing stages in the supply chain. With the onset of worldwide food shortages, interest in reducing postharvest losses in cassava has been increasing. In this research, the main goal was to evaluate biochemical changes and identify the metabolites involved in the deterioration of cassava roots. We found that high levels of ascorbic acid (AsA), polyphenol oxidase (PPO), dry matter, and proteins are correlated with overall lower rates of deterioration. On the other hand, soluble sugars such as glucose and fructose, as well as organic acids, mainly, succinic acid, seem to be upregulated during storage and may play a role in the deterioration of cassava roots. Cultivar Branco (BRA) was most resilient to postharvest physiological deterioration (PPD), while Oriental (ORI) was the most susceptible. Our findings suggest that PPO, AsA, and proteins may play a distinct role in PPD delay. PMID:27247771

  17. Sensors, Volume 3, Part II, Chemical and Biochemical Sensors Part II

    NASA Astrophysics Data System (ADS)

    Göpel, Wolfgang; Jones, T. A.; Kleitz, Michel; Lundström, Ingemar; Seiyama, Tetsuro

    1997-06-01

    'Sensors' is the first self-contained series to deal with the whole area of sensors. It describes general aspects, technical and physical fundamentals, construction, function, applications and developments of the various types of sensors. This is the second of two volumes focusing on chemical and biochemical sensors. It includes a detailed description of biosensors which often make use of transducer properties of the basic sensors and usually have additional biological components. This volume provides a unique overview of the applications, the possibilities and limitations of sensors in comparison with conventional instrumentation in analytical chemistry. Specific facettes of applications are presented by specialists from different fields including environmental, biotechnological, medical, or chemical process control. This book is an indispensable reference work for both specialits and newcomers, researchers and developers.

  18. Data on biochemical indexes of HFD-fed mice treatment with metformin or resveratrol.

    PubMed

    Zhao, Wenjun; Li, Aiyun; Feng, Xin; Hou, Ting; Liu, Kang; Liu, Baolin; Zhang, Ning

    2016-09-01

    To investigate the changes of physiological and biochemical indexes, male mice were fed a regular diet or short time high fat diet (HFD) for 10 days with oral administration of saline, metformin, resveratrol, or injected intraperitoneally (ip) with digoxin respectively every day. Food intake and body weight were recorded simultaneously. Blood was collected after mice were sacrificed and then tested with commercial kits. The data manifested that metformin and resveratrol only ameliorate free fatty acids and glycerol in HFD-fed mice. Data interpretation of this part can be found in the research article "Metformin and resveratrol ameliorate muscle insulin resistance through preventing lipolysis and inflammation in hypoxic adipose tissue" (Zhao et al.,) [1]. PMID:27547796

  19. Biochemical basis of drought tolerance in hybrid Populus grown under field production conditions. CRADA final report

    SciTech Connect

    Tschaplinski, T.J.; Tuskan, G.A.; Wierman, C.

    1997-04-01

    The purpose of this cooperative effort was to assess the use of osmotically active compounds as molecular selection criteria for drought tolerance in Populus in a large-scale field trial. It is known that some plant species, and individuals within a plant species, can tolerate increasing stress associated with reduced moisture availability by accumulating solutes. The biochemical matrix of such metabolites varies among species and among individuals. The ability of Populus clones to tolerate drought has equal value to other fiber producers, i.e., the wood products industry, where irrigation is used in combination with other cultural treatments to obtain high dry weight yields. The research initially involved an assessment of drought stress under field conditions and characterization of changes in osmotic constitution among the seven clones across the six moisture levels. The near-term goal was to provide a mechanistic basis for clonal differences in productivity under various irrigation treatments over time.

  20. Hematologic and Biochemical Biologic Variation in Laboratory Cats.

    PubMed

    Trumel, Catherine; Monzali, Céline; Geffré, Anne; Concordet, Didier V; Hourqueig, Louise; Braun, Jean-Pierre D; Bourgès-Abella, Nathalie H

    2016-01-01

    The biologic variation associated with a clinical pathology result is important to consider before reference intervals (RI) are used. Most available RI are population-based RI, in which the analytical variability, interindividual variability, and intraindividual variability are confounded. In addition, when the intraindividual variability is considerably less than the interindividual variability, a population-based RI is insufficiently sensitive to detect changes in a subject over time. Here we determined the biologic variation and reference change value (RCV) of hematologic and biochemical variables in laboratory cats. Blood specimens from 14 (7 females and 7 males) overnight-fasted laboratory cats sampled 7 times (days 1, 2, 7, 14, 31, 42, and 100) were analyzed regarding hematology and biochemistry variables. For each variable, analytical, intraindividual, and interindividual coefficients of variation were estimated prior to calculation of the index of individuality and the RCV. RBC variables (count, Hgb, Hct, MCV, MCH, MCHC, and RBC distribution width) and 5 biochemical analytes (cholesterol, creatinine, triglycerides, ALP, and calcium) exhibited marked individuality, therefore indicating that subject-based reference intervals or RCV would be preferable when monitoring these variables in laboratory cats. Population-based RI were shown to be adequate for glucose and sodium, and both types of population and individual RI were similarly efficient for albumin, total protein, urea, ALT, AST, creatine kinase, chloride, carbon dioxide, iron, magnesium, inorganic phosphate, and potassium and reticulocyte, WBC, neutrophil, lymphocyte, monocyte, eosinophil, and platelet counts. The RCV determined in the present study provide a valuable tool for monitoring hematologic and biochemical variables in healthy laboratory cats. PMID:27657703

  1. Biochemical thermodynamics and rapid-equilibrium enzyme kinetics.

    PubMed

    Alberty, Robert A

    2010-12-30

    Biochemical thermodynamics is based on the chemical thermodynamics of aqueous solutions, but it is quite different because pH is used as an independent variable. A transformed Gibbs energy G' is used, and that leads to transformed enthalpies H' and transformed entropies S'. Equilibrium constants for enzyme-catalyzed reactions are referred to as apparent equilibrium constants K' to indicate that they are functions of pH in addition to temperature and ionic strength. Despite this, the most useful way to store basic thermodynamic data on enzyme-catalyzed reactions is to give standard Gibbs energies of formation, standard enthalpies of formation, electric charges, and numbers of hydrogen atoms in species of biochemical reactants like ATP. This makes it possible to calculate standard transformed Gibbs energies of formation, standard transformed enthalpies of formation of reactants (sums of species), and apparent equilibrium constants at desired temperatures, pHs, and ionic strengths. These calculations are complicated, and therefore, a mathematical application in a computer is needed. Rapid-equilibrium enzyme kinetics is based on biochemical thermodynamics because all reactions in the mechanism prior to the rate-determining reaction are at equilibrium. The expression for the equilibrium concentration of the enzyme-substrate complex that yields products can be derived by applying Solve in a computer to the expressions for the equilibrium constants in the mechanism and the conservation equation for enzymatic sites. In 1979, Duggleby pointed out that the minimum number of velocities of enzyme-catalyzed reactions required to estimate the values of the kinetic parameters is equal to the number of kinetic parameters. Solve can be used to do this with steady-state rate equations as well as rapid-equilibrium rate equations, provided that the rate equation is a polynomial. Rapid-equilibrium rate equations can be derived for complicated mechanisms that involve several reactants

  2. [Biochemical diagnostics in acute pancreatitis recognition and outcome predicition].

    PubMed

    Olczyk, Paweł; Kozma, Ewa M; Olczyk, Krystyna; Komosińska-Vassev, Katarzyna

    2004-01-01

    Acute pancreatitis (AP) is a common disease associated with an improper activation of pancreatic zymogens leading to autodigestion of the gland and if excessive--to multiple organ dysfunction. Acute necrotizing pancreatitis manifested by 20% of patients with acute pancreatitis is a life threatening disorder requiring subsequent management in intensive care unit. Unfortunately, none of biochemical tests presently used for laboratory assessment of acute pancreatitis at the early stage of the disease is able to estimate accurately: diagnosis, etiology and severity. At present, diagnosis of acute pancreatitis is based on evaluation of serum amylase and lipase activity due to easy availability and simplicity of these enzymatic tests. Low specificity of the mentioned enzymes resulted in studies concerning pancreatic isoamylase, elastase-1, chymotrypsine, procarboxy-peptidase B, trypsinogen-2 and immunoreactive trypsinogen usefulness in the laboratory diagnosis of AP. The prediction of severity in acute pancreatitis using multifactorial scoring systems is cumbersome especially due to their complexity. On the other hand the biochemical method of choice, estimation of serum C reactive protein, is useless in the early phase of disease. Unfortunately, the computed tomography--the most accurate method in severity assessing--is not always available. Recent studies have brought some progress in severity predicting, such as phospholipase A2, cellular immunity markers, cytokines, activation peptides of trypsinogen and carboxypeptidase B, procalcitonine, pancreatitis associated protein and serum amyloid A. All these newly introduced biochemical methods allow to look optimistically into the future of laboratory diagnostics of the acute pancreatitis believing that the problem of diagnosing and predicting the AP severity will be solved. PMID:15850341

  3. [Biochemical diagnostics in acute pancreatitis recognition and outcome predicition].

    PubMed

    Olczyk, Paweł; Kozma, Ewa M; Olczyk, Krystyna; Komosińska-Vassev, Katarzyna

    2004-01-01

    Acute pancreatitis (AP) is a common disease associated with an improper activation of pancreatic zymogens leading to autodigestion of the gland and if excessive--to multiple organ dysfunction. Acute necrotizing pancreatitis manifested by 20% of patients with acute pancreatitis is a life threatening disorder requiring subsequent management in intensive care unit. Unfortunately, none of biochemical tests presently used for laboratory assessment of acute pancreatitis at the early stage of the disease is able to estimate accurately: diagnosis, etiology and severity. At present, diagnosis of acute pancreatitis is based on evaluation of serum amylase and lipase activity due to easy availability and simplicity of these enzymatic tests. Low specificity of the mentioned enzymes resulted in studies concerning pancreatic isoamylase, elastase-1, chymotrypsine, procarboxy-peptidase B, trypsinogen-2 and immunoreactive trypsinogen usefulness in the laboratory diagnosis of AP. The prediction of severity in acute pancreatitis using multifactorial scoring systems is cumbersome especially due to their complexity. On the other hand the biochemical method of choice, estimation of serum C reactive protein, is useless in the early phase of disease. Unfortunately, the computed tomography--the most accurate method in severity assessing--is not always available. Recent studies have brought some progress in severity predicting, such as phospholipase A2, cellular immunity markers, cytokines, activation peptides of trypsinogen and carboxypeptidase B, procalcitonine, pancreatitis associated protein and serum amyloid A. All these newly introduced biochemical methods allow to look optimistically into the future of laboratory diagnostics of the acute pancreatitis believing that the problem of diagnosing and predicting the AP severity will be solved.

  4. Biochemical and Clinical Profile in Type 2 Diabetics with Depression

    PubMed Central

    Bodi, Akhil Venkata; Sudagani, Jaidev

    2016-01-01

    Introduction There were 72 million adults with Diabetes Mellitus (DM) in 2013 in the South East Asian region of which India is a part. This figure is expected to rise to more than 123 million by 2035. Some studies have also shown that there is an increased risk of depression in subjects with Type 2 Diabetes Mellitus (T2DM). The present study is an attempt to decipher whether there is any difference in the metabolic and clinical profile between patients having T2DM with depression and without depression. Aim To study the clinical and biochemical profile of subjects with T2DM and depression and compare a non-depressed diabetic cohort on the same parameters. Materials and Methods The cross-sectional study was conducted at a tertiary care teaching hospital in rural Andhra Pradesh. Patients with T2DM who fulfilled the inclusion and exclusion criteria and attending the outpatient clinic of the General Medicine department were the subjects of this study. The subjects with T2DM were categorized as depressed or non-depressed after administering the Patient Health Questionnare-9. Out of them 30 subjects with depression and 30 without depression were selected. Samples for blood were collected and analysed for glucose, urea, creatinine, lipid profile and glycated haemoglobin. Urine micro protein was estimated. Anthropometric measurements, blood pressure and chronic complications were recorded. Results The two groups were similar on most of the socio-demographic parameters, biochemical and many of the clinical parameters like age, waist circumference, glycated haemoglobin, lipid profile and insulin use. The Chi-square test for association between the categorical variables like use of insulin, gender predilection, exercise and complications with depression were not significant. Conclusion The study did not show any significant difference between the two groups in terms of the biochemical and clinical profile. PMID:27656433

  5. Synchronization in Biochemical Substance Exchange Between Two Cells

    NASA Astrophysics Data System (ADS)

    Mihailović, Dragutin T.; Balaž, Igor

    In this paper, Mihailović et al. [Mod. Phys. Lett. B 25 (2011) 2407-2417] introduce a simplified model of cell communication in a form of coupled difference logistic equations. Then we investigated stability of exchange of signaling molecules under variability of internal and external parameters. However, we have not touched questions about synchronization and effect of noise on biochemical substance exchange between cells. In this paper, we consider synchronization in intercellular exchange in dependence of environmental and cell intrinsic parameters by analyzing the largest Lyapunov exponent, cross sample entropy and bifurcation maps.

  6. Biochemical properties of ricin in immature castor seed.

    PubMed

    Chakravartula, Srinivas V S; Guttarla, Nagaraj

    2008-05-10

    The biochemical properties of ricin at different stages of seed i.e. from immature to mature seed were studied. Hemagglutination, SDS-PAGE and UV-spectrometry studies showed total absence of RCA protein in the immature seed. Interestingly, ricin extract on SDS-PAGE showed only one protein band with a molecular weight of 29,000 dalton corresponding to the molecular weight of A chain of ricin. Our results have shown that at immature seed level only the toxic moiety of ricin (A chain) is being synthesized first and gradually the RCA and B chain of ricin. PMID:18569697

  7. Biochemical and electrophysiological characteristics of mammalian GABA receptors.

    PubMed

    Enna, S J; Gallagher, J P

    1983-01-01

    The concept that GABA is a neurotransmitter in the mammalian CNS is supported by both electrophysiological and biochemical data. Whereas the electrophysiological studies are essential for demonstrating a specific functional response to GABA, the biochemical approach is useful for characterizing the molecular properties of this site. As a result of these studies the concept of the GABA receptor has progressed from a simple model of a single recognition site associated with a chloride channel to a more complex structure having a variety of interacting components. Thus, both electrophysiological and biochemical data support the existence of at least two pharmacologically distinct types of GABA receptors, based on the sensitivity to bicuculline. Also, anatomically, there appear to be two different types of receptors, those located postsynaptically on the soma or dendrites of a neighboring cell and those found presynaptically on GABAergic and other neurotransmitter terminals. From biochemical studies it appears that the GABA receptor may be composed of at least three distinct interacting components. One of these, the recognition site, may exist in two conformations, with one preferring agonists and the other having a higher affinity for antagonists. Ion channels may be considered a second component, with some of these regulating the passage of chloride ion, whereas others may be associated with calcium transport. The third major element of GABA receptors appears to be a benzodiazepine recognition site, although only a certain population of GABA receptors may be endowed with this property. In addition to these, the GABA receptor complex appears to contain substances that modulate the recognition site by influencing the availability of higher affinity binding proteins. It would appear therefore that changes affecting any one of these constituents can influence the characteristics of the others. While increasing the complexity of the system, this arrangement makes for a

  8. Morphological and biochemical characteristics of bacterial isolates degrading crude oil

    SciTech Connect

    Janiyani, K.L.; Wate, S.R.; Joshi, S.R. )

    1993-01-01

    A mixed bacterial culture developed by soil enrichment procedure using crude oil as a substrate was screened for individual bacterial species. Studies on morphological and biochemical characterization of eleven dominant bacterial isolates revealed that most of the cultures were gram-negative motile rods, and were catalase and oxidase positive. It was observed that four bacterial isolates were efficient in degrading pure hydrocarbons, model petroleum and crude oil. Identification of dominant bacterial cultures confirmed the isolates as Pseudomonas stutzeri, Pseudomonas aeruginoss, Bacillus cereus and Pseudomonas fluorescens. 28 refs., 8 tabs.

  9. Biochemical Effects of Ozone on Asthma During Postnatal Development

    PubMed Central

    Auten, Richard L.; Foster, W. Michael

    2011-01-01

    Background Ozone exposure during early life has the potential to contribute to the development of asthma as well as to exacerbate underlying allergic asthma. Scope of Review Developmentally regulated aspects of sensitivity to ozone exposure and downstream biochemical and cellular responses. Major Conclusions Developmental differences in antioxidant defense responses, respiratory physiology, and vulnerabilities to cellular injury during particular developmental stages all contribute to disparities in the health effects of ozone exposure between children and adults. General Significance Ozone exposure has the capacity to affect multiple aspects of the “effector arc” of airway hyperresponsiveness, ranging from initial epithelial damage and neural excitation to neural reprogramming during infancy. PMID:21276837

  10. Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production

    PubMed Central

    Lai, Martin C.; Lan, Ethan I.

    2015-01-01

    Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central metabolism and rerouting carbon flux towards desirable compound production, cyanobacteria are engineered to directly convert CO2 into various chemicals. This review discusses the diversity of bioproducts synthesized by engineered cyanobacteria, the metabolic pathways used, and the current engineering strategies used for increasing their titers. PMID:26516923

  11. Laser induced fluorescence of biochemical for UV LIDAR application.

    PubMed

    Gupta, L; Sharma, R C; Razdan, A K; Maini, A K

    2014-05-01

    Laser induced fluorescence spectroscopy in the ultraviolet regime has been used for the detection of biochemical through a fiber coupled CCD detector from a distance of 2 m. The effect of concentration and laser excitation energy on the fluorescence spectra of nicotinamide adenine dinucleotide (NADH) has been investigated. The signature fluorescence peak of NADH was centred about 460 nm. At lower concentration Raman peak centred at 405 nm was also observed. The origin of this peak has been discussed. Detection limit with the proposed set up is found to be 1 ppm.

  12. [Correlation of some biochemical and coagulological parameters in carotid atherosclerosis].

    PubMed

    Akhvlediani, M V; Vorob'eva, E O; Emukhvari, M G; Sharashidze, N A; Kupreishvili, S B

    2009-11-01

    It has been established positive correlation of the degree of stenosis and intima-media thickness of carotid arteries with the following biochemical parameters: total cholesterol, LDL cholesterol, Apo-B, Lp(a), triglycerides, hs-C-reactive protein(CRP), interleukines (IL-1beta and IL-6), fibrinogen, D-dimers. Negative correlation was stated with respect to HDL cholesterol, Apo-A-1, protein C. Relation between the parameters of the blood lipid spectre, proteins and mediators of inflammation as well as those of hemostasis enables us to approach pathophysiological mechanisms of carotid atherosclerosis, define the processes of inflammation and atherosclerosis.

  13. Fibre optic system for biochemical and microbiological sensing

    NASA Astrophysics Data System (ADS)

    Penwill, L. A.; Slater, J. H.; Hayes, N. W.; Tremlett, C. J.

    2007-07-01

    This poster will discuss state-of-the-art fibre optic sensors based on evanescent wave technology emphasising chemophotonic sensors for biochemical reactions and microbe detection. Devices based on antibody specificity and unique DNA sequences will be described. The development of simple sensor devices with disposable single use sensor probes will be illustrated with a view to providing cost effective field based or point of care analysis of major themes such as hospital acquired infections or bioterrorism events. This presentation will discuss the nature and detection thresholds required, the optical detection techniques investigated, results of sensor trials and the potential for wider commercial application.

  14. Biochemical nature of cellulases from mutants of Trichoderma reesei

    SciTech Connect

    Montenecourt, B.S.; Kelleher, T.J.; Eveleigh, D.E.; Pettersson, L.G.

    1980-01-01

    The cellulases of two new mutants of T. reesei, RUT-NG14 and RUT-C30, have been examined with respect to the separation and biochemical characterization of the various components in the cellulase complex. The cellulase of both mutants has been shown to contain enhanced proportions of a cellobiohydrolase by quantitative immune precipitation. Application of ion-exchange high-pressure liquid chromatography protein separations affords a rapid (30 min) and simple method of separating and comparing cellulase components from potential high-yielding cellulase mutants.

  15. Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production.

    PubMed

    Lai, Martin C; Lan, Ethan I

    2015-01-01

    Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central metabolism and rerouting carbon flux towards desirable compound production, cyanobacteria are engineered to directly convert CO₂ into various chemicals. This review discusses the diversity of bioproducts synthesized by engineered cyanobacteria, the metabolic pathways used, and the current engineering strategies used for increasing their titers. PMID:26516923

  16. Single-molecule detection: applications to ultrasensitive biochemical analysis

    NASA Astrophysics Data System (ADS)

    Castro, Alonso; Shera, E. Brooks

    1995-06-01

    Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

  17. Biochemical and Hematological Evaluations of Bryonia Epigaea Tubers

    PubMed Central

    Sinha, B.N.; Sasmal, D.; Basu, S.P.

    1999-01-01

    Bryonia epigaea (cucurbitaceae) has been evaluated on various inflammatory models in rats in our laboratory. Ana anti-inflammatory drug(s) irrespective of its potency may not be devoid of undesirable effects on biochemical and hematological parameters. Alcoholic extract of Bryonia epigaaea (BE-Extract) at the dose of 50 mg/kg body weight, was administered to rats. Hepatotxic and nephrotoxic effects of BE-Extract were studies by measuring cholesterol, urea, uric acid, SGOT, SGPT and glucose levels in blood. Effects of BE-Extract on RBC count, WBC count, platelet count, hemoglobin content, clotting and bleeding time were also studied. PMID:22556913

  18. Rieger syndrome: a clinical, molecular, and biochemical analysis.

    PubMed

    Amendt, B A; Semina, E V; Alward, W L

    2000-10-01

    Rieger syndrome (RIEG 1; MIM 180500) is an autosomal dominant disorder of morphogenesis. It is a phenotypically heterogeneous disorder characterized by malformations of the eyes, teeth, and umbilicus. RIEG belongs to the Axenfeld-Rieger group of anomalies, which includes Axenfeld anomaly and Rieger anomaly (or Rieger eye malformation), which display ocular features only. Recently, mutations in the homeodomain transcription factor, PITX2, have been shown to be associated with Rieger syndrome. This review discusses the clinical manifestations of Rieger syndrome and how they correlate with the current molecular and biochemical studies on this human disorder. PMID:11092457

  19. Laser induced fluorescence of biochemical for UV LIDAR application.

    PubMed

    Gupta, L; Sharma, R C; Razdan, A K; Maini, A K

    2014-05-01

    Laser induced fluorescence spectroscopy in the ultraviolet regime has been used for the detection of biochemical through a fiber coupled CCD detector from a distance of 2 m. The effect of concentration and laser excitation energy on the fluorescence spectra of nicotinamide adenine dinucleotide (NADH) has been investigated. The signature fluorescence peak of NADH was centred about 460 nm. At lower concentration Raman peak centred at 405 nm was also observed. The origin of this peak has been discussed. Detection limit with the proposed set up is found to be 1 ppm. PMID:24337816

  20. Biochemical and cultural characteristics of invasive Escherichia coli.

    PubMed Central

    Silva, R M; Toledo, M R; Trabulsi, L R

    1980-01-01

    The biochemical characteristics of 97 invasive Escherichia coli strains of different O serogroups were studied. Considered as a group, the behavior of the strains was quite variable. However, none of them decarboxylated lysine and all but seven strains, belonging to the O124 serogroup, were nonmotile. The growth of 25 strains obtained on MacConkey, salmonella-shigella, xylose-lysine-desoxycholate, and Hektoen enteric agars was compared. MacConkey and Hektoen enteric agars yielded the highest average growth for these strains, whereas salmonella-shigella agar had the lowest average counts. PMID:6991526

  1. The rat adequately reflects human responses to exercise in blood biochemical profile: a comparative study

    PubMed Central

    Goutianos, Georgios; Tzioura, Aikaterini; Kyparos, Antonios; Paschalis, Vassilis; Margaritelis, Nikos V; Veskoukis, Aristidis S; Zafeiridis, Andreas; Dipla, Konstantina; Nikolaidis, Michalis G; Vrabas, Ioannis S

    2015-01-01

    Animal models are widely used in biology and the findings of animal research are traditionally projected to humans. However, recent publications have raised concerns with regard to what extent animals and humans respond similar to physiological stimuli. Original data on direct in vivo comparison between animals and humans are scarce and no study has addressed this issue after exercise. We aimed to compare side by side in the same experimental setup rat and human responses to an acute exercise bout of matched intensity and duration. Rats and humans ran on a treadmill at 86% of maximal velocity until exhaustion. Pre and post exercise we measured 30 blood chemistry parameters, which evaluate iron status, lipid profile, glucose regulation, protein metabolism, liver, and renal function. ANOVA indicated that almost all biochemical parameters followed a similar alteration pattern post exercise in rats and humans. In fact, there were only 2/30 significant species × exercise interactions (in testosterone and globulins), indicating different responses to exercise between rats and humans. On the contrary, the main effect of exercise was significant in 15/30 parameters and marginally nonsignificant in other two parameters (copper, P = 0.060 and apolipoprotein B, P = 0.058). Our major finding is that the rat adequately mimics human responses to exercise in those basic blood biochemical parameters reported here. The physiological resemblance of rat and human blood responses after exercise to exhaustion on a treadmill indicates that the use of blood chemistry in rats for exercise physiology research is justified. PMID:25677548

  2. Biochemical process of low level radioactive liquid simulation waste containing detergent

    SciTech Connect

    Kundari, Noor Anis Putra, Sugili; Mukaromah, Umi

    2015-12-29

    Research of biochemical process of low level radioactive liquid waste containing detergent has been done. Thse organic liquid wastes are generated in nuclear facilities such as from laundry. The wastes that are cotegorized as hazard and poison materials are also radioactive. It must be treated properly by detoxification of the hazard and decontamination of the radionuclides to ensure that the disposal of the waste meets the requirement of standard quality of water. This research was intended to determine decontamination factor and separation efficiensies, its kinetics law, and to produce a supernatant that ensured the environmental quality standard. The radioactive element in the waste was thorium with activity of 5.10{sup −5} Ci/m{sup 3}. The radioactive liquid waste which were generated in simulation plant contains detergents that was further processed by aerobic biochemical process using SGB 103 bacteria in a batch reactor equipped with aerators. Two different concentration of samples were processed and analyzed for 212 hours and 183 hours respectively at a room temperature. The product of this process is a liquid phase called as supernatant and solid phase material called sludge. The chemical oxygen demand (COD), biological oxygen demand (BOD), suspended solid (SS), and its alpha activity were analyzed. The results show that the decontamination factor and the separation efficiency of the lower concentration samples are higher compared to the samples with high concentration. Regarding the decontamination factor, the result for 212 hours processing of waste with detergent concentration of 1.496 g/L was 3.496 times, whereas at the detergent concentration of 0.748 g/L was 15.305 times for 183 hours processing. In case of the separation efficiency, the results for both samples were 71.396% and 93.465% respectively. The Bacterial growth kinetics equation follow Monod’s model and the decreasing of COD and BOD were first order with the rate constant of 0

  3. Biochemical process of low level radioactive liquid simulation waste containing detergent

    NASA Astrophysics Data System (ADS)

    Kundari, Noor Anis; Putra, Sugili; Mukaromah, Umi

    2015-12-01

    Research of biochemical process of low level radioactive liquid waste containing detergent has been done. Thse organic liquid wastes are generated in nuclear facilities such as from laundry. The wastes that are cotegorized as hazard and poison materials are also radioactive. It must be treated properly by detoxification of the hazard and decontamination of the radionuclides to ensure that the disposal of the waste meets the requirement of standard quality of water. This research was intended to determine decontamination factor and separation efficiensies, its kinetics law, and to produce a supernatant that ensured the environmental quality standard. The radioactive element in the waste was thorium with activity of 5.10-5 Ci/m3. The radioactive liquid waste which were generated in simulation plant contains detergents that was further processed by aerobic biochemical process using SGB 103 bacteria in a batch reactor equipped with aerators. Two different concentration of samples were processed and analyzed for 212 hours and 183 hours respectively at a room temperature. The product of this process is a liquid phase called as supernatant and solid phase material called sludge. The chemical oxygen demand (COD), biological oxygen demand (BOD), suspended solid (SS), and its alpha activity were analyzed. The results show that the decontamination factor and the separation efficiency of the lower concentration samples are higher compared to the samples with high concentration. Regarding the decontamination factor, the result for 212 hours processing of waste with detergent concentration of 1.496 g/L was 3.496 times, whereas at the detergent concentration of 0.748 g/L was 15.305 times for 183 hours processing. In case of the separation efficiency, the results for both samples were 71.396% and 93.465% respectively. The Bacterial growth kinetics equation follow Monod's model and the decreasing of COD and BOD were first order with the rate constant of 0.01 hour-1.

  4. Serum biochemical analysis to indicate pathogenic risk on mouse Mus musculus exposure to source of drinking water.

    PubMed

    Yun, Shi Feng; Tian, Xiao Yun; Cheng, Shu Pei; Zhang, Yan; Li, Ai Min; Zhang, Li Bo; Zhang, Xu Xiang; Chen, Li; Wu, Bing; Guo, Lian Qin; Shi, Yun Zhong

    2011-07-01

    The 18 biochemical parameters of serum were measured to analyze the pathogenic risks of the Yangtze River Source of Drinking Water in Nanjing area (YZR-SDW-NJ) on mouse Mus musculus for protection of human health in this research. The male mice Mus musculus were sampled and fed with YZR-SDW-NJ for 90 days then the eighteen serum biochemical levels were measured with Automatic Biochemical Analysis/RerLi 600. And the parameter data were treated by One-Way ANOVA statistic approach. The results showed that five parameter levels for the sample group mice were different from those for the control group significantly (0.01 < P or 0.05 < P). Four 4 of the 5 altered parameter levels were decreased including glutamate pyruvate transaminase 38% lower, glutamine-oxaloacetic transaminase 24% lower, triglyceride 76% lower and cystatin C 73% lower, only creatinine level was 26% higher than that in the control group. The data suggest that YZR-SDW-NJ had toxicity on the mouse and the organic pollutants in YZR-SDW-NJ might lead to liver, kidney, cardiovascular and metabolic pathogenic risks on the human beings. The results might be cited as evidence to control pollutants in the source water for the protection of NJ people's health.

  5. Biochemical analysis of the crude extract of Momordica charantia (L.).

    PubMed

    Dar, Ume Kalsoom; Owais, Farah; Ahmad, Manzoor; Rizwani, Ghazala H

    2014-11-01

    Momordica charantia (L.) commonly referred as bitter gourd, karela and balsam pear. Its fruit is used for the treatment of diabetes and related conditions amongst the indigenous populations of Asia, South America, India and East Africa. The study was conducted to find out the biochemical aspects of crude extract of whole fruit of M. charantia including seeds which includes blood test (Hemoglobin, RBC, Total leukocyte count, platelets count, HbA1C (Glycocylated heamoglobin Type A1C)), Lipid profile test and electrolyte balance. Hemoglobin (7.1±0.14), platelets count (827 ×109±1.95), Cholesterol level (111±2), HDL (high density lipoproteins) (20±1.22) at 10mg shows marked increase in values as compared to control. While 25 mg dose shows insignificant result. Electrolyte balance are found significant at 10mg and 25mg except bicarbonates (Na(+¬)=143±1.87, K-=3.45±0.35, Cl(-) =108±1.48). Another important property of M. charantia is the elevation of platelet counts, heamoglobin and specifically high-density lipoproteins (HDL). It also controls cholesterol, triglycerides, HDL, LDL and VLDL at low dosage (10mg). Further studies can be conducted to find out which phytochemical components acts on specific biochemical activity. PMID:26045386

  6. Investigation on energy conversion technology using biochemical reaction elements, 2

    NASA Astrophysics Data System (ADS)

    1994-03-01

    For measures taken for resource/energy and environmental issues, a study is made on utilization of microbial biochemical reaction. As a reaction system using chemical energy, cited is production of petroleum substitution substances and food/feed by CO2 fixation using hydrogen energy and hydrogen bacteria. As to photo energy utilization, regarded as promising are CO2 fixation using photo energy and microalgae, and production of hydrogen and useful carbon compound using photosynthetic organisms. As living organism/electric energy interconversion, cited is the culture of chemoautotrophic bacteria which fix CO2 using electric energy. For enhancing its conversion efficiency, it is important to develop a technology of gene manipulation of the bacteria and a system to use functional biochemical elements adaptable to the electrode reaction. With regard to utilization of the microorganism metabolic function, the paper presents emission of soluble nitrogen in the hydrosphere into the atmosphere using denitrifying bacteria, removal of phosphorus, reduction in environmental pollution caused by heavy metal dilute solutions, and recovery as resources, etc.

  7. The application of information theory to biochemical signaling systems

    PubMed Central

    Rhee, Alex; Cheong, Raymond; Levchenko, Andre

    2012-01-01

    Cell signaling can be thought of fundamentally as an information transmission problem in which chemical messengers relay information about the external environment to the decision centers within a cell. Due to the biochemical nature of cellular signal transduction networks, molecular noise will inevitably limit the fidelity of any messages received and processed by a cell’s signal transduction networks, leaving it with an imperfect impression of its environment. Fortunately, Shannon’s information theory provides a mathematical framework independent of network complexity that can quantify the amount of information that can be transmitted despite biochemical noise. In particular, the channel capacity can be used to measure the maximum number of stimuli a cell can distinguish based upon the noisy responses of its signaling systems. Here, we provide a primer for quantitative biologists that covers fundamental concepts of information theory, highlights several key considerations when experimentally measuring channel capacity, and describes successful examples of the application of information theoretic analysis to biological signaling. PMID:22872091

  8. DNA damaging and biochemical effects of potassium tetraborate

    PubMed Central

    Çelikezen, Fatih Çaglar; Turkez, Hasan; Togar, Basak; Izgi, Mehmet Sait

    2014-01-01

    Potassium tetraborate (PTB) is a product resulting from the controlled reaction of potassium hydroxide, water and boric acid (BA). It is used in many areas of industry such as disinfectant, detergent and treatment of contact lenses. PTB is one of the boron compounds which is most commonly used in many areas of industry although very limited information is available concerning its toxicity. Therefore, in this study, it is aimed to determine genetic and biochemical effects of PTB in human blood cell cultures (n=4). PTB was added into culture tubes at various concentrations (0-1280 µg/ml). Micronucleus (MN) and chromosomal aberration (CA) tests were performed for genotoxic damage influences estimation. In addition, biochemical parameters (total antioxidant capacity (TAC) and total oxidative status (TOS) were examined to determine oxidative effects. The results indicated that all tested concentrations of PTB were found to be non-genotoxic. In addition, low concentrations (1.25, 2.5 and 5 µg/ml) of PTB caused increases of TAC levels. Furthermore, all concentrations of PTB were not changed the TOS levels in cultured human blood cells. Based on these results, in this study it has been reported for the first time that PTB is not genotoxic and it increases the antioxidant capacity in human peripheral blood lymphocytes. PMID:26417271

  9. Hepatic histological alterations and biochemical changes induced by sildenafil overdoses.

    PubMed

    Jarrar, Bashir Mahmoud; Almansour, Mansour Ibrahim

    2015-11-01

    Sildenafil is used for the treatment of erectile dysfunction and is helping millions of men around the world to achieve and maintain a long lasting erection. Fifty healthy male rabbits (Oryctolagus cuniculus) were used in the present study and exposed daily to sildenafil (0, 1, 3, 6, 9 mg/kg) for 5 days per week for 7 weeks to investigate the biochemical changes and alterations in the hepatic tissues induced by this drug overdosing. In comparison with respective control rabbits, sildenafil overdoses elevated significantly (p-value<0.05, ANOVA test) alanine aminotransferase (ALT), aspartate aminotransferase (AST), testosterone, follicular stimulating hormone and total protein, while creatinine and urea were lowered with no significant alteration was observed in uric acid and luteinizing hormone concentration. Also sildenafil provoked hepatocytes nuclear alterations, necrosis, hydropic degeneration, bile duct hyperplasia, Kupffer cells hyperplasia, inflammatory cells infiltration, hepatic vessels congestion and evident partial depletion of glycogen content. The results show that subchronic exposure to sildenafil overdoses exhibits significant biochemical and alterations in the hepatic tissues that might affect the functions of the liver and other vital organs. PMID:26639481

  10. Millisecond-Scale Biochemical Response to Change in Strain

    PubMed Central

    Bickham, Dale C.; West, Timothy G.; Webb, Martin R.; Woledge, Roger C.; Curtin, Nancy A.; Ferenczi, Michael A.

    2011-01-01

    Muscle fiber contraction involves the cyclical interaction of myosin cross-bridges with actin filaments, linked to hydrolysis of ATP that provides the required energy. We show here the relationship between cross-bridge states, force generation, and Pi release during ramp stretches of active mammalian skeletal muscle fibers at 20°C. The results show that force and Pi release respond quickly to the application of stretch: force rises rapidly, whereas the rate of Pi release decreases abruptly and remains low for the duration of the stretch. These measurements show that biochemical change on the millisecond timescale accompanies the mechanical and structural responses in active muscle fibers. A cross-bridge model is used to simulate the effect of stretch on the distribution of actomyosin cross-bridges, force, and Pi release, with explicit inclusion of ATP, ADP, and Pi in the biochemical states and length-dependence of transitions. In the simulation, stretch causes rapid detachment and reattachment of cross-bridges without release of Pi or ATP hydrolysis. PMID:22098743

  11. How spatial heterogeneity shapes multiscale biochemical reaction network dynamics.

    PubMed

    Pfaffelhuber, Peter; Popovic, Lea

    2015-03-01

    Spatial heterogeneity in cells can be modelled using distinct compartments connected by molecular movement between them. In addition to movement, changes in the amount of molecules are due to biochemical reactions within compartments, often such that some molecular types fluctuate on a slower timescale than others. It is natural to ask the following questions: how sensitive is the dynamics of molecular types to their own spatial distribution, and how sensitive are they to the distribution of others? What conditions lead to effective homogeneity in biochemical dynamics despite heterogeneity in molecular distribution? What kind of spatial distribution is optimal from the point of view of some downstream product? Within a spatially heterogeneous multiscale model, we consider two notions of dynamical homogeneity (full homogeneity and homogeneity for the fast subsystem), and consider their implications under different timescales for the motility of molecules between compartments. We derive rigorous results for their dynamics and long-term behaviour, and illustrate them with examples of a shared pathway, Michaelis-Menten enzymatic kinetics and autoregulating feedbacks. Using stochastic averaging of fast fluctuations to their quasi-steady-state distribution, we obtain simple analytic results that significantly reduce the complexity and expedite simulation of stochastic compartment models of chemical reactions.

  12. Applications of biochemical processes in geothermal and other industries

    SciTech Connect

    Premuzic, E.T.; Lin, M.S.; Jin, J.Z.

    1994-06-01

    Laboratory studies aimed at the development of economically and technically feasible, and environmentally acceptable technology for the disposal of geothermal sludges and wastes have led to the development of biochemical processes which meet the above conditions. A pilot-scale plant has been constructed and used to identify process variables and optimize processing conditions. The total process is flexible and can be used in several modes of operation which include (1) solubilization and removal of many metals, including radionuclides, from brines and sludges; (2) selective removal of a few metals; (3) concentration of metals; (4) recovery of metals; and (5) recovery of salts. The end product is a silica-type material which meets regulatory requirements, while the aqueous phase meets drinking water standards and can be reinjected and/or used for irrigation. Preliminary engineering studies of the metal and salt recovery technologies have indicated that significant cost benefits could be obtained by means of combined processing. Recent accomplishments in the development of new biochemical technologies will be discussed in this paper.

  13. In vitro reparative dentin: a biochemical and morphological study.

    PubMed

    Teti, G; Salvatore, V; Ruggeri, A; Manzoli, L; Gesi, M; Orsini, G; Falconi, M

    2013-08-06

    In this study, starting from human dental pulp cells cultured in vitro, we simulated reparative dentinogenesis using a medium supplemented with different odontogenic inductors. The differentiation of dental pulp cells in odontoblast-like cells was evaluated by means of staining, and ultramorphological, biochemical and biomolecular methods. Alizarin red staining showed mineral deposition while transmission electron microscopy revealed a synthesis of extracellular matrix fibers during the differentiation process. Biochemical assays demonstrated that the differentiated phenotype expressed odontoblast markers, such as Dentin Matrix Protein 1 (DMP1) and Dentin Sialoprotein (DSP), as well as type I collagen. Quantitative data regarding the mRNA expression of DMP1, DSP and type I collagen were obtained by Real Time PCR. Immunofluorescence data demonstrated the various localizations of DSP and DMP1 during odontoblast differentiation. Based on our results, we obtained odontoblast-like cells which simulated the reparative dentin processes in order to better investigate the mechanism of odontoblast differentiation, and dentin extracellular matrix deposition and mineralization.

  14. Biochemical and functional characterization of Helicobacter pylori vesicles

    PubMed Central

    Olofsson, Annelie; Vallström, Anna; Petzold, Katja; Tegtmeyer, Nicole; Schleucher, Jürgen; Carlsson, Sven; Haas, Rainer; Backert, Steffen; Wai, Sun Nyunt; Gröbner, Gerhard; Arnqvist, Anna

    2010-01-01

    Helicobacter pylori can cause peptic ulcer disease and/or gastric cancer. Adhesion of bacteria to the stomach mucosa is an important contributor to the vigour of infection and resulting virulence. H. pylori adheres primarily via binding of BabA adhesins to ABO/Lewis b (Leb) blood group antigens and the binding of SabA adhesins to sialyl-Lewis x/a (sLex/a) antigens. Similar to most Gram-negative bacteria, H. pylori continuously buds off vesicles and vesicles derived from pathogenic bacteria often include virulence-associated factors. Here we biochemically characterized highly purified H. pylori vesicles. Major protein and phospholipid components associated with the vesicles were identified with mass spectroscopy and nuclear magnetic resonance. A subset of virulence factors present was confirmed by immunoblots. Additional functional and biochemical analysis focused on the vesicle BabA and SabA adhesins and their respective interactions to human gastric epithelium. Vesicles exhibit heterogeneity in their protein composition, which were specifically studied in respect to the BabA adhesin. We also demonstrate that the oncoprotein, CagA, is associated with the surface of H. pylori vesicles. Thus, we have explored mechanisms for intimate H. pylori vesicle–host interactions and found that the vesicles carry effector-promoting properties that are important to disease development. PMID:20659286

  15. Transient amplification limits noise suppression in biochemical networks

    NASA Astrophysics Data System (ADS)

    Dixon, John; Lindemann, Anika; McCoy, Jonathan H.

    2016-01-01

    Cell physiology is orchestrated, on a molecular level, through complex networks of biochemical reactions. The propagation of random fluctuations through these networks can significantly impact cell behavior, raising challenging questions about how network design shapes the cell's ability to suppress or exploit these fluctuations. Here, drawing on insights from statistical physics, fluid dynamics, and systems biology, we explore how transient amplification phenomena arising from network connectivity naturally limit a biochemical system's ability to suppress small fluctuations around steady-state behaviors. We find that even a simple system consisting of two variables linked by a single interaction is capable of amplifying small fluctuations orders of magnitude beyond the levels predicted by linear stability theory. We also find that adding additional interactions can promote further amplification, even when these interactions implement classic design strategies known to suppress fluctuations. These results establish that transient amplification is an essential factor determining baseline noise levels in stable intracellular networks. Significantly, our analysis is not bound to specific systems or interaction mechanisms: we find that noise amplification is an emergent phenomenon found near steady states in any network containing sufficiently strong interactions, regardless of its form or function.

  16. The human sunburn reaction: histologic and biochemical studies

    SciTech Connect

    Gilchrest, B.A.; Soter, N.A.; Stoff, J.S.; Mihm, M.C. Jr.

    1981-01-01

    The ultraviolet-induced erythema reaction was investigated histologically and biochemically in four subjects, utilizing suction blister aspirates, analyzed for histamine and prostaglandin E2 (PGE2), and Epon-embedded 1-mu skin biopsy sections from control skin and from irradiated skin at intervals for 72 hours after exposure to a Hanovia lamp. Major histologic alterations in the epidermis included dyskeratotic and vacuolated keratinocytes (sunburn cells), and disappearance of Langerhans cells. In the dermis the major changes were vascular, involving both the superficial and deep venular plexuses. Endothelial cell enlargement was first apparent within 30 minutes of irradiation, peaked at 24 hours, and persisted throughout the 72-hour study period. Mast cell degranulation and associated perivenular edema were first apparent at 1 hour and striking at the onset of erythema, 3 to 4 hours postirradiation; edema was absent and mast cells were again normal in number and granule content at 24 hours. Histamine levels rose approximately fourfold above control values immediately after the onset of erythema and returned to baseline within 24 hours. PGE2 levels were statistically elevated even before the onset of erythema and reached approximately 150% of the control value at 24 hours. These data provide the first evidence that histamine may mediate the early phase of the human sunburn reaction and increase our understanding of its complex histologic and biochemical sequelae.

  17. Structure and Biochemical Activities of Escherichia coli MgsA

    SciTech Connect

    Page, Asher N.; George, Nicholas P.; Marceau, Aimee H.; Cox, Michael M.; Keck, James L.

    2012-02-27

    Bacterial 'maintenance of genome stability protein A' (MgsA) and related eukaryotic enzymes play important roles in cellular responses to stalled DNA replication processes. Sequence information identifies MgsA enzymes as members of the clamp loader clade of AAA{sup +} proteins, but structural information defining the family has been limited. Here, the x-ray crystal structure of Escherichia coli MgsA is described, revealing a homotetrameric arrangement for the protein that distinguishes it from other clamp loader clade AAA{sup +} proteins. Each MgsA protomer is composed of three elements as follows: ATP-binding and helical lid domains (conserved among AAA{sup +} proteins) and a tetramerization domain. Although the tetramerization domains bury the greatest amount of surface area in the MgsA oligomer, each of the domains participates in oligomerization to form a highly intertwined quaternary structure. Phosphate is bound at each AAA{sup +} ATP-binding site, but the active sites do not appear to be in a catalytically competent conformation due to displacement of Arg finger residues. E. coli MgsA is also shown to form a complex with the single-stranded DNA-binding protein through co-purification and biochemical studies. MgsA DNA-dependent ATPase activity is inhibited by single-stranded DNA-binding protein. Together, these structural and biochemical observations provide insights into the mechanisms of MgsA family AAA{sup +} proteins.

  18. The propagation approach for computing biochemical reaction networks.

    PubMed

    Henzinger, Thomas A; Mateescu, Maria

    2013-01-01

    We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its next operator propagates mass values through this set of nodes. We propose an approximate implementation of the next operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.

  19. Drug resistance and biochemical characteristics of Salmonella from turkeys.

    PubMed Central

    Poppe, C; Kolar, J J; Demczuk, W H; Harris, J E

    1995-01-01

    A study was conducted to determine the antibiotic resistance and biochemical characteristics of 2690 Salmonella strains belonging to 52 serovars and isolated from environmental and feed samples from 270 turkey flocks in Canada. Resistance of the Salmonella strains to the aminoglycoside antibiotics varied widely; none of the strains were resistant to amikacin, 14.2% were resistant to neomycin, 25.8% were resistant to gentamicin, and 27.7% of the strains were resistant to kanamycin. Most strains (97.6%) were resistant to the aminocyclitol, spectinomycin. Regarding resistance to the beta-lactam antibiotics, 14.3% and 14.4% of the strains were resistant to ampicillin and carbenicillin, respectively, whereas only 5 (0.2%) of the strains were resistant to cephalothin. None of the strains were resistant to the fluoroquinolone ciprofloxacin or to polymyxin B. Resistance to chloramphenicol and nitrofurantoin was found in 2.4% and 7% of the strains, respectively. Only 1.7% of the strains were resistant to the trimethoprimsulfamethoxazole combination, whereas 58.1% were resistant to sulfisoxazole. Thirty-eight percent of the strains were resistant to tetracycline. Salmonella serovars differed markedly in their drug resistance profiles. Biochemical characterization of the Salmonella showed that the S. anatum, S. saintpaul and S. reading serovars could be divided into distinct biotypes. PMID:8548684

  20. Biochemical and pathogenic properties of Shewanella alga and Shewanella putrefaciens.

    PubMed

    Khashe, S; Janda, J M

    1998-03-01

    We characterized 49 strains of Shewanella spp. from clinical (n = 31) and nonhuman (n = 18) sources. Most Shewanella alga organisms (Gilardi biovar 2; Centers for Disease Control and Prevention [CDC] biotype 2) originated from clinical material (92%), failed to produce acid from carbohydrates other than D-ribose, and were biochemically and enzymatically fairly homogeneous. In contrast, Shewanella putrefaciens organisms (Gilardi biovars 1 and 3; CDC biotype 1) were more often associated with nonhuman sources (70%), were able to utilize a number of sugars (sucrose, L-arabinose, and maltose), and were found to exhibit wider variations in biochemical characteristics; three biotypes within S. putrefaciens were detected. Notable differences between the two species in enzymatic activity, determined with the API-ZYM system (bioMérieux, Hazelwood, Mo.), and cellular fatty acid profiles, determined by the MIDI system (Microbial ID Inc., Newark, Del.), were also detected. Pathogenicity studies of mice indicate that S. alga appears to be the more virulent species, possibly due to the production of a hemolytic substance.

  1. Biochemical oxygen demand sensor using Serratia marcescens LSY 4.

    PubMed

    Kim, M N; Kwon, H S

    1999-01-01

    A microbial biochemical oxygen demand (BOD) sensor consisting of Serratia marcescens LSY 4 and an oxygen electrode was prepared for estimation of the biochemical oxygen demand. The response of the BOD sensor was insensitive to pH in the range of pH 6.0-8.0, and the baseline drift of the signal was nearly absent even in unbuffered aqueous solution. Because heavy metal ions were precipitated from the phosphate buffer solution, unbuffered solution was used to investigate the effect of the concentration of heavy metal ions on the sensor response. Contrary to previous studies, not only Cu2+ and Ag+ but also Cd2+ and Zn2+ significantly decreased the response of the BOD sensor in unbuffered solution. Graft polymerization of sodium styrene sulfonate on the surface of the porous teflon membrane was carried out to absorb the heavy metal ions permeating through the membrane. Tolerance against Zn2+ was induced for S. marcescens LSY 4 to make the cells less sensitive to the presence of heavy metal ions. The membrane modification and the Zn2+ tolerance induction showed some positive effects in such a way that they reduced the inhibitory effects of Zn2+ and Cd2+ on the sensitivity of the BOD sensor. However, they had no effect on the protection of the cells against the interference of Cu2+ and Ag+ on the performance of the sensor.

  2. Biochemical Effects of Technetium-99-Pertechnetate on Microorganisms 1

    PubMed Central

    Gearing, Patrick; Van Baalen, Chase; Parker, Patrick L.

    1975-01-01

    The biochemical effects of technetium-99 as pertechnetate (TcO4−) were investigated in a variety of microorganisms (a nonsulfur purple bacterium, five blue-green algae, a protozoan, a diatom, two heterotrophic bacteria, a red alga and two green algae). Sensitivity to pertechnetate as measured by growth ranged from marked inhibition at 1 μg Tc/ml (nonsulfur purple bacterium) to no effect at 600 μg Tc ml (both green algae). No correlation between organism type and growth susceptibility to pertechnetate was apparent. The blue-green alga, Agmenellum quadruplicatum strain PR-6, bound technetium-99 to a level of 3 μg/mg dry weight cells (from medium containing 1.5 mm pertechnetate) in the light, but little or none in the dark; cell death occurred only with uptake. Addition of TcO4− to the medium caused a rapid but temporary increase in ATP levels of PR-6 (in the light only) and Tetrahymena pyriformis strain WH14. Respiration of organisms WH14 and Bacillus subtilis and photosynthesis of organism PR-6 were immediately slowed by the introduction of pertechnetate. Technetium as pertechnetate has a possible biochemical effect on cells, unrelated to its radioactivity or to a general oxidation effect. PMID:16659059

  3. Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

    SciTech Connect

    Nemenman, Ilya; Sinitsyn, Nikolai; Hengartner, Nick

    2008-01-01

    We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

  4. Biochemical composition of three species of unionid mussels after emersion

    USGS Publications Warehouse

    Greseth, Shari L.; Cope, W.G.; Rada, R.G.; Waller, D.L.; Bartsch, M.R.

    2003-01-01

    Freshwater mussels are emersed (exposed to air) during conservation activities such as surveys and relocations. Success of these activities depends upon the ability of mussels to survive emersion and to re-burrow in the substratum. We evaluated the acute sublethal effects of emersion on three species of unionid mussels [pocketbook, Lampsilis cardium (Rafinesque, 1820); pimpleback, Quadrula pustulosa pustulosa (I. Lea, 1831); spike, Elliptio dilatata (Rafinesque, 1820)] by measuring three biochemicals (carbohydrate, lipid, protein) indicative of biochemical function and energy storage. Mussels were acclimated in water at 25??C and exposed to five air temperatures (15, 20, 25, 35 and 45??C) for 15, 30 and 60 min. After emersion, mussels were returned to water at 25??C and observed for 14 days. Samples of mantle tissue were taken after the 14-day postexposure period and analysed for carbohydrate, lipid and protein. Three-way analysis of variance (ANOVA) did not reveal consistent trends in carbohydrate, lipid or protein concentrations due to sex of mussels, duration of emersion, air temperature or their interaction terms that indicated biological compensation to stress. Overall mean carbohydrate concentrations were greatest (range 447-615 mg/g dry wt) among the species, followed by protein (179-289 mg/g dry wt) and lipids (26.7-38.1 mg/g dry wt). These results have positive implications for conducting conservation activities, because emersion over the range of temperatures (15-35??C) and durations (15-60 min) examined did not appear acutely harmful to mussels.

  5. Specificity and completion time distributions of biochemical processes

    SciTech Connect

    Munsky, Brian; Nemenman, Ilya; Bel, Golan

    2009-01-01

    In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common mqdel used to explain this high specificity is kinetic proofreading, which has been extended to a variety of systems from detection of DNA mismatch to cell signaling processes. While the specification properties of the kinetic proofreading model are well known and were studied in various contexts, very little is known about its temporal behavior. In this work, we study the dynamical properties of discrete stochastic two-branch kinetic proofreading schemes. Using the Laplace transform of the corresponding chemical master equation, we obtain an analytical solution for the completion time distribution. In particular we provide expressions for the specificity and the mean and the variance of the process completion times. We also show that, for a wide range of parameters a process distinguishing between two different products can be reduced to a much simpler three point process. Our results allow for the systematic study of the interplay between specificity and completion times as well as testing the validity of the kinetic proofreading model in biological systems.

  6. Biochemical and mechanical environment cooperatively regulate skeletal muscle regeneration

    PubMed Central

    Calve, Sarah; Simon, Hans-Georg

    2012-01-01

    During forelimb regeneration in the newt Notophthalmus viridescens, the dynamic expression of a transitional matrix rich in hyaluronic acid, tenascin-C, and fibronectin controls muscle cell behavior in vivo and in vitro. However, the influence of extracellular matrix (ECM) remodeling on tissue stiffness and the cellular response to mechanical variations during regeneration was unknown. By measuring the transverse stiffness of tissues in situ, we found undifferentiated regenerative blastemas were less stiff than differentiated stump muscle (13.3±1.6 vs. 16.6±1.2 kPa). To directly determine how ECM and stiffness combine to affect skeletal muscle fragmentation, migration, and fusion, we coated silicone-based substrates ranging from 2 to 100 kPa with matrices representative of transitional (tenascin-C and fibronectin) and differentiated environments (laminin and Matrigel). Using live-cell imaging, we found softer tenascin-C-coated substrates significantly enhanced migration and fragmentation of primary newt muscle cells. In contrast, stiffer substrates coated with laminin, Matrigel, or fibronectin increased differentiation while suppressing migration and fragmentation. These data support our in vivo observations that a transitional matrix of reduced stiffness regulates muscle plasticity and progenitor cell recruitment into the regenerative blastema. These new findings will enable the determination of how biochemical and mechanical cues from the ECM control genetic pathways that drive regeneration.—Calve, S., Simon, H.-G. Biochemical and mechanical environment cooperatively regulate skeletal muscle regeneration. PMID:22415307

  7. Researcher / Researched: Repositioning Research Paradigms

    ERIC Educational Resources Information Center

    Meerwald, Agnes May Lin

    2013-01-01

    "Researcher / Researched" calls for a complementary research methodology by proposing autoethnography as both a method and text that crosses the boundaries of conventional and alternative methodologies in higher education. Autoethnography rearticulates the researcher / researched positions by blurring the boundary between them. This…

  8. Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists.

    PubMed

    Bajic, Vladimir B; Veronika, Merlin; Veladandi, Pardha Sarathi; Meka, Archana; Heng, Mok-Wei; Rajaraman, Kanagasabai; Pan, Hong; Swarup, Sanjay

    2005-08-01

    We introduce a tool for text mining, Dragon Plant Biology Explorer (DPBE) that integrates information on Arabidopsis (Arabidopsis thaliana) genes with their functions, based on gene ontologies and biochemical entity vocabularies, and presents the associations as interactive networks. The associations are based on (1) user-provided PubMed abstracts; (2) a list of Arabidopsis genes compiled by The Arabidopsis Information Resource; (3) user-defined combinations of four vocabulary lists based on the ones developed by the general, plant, and Arabidopsis GO consortia; and (4) three lists developed here based on metabolic pathways, enzymes, and metabolites derived from AraCyc, BRENDA, and other metabolism databases. We demonstrate how various combinations can be applied to fields of (1) gene function and gene interaction analyses, (2) plant development, (3) biochemistry and metabolism, and (4) pharmacology of bioactive compounds. Furthermore, we show the suitability of DPBE for systems approaches by integration with "omics" platform outputs. Using a list of abiotic stress-related genes identified by microarray experiments, we show how this tool can be used to rapidly build an information base on the previously reported relationships. This tool complements the existing biological resources for systems biology by identifying potentially novel associations using text analysis between cellular entities based on genome annotation terms. Thus, it allows researchers to efficiently summarize existing information for a group of genes or pathways, so as to make better informed choices for designing validation experiments. Last, DPBE can be helpful for beginning researchers and graduate students to summarize vast information in an unfamiliar area. DPBE is freely available for academic and nonprofit users at http://research.i2r.a-star.edu.sg/DRAGON/ME2/.

  9. IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN). Recommendations for nomenclature and tables in biochemical thermodynamics. Recommendations 1994.

    PubMed

    Alberty, R A

    1996-08-15

    Chemical equations are written in terms of specific ionic and elemental species and balance elements and charge, whereas biochemical equations are written in terms of reactants that often consist of species in equilibrium with each other and do not balance elements that are assumed fixed such as hydrogen at constant pH. Both kinds of reaction equations are needed in biochemistry. When the pH and the free concentrations of certain metal ions are specified, the apparent equilibrium constant K' for a biochemical reaction is written in terms of sums of species and can be used to calculate a standard transformed Gibbs energy of reaction deltarG'o. Transformed thermodynamic properties can be calculated directly from conventional thermodynamic properties of species. Calorimetry or the dependence of K' on temperature can be used to obtain the standard transformed enthalpy of reaction deltarH'o. Standard transformed Gibbs energies of formation deltafG'o(i) and standard transformed enthalpies of formation deltafH'o(i) for reactants (sums of species) can be calculated at various T, pH, pMg, and ionic strength (I) if sufficient information about the chemical reactions involved is available. These quantities can also be calculated from measurement if K' for a number of reactions under the desired conditions. Tables can be used to calculate deltafG'o and deltarH'o for many more reactions.

  10. Posttraumatic knee osteoarthritis following anterior cruciate ligament injury: Potential biochemical mediators of degenerative alteration and specific biochemical markers

    PubMed Central

    LI, HONG; CHEN, CHEN; CHEN, SHIYI

    2015-01-01

    As a common injury, anterior cruciate ligament (ACL) injury is unable to heal itself naturally, which possibly increases knee instability, accelerates the risk of joint degeneration and leads to knee osteoarthritis (OA) in the ACL-injured knee. Thus, ACL reconstruction using an autograft or allograft tendon is proposed to maintain the biomechanical stability of the knee joint. However, previous studies demonstrate that surgical management of ACL reconstruction failed to abrogate the development of OA completely, indicating that biochemical disturbance is responsible for the osteoarthritic changes observed following ACL injury. Inflammatory mediators are elevated subsequent to ACL injury or rupture, inducing matrix metalloproteinase production, proteoglycan degradation, collagen destruction, chondrocyte necrosis and lubricin loss. These potential biochemical mediators may aid in the development of effective biological management to reduce the onset of future posttraumatic OA. Furthermore, during the degenerative process of cartilage, there are a number of cartilage-specific biomarkers, which play a critical step in the loss of structural and functional integrity of cartilage. The present review illustrates several specific biomarkers in the ACL-injured knee joint, which may provide effective diagnostic and prognostic tools for investigating cartilage degenerative progression and future posttraumatic OA of ACL-injured patients. PMID:25798238

  11. Mathematical modeling and analysis in biochemical engineering: past accomplishments and future opportunities.

    PubMed

    Bailey, J E

    1998-01-01

    This is a personal commentary on the history and future prospects of mathematical modeling and analysis in biochemical engineering. Major transitions in these fields were driven by the appearance of the Aiba, Humphrey, and Millis text, Fredrickson's guidance on conceptualizing mathematical representations of cell populations, and Ramkrishna's development of the cybernetic modeling approach. The value of mathematical models to organize data, to consider interactions in complex systems in a rational way, to correct the conventional wisdom, and to understand essential qualitative features of biological systems has been clearly documented in prior research. The impact of this research in biotechnology discovery has so far been limited, but this will change in the future if we are adept in recognizing emerging opportunities and in integrating new concepts and tools into our research. Mathematical structures and methods, allied with extraordinary contemporary computing power, are essential to the emerging field of functional genomics. Important in this quest is a hierarchy of powerful modeling, analysis, and computational tools which can capture essential quantitative features of available experimental data and use these effectively for analysis and design of metabolism. PMID:9496667

  12. Mathematical modeling and analysis in biochemical engineering: past accomplishments and future opportunities.

    PubMed

    Bailey, J E

    1998-01-01

    This is a personal commentary on the history and future prospects of mathematical modeling and analysis in biochemical engineering. Major transitions in these fields were driven by the appearance of the Aiba, Humphrey, and Millis text, Fredrickson's guidance on conceptualizing mathematical representations of cell populations, and Ramkrishna's development of the cybernetic modeling approach. The value of mathematical models to organize data, to consider interactions in complex systems in a rational way, to correct the conventional wisdom, and to understand essential qualitative features of biological systems has been clearly documented in prior research. The impact of this research in biotechnology discovery has so far been limited, but this will change in the future if we are adept in recognizing emerging opportunities and in integrating new concepts and tools into our research. Mathematical structures and methods, allied with extraordinary contemporary computing power, are essential to the emerging field of functional genomics. Important in this quest is a hierarchy of powerful modeling, analysis, and computational tools which can capture essential quantitative features of available experimental data and use these effectively for analysis and design of metabolism.

  13. Physiological and biochemical responses of Ricinus communis seedlings to different temperatures: a metabolomics approach

    PubMed Central

    2014-01-01

    to be the main biochemical response to support growth at higher temperatures. The biochemical changes observed in response to the increasing temperature provide leads into understanding plant adaptation to harsh environmental conditions, which will be very helpful in developing strategies for R. communis crop improvement research. PMID:25109402

  14. Phase-sensitive flow cytometry: New technology for analyzing biochemical, functional, and structural features in fluorochrome- labeled cells/particles

    SciTech Connect

    Steinkamp, J.A.

    1993-12-01

    Flow cytometry (FCM) instruments rapidly measure biochemical, functional, and cytological properties of individual cells and macromolecular components, e.g., chromosomes, for clinical diagnostic medicine and biomedical and envirorunental research applications. These measurements are based on labeling cells with multiple fluorochromes for correlated analysis of macromolecules, such as DNA RNA, protein, and cell-surface receptors. This report describes the development of a phase-sensitive flow cytometer that provides unique capabilities for making laser-excited, phase-resolved measurements on fluorochrome-labelled cells and particles.

  15. Extraction, partial purification and determination of some biochemical properties of β-glucosidase from Tea Leaves (Camellia sinensis L.).

    PubMed

    Şener, Aysun

    2015-12-01

    This research was carried out to determine biochemical properties of β-glucosidase (β-D-glucoside glucohydrolase, EC 3.2.1.21) isolated from Turkish tea leaves. Two protein peaks containing β-glucosidase activity were recovered and characterized, which were denoted as isoenzyme A and isoenzyme B. Their pH optimum, thermal resistances, affinity towards p-nitrophenyl-β-D-glucopyranoside differed markedly. They both displayed maximal activity at pH 5.0. The effects of the inhibitors tested varied in a dose dependent manner.

  16. Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase

    PubMed Central

    Lazarus, Hilary

    2016-01-01

    ABSTRACT Middle East respiratory syndrome coronavirus (MERS-CoV) helicase is a superfamily 1 helicase containing seven conserved motifs. We have cloned, expressed, and purified a Strep-fused recombinant MERS-CoV nonstructural protein 13 (M-nsp13) helicase. Characterization of its biochemical properties showed that it unwound DNA and RNA similarly to severe acute respiratory syndrome CoV nsp13 (S-nsp13) helicase. We showed that M-nsp13 unwound in a 5′-to-3′ direction and efficiently unwound the partially duplex RNA substrates with a long loading strand relative to those of the RNA substrates with a short or no loading strand. Moreover, the Km of ATP for M-nsp13 is inversely proportional to the length of the 5′ loading strand of the partially duplex RNA substrates. Finally, we also showed that the rate of unwinding (ku) of M-nsp13 is directly proportional to the length of the 5′ loading strand of the partially duplex RNA substrate. These results provide insights that enhance our understanding of the biochemical properties of M-nsp13. IMPORTANCE Coronaviruses are known to cause a wide range of diseases in humans and animals. Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus discovered in 2012 and is responsible for acute respiratory syndrome in humans in the Middle East, Europe, North Africa, and the United States of America. Helicases are motor proteins that catalyze the processive separation of double-stranded nucleic acids into two single-stranded nucleic acids by utilizing the energy derived from ATP hydrolysis. MERS-CoV helicase is one of the most important viral replication enzymes of this coronavirus. Herein, we report the first bacterial expression, enzyme purification, and biochemical characterization of MERS-CoV helicase. The knowledge obtained from this study might be used to identify an inhibitor of MERS-CoV replication, and the helicase might be used as a therapeutic target.

  17. Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase

    PubMed Central

    Lazarus, Hilary

    2016-01-01

    ABSTRACT Middle East respiratory syndrome coronavirus (MERS-CoV) helicase is a superfamily 1 helicase containing seven conserved motifs. We have cloned, expressed, and purified a Strep-fused recombinant MERS-CoV nonstructural protein 13 (M-nsp13) helicase. Characterization of its biochemical properties showed that it unwound DNA and RNA similarly to severe acute respiratory syndrome CoV nsp13 (S-nsp13) helicase. We showed that M-nsp13 unwound in a 5′-to-3′ direction and efficiently unwound the partially duplex RNA substrates with a long loading strand relative to those of the RNA substrates with a short or no loading strand. Moreover, the Km of ATP for M-nsp13 is inversely proportional to the length of the 5′ loading strand of the partially duplex RNA substrates. Finally, we also showed that the rate of unwinding (ku) of M-nsp13 is directly proportional to the length of the 5′ loading strand of the partially duplex RNA substrate. These results provide insights that enhance our understanding of the biochemical properties of M-nsp13. IMPORTANCE Coronaviruses are known to cause a wide range of diseases in humans and animals. Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus discovered in 2012 and is responsible for acute respiratory syndrome in humans in the Middle East, Europe, North Africa, and the United States of America. Helicases are motor proteins that catalyze the processive separation of double-stranded nucleic acids into two single-stranded nucleic acids by utilizing the energy derived from ATP hydrolysis. MERS-CoV helicase is one of the most important viral replication enzymes of this coronavirus. Herein, we report the first bacterial expression, enzyme purification, and biochemical characterization of MERS-CoV helicase. The knowledge obtained from this study might be used to identify an inhibitor of MERS-CoV replication, and the helicase might be used as a therapeutic target. PMID:27631026

  18. Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase.

    PubMed

    Adedeji, Adeyemi O; Lazarus, Hilary

    2016-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) helicase is a superfamily 1 helicase containing seven conserved motifs. We have cloned, expressed, and purified a Strep-fused recombinant MERS-CoV nonstructural protein 13 (M-nsp13) helicase. Characterization of its biochemical properties showed that it unwound DNA and RNA similarly to severe acute respiratory syndrome CoV nsp13 (S-nsp13) helicase. We showed that M-nsp13 unwound in a 5'-to-3' direction and efficiently unwound the partially duplex RNA substrates with a long loading strand relative to those of the RNA substrates with a short or no loading strand. Moreover, the Km of ATP for M-nsp13 is inversely proportional to the length of the 5' loading strand of the partially duplex RNA substrates. Finally, we also showed that the rate of unwinding (ku) of M-nsp13 is directly proportional to the length of the 5' loading strand of the partially duplex RNA substrate. These results provide insights that enhance our understanding of the biochemical properties of M-nsp13. IMPORTANCE Coronaviruses are known to cause a wide range of diseases in humans and animals. Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus discovered in 2012 and is responsible for acute respiratory syndrome in humans in the Middle East, Europe, North Africa, and the United States of America. Helicases are motor proteins that catalyze the processive separation of double-stranded nucleic acids into two single-stranded nucleic acids by utilizing the energy derived from ATP hydrolysis. MERS-CoV helicase is one of the most important viral replication enzymes of this coronavirus. Herein, we report the first bacterial expression, enzyme purification, and biochemical characterization of MERS-CoV helicase. The knowledge obtained from this study might be used to identify an inhibitor of MERS-CoV replication, and the helicase might be used as a therapeutic target. PMID:27631026

  19. Biochemical Mechanisms Controlling Terminal Electron Transfer in Geobacter sulfurreducens

    NASA Astrophysics Data System (ADS)

    Helmus, R.; Liermann, L. J.; Brantley, S. L.; Tien, M.

    2009-04-01

    The ability of Geobacter sulfurreducens to use a variety of metals as terminal electron acceptors (TEAs) for cellular respiration makes it attractive for use in bioremediation and implies its importance to mineral cycling in the environment. This study is aimed at understanding the biochemical mechanisms that allow Geobacter sulfurreducens to use soluble and insoluble iron and manganese forms as TEAs for cellular respiration and is the first of its kind to address the kinetics of manganese use as a TEA by G. sulfurreducens. First, G. sulfurreducens was conditioned to grow on various soluble and insoluble iron and manganese forms. G. sulfurreducens demonstrated enhanced growth rates when cultured using soluble TEAs compared with insoluble TEAs. However, the lower growth rate on insoluble iron compared with soluble iron was observed concomitantly with a 1-2 log lower cell density in stationary phase in insoluble iron cultures and a lower growth yield per electron donor used in log growth phase. Furthermore, the growth yield per electron was similar with both soluble and insoluble iron. These results suggest that the net amount of energy available for biomass production achieved from reducing insoluble iron is lower than with soluble iron, which may be due to a different biochemical mechanism catalyzing the electron transfer to TEA dependent upon the solubility of the TEA. One scenario consistent with this notion is that protein(s) in the outer membrane of G. sulfurreducens that transfers electrons to insoluble TEAs does so in a manner that uncouples electron flow from the proton pump in the cellular membrane, similar to what we have observed with Shewanella oneidensis MR-1. Both the growth rate and growth yield of G. sulfurreducens on insoluble manganese were higher than on insoluble iron, indicating that there is a difference in the flow of electrons to the TEA in these two situations. While the different redox potentials of these elements may affect these values

  20. Physiological and biochemical effect of neem and other Meliaceae plants secondary metabolites against Lepidopteran insects

    PubMed Central

    Senthil-Nathan, Sengottayan

    2013-01-01

    This review described the physiological and biochemical effects of various secondary metabolites from Meliaceae against major Lepidopteran insect pest including, Noctuidae and Pyralidae. The biochemical effect of major Meliaceae secondary metabolites were discussed more in this review. Several enzymes based on food materials have critical roles in nutritional indices (food utilization) of the insect pest population. Several research work has been referred and the effect of Meliaceae secondary metabolites on feeding parameters of insects by demonstrating food consumption, approximate digestibility of consumed food, efficiency of converting the ingested food to body substance, efficiency of converting digested food to body substance and consumption index was reviewed in detail. Further how the digestive enzymes including a-Amylases, α and β-glucosidases (EC 3.2.1.1), lipases (EC 3.1.1) Proteases, serine, cysteine, and aspartic proteinases affected by the Meliaceae secondary metabolites was reviewed. Further effect of Meliaceae secondary metabolites on detoxifying enzymes have been found to react against botanical insecticides including general esterases (EST), glutathione S-transferase (GST) and phosphatases was reviewed. Alkaline phosphatase (ALP, E.C.3.1.3.1) and acid phosphatase (ACP, E.C.3.1.3.2) are hydrolytic enzymes, which hydrolyze phosphomonoesters under alkaline or acid conditions, respectively. These enzymes were affected by the secondary metabolites treatment. The detailed mechanism of action was further explained in this review. Acethylcholine esterase (AChE) is a key enzyme that terminates nerve impulses by catalyzing the hydrolysis of neurotransmitter, acetylcholine, in the nervous system of various organisms. How the AChE activity was altered by the Meliaceae secondary metabolites reviewed in detail. PMID:24391591

  1. Localized Modeling of Biochemical and Flow Interactions during Cancer Cell Adhesion

    PubMed Central

    Behr, Julie; Gaskin, Byron; Fu, Changliang; Dong, Cheng; Kunz, Robert

    2015-01-01

    This work focuses on one component of a larger research effort to develop a simulation tool to model populations of flowing cells. Specifically, in this study a local model of the biochemical interactions between circulating melanoma tumor cells (TC) and substrate adherent polymorphonuclear neutrophils (PMN) is developed. This model provides realistic three-dimensional distributions of bond formation and attendant attraction and repulsion forces that are consistent with the time dependent Computational Fluid Dynamics (CFD) framework of the full system model which accounts local pressure, shear and repulsion forces. The resulting full dynamics model enables exploration of TC adhesion to adherent PMNs, which is a known participating mechanism in melanoma cell metastasis. The model defines the adhesion molecules present on the TC and PMN cell surfaces, and calculates their interactions as the melanoma cell flows past the PMN. Biochemical rates of reactions between individual molecules are determined based on their local properties. The melanoma cell in the model expresses ICAM-1 molecules on its surface, and the PMN expresses the β-2 integrins LFA-1 and Mac-1. In this work the PMN is fixed to the substrate and is assumed fully rigid and of a prescribed shear-rate dependent shape obtained from micro-PIV experiments. The melanoma cell is transported with full six-degrees-of-freedom dynamics. Adhesion models, which represent the ability of molecules to bond and adhere the cells to each other, and repulsion models, which represent the various physical mechanisms of cellular repulsion, are incorporated with the CFD solver. All models are general enough to allow for future extensions, including arbitrary adhesion molecule types, and the ability to redefine the values of parameters to represent various cell types. The model presented in this study will be part of a clinical tool for development of personalized medical treatment programs. PMID:26366568

  2. Biochemical characterization of a factor X activator protein purified from Walterinnesia aegyptia venom.

    PubMed

    Khan, Sami U; Al-Saleh, Saad S

    2015-10-01

    Factor X of blood coagulation cascade can be activated by both intrinsic and extrinsic activating complex, trypsin and some kind of snake venom. A factor X activator protein is reported in Elapidae snake venom. The aim of this study was to evaluate biochemical properties of factor X activator protein because of its prospective application in biochemical research and therapeutics. Crude venom was fractionated on a HPLC system Gold 126/1667 using a combination of Protein PAK 125 and Protein PAK 60 Columns. Molecular weight was determined using SDS-PAGE. Walterinnesia aegyptia venom was fractionated into several protein peaks, but procoagulant and factor X activation activity coexisted into peak no.6. It appeared as single band on native PAGE and molecular weight was 60,000 ± 3. Purified up to 37-fold over crude venom. It shortened recalcification time, effect was dose-dependent and strictly Ca(2++)-dependent. Factor X activator seems to be able to activate factor X specifically because it showed no activation activity on human prothrombin, plasminogen, or protein C. It did not hydrolyze factor Xa substrate S-2222, thrombin substrate S-2238, plasmin substrate S-2251 or S-2302 and kalikrein substrate S-2266. It did not hydrolyze synthetic ester benzoyl arginine ethyl ester. Procoagulant activity was completely inhibited by irreversible serine protease inhibitors phenylmethylsulphonyl fluoride and N-p-tosylphenylalanine chloromethyl ketone. This study illustrates that factor X activator from W. aegyptia is though different in many aspects from factor X activators of Viperidae and Crotalidae venoms, but shows several properties identical to factor X activators from Elapidae venoms. PMID:26407136

  3. Chemical and Biochemical Approaches in the Study of Histone Methylation and Demethylation

    PubMed Central

    Li, Keqin Kathy; Luo, Cheng; Wang, Dongxia; Jiang, Hualiang; Zheng, Y. George

    2014-01-01

    Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and provide information otherwise difficulty to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation (ChIP), chemical ligation, mass spectrometry (MS), biochemical assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of the biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic application in the clinic. PMID:22777714

  4. Chemical and biochemical approaches in the study of histone methylation and demethylation.

    PubMed

    Li, Keqin Kathy; Luo, Cheng; Wang, Dongxia; Jiang, Hualiang; Zheng, Y George

    2012-07-01

    Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and offer information otherwise difficult to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation, chemical ligation, mass spectrometry, biochemical methylation and demethylation assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes, or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic applications in the clinic.

  5. Accelerator mass spectrometry in biomedical research

    SciTech Connect

    Vogel, J.S.; Turteltaub, K.W.

    1993-10-20

    Biological effects occur in natural systems at chemical concentrations of parts per billion (1:10{sup 9}) or less. Affected biomolecules may be separable in only milligram or microgram quantities. Quantification at attomole sensitivity is needed to study these interactions. AMS measures isotope concentrations to parts per 10{sup 13--15} on milligram-sized samples and is ideal for quantifying long-lived radioisotopic labels that are commonly used to trace biochemical pathways in natural systems. {sup 14}C-AMS has now been coupled to a variety of organic separation and definition technologies. The primary research investigates pharmacokinetics and genotoxicities of toxins and drugs at very low doses. Human subject research using AMS includes nutrition, toxicity and elemental balance studies. {sup 3} H, {sup 41}Ca and {sup 26}Al are also traced by AMS for fundamental biochemical kinetic research. Expansion of biomedical AMS awaits further development of biochemical and accelerator technologies designed specifically for these applications.

  6. Using Fermentation and Catalysis to Make Fuels and Products: Biochemical Conversion

    SciTech Connect

    2010-09-01

    Information about the Biomass Program's collaborative projects to improve processing routes for biochemical conversion, which entails breaking down biomass to make the carbohydrates available for conversion into sugars.

  7. Biochemical and histochemical studies of the sarcocyst of Sarcocystis fusiformis of buffalo Bubalus bubalis.

    PubMed

    Chaudhry, R K; Kushwah, H S; Shah, H L

    1986-10-01

    The glycogen content and activities of alkaline and acid phosphatases of sarcocysts of Sarcocystis fusiformis from naturally infected Indian water buffalo (Bubalus bubalis) were determined biochemically and histochemically.

  8. Structural and biochemical analysis of a bacterial glycosyltransferase

    PubMed Central

    Zhu, Fan; Wu, Ren; Zhang, Hua; Wu, Hui

    2014-01-01

    Summary Glycosyltransferases (GTs) are a large family of enzymes that specifically transfer sugar moieties to a diverse range of substrates. The process of bacterial glycosylation (such as biosynthesis of glycolipids, glycoproteins, and polysaccharides) has been studied extensively, yet the majority of GTs involved remains poorly characterized. Besides predicting enzymatic parameters of GTs, the resolution of three-dimensional structures of GTs can help to determine activity, donor sugar binding, and acceptor substrate binding sites. It also facilitates amino acid sequence-based structural modeling and biochemical characterization of their homologues. Here we describe a general procedure to accomplish expression and purification of soluble and active recombinant GTs. Enzymatic characterization, and crystallization of GTs, and data refinement for structural analysis are also covered in this protocol. PMID:23765651

  9. A biochemical and genetic study of Leishmania donovani pyruvate kinase.

    PubMed

    Sandoval, Will; Isea, Raúl; Rodriguez, Evelyn; Ramirez, Jose Luis

    2008-11-15

    Here we present a biochemical and molecular biology study of the enzyme pyruvate kinase (PYK) from the parasitic protozoa Leishmania donovani. The PYK gene was cloned, mutagenised and over expressed and its kinetic parameters determined. Like in other kinetoplastids, L. donovani PYK is allosterically stimulated by the effector fructose 2,6 biphosphate and not by fructose 1,6 biphosphate. When the putative effector binding site of L. donovani PYK was mutagenised, we obtained two mutants with extreme kinetic behavior: Lys453Leu, which retained a sigmoidal kinetics and was little affected by the effector; and His480Gln, which deployed a hyperbolic kinetics that was not changed by the addition of the effector. Molecular Dynamics (MD) studies revealed that the mutations not only altered the effector binding site of L. donovani PYK but also changed the folding of its domain C. PMID:18725273

  10. Biochemical biomarkers in barnacles Balanus improvisus: pollution and seasonal effects.

    PubMed

    Zanette, Juliano; Monserrat, José Maria; Bianchini, Adalto

    2015-02-01

    Biochemical biomarkers were evaluated in the barnacle Balanus improvisus (Crustacea: Cirripedia) sampled from both polluted and reference sites in the Patos Lagoon Estuary, Southern Brazil. During winter, higher glutathione S-transferase (GST) activity was recorded in the barnacles from the polluted sites, indicating environmental exposure to contaminants. Relatively low lipid peroxide levels (LPO) were also observed in barnacles from polluted sites, indicating that oxidative stress by lipid peroxidation was not a major threat in barnacles from those sites. Seasonal differences in the GST and total oxyradical scavenging capacity (TOSC) could have contributed to the low LPO levels in the summer relative to the levels in the winter. Catalase activity and metallothionein levels were not affected by contamination or seasonality. The seasonal changes observed in biomarker responses were paralleled by the differences in temperature, which could have affected physiological responses, including the balance between pro-oxidants and antioxidants. PMID:25460064

  11. Biliary casts after liver transplantation: Morphology and biochemical analysis

    PubMed Central

    Yang, Yu-Long; Zhang, Cheng; Lin, Mei-Ju; Shi, Li-Jun; Zhang, Hong-Wei; Li, Jing-Yi; Yu, Qiang

    2013-01-01

    AIM: To investigate the pathogenesis of biliary casts after liver transplantation relative to their morphology and biochemical markers. METHODS: The microstructure of biliary casts was assessed using scanning electron microscopy and Hematoxylin and eosin staining assessed their histology. The expression levels of CD3, CD5, CD34, CD68 and CD79a in these biliary casts were evaluated immunohistochemically. RESULTS: Biliary casts differed widely in their microstructure, with some containing blood vessels positive for CD34 and collagen fibers with positive Masson staining. Large numbers of neutrophils and other inflammatory cells were present, but only on the edge of the biliary casts; although the boundaries were clear without crossover. None of the biliary casts contained T-lymphocytes, B-lymphocytes, macrophages and other inflammatory cells. CONCLUSION: The microcostructure of biliary casts differed. Bacteria and acute rejection are not clearly related to their formation. PMID:24282366

  12. Some specific features of the biochemical properties of soils

    NASA Astrophysics Data System (ADS)

    Karpachevskii, L. O.; Zubkova, T. A.

    2008-12-01

    Soil can be perceived as a matric system with certain compartments. The mineral, organic, and organomineral matrices can be distinguished in it. The synthesis of humus in the soil is a continuous process with an abiotic final stage. The synthesis of polymers takes place on mineral and organomineral matrices. The development of humus horizon considerably reduces the migration of organic substances in the soil. Three different types of element associations can be distinguished in the soil: the geochemical association inherited from the parent material, the biochemical association inherited from the remains of living organisms entering the soil, and the biogeochemical (or proper pedogenic) association appearing in the course of interaction between the first two element associations under the given type of the soil water regime. The inhibitors and, probably, stimulators of plant growth also exist in the soil.

  13. Optimization of multiple-slot waveguides for biochemical sensing.

    PubMed

    Khodadad, Iman; Clarke, Nigel; Khorasaninejad, Mohammadreza; Henneke, Dale; Saini, Simarjeet S

    2014-08-10

    In this work, we analyze and optimize an optical biochemical sensor using silicon multiple-slot waveguides. The rigorous optimization procedure considers parameters such as ridge width, slot width, the number of slots, and the effect of residual silicon left at the bottom of the slot region. These parameters are then optimized using a figure of merit to achieve the highest possible sensitivity to bulk and surface changes in the upper cladding of the sensor. The multiple-slot structure is then studied in a bend configuration in order to construct ring-resonator-based sensors. A bulk sensitivity of 912 nm/refractive index unit is achieved for a change in bulk refractive index, which is three times better than single-slot waveguides. PMID:25320926

  14. Biochemical methane potential (BMP) of artichoke waste: the inoculum effect.

    PubMed

    Fabbri, Andrea; Serranti, Silvia; Bonifazi, Giuseppe

    2014-03-01

    The aim of this work was to investigate anaerobic digestibility of artichoke waste resulting from industrial transformation. A series of batch anaerobic digestion tests was performed in order to evaluate the biochemical methane potential of the matrix in respect of the process. A comparison of the different performances of the laboratory-scale reactors operating in mesophilic conditions and utilizing three different values of the inoculum/substrate ratio was carried out. The best performance was achieved with an inoculum/substrate ratio of 2. Artichoke-processing byproducts showed a classical organic waste decomposition behaviour: a fast start-up phase, an acclimation stage, and a final stabilization phase. Following this approach, artichoke waste reached chemical oxygen demand removal of about 90% in 40 days. The high methane yield (average 408.62 mL CH4 gvs (-1) voltatile solids), makes artichoke waste a good product to be utilized in anaerobic digestion plants for biogas production. PMID:24616343

  15. Effects of mefenoxam fungicide on soil biochemical properties.

    PubMed

    Gómez, Isidoro; García-Martínez, Ana María; Osta, Paloma; Parrado, Juan; Tejada, Manuel

    2015-05-01

    We studied the effect of mefenoxam on soil biochemical properties. Soil was mixed with three rates of mefenoxam (0.5, 1 and 2 L ha(-1)) and incubated for 83 days. Fungicide was applied to the soil four times during the experiment, according to the manufacturer's instructions. Soil ergosterol, dehydrogenase, urease, β-glucosidase, and phosphatase activities were measured during the experiment. Compared to controls, soils with the highest doses of mefenoxam demonstrated decreased ergosterol and dehydrogenase activities by 81 and 27 %, respectively; whereas, urease, β-glucosidase, and phosphatase activities increased. These results suggest that mefenoxam may possibly have consequences for agronomic crop production due to the negative effect on soil fungal populations and stimulation of the growth of soil bacterial activity.

  16. SIMULATING BIOCHEMICAL SIGNALING NETWORKS IN COMPLEX MOVING GEOMETRIES.

    PubMed

    Strychalski, Wanda; Adalsteinsson, David; Elston, Timothy C

    2010-01-01

    Signaling networks regulate cellular responses to environmental stimuli through cascades of protein interactions. External signals can trigger cells to polarize and move in a specific direction. During migration, spatially localized activity of proteins is maintained. To investigate the effects of morphological changes on intracellular signaling, we developed a numerical scheme consisting of a cut cell finite volume spatial discretization coupled with level set methods to simulate the resulting advection-reaction-diffusion system. We then apply the method to several biochemical reaction networks in changing geometries. We found that a Turing instability can develop exclusively by cell deformations that maintain constant area. For a Turing system with a geometry-dependent single or double peak solution, simulations in a dynamically changing geometry suggest that a single peak solution is the only stable one, independent of the oscillation frequency. The method is also applied to a model of a signaling network in a migrating fibroblast. PMID:24086102

  17. Biochemically designed polymers as self-organized materials

    NASA Astrophysics Data System (ADS)

    Alva, Shridhara; Sarma, Rupmoni; Marx, Kenneth A.; Kumar, Jayant; Tripathy, Sukant K.; Akkara, Joseph A.; Kaplan, David L.

    1997-02-01

    Self assembled molecular systems are a focus of attention for material scientists as they provide an inherent molecular level organization responsible for enhanced material properties. We have developed polymeric molecular systems with interesting optical properties by biochemical engineering, which can be self assembled to thin films. Horseradish peroxidase catalyzed polymerizations of phenolic monomers: 9-hydroxyquinoline-5-sulfonic acid, acid red and decyl ester (d&l isomers) of tyrosine, have been achieved in the presence of hydrogen peroxide. The polymer of 8- hydroxyquinoline-5-sulfonic acid acts as a polymeric ligand that can be used for metal ion sensing. The polymer of acid red, with azo functional groups in the polymer backbone, shows interesting optical properties. Amphiphilic derivatives of tyrosine self assemble into tubules from micelles in aqueous solutions. These tubules have been enzymatically polymerized to polymeric tubules. The tubules are of 5 micrometers average diameter and > 200 micrometers length. The formation and properties of these tubules are discussed.

  18. Integration of biochemical sensors into wearable biomaterial platforms

    NASA Astrophysics Data System (ADS)

    Jandhyala, Sidhartha; Walper, Scott A.; Cargill, Allison A.; Ozual, Abigail; Daniele, Michael A.

    2016-05-01

    With rapidly inflating healthcare costs, a limited supply of physicians and an alarming surge in lifestyle diseases, radical changes must be made to improve preventative medicine and ensure a sustainable healthcare system. A compelling solution is to equip the population with wearable health monitors to continuously record representative and actionable physiological data. Herein, we present a preliminary design and evaluation of a biochemical sensor node enabled by a substrate comprised of a nanocellulose thin-film that conforms to the skin and carries a printed sensor element. The nanocellulose layer ensures conformal and biocompatible contact with the skin, while a printed layer provides a high surface-area electrode. While the recognition/transduction element can be exchanged for many different sensing motifs, we utilize the general structure of an electrochemical glucose sensor.

  19. The biochemical basis for thermoregulation in heat-producing flowers.

    PubMed

    Umekawa, Yui; Seymour, Roger S; Ito, Kikukatsu

    2016-01-01

    Thermoregulation (homeothermy) in animals involves a complex mechanism involving thermal receptors throughout the body and integration in the hypothalamus that controls shivering and non-shivering thermogenesis. The flowers of some ancient families of seed plants show a similar degree of physiological thermoregulation, but by a different mechanism. Here, we show that respiratory control in homeothermic spadices of skunk cabbage (Symplocarpus renifolius) is achieved by rate-determining biochemical reactions in which the overall thermodynamic activation energy exhibits a negative value. Moreover, NADPH production, catalyzed by mitochondrial isocitrate dehydrogenase in a chemically endothermic reaction, plays a role in the pre-equilibrium reaction. We propose that a law of chemical equilibrium known as Le Châtelier's principle governs the homeothermic control in skunk cabbage. PMID:27095582

  20. High-resolution mapping of bifurcations in nonlinear biochemical circuits.

    PubMed

    Genot, A J; Baccouche, A; Sieskind, R; Aubert-Kato, N; Bredeche, N; Bartolo, J F; Taly, V; Fujii, T; Rondelez, Y

    2016-08-01

    Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

  1. Biochemical biomarkers in barnacles Balanus improvisus: pollution and seasonal effects.

    PubMed

    Zanette, Juliano; Monserrat, José Maria; Bianchini, Adalto

    2015-02-01

    Biochemical biomarkers were evaluated in the barnacle Balanus improvisus (Crustacea: Cirripedia) sampled from both polluted and reference sites in the Patos Lagoon Estuary, Southern Brazil. During winter, higher glutathione S-transferase (GST) activity was recorded in the barnacles from the polluted sites, indicating environmental exposure to contaminants. Relatively low lipid peroxide levels (LPO) were also observed in barnacles from polluted sites, indicating that oxidative stress by lipid peroxidation was not a major threat in barnacles from those sites. Seasonal differences in the GST and total oxyradical scavenging capacity (TOSC) could have contributed to the low LPO levels in the summer relative to the levels in the winter. Catalase activity and metallothionein levels were not affected by contamination or seasonality. The seasonal changes observed in biomarker responses were paralleled by the differences in temperature, which could have affected physiological responses, including the balance between pro-oxidants and antioxidants.

  2. Lead-induced biochemical changes in freshwater fish Oreochromis mossambicus

    SciTech Connect

    Ruparelia, S.G.; Verma, Y.; Mehta, N.S.; Salyed, S.R. )

    1989-08-01

    Lead, a non-essential and non-beneficial element has considerably added the problem of health hazard to human and experimental mammals. It has also received much attention over the past few years as potentially important aquatic pollutant. Fishes are of great nutritional significance and their intoxication by lead causes retardation of growth and deterioration in the nutritional value. Very little attention has been paid to biochemical changes which develop more quickly in response to toxicants than any apparent morphological changes. Therefore, the present investigation was undertaken to evaluate the effect of lead on plasma chemistry of freshwater fish Oreochromis mossambicus. This fish was selected because of its wide availability, edibility in India and its suitability as a model fish for toxicity testing. The variables such as glucose, cholesterol and protein representing carbohydrate, lipid and protein metabolism were studied.

  3. Overview of the biochemical and genetic processes in malignant mesothelioma.

    PubMed

    Assis, Leonardo Vinícius Monteiro de; Isoldi, Mauro César

    2014-01-01

    Malignant mesothelioma (MM) is a highly aggressive form of cancer, has a long latency period, and is resistant to chemotherapy. It is extremely fatal, with a mean survival of less than one year. The development of MM is strongly correlated with exposure to asbestos and with other factors, such as erionite and simian virus 40 [corrected]. Although various countries have banned the use of asbestos, MM has proven to be difficult to control and there appears to be a trend toward an increase in its incidence in the years to come. In Brazil, MM has not been widely studied from a genetic or biochemical standpoint. In addition, there have been few epidemiological studies of the disease, and the profile of its incidence has yet to be well established in the Brazilian population. The objective of this study was to review the literature regarding the processes of malignant transformation, as well as the respective mechanisms of tumorigenesis, in MM.

  4. [The biochemical carcinogenesis of selected heavy metals in bladder cancer].

    PubMed

    Rorbach-Dolata, Anna; Marchewka, Zofia; Piwowar, Agnieszka

    2015-01-01

    Bladder cancer takes the second place in the classification of morbidity of urinary system cancers. Many chemical factors take part in cancerogenesis. It is suggested that exposure to heavy metals such as arsenic, chromium, nickel and cadmium as well as its metabolites may trigger the bladder cancer through inducing excessive reactive oxygen species production and oxidative stress formation which are responsible for DNA damage. In patients with bladder cancer is observed the disorder of processes regulated by p-53, including apoptosis. There are many patients with bladder cancer with confirmed absence of retinoblastoma protein, which is responsible of holding on the process of coming up the cells with mutation into synthesis, where the replication process undergoes. It is mentioned that excessive expression of proto-oncogenes may also cause the bladder cancer. The article concerns biochemical effects of exposure to chosen heavy metals and their potential role in bladder cancer progression. PMID:26689010

  5. High-resolution mapping of bifurcations in nonlinear biochemical circuits

    NASA Astrophysics Data System (ADS)

    Genot, A. J.; Baccouche, A.; Sieskind, R.; Aubert-Kato, N.; Bredeche, N.; Bartolo, J. F.; Taly, V.; Fujii, T.; Rondelez, Y.

    2016-08-01

    Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator–prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

  6. Bone Health in Childhood: Usefulness of Biochemical Biomarkers

    PubMed Central

    Eapen, E.; Grey, V.; Don-Wauchope, A.; Atkinson, S. A.

    2008-01-01

    Development of the human skeleton begins in early embryonic life and continues through childhood into early adulthood. The acquisition of peak bone mass during these vulnerable periods may impact on skeletal fragility in later adult years. Once the skeleton has reached maturity, bone remodelling continues with periodic replacement of old bone with new at the same location. Bone biomarkers are specifically derived biomarkers that reflect both formation by osteoblasts and resorption by osteoclasts. Children have significantly higher concentrations of bone biomarkers than adults due to both skeletal growth and rapid bone turnover during childhood and adolescence. Biochemical assessment of markers of bone turnover may be important in the diagnosis, prognosis and management of metabolic bone disease. This review will discuss the various serum bone markers used for assessing bone health and the factors that influence their utility.

  7. A Biochemical Phenotype for a Disease Resistance Gene of Maize.

    PubMed Central

    Meeley, RB; Johal, GS; Briggs, SP; Walton, JD

    1992-01-01

    In maize, major resistance to the pathogenic fungus Cochliobolus (Helminthosporium) carbonum race 1 is determined by the dominant allele of the nuclear locus hm. The interaction between C. carbonum race 1 and maize is mediated by a pathogen-produced, low molecular weight compound called HC-toxin. We recently described an enzyme from maize, called HC-toxin reductase, that inactivates HC-toxin by pyridine nucleotide-dependent reduction of an essential carbonyl group. We now report that this enzyme activity is detectable only in extracts of maize that are resistant to C. carbonum race 1 (genotype Hm/Hm or Hm/hm). In several genetic analyses, in vitro HC-toxin reductase activity was without exception associated with resistance to C. carbonum race 1. The results indicate that detoxification of HC-toxin is the biochemical basis of Hm-specific resistance of maize to infection by C. carbonum race 1. PMID:12297630

  8. Biochemical physics modeling of biological nano-motors

    SciTech Connect

    Santamaría-Holek, I.; López-Alamilla, N. J.

    2014-01-14

    We present a biochemical physics model accounting for the dynamics and energetics of both translational and rotational protein motors. A modified version of the hand-over-hand mechanism considering competitive inhibition by ADP is presented. Transition state-like theory is used to reconstruct the time dependent free-energy landscape of the cycle catalyst process that allows to predicting the number of steps or rotations that a single motor can perform. In addition, following the usual approach of chemical kinetics, we calculate the average translational velocity and also the stopping time of processes involving a collectivity of motors, such as exocytosis and endocytosis processes. Finally, we formulate a stochastic model reproducing very well single realizations of kinesin and rotary ATPases.

  9. Applications of MEMS-based biochemical analytical instrumentation

    SciTech Connect

    Morse, J. D., LLNL

    1997-05-21

    The MicroTechnology Center at Lawrence Livermore National Laboratory is developing a variety of MEMS-Based analytical instrumentation systems in support of programmatic needs, along with numerous external customers. Several of the applications of interest are in the area of biochemical identification and analysis. These applications range from DNA fragment analysis and collection in support of the Human Genome Project, to detection of viruses or biological warfare agents. Each of the applications of interest has focused in micro-machined MEMS technology for reduced cost, higher throughput, and faster results. Development of these analytical instrumentation systems will have long term benefits for the medical community as well. The following describes the technologies several specific applications.

  10. [Molecular hyperspectral imaging (MHSI) system and application in biochemical medicine].

    PubMed

    Liu, Hong-Ying; Li, Qing-Li; Wang, Yi-Ting; Liu, Jin-Gao; Xue, Yong-Qi

    2011-10-01

    A novel molecular hyperspectral imaging (MHSI) system based on AOTF (acousto-optic tunable filters) was presented. The system consists of microscope, AOTF-based spectrometer, matrix CCD, image collection card and computer. The spectral range of the MHSI is from 550 to 1 000 nm. The spectral resolution is less than 2 nm, and the spatial resolution is about 0.3 microm. This paper has also presented that spectral curves extracted from the corrected hyperspectral data of the sample, which have been preprocessed by the gray correction coefficient, can more truly represent biochemical characteristic of the sample. The system can supply not only single band images in the visible range, but also spectrum curve of random pixel of sample image. This system can be widely used in various fields of biomedicine, clinical medicine, material science and microelectronics. PMID:22250515

  11. [Gaucher's and Fabry's diseases: biochemical and genetic aspects].

    PubMed

    Caillaud, Catherine; Poenaru, Livia

    2002-01-01

    Gaucher and Fabry's diseases are lysosomal storage disorders. They are due to glucocerebrosidase or alpha galactosidase deficiency, respectively. Gaucher disease, transmitted as an autosomal recessive trait, is frequent among Ashkenazi Jews. Cloning of the gene has allowed the characterization of few common mutations. Some of them have a prognosis value, in favour of either a non neurological form (type 1) or more severe forms (types 2 and 3). There mutations were found in 70% of the alleles, the other alleles carrying private mutations. Fabry disease is transmitted as an X-linked recessive trait. Genetic counselling in at-risk families relies on the detection of carrier females. As the alpha galactosidase gene shows various mutations, the establishment of phenotype-genotype correlations is limited. These two diseases, well defined at the biochemical and genetic level, are good models of inherited diseases for the development of specific therapies.

  12. Gender Differences in Cardiovascular Disease: Hormonal and Biochemical Influences

    PubMed Central

    Pérez-López, Faustino R.; Larrad-Mur, Luis; Kallen, Amanda; Chedraui, Peter; Taylor, Hugh S.

    2011-01-01

    Objective Atherosclerosis is a complex process characterized by an increase in vascular wall thickness owing to the accumulation of cells and extracellular matrix between the endothelium and the smooth muscle cell wall. There is evidence that females are at lower risk of developing cardiovascular disease (CVD) as compared to males. This has led to an interest in examining the contribution of genetic background and sex hormones to the development of CVD. The objective of this review is to provide an overview of factors, including those related to gender, that influence CVD. Methods Evidence analysis from PubMed and individual searches concerning biochemical and endocrine influences and gender differences, which affect the origin and development of CVD. Results Although still controversial, evidence suggests that hormones including estradiol and androgens are responsible for subtle cardiovascular changes long before the development of overt atherosclerosis. Conclusion Exposure to sex hormones throughout an individual's lifespan modulates many endocrine factors involved in atherosclerosis. PMID:20460551

  13. High-resolution mapping of bifurcations in nonlinear biochemical circuits

    NASA Astrophysics Data System (ADS)

    Genot, A. J.; Baccouche, A.; Sieskind, R.; Aubert-Kato, N.; Bredeche, N.; Bartolo, J. F.; Taly, V.; Fujii, T.; Rondelez, Y.

    2016-08-01

    Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

  14. Improved Biochemical Strategies for Targeted Delivery of Taxoids

    PubMed Central

    Ganesh, Thota

    2008-01-01

    Paclitaxel (Taxol ®) and docetaxel (Taxotere ®) are very important anti-tumor drugs in clinical use for cancer. However, their clinical utility is limited due to systemic toxicity, low solubility and inactivity against drug resistant tumors. To improve chemotherapeutic levels of these drugs, it would be highly desirable to design strategies which bypass the above limitations. In this respect various prodrug and drug targeting strategies have been envisioned either to improve oral bioavailability or tumor specific delivery of taxoids. Abnormal properties of cancer cells with respect to normal cells have guided in designing of these protocols. This review article records the designed biochemical strategies and their biological efficacies as potential taxoid chemotherapeutics. PMID:17419065

  15. Parameter uncertainty in biochemical models described by ordinary differential equations.

    PubMed

    Vanlier, J; Tiemann, C A; Hilbers, P A J; van Riel, N A W

    2013-12-01

    Improved mechanistic understanding of biochemical networks is one of the driving ambitions of Systems Biology. Computational modeling allows the integration of various sources of experimental data in order to put this conceptual understanding to the test in a quantitative manner. The aim of computational modeling is to obtain both predictive as well as explanatory models for complex phenomena, hereby providing useful approximations of reality with varying levels of detail. As the complexity required to describe different system increases, so does the need for determining how well such predictions can be made. Despite efforts to make tools for uncertainty analysis available to the field, these methods have not yet found widespread use in the field of Systems Biology. Additionally, the suitability of the different methods strongly depends on the problem and system under investigation. This review provides an introduction to some of the techniques available as well as gives an overview of the state-of-the-art methods for parameter uncertainty analysis.

  16. Spongiosa primary development: a biochemical hypothesis by Turing patterns formations.

    PubMed

    López-Vaca, Oscar Rodrigo; Garzón-Alvarado, Diego Alexander

    2012-01-01

    We propose a biochemical model describing the formation of primary spongiosa architecture through a bioregulatory model by metalloproteinase 13 (MMP13) and vascular endothelial growth factor (VEGF). It is assumed that MMP13 regulates cartilage degradation and the VEGF allows vascularization and advances in the ossification front through the presence of osteoblasts. The coupling of this set of molecules is represented by reaction-diffusion equations with parameters in the Turing space, creating a stable spatiotemporal pattern that leads to the formation of the trabeculae present in the spongy tissue. Experimental evidence has shown that the MMP13 regulates VEGF formation, and it is assumed that VEGF negatively regulates MMP13 formation. Thus, the patterns obtained by ossification may represent the primary spongiosa formation during endochondral ossification. Moreover, for the numerical solution, we used the finite element method with the Newton-Raphson method to approximate partial differential nonlinear equations. Ossification patterns obtained may represent the primary spongiosa formation during endochondral ossification.

  17. Stochastic magnetization dynamics of biochemically bound magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Reeves, Daniel; Weaver, John

    2015-03-01

    Understanding the dynamics of magnetic nanoparticles in applied magnetic fields is critical for biosensing and therapeutic applications. In biological environments, the nanoparticles may clump together and the resultant dynamics are interesting and important. We show simulation schemes using stochastic Langevin equations that describe the particle rotations in various conditions and suggest ways to improve the applications. Biochemical binding is described in terms of changes of the size distribution from network theory perspective. Also, using log-normally size distributed particles, a master variable is derived that contains all the significant variables. This compacts the parameter space, quickens simulation, and improves intuition. An approximate closed form solution to the magnetization harmonics in an oscillating field is given in terms of this variable using the Langevin function.

  18. [Cardiorenal syndrome: the role of new biochemical markers].

    PubMed

    Vernuccio, Federica; Grutta, Giuseppe; Ferrara, Filippo; Novo, Giuseppina; Novo, Salvatore

    2012-12-01

    Cardiorenal syndrome is a pathophysiological heart and kidney disorder, in which acute or chronic dysfunction of one organ induces a damage in the other. It's a syndrome more and more often encountered in clinical practice and this implies the need to recognize the syndrome through biochemical markers with a good sensitivity and specificity, since its earliest stages in order to optimize therapy. In addition to widely validated biomarkers, such as BNP, pro BNP, creatinine, GFR and cystatin C, other promising molecules are available, like NGAL (neutrophil gelatinase-associated lipocalin, KIM-1 (kidney injury molecule-1), MCP-1 (monocyte chemotactic peptide), Netrin-1, interleuchin 18 and NAG (N-acetyl-β-glucosa-minidase). The role of these emerging biomarkers is still not completely clarified: hence the need of new clinical trials. PMID:23258238

  19. Mutagenesis and biochemical analysis of recombinant yeast prenyltransferases.

    PubMed

    Caplin, B E; Marshall, M S

    1995-01-01

    The use of the S. cerevisiae protein prenyltransferases as a model system for general prenyltransferase study is justified by the similarity of mechanism, substrate specificity, and evolutionarily conserved substrates with the mammalian prenyltransferases. Genetic identification of potential structural genes involved in prenyltransferase activity can be easily confirmed with biochemical assays using recombinant enzyme reconstitution. Yeast FTase and GGTase I produced in E. coli are indistinguishable from the native proteins and can be studied without interference from contaminating cellular protein prenyltransferases. Structure-function analysis of the yeast prenyltransferase subunits is also simplified by the rapidity with which mutant enzymes can be analyzed in E. coli and their biological activity characterized in yeast defective for the particular subunit gene.

  20. A novel nanoarchitecture with optical, solar, medical and biochemical utility

    NASA Astrophysics Data System (ADS)

    Naughton, M. J.; Kempa, K.; Ren, Z. F.

    2009-03-01

    We discuss a nanoscale platform offering widespread utility in nanophotonics, photovoltaics, visual prosthetics, and biological and chemical sensing. As a subwavelength wave-guide architecture, these nanostructures can be used in array form for high efficiency solar cells, as well as in a wide range of nanoscale manipulations of light without deleterious plasmonic effects. They are also being developed as a high electrode-density (10^8/cm^2) retinal implant. Finally, a modification of the basic structure enables the fabrication of a highly sensitive ``nanocavity'' biochemical sensor. We will report on aspects of each application. We also thank the following collaborators: N. Argenti, D. Cai, T.C. Chiles, P. Dhakal, Y. Gao, T. Kirkpatrick, Y.C. Lan, G. McMahon, J.I. Oh, B. Rizal, J. Rybczynski.