Science.gov

Sample records for aldrich research biochemicals

  1. Neuropsychological Profile of a Girl with Wiskott-Aldrich Syndrome.

    PubMed

    Byrne, Andrea M; Schechter, Tal; Westmacott, Robyn

    2018-03-01

    We report the neuropsychological profile of a 6-year-old girl with Wiskott-Aldrich syndrome, a rare X-linked immunodeficiency disorder associated with thrombocytopenia, eczema, recurrent infections, and malignancy. Wiskott-Aldrich syndrome occurs almost exclusively in males and is extremely rare in females, with no known research focused on cognitive and academic functioning in this population. Our patient was referred due to concerns about her memory and academic functioning. She had a history of progressive thrombocytopenia and hematopoietic stem cell transplantation at age 15 months. Standardized measures of intellectual ability, language, visual-spatial and visual-motor skills, attention, memory, and academic achievement were administered. The results showed average to above-average performance in multiple areas of cognitive and academic functioning, with weaknesses in phonological awareness and rapid naming. The advent of hematopoietic stem cell transplantation has led to considerable improvement in the long-term prognosis of children with Wiskott-Aldrich syndrome. Although the impact of this syndrome and related conditions on neurocognitive development is presently unknown, this case highlights both the importance of considering base rates for commonly occurring conditions and the significant role neuropsychology can play in identifying cognitive strengths and weaknesses in the context of the developing brain.

  2. 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.

  3. Wiskott-Aldrich Syndrome (WAS)

    MedlinePlus

    ... Networks Research Conducted at NIAID Research Rules & Policies Sequencing Assay Project Specific Metadata Standards Core Sample Core ... Priority Areas of Interest Division of Microbiology and Infectious Diseases High-Priority Areas of Interest Small Business ...

  4. The Design of Advanced Learning Engines: An Interview with Clark Aldrich

    ERIC Educational Resources Information Center

    Foreman, Joel; Aldrich, Clark

    2005-01-01

    This article presents an interview with Clark Aldrich, whose expertise as an "e-learning guru" (one of three identified by "Fortune" magazine in November 2000) rests on substantial foundations: his service as the Gartner Group research director who initiated and developed the firm's e-learning coverage, his leadership of the world class team that…

  5. In memoriam: John Warren Aldrich, 1906-1995

    USGS Publications Warehouse

    Banks, Richard C.

    1997-01-01

    John Aldrich was born in Providence, Rhode Island, on 23 February 1906, and went to the Providence public schools. He developed a broad interest in natural history at an early age, being stimulated by his mother, a kindergarten teacher, who introduced him to nature books. His interest was strengthened by Harold L. Madison, Director of the Park Museum in Providence, an Associate ( = member) of the AOU. As a high school student, John taught nature study at the Rhode Island Boy Scout Camp in summers. John was President of his class at Classical High School, and manager of the school's football team in his senior year. Also in that year, 1923, John published his first paper, a note in Bird-Lore on the occurrence of the Mockingbird in Rhode Island. That paper is a literary gem, showing that his skill in writing developed as early as his knowledge of birds. His early interest in football continued as well; he was a devoted fan of the Washington Redskins in his later years.

  6. 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. Published by Elsevier Inc.

  7. Close linkage of hypervariable marker DXS255 to disease locus of Wiskott-Aldrich syndrome.

    PubMed

    de Saint Basile, G; Arveiler, B; Fraser, N J; Boyd, Y; Graig, I W; Griscelli, G; Fischer, A

    1989-12-02

    Linkage analyses in 5 families with Wiskott-Aldrich syndrome show that a novel hypervariable locus, DXS255, is very closely linked to the disease gene on the proximal short arm of the X chromosome. DXS255, with a maximum lod score of 5.42 at theta = 0.00 (90% confidence interval 0.00, 0.10) and heterozygosity of over 90%, is likely to be the closest available marker to the Wiskott-Aldrich gene and to be helpful in genetic counselling of affected families.

  8. Biochem-Env: a platform of biochemistry for research in environmental and agricultural sciences.

    PubMed

    Cheviron, Nathalie; Grondin, Virginie; Mougin, Christian

    2018-03-01

    Biochemical indicators are potent tools to assess ecosystem functioning under anthropic and global pressures. Nevertheless, additional work is needed to improve the methods used for the measurement of these indicators, and for a more relevant interpretation of the obtained results. To face these challenges, the platform Biochem-Env aims at providing innovative and standardized measurement protocols, as well as database and information system favoring result interpretation and opening. Its skills and tools are also offered for expertise, consulting, training, and standardization. In addition, the platform is a service of a French Research Infrastructure for Analysis and Experimentation on Ecosystems, for research in environmental and agricultural sciences.

  9. Critical requirement for the Wiskott-Aldrich syndrome protein in Th2 effector function

    USDA-ARS?s Scientific Manuscript database

    The Wiskott-Aldrich syndrome protein (WASp) regulates actin polymerization via activation of Arp2/3 and plays a role in the dynamics of the immunological synapse. How these events influence subsequent gene expression and effector function is unclear. We studied the role of WASp in CD4+ T cell effe...

  10. 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.

  11. 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

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

    PubMed

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

    2015-09-01

    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.

  13. 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. © FASEB.

  14. 77 FR 47106 - Manufacturer of Controlled Substances; Notice of Application; SA INTL GMBH C/O., Sigma Aldrich Co...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Manufacturer of Controlled Substances; Notice of Application; SA INTL GMBH C/O., Sigma Aldrich Co. LLC Pursuant to Title 21 Code of Federal Regulations 1301.34 (a), this is notice that on May 2, 2012, SA INTL GMBH C/O.,...

  15. 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 of Tuesday, August 7, 2012, make the...

  16. 78 FR 19015 - Importer of Controlled Substances; Notice of Application; SA INTL GMBH C/O., Sigma Aldrich Co. LLC

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-28

    ... 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 Pursuant to Title 21 Code of Federal Regulations 1301.34 (a), this is notice that on February 1, 2013, SA INTL GMBH C/O.,...

  17. Tricornered Kinase Regulates Synapse Development by Regulating the Levels of Wiskott-Aldrich Syndrome Protein.

    PubMed

    Natarajan, Rajalaxmi; Barber, Kara; Buckley, Amanda; Cho, Phillip; Egbejimi, Anuoluwapo; Wairkar, Yogesh P

    2015-01-01

    Precise regulation of synapses during development is essential to ensure accurate neural connectivity and function of nervous system. Many signaling pathways, including the mTOR (mechanical Target of Rapamycin) pathway operate in neurons to maintain genetically determined number of synapses during development. mTOR, a kinase, is shared between two functionally distinct multi-protein complexes- mTORC1 and mTORC2, that act downstream of Tuberous Sclerosis Complex (TSC). We and others have suggested an important role for TSC in synapse development at the Drosophila neuromuscular junction (NMJ) synapses. In addition, our data suggested that the regulation of the NMJ synapse numbers in Drosophila largely depends on signaling via mTORC2. In the present study, we further this observation by identifying Tricornered (Trc) kinase, a serine/threonine kinase as a likely mediator of TSC signaling. trc genetically interacts with Tsc2 to regulate the number of synapses. In addition, Tsc2 and trc mutants exhibit a dramatic reduction in synaptic levels of WASP, an important regulator of actin polymerization. We show that Trc regulates the WASP levels largely, by regulating the transcription of WASP. Finally, we show that overexpression of WASP (Wiskott-Aldrich Syndrome Protein) in trc mutants can suppress the increase in the number of synapses observed in trc mutants, suggesting that WASP regulates synapses downstream of Trc. Thus, our data provide a novel insight into how Trc may regulate the genetic program that controls the number of synapses during development.

  18. Lentivirus-based Gene Therapy of Hematopoietic Stem Cells in Wiskott-Aldrich Syndrome

    PubMed Central

    Aiuti, Alessandro; Biasco, Luca; Scaramuzza, Samantha; Ferrua, Francesca; Cicalese, Maria Pia; Baricordi, Cristina; Dionisio, Francesca; Calabria, Andrea; Giannelli, Stefania; Castiello, Maria Carmina; Bosticardo, Marita; Evangelio, Costanza; Assanelli, Andrea; Casiraghi, Miriam; Di Nunzio, Sara; Callegaro, Luciano; Benati, Claudia; Rizzardi, Paolo; Pellin, Danilo; Di Serio, Clelia; Schmidt, Manfred; Von Kalle, Christof; Gardner, Jason; Mehta, Nalini; Neduva, Victor; Dow, David J.; Galy, Anne; Miniero, Roberto; Finocchi, Andrea; Metin, Ayse; Banerjee, Pinaki; Orange, Jordan; Galimberti, Stefania; Valsecchi, Maria Grazia; Biffi, Alessandra; Montini, Eugenio; Villa, Anna; Ciceri, Fabio; Roncarolo, Maria Grazia; Naldini, Luigi

    2015-01-01

    Wiskott-Aldrich Syndrome (WAS) is an inherited immunodeficiency caused by mutations in the gene encoding WASP, a protein regulating the cytoskeleton. Hematopoietic stem/progenitor cell (HSPC) transplants can be curative but, when matched donors are unavailable, infusion of autologous HSPCs modified ex vivo by gene therapy is an alternative approach. We used a lentiviral vector encoding functional WASP to genetically correct HSPCs from three WAS patients and re-infused the cells after reduced-intensity conditioning regimen. All three patients showed stable engraftment of WASP-expressing cells and improvements in platelet counts, immune functions, and clinical score. Vector integration analyses revealed highly polyclonal and multi-lineage haematopoiesis resulting from the gene corrected HSPCs. Lentiviral gene therapy did not induce selection of integrations near oncogenes and no aberrant clonal expansion was observed after 20–32 months. Although extended clinical observation is required to establish long-term safety, lentiviral gene therapy represents a promising treatment for WAS. PMID:23845947

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

    PubMed Central

    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. PMID:26305109

  20. Improved lentiviral vectors for Wiskott-Aldrich syndrome gene therapy mimic endogenous expression profiles throughout haematopoiesis.

    PubMed

    Frecha, C; Toscano, M G; Costa, C; Saez-Lara, M J; Cosset, F L; Verhoeyen, E; Martin, F

    2008-06-01

    Wiskott-Aldrich syndrome (WAS) gene therapy requires highly efficient and well-controlled vectors. Here we studied the performance of a lentiviral vector (LV) harbouring a 500-bp fragment of the WAS proximal promoter (WW), which we previously characterized as haematopoietic-specific and capable of restoring WAS phenotype in patients' T cells. We used an LV (WE) expressing eGFP to evaluate whether this promoter was following the expression pattern of endogenous WASp. Transgene expression was analysed in WE-transduced hCD34+ population and its progeny after in vitro and in vivo differentiation in the Rag2-/-, gammac-/- humanized mouse. We revealed very poor expression from the WE internal promoter in macrophages and erythroid cells. Therefore, we designed a novel LV including a fragment of the alternative WAS promoter in WE vector (AWE). This new vector sustained high transgene levels along the whole lymphoid lineage in vivo. Most importantly, the performance of AWE vector was highly superior to WE vector since AWE clearly improved transgene levels in in vitro and in vivo hCD34+-derived macrophages, erythroid cells, megakaryocytes and B cells while supporting a high expression in human T cells. This emphasizes that it is a suitable LV backbone for gene therapy of haematopoietic diseases such as WAS.

  1. 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, subsoilingmore » 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.« less

  2. 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.

  3. Unraveling the molecular effects of mutation L270P on Wiskkot-Aldrich syndrome protein: insights from molecular dynamics approach.

    PubMed

    Palaniappan, Chandrasekaran; Rao, Sethumadhavan; Ramalingam, Rajasekaran

    2016-09-01

    Missense mutation L270P disrupts the auto-inhibited state of "Wiskkot-Aldrich syndrome protein" (WASP), thereby constitutively activating the mutant structure, a key event for pathogenesis of X-linked neutropenia (XLN). In this study, we comprehensively deciphered the molecular feature of activated mutant structure by all atom molecular dynamics (MD) approach. MD analysis revealed that mutant structure exposed a wide variation in the spatial environment of atoms, resulting in enhanced residue flexibility. The increased flexibility of residues favored to decrease the number of intra-molecular hydrogen bonding interactions in mutant structure. The reduction of hydrogen bonds in the mutant structure resulted to disrupt the local folding of secondary structural elements that eventually affect the proper folding of mutants. The unfolded state of mutant structure established more number of inter-molecular hydrogen bonding interaction at interface level due to the conformational variability, thus mediated high binding affinity with its interacting partner, Cdc42.

  4. 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

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

    PubMed

    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

    2015-09-01

    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. 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. 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. 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 CD21(low) B cells and a reduction in B cell-activating factor levels. Immunoglobulin serum levels and autoantibody production improved in all treated patients. 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 improvement in patients with WAS. Copyright

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

    PubMed Central

    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

    2016-01-01

    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. PMID:27025963

  7. R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome.

    PubMed

    Sarkar, Koustav; Han, Seong-Su; Wen, Kuo-Kuang; Ochs, Hans D; Dupré, Loïc; Seidman, Michael M; Vyas, Yatin M

    2017-12-15

    Wiskott-Aldrich syndrome (WAS), X-linked thrombocytopenia (XLT), and X-linked neutropenia, which are caused by WAS mutations affecting Wiskott-Aldrich syndrome protein (WASp) expression or activity, manifest in immunodeficiency, autoimmunity, genomic instability, and lymphoid and other cancers. WASp supports filamentous actin formation in the cytoplasm and gene transcription in the nucleus. Although the genetic basis for XLT/WAS has been clarified, the relationships between mutant forms of WASp and the diverse features of these disorders remain ill-defined. We sought to define how dysfunctional gene transcription is causally linked to the degree of T H cell deficiency and genomic instability in the XLT/WAS clinical spectrum. In human T H 1- or T H 2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double-strand breaks (DSBs) were monitored in multiple samples from patients with XLT and WAS and in normal T cells depleted of WASp. WASp deficiency provokes increased R-loops and R-loop-mediated DSBs in T H 1 cells relative to T H 2 cells. Mechanistically, chromatin occupancy of serine 2-unphosphorylated RNA polymerase II is increased, and that of topoisomerase 1, an R-loop preventing factor, is decreased at R-loop-enriched regions of IFNG and TBX21 (T H 1 genes) in T H 1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (T H 2 gene). Significantly, increased cellular load of R-loops and DSBs, which are normalized on RNaseH1-mediated suppression of ectopic R-loops, inversely correlates with disease severity scores. Transcriptional R-loop imbalance is a novel molecular defect causative in T H 1 immunodeficiency and genomic instability in patients with WAS. The study proposes that cellular R-loop load could be used as a potential biomarker for monitoring symptom severity and prognostic outcome in the XLT-WAS clinical spectrum

  8. 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

  9. Scar/WAVE-1, a Wiskott–Aldrich syndrome protein, assembles an actin-associated multi-kinase scaffold

    PubMed Central

    Westphal, Ryan S.; Soderling, Scott H.; Alto, Neal M.; Langeberg, Lorene K.; Scott, John D.

    2000-01-01

    WAVE proteins are members of the Wiskott–Aldrich syndrome protein (WASP) family of scaffolding proteins that coordinate actin reorganization by coupling Rho-related small molecular weight GTPases to the mobilization of the Arp2/3 complex. We identified WAVE-1 in a screen for rat brain A kinase-anchoring proteins (AKAPs), which bind to the SH3 domain of the Abelson tyrosine kinase (Abl). Recombinant WAVE-1 interacts with cAMP-dependent protein kinase (PKA) and Abl kinases when expressed in HEK-293 cells, and both enzymes co-purify with endogenous WAVE from brain extracts. Mapping studies have defined binding sites for each kinase. Competition experiments suggest that the PKA–WAVE-1 interaction may be regulated by actin as the kinase binds to a site overlapping a verprolin homology region, which has been shown to interact with actin. Immunocytochemical analyses in Swiss 3T3 fibroblasts suggest that the WAVE-1 kinase scaffold is assembled dynamically as WAVE, PKA and Abl translocate to sites of actin reorganization in response to platelet-derived growth factor treatment. Thus, we propose a previously unrecognized function for WAVE-1 as an actin-associated scaffolding protein that recruits PKA and Abl. PMID:10970852

  10. Dendritic cell functional improvement in a preclinical model of lentiviral-mediated gene therapy for Wiskott-Aldrich syndrome

    PubMed Central

    Catucci, Marco; Prete, Francesca; Bosticardo, Marita; Castiello, Maria Carmina; Draghici, Elena; Locci, Michela; Roncarolo, Maria Grazia; Aiuti, Alessandro; Benvenuti, Federica; Villa, Anna

    2011-01-01

    Wiskott-Aldrich syndrome (WAS) is a rare X-linked primary immunodeficiency caused by the defective expression of the WAS protein (WASP) in hematopoietic cells. It has been shown that dendritic cells (DCs) are functionally impaired in WAS patients and was−/− mice. We have previously demonstrated the efficacy and safety of a murine model of WAS gene therapy (GT), using stem cells transduced with a lentiviral vector. The aim of this study was to investigate whether GT can correct DC defects in was−/− mice. As DCs expressing WASP were detected in the secondary lymphoid organs of the treated mice, we tested the in vitro and in vivo function of bone marrow-derived DCs (BMDCs). The BMDCs showed efficient in vitro uptake of latex beads and Salmonella typhimurium. When BMDCs from the treated mice (GT BMDCs) and the was−/− mice were injected into wild type hosts, we found a higher number of cells that had migrated to the draining lymph nodes compared to mice injected with was−/− BMDCs. Finally, we found that OVA-pulsed GT BMDCs or vaccination with anti-DEC205 OVA fusion protein can efficiently induce antigen-specific T cell activation in vivo. These findings show that WAS GT significantly improves DC function, thus adding new evidence of the preclinical efficacy of lentiviral vector-mediated WAS GT. PMID:22189416

  11. 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 sialophorinmore » 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.« less

  12. 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…

  13. Biochemical Education in Nigerian Universities.

    ERIC Educational Resources Information Center

    Josefsson, Lars

    1987-01-01

    Reports on a conference on Biochemical Education and National Development held at the University of Lagos (Nigeria). Includes the author's personal impressions on biochemical education at Nigerian universities. Summarizes the sessions held at the conference regarding undergraduate, graduate, and research programs in those universities. (TW)

  14. 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)…

  15. 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

  16. Wiskott-Aldrich syndrome protein is required for NK cell cytotoxicity and colocalizes with actin to NK cell-activating immunologic synapses

    NASA Astrophysics Data System (ADS)

    Orange, Jordan S.; Ramesh, Narayanaswamy; Remold-O'Donnell, Eileen; Sasahara, Yoji; Koopman, Louise; Byrne, Michael; Bonilla, Francisco A.; Rosen, Fred S.; Geha, Raif S.; Strominger, Jack L.

    2002-08-01

    The Wiskott-Aldrich syndrome (WAS) is a primary immunodeficiency disorder caused by a mutation in WAS protein (WASp) that results in defective actin polymerization. Although the function of many hematopoietic cells requires WASp, the specific expression and function of this molecule in natural killer (NK) cells is unknown. Here, we report that WAS patients have increased percentages of peripheral blood NK cells and that fresh enriched NK cells from two patients with a WASp mutation have defective cytolytic function. In normal NK cells, WASp was expressed and localized to the activating immunologic synapse (IS) with filamentous actin (F-actin). Perforin also localized to the NK cell-activating IS but at a lesser frequency than F-actin and WASp. The accumulation of F-actin and WASp at the activating IS was decreased significantly in NK cells that had been treated with the inhibitor of actin polymerization, cytochalasin D. NK cells from WAS patients lacked expression of WASp and accumulated F-actin at the activating IS infrequently. Thus, WASp has an important function in NK cells. In patients with WASp mutations, the resulting NK cell defects are likely to contribute to their disease.

  17. Cutting edge: selective requirement for the Wiskott-Aldrich syndrome protein in cytokine, but not chemokine, secretion by CD4+ T cells.

    PubMed

    Morales-Tirado, Vanessa; Johannson, Sara; Hanson, Elaine; Howell, Alan; Zhang, Jinyi; Siminovitch, Katherine A; Fowell, Deborah J

    2004-07-15

    The mechanism of cytokine secretion is not well understood, but cytokines appear to be synthesized and released in a polarized fashion toward an Ag-specific target cell. In this study, we demonstrate that the Wiskott-Aldrich syndrome protein (WASp) is an essential component of the cytokine secretory pathway in CD4(+) T cells. Murine WASp-deficient CD4(+) T cells fail to polarize cytokines toward a target and show an unexpected and striking block in cytokine secretion. In contrast, chemokine secretion and trafficking of plasma membrane proteins, transported via the constitutive secretory pathway, are unaffected by the lack of WASp. These results suggest that CD4(+) T cell cytokines require a specialized, WASp-dependent pathway for cellular traffic and/or vesicle release that is distinct from that required for chemokine release. We propose that the use of different secretory pathways for cytokines and chemokines enables CD4(+) T cell activity to be further fine-tuned to serve specialized effector functions.

  18. Neural Wiskott-Aldrich syndrome protein is involved in hepatocyte growth factor-induced migration, invasion, and tubulogenesis of epithelial cells.

    PubMed

    Yamaguchi, Hideki; Miki, Hiroaki; Takenawa, Tadaomi

    2002-05-01

    Neural Wiskott-Aldrich syndrome protein (N-WASP), a member of the WASP family, regulates reorganization of the actin cytoskeleton through activation of the Arp2/3 complex. To date, most studies of N-WASP have focused on intracellular and morphological phenomena, such as vesicle transport and filopodium formation. We investigated the importance of N-WASP in epithelial morphogenesis, using Madin-Darby canine kidney epithelial cells, which form branching tubules when cultured with hepatocyte growth factor (HGF) in collagen gel. We established MDCK cell lines that overexpress wild-type N-WASP (WT-NW) or a dominant-negative form of N-WASP (DN-NW). WT-NW and parental Madin-Darby canine kidney cells formed branching tubules in collagen gel in response to HGF. However, formation of branching tubules was suppressed in DN-NW cells. During tubulogenesis, endogenous N-WASP accumulated at cell extensions protruding from the walls of the cysts and at the tips of the extending tubules. Gross cell morphology, cell-cell adhesion, cell polarity, and scattering in response to HGF were unaffected in WT-NW and DN-NW cells. In contrast, directed cell migration and HGF-induced invasion were significantly repressed in DN-NW cells. These results indicate that N-WASP regulates HGF-induced cell migration and invasion, which are required for epithelial tubulogenesis.

  19. MicroRNA-214-5p Inhibits the Invasion and Migration of Hepatocellular Carcinoma Cells by Targeting Wiskott-Aldrich Syndrome Like.

    PubMed

    Li, Hongdan; Wang, Haoqi; Ren, Zhen

    2018-01-01

    This study aims to explore the effects of microRNA-214-5p (miR-214-5p) on the invasion and migration of Hepatocellular Carcinoma cells (HCC). Hepatocellular Carcinoma tissues and adjacent normal tissues from 44 hepatocellular carcinoma patients were prepared for this study. The HepG2 and BEL-7402 cells were transfected with miR-214-5p mimic and inhibitor. qRT-PCR was performed to detect the expressions of miR-214-5p. Transwell assays were used to detect the invasion and migration assays in HepG2 and BEL-7402 cells. A dual-luciferase reporter assay was conducted to examine the effect of miR-214-5p on Wiskott-Aldrich Syndrome Like (WASL/ N-WASP). Western blot and qRT-PCR were used to measure the expressions of the E-cadherin, N-cadherin and Vimentin proteins. Transwell chamber assays were performed to detect cell invasion and migration. Compared with normal tissues, HCC tissues demonstrated significantly lower expression of miR-214-5p. Overexpression of miR-214-5p significantly inhibited the migration and invasion of HCC cells and inhibition of miR-214-5p promoted the migration and invasion. Additionally, miR-214-5p suppressed the epithelial-mesenchymal transition (EMT). Further study showed WASL was a putative target gene of miR-214-5p. Up-regulating the expression of WASL could reverse the inhibition effect of miR-214-5p on invasion and migration. Our data suggested that miR-214-5p inhibited the invasion and migration of HepG2 and BEL-7402 by targeting WASL in Hepatocellular carcinoma. © 2018 The Author(s). Published by S. Karger AG, Basel.

  20. The Saccharomyces cerevisiae Homologue of Human Wiskott–Aldrich Syndrome Protein Las17p Interacts with the Arp2/3 Complex

    PubMed Central

    Madania, Ammar; Dumoulin, Pascal; Grava, Sandrine; Kitamoto, Hiroko; Schärer-Brodbeck, Claudia; Soulard, Alexandre; Moreau, Violaine; Winsor, Barbara

    1999-01-01

    Yeast Las17 protein is homologous to the Wiskott–Aldrich Syndrome protein, which is implicated in severe immunodeficiency. Las17p/Bee1p has been shown to be important for actin patch assembly and actin polymerization. Here we show that Las17p interacts with the Arp2/3 complex. LAS17 is an allele-specific multicopy suppressor of ARP2 and ARP3 mutations; overexpression restores both actin patch organization and endocytosis defects in ARP2 temperature-sensitive (ts) cells. Six of seven ARP2 ts mutants and at least one ARP3 ts mutant are synthetically lethal with las17Δ ts confirming functional interaction with the Arp2/3 complex. Further characterization of las17Δ cells showed that receptor-mediated internalization of α factor by the Ste2 receptor is severely defective. The polarity of normal bipolar bud site selection is lost. Las17-gfp remains localized in cortical patches in vivo independently of polymerized actin and is required for the polarized localization of Arp2/3 as well as actin. Coimmunoprecipitation of Arp2p with Las17p indicates that Las17p interacts directly with the complex. Two hybrid results also suggest that Las17p interacts with actin, verprolin, Rvs167p and several other proteins including Src homology 3 (SH3) domain proteins, suggesting that Las17p may integrate signals from different regulatory cascades destined for the Arp2/3p complex and the actin cytoskeleton. PMID:10512884

  1. 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)

  2. 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.

  3. 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.

  4. Use of zinc-finger nucleases to knock out the WAS gene in K562 cells: a human cellular model for Wiskott-Aldrich syndrome.

    PubMed

    Toscano, Miguel G; Anderson, Per; Muñoz, Pilar; Lucena, Gema; Cobo, Marién; Benabdellah, Karim; Gregory, Philip D; Holmes, Michael C; Martin, Francisco

    2013-03-01

    Mutations in the WAS gene cause Wiskott-Aldrich syndrome (WAS), which is characterized by eczema, immunodeficiency and microthrombocytopenia. Although the role of WASP in lymphocytes and myeloid cells is well characterized, its role on megakaryocyte (MK) development is poorly understood. In order to develop a human cellular model that mimics the megakaryocytic-derived defects observed in WAS patients we used K562 cells, a well-known model for study of megakaryocytic development. We knocked out the WAS gene in K562 cells using a zinc-finger nuclease (ZFN) pair targeting the WAS intron 1 and a homologous donor DNA that disrupted WASP expression. Knockout of WASP on K562 cells (K562WASKO cells) resulted in several megakaryocytic-related defects such as morphological alterations, lower expression of CD41, lower increments in F-actin polymerization upon stimulation, reduced CD43 expression and increased phosphatidylserine exposure. All these defects have been previously described either in WAS-knockout mice or in WAS patients, validating K562WASKO as a cell model for WAS. However, K562WASPKO cells showed also increased basal F-actin and adhesion, increased expression of CD61 and reduced expression of TGFβ and Factor VIII, defects that have never been described before for WAS-deficient cells. Interestingly, these phenotypic alterations correlate with different roles for WASP in megakaryocytic differentiation. All phenotypic alterations observed in K562WASKO cells were alleviated upon expression of WAS following lentiviral transduction, confirming the role of WASP in these phenotypes. In summary, in this work we have validated a human cellular model, K562WASPKO, that mimics the megakaryocytic-related defects found in WAS-knockout mice and have found evidences for a role of WASP as regulator of megakaryocytic differentiation. We propose the use of K562WASPKO cells as a tool to study the molecular mechanisms involved in the megakaryocytic-related defects observed in WAS

  5. Use of zinc-finger nucleases to knock out the WAS gene in K562 cells: a human cellular model for Wiskott-Aldrich syndrome

    PubMed Central

    Toscano, Miguel G.; Anderson, Per; Muñoz, Pilar; Lucena, Gema; Cobo, Marién; Benabdellah, Karim; Gregory, Philip D.; Holmes, Michael C.; Martin, Francisco

    2013-01-01

    SUMMARY Mutations in the WAS gene cause Wiskott-Aldrich syndrome (WAS), which is characterized by eczema, immunodeficiency and microthrombocytopenia. Although the role of WASP in lymphocytes and myeloid cells is well characterized, its role on megakaryocyte (MK) development is poorly understood. In order to develop a human cellular model that mimics the megakaryocytic-derived defects observed in WAS patients we used K562 cells, a well-known model for study of megakaryocytic development. We knocked out the WAS gene in K562 cells using a zinc-finger nuclease (ZFN) pair targeting the WAS intron 1 and a homologous donor DNA that disrupted WASP expression. Knockout of WASP on K562 cells (K562WASKO cells) resulted in several megakaryocytic-related defects such as morphological alterations, lower expression of CD41ɑ, lower increments in F-actin polymerization upon stimulation, reduced CD43 expression and increased phosphatidylserine exposure. All these defects have been previously described either in WAS-knockout mice or in WAS patients, validating K562WASKO as a cell model for WAS. However, K562WASPKO cells showed also increased basal F-actin and adhesion, increased expression of CD61 and reduced expression of TGFβ and Factor VIII, defects that have never been described before for WAS-deficient cells. Interestingly, these phenotypic alterations correlate with different roles for WASP in megakaryocytic differentiation. All phenotypic alterations observed in K562WASKO cells were alleviated upon expression of WAS following lentiviral transduction, confirming the role of WASP in these phenotypes. In summary, in this work we have validated a human cellular model, K562WASPKO, that mimics the megakaryocytic-related defects found in WAS-knockout mice and have found evidences for a role of WASP as regulator of megakaryocytic differentiation. We propose the use of K562WASPKO cells as a tool to study the molecular mechanisms involved in the megakaryocytic-related defects observed

  6. 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)

  7. Biochemical markers of impending psychosis.

    PubMed

    Emanuele, Enzo; Martinelli, Valentina; Abbiati, Vera; Fusar-Poli, Paolo; Politi, Pierluigi

    2012-01-01

    Recent years have witnessed numerous attempts at identifying the biological correlates of impending psychosis. Biochemical markers may theoretically provide a powerful approach to identify at-risk individuals, potentially leading to more effective intervention strategies to treat them. Hopefully, future developments in the field of research biochemistry in patients with at risk mental states or prodromal symptoms will make this approach ideal for screening and monitoring purposes. In this review, we provide an overview of the different biochemical markers which have been recently demonstrated to be altered in the biological fluids of patients with impending psychosis. We will also examine the practical issues that seem to be limiting the effective integration of biomarkers into clinical development.

  8. Complete biochemical (prostate-specific antigen) response to sipuleucel-T with enzalutamide in castration-resistant prostate cancer: a case report with implications for future research.

    PubMed

    Graff, Julie N; Drake, Charles G; Beer, Tomasz M

    2013-02-01

    To describe the case of a patient with castration-resistant, metastatic prostate cancer who achieved a complete and durable biochemical response after treatment with sipuleucel-T while continuing with enzalutamide and to explore the immunologic basis for such a response. We obtained serial prostate-specific antigen (PSA) measurements and bone scans to assess the patient's response to enzalutamide followed by the addition of sipuleucel-T. Using preclinical and clinical data, we describe his response through known immunobiologic mechanisms. This patient's PSA level became undetectable during treatment with enzalutamide and began to increase again after 14 months. He opted for treatment with sipuleucel-T, while continuing with the enzalutamide. This resulted in another complete PSA response 6 months after exposure to sipuleucel-T. Sipuleucel-T typically does not produce significant PSA reductions, and, to the best of our knowledge, only 1 previous report of a durable complete PSA response in a patient with metastatic disease has been published. The timing of this response supports an immune mechanism. The biologic rationale for the combination, coupled with the clinical result observed in our patient, provides a basis for studies of the combination of sipuleucel-T and enzalutamide. Published by Elsevier Inc.

  9. CDC’s Second National Report on Biochemical Indicators of Diet and Nutrition in the US Population is a valuable tool for researchers and policy makers123

    PubMed Central

    Pfeiffer, Christine M.; Sternberg, Maya R.; Schleicher, Rosemary L.; Haynes, Bridgette M.H.; Rybak, Michael E.; Pirkle, James L.

    2016-01-01

    The CDC’s National Report on Biochemical Indicators of Diet and Nutrition in the US Population (Nutrition Report) is a serial publication that provides ongoing assessment of the population’s nutritional status. The Nutrition Report presents data on blood and urine biomarker concentrations (selected water- and fat-soluble vitamins and nutrients, trace elements, dietary bioactive compounds) from a representative sample of the population participating in the NHANES. The Second Nutrition Report (released in 2012) contains reference information (means and percentiles) for 58 biomarkers measured during all or part of 2003–2006, stratified by age, sex, and race-ethnicity. Where available, we presented cutpoint-based prevalence data during 2003–2006, and data on changes in biomarker concentrations or prevalence since 1999. Blood vitamin concentrations were generally higher in older (≥60 y) compared to younger (20–39 y) adults and lower in Mexican Americans and non-Hispanic blacks compared to non-Hispanic whites. Nearly 80% of Americans (≥6 y) were not at risk for deficiencies in any of the 7 vitamins studied (A, B-6, B-12, C, D, E and folate). Deficiency rates varied by age, sex, and race-ethnicity. About 90% of women (12–49 y) were not at risk for iron deficiency, but only 68% were not at risk for deficiencies in iron and all 7 vitamins. Young women (20–39 y) had median urine iodine concentrations bordering on insufficiency. First-time data are presented on plasma concentrations of 24 saturated, mono- and polyunsaturated fatty acids. Tabulation and graphical presentation of NHANES data in the Second Nutrition Report benefits those organizations involved in developing and evaluating nutrition policy. PMID:23596164

  10. Biochemical upgrading of oils

    DOEpatents

    Premuzic, Eugene T.; Lin, Mow 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 in organic sulfur, organic nitrogen and trace metals. Adapted microorganisms which have been modified under challenged growth processes are also disclosed.

  11. 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.

  12. 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)

  13. 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

  14. Physical forcing and physical/biochemical variability of the Mediterranean Sea: a review of unresolved issues and directions for future research

    NASA Astrophysics Data System (ADS)

    Malanotte-Rizzoli, P.; Artale, V.; Borzelli-Eusebi, G. L.; Brenner, S.; Civitarese, G.; Crise, A.; Font, J.; Gacic, M.; Kress, N.; Marullo, S.; Ozsoy, E.; Ribera d'Alcalà, M.; Roether, W.; Schroeder, K.; Sofianos, S.; Tanhua, T.; Theocharis, A.; Alvarez, M.; Ashkenazy, Y.; Bergamasco, A.; Cardin, V.; Carniel, S.; D'Ortenzio, F.; Garcia-Ladona, E.; Garcia-Lafuente, J. M.; Gogou, A.; Gregoire, M.; Hainbucher, D.; Kontoyannis, H.; Kovacevic, V.; Krasakapoulou, E.; Krokos, G.; Incarbona, A.; Mazzocchi, M. G.; Orlic, M.; Pascual, A.; Poulain, P.-M.; Rubino, A.; Siokou-Frangou, J.; Souvermezoglou, E.; Sprovieri, M.; Taupier-Letage, I.; Tintoré, J.; Triantafyllou, G.

    2013-07-01

    convection cells are much more amenable to direct observational surveys and mooring arrays. An ubiquitous, energetic mesoscale and sub-mesoscale eddy field is superimposed to and interacts with the sub-basin scale, wind-driven gyres that characterize the upper thermocline circulation. Three different scales of motion are therefore superimposed producing a richness of interaction processes which typify similar interactions in unexplored ocean regions. Both wide and narrow shelves are present separated by steep continental slopes from the deep interiors. Cross-shelf fluxes of physical as well biogeochemical parameters are crucial in determining the properties of the shallow versus deep local ecosystems and their trophic chain. Most importantly, the Mediterranean Sea is a basin of contrasting ecosystems, from the strongly oligotrophic deep interiors to the fully eutrophic northern Adriatic characterized by recurrent, anomalous algal blooms and related anoxia events. This review focuses on the identification of the major unresolved scientific issues and wants also to provide directions for future research which may lead to the formulation of interdisciplinary, collaborative implementation plans to address these issues both theoretically and observationally.

  15. Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex.

    PubMed

    Luan, Qing; Zelter, Alex; MacCoss, Michael J; Davis, Trisha N; Nolen, Brad J

    2018-02-13

    Arp2/3 complex nucleates branched actin filaments important for cellular motility and endocytosis. WASP family proteins are Arp2/3 complex activators that play multiple roles in branching nucleation, but little is known about the structural bases of these WASP functions, owing to an incomplete understanding of how WASP binds Arp2/3 complex. Recent data show WASP binds two sites, and biochemical and structural studies led to models in which the WASP C segment engages the barbed ends of the Arp3 and Arp2 subunits while the WASP A segment binds the back side of the complex on Arp3. However, electron microscopy reconstructions showed density for WASP inconsistent with these models on the opposite (front) side of Arp2/3 complex. Here we use chemical cross-linking and mass spectrometry (XL-MS) along with computational docking and structure-based mutational analysis to map the two WASP binding sites on the complex. Our data corroborate the barbed end and back side binding models and show one WASP binding site on Arp3, on the back side of the complex, and a second site on the bottom of the complex, spanning Arp2 and ARPC1. The XL-MS-identified cross-links rule out the front side binding model and show that the A segment of WASP binds along the bottom side of the ARPC1 subunit, instead of at the Arp2/ARPC1 interface, as suggested by FRET experiments. The identified binding sites support the Arp3 tail release model to explain WASP-mediated activating conformational changes in Arp2/3 complex and provide insight into the roles of WASP in branching nucleation.

  16. Early Salvage Hormonal Therapy for Biochemical Failure Improved Survival in Prostate Cancer Patients After Neoadjuvant Hormonal Therapy Plus Radiation Therapy-A Secondary Analysis of Irish Clinical Oncology Research Group 97-01

    SciTech Connect

    Mydin, Aminudin R., E-mail: aminudinrahman@googlemail.com; Dunne, Mary T.; Finn, Marie A.

    2013-01-01

    Purpose: To assess the survival benefit of early vs late salvage hormonal therapy (HT), we performed a secondary analysis on patients who developed recurrence from Irish Clinical Oncology Research Group 97-01, a randomized trial comparing 4 vs 8 months neoadjuvant HT plus radiation therapy (RT) in intermediate- and high-risk prostate adenocarcinoma. Methods and Materials: A total of 102 patients from the trial who recurred were analyzed at a median follow-up of 8.5 years. The patients were divided into 3 groups based on the timing of salvage HT: 57 patients had prostate-specific antigen (PSA) {<=}10 ng/mL and absent distant metastases (groupmore » 1, early), 21 patients had PSA >10 ng/mL and absent distant metastases (group 2, late), and 24 patients had distant metastases (group 3, late). The endpoint analyzed was overall survival (OS) calculated from 2 different time points: date of enrolment in the trial (OS1) and date of initiation of salvage HT (OS2). Survival was estimated using Kaplan-Meier curves and a Cox regression model. Results: The OS1 differed significantly between groups (P<.0005): OS1 at 10 years was 78% in group 1, 42% in group 2, and 29% in group 3. The OS2 also differed significantly between groups (P<.0005): OS2 at 6 years was 70% in group 1, 47% in group 2, and 22% in group 3. Group 1 had the longest median time from end of RT to biochemical failure compared with groups 2 and 3 (3.3, 0.9, and 1.7 years, respectively; P<.0005). Group 1 also had the longest median PSA doubling time compared with groups 2 and 3 (9.9, 3.6, and 2.4 months, respectively; P<.0005). On multivariate analysis, timing of salvage HT, time from end of RT to biochemical failure, and PSA nadir on salvage HT were significant predictors of survival. Conclusion: Early salvage HT based on PSA {<=}10 ng/mL and absent distant metastases improved survival in patients with prostate cancer after failure of initial treatment with neoadjuvant HT plus RT.« less

  17. 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

  18. 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)

  19. 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. Copyright 2002 Wiley-Liss, Inc.

  20. Explorations into Chemical Reactions and Biochemical Pathways.

    PubMed

    Gasteiger, Johann

    2016-12-01

    A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Genetics Home Reference: Wiskott-Aldrich syndrome

    MedlinePlus

    ... Accessibility FOIA Viewers & Players U.S. Department of Health & Human Services National Institutes of Health National Library of Medicine Lister Hill National Center for Biomedical Communications 8600 Rockville Pike, Bethesda, MD 20894, USA HONCode ...

  2. Epstein-Barr-virus-transformed lymphoblastoid cell lines derived from patients with X-linked agammaglobulinaemia and Wiskott-Aldrich syndrome: responses to B cell growth and differentiation factors.

    PubMed Central

    Lau, Y L; Shields, J G; Levinsky, R J; Callard, R E

    1989-01-01

    Epstein-Barr-virus-transformed B lymphoblastoid cell lines (EBV-transformed LCL) from three patients with X-linked agammaglobulinaemia (XLA), six patients with Wiskott-Aldrich Syndrome (WAS), and seven normal donors, were tested for growth and differentiation in response to human recombinant IL-4, a commercially available, low molecular weight B cell growth factor (BCGFlow), and B cell differentiation factor (BCDF) secreted by the T24 cell line, now known to be IL-6. Proliferation (3H-TdR uptake) by EBV-transformed LCL from both XLA and WAS patients in response to BCGFlow was similar to that obtained with the normal cell lines. In addition, three normal and three WAS, but none of the XLA EBV-transformed LCL, proliferated a little in response to IL-4. All the normal B cell lines secreted IgM, and six out of the seven secreted IgG in response to BCGFlow and BCDF. A similar pattern of response was obtained with the WAS EBV-transformed LCL (6/6 secreted IgM and 4/6 secreted IgG). Several of the normal and WAS EBV-transformed LCL also secreted IgM and IgG in response to IL-4. In contrast, the lines from the XLA patients were abnormal. One secreted large amounts of IgM and two secreted small amounts, but none of the XLA lines secreted IgG constitutively or in response to any of the factors (IL-4, BCDF). The lack of detectable IgG secretion by the XLA lines was probably due to an absence of precommitted IgG B cell precursors transformed by EBV rather than an intrinsic inability to respond to BCGF and BCDF. All of the lines, including those derived from XLA patients, were shown to secrete B cell growth and differentiation factors detected on indicator B cell lines. These results suggest that the abnormal X-linked genes responsible for XLA and WAS do not interfere with B cell responses to B cell growth and differentiation factors. PMID:2539277

  3. Conditioning Regimen with Plerixafor is Safe and Improves the Outcome of TCRαβ+ and CD19+ Cell-Depleted Stem Cell Transplantation in Wiskott-Aldrich Syndrome Patients.

    PubMed

    Balashov, Dmitry; Laberko, Alexandra; Shcherbina, Anna; Trakhtman, Pavel; Abramov, Dmitrii; Gutovskaya, Elena; Kozlovskaya, Svetlana; Shelikhova, Larisa; Novichkova, Galina; Maschan, Michael; Rumiantsev, Alexander; Maschan, Alexei

    2018-03-14

    Our initial experience of hematopoietic stem cell transplantation (HSCT) from a matched unrelated donor (MUD; n=12) or a haploidentical related donor (n=6) with TCRαβ+/CD19+ graft depletion for Wiskott-Aldrich syndrome (WAS) patients (n=18) showed a dramatic decrease in the incidence of graft-versus-host disease (GVHD) and transplant-related mortality, with an increased rate of overall survival (OS) of 88,9%. Unfortunately, the treatment was associated with mixed myeloid donor chimerism and secondary graft dysfunction (severe thrombocytopenia, n=2; graft rejection, n=5). To improve the outcome, we hypothesized that the addition of G-CSF and plerixafor to the conditioning chemotherapy would result in a more complete donor stem cell engraftment. This trial was registered at www.clinicaltrials.gov (NCT03019809). A study group of WAS patients (n=16) received TCRαβ+/CD19+-depleted HSCT (MUD, n=6; haploidentical, n=10). The conditioning regimen was treosulfan-fludarabine-rATG-melphalan (or thiophosphamide in 1 patient) with G-CSF (10µg/kg daily for 5 days starting on day -8) and plerixafor (240 µg/kg daily for 3 days starting on day -6). The clinical outcomes in this study were compared to historical data set (n=18). No patients had grade III/IV acute GVHD in either the study or the historical control group. Importantly, among all patients with WAS, there was no statistical significance in OS after HSCT from haploidentical (93,8%) in comparison with MUD (88,5%) donors (p=0,612). All patients in the study group had full donor chimerism in whole blood and in the CD3+ compartments. The OS was 93,8%, and there were no cases of graft dysfunction. The present work shows the efficacy of G-CSF/plerixafor addition to the conditioning regimen before HSCT with TCRαβ+/C D19+ graft depletion in WAS patients. Copyright © 2018. Published by Elsevier Inc.

  4. Zyxin, axin, and Wiskott-Aldrich syndrome protein are adaptors that link the cadherin/catenin protein complex to the cytoskeleton at adherens junctions in the seminiferous epithelium of the rat testis.

    PubMed

    Lee, Nikki P Y; Mruk, Dolores D; Conway, Anne M; Cheng, C Yan

    2004-01-01

    During spermatogenesis, the movement of germ cells across the seminiferous epithelium is associated with extensive junction restructuring. Yet the underlying mechanism (or mechanisms) that regulates these events is largely unknown. If the molecular architecture of the cell-cell actin-based adherens junction (AJ), such as ectoplasmic specialization (ES) and tubulobulbar complex- two testis-specific AJ types, is known, many functional mechanistic studies can be designed. We thus undertook an investigation to study 3 adaptors in the seminiferous epithelium: zyxin, axin, and Wiskott-Aldrich syndrome protein (WASP). All 3 adaptors were shown to be products of Sertoli and germ cells. Zyxin was shown to be a stage-specific protein that was most prominent during stages V-VII and restricted mostly to pachytene spermatocytes, but it could also be detected at the site of basal and apical ectoplasmic specialization (ES). Zyxin, axin, and WASP were shown to be structurally linked to the N-cadherin/beta-catenin/alpha-actinin/actin complex but not to the nectin-3/afadin or the beta 1-integrin-mediated protein complexes. Interestingly, zyxin, axin, and WASP are also structurally linked to vimentin (an intermediate filament protein) and alpha-tubulin (the subunit of a microtubule), which suggests that they have a role (or roles) in the regulation of the dynamics of the desmosome-like junction and microtubule. These results illustrate that zyxin, axin, and WASP are adaptors in both AJs and intermediate filament-based desmosome-like junctions. This raises the possibility that classic cadherins are also associated with vimentin-based intermediate filaments via these adaptors in the testis. While virtually no N-cadherin was found to associate with vimentin in the seminiferous tubules, it did associate with vimentin when testis lysates were used. Interestingly, about 5% of the E-cadherin associated with vimentin in isolated seminiferous tubules, and about 50% of the E-cadherin in the

  5. 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)

  6. Interferometric biochemical and chemical sensors

    NASA Astrophysics Data System (ADS)

    Gauglitz, Guenter; Brecht, Andreas; Kraus, Gerolf

    1995-09-01

    Interferometric principles have gained wide acceptance in the field of chemical and biochemical sensing. Reflectometric interference spectrometry sensors using white light multiple reflections at thin layers, structures of polymers, or monolayers of biochemicals are discussed in a survey. These are compared to other techniques, especially methods using surface plasmon resonance and grating couplers. Applications in the area of environmental monitoring in public safety are given, demonstrating the results for halogenated hydrocarbons in air and water as well as pesticides in ground water. Calibration curves, limits of decision, of detection, and of determination are specified and discussed with respect to EU limits. The application of multivariate data analysis is considered including artificial neuronal networks for multisensor systems and referencing in the case of gas sensors.

  7. Development of Biochemical Cyanide Antidotes

    DTIC Science & Technology

    1990-11-30

    04318 ,,’,, 3 / ,30 30 November 1990 Midterm Report ( 2 /1/89 - 11/1/90) DEVELOPMENT OF BIOCHEMICAL CYANIDE ANTIDOTES Contract No. DAMD17-89-C-9033...calcium 3 . Peroxide generation 4 . Cytochrome oxidase inhibition 5. Dopamine release Chemicals selected as potential antidotes included anti- convulsants...to determine resting activity of each of the above parameters. Experiments were generally repeated 2 to 4 times to establish the validity of the

  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. Optofluidics in bio-chemical analysis

    NASA Astrophysics Data System (ADS)

    Guo, Yunbo; Fan, Xudong

    2012-01-01

    Optofluidics organically integrates microfluidics and photonics and is an emerging technology in biological and chemical analysis. In this paper, we overview the recent studies in bio-chemical sensing applications of optofluidics. Particularly, we report the research progress in our lab in developing diverse optofluidic devices using two unique configurations: thin-walled capillary based optofluidic ring resonator (OFRR) and multi-hole capillary based optofluidic platforms. The first one has been developed to be OFRR-based label-free biosensor, microfluidic laser based intra-cavity sensors, and on-column optical detectors for micro-gas chromatography (μGC), while the second one has been developed to be optofluidic Fabry-Pérot based label-free biosensor and optofluidic Surface-Enhanced Raman Spectroscopy (SERS) biosensor. All of these devices take advantage of superior fluidic handling capability and high sensitivity, and have been used in detecting various biological and chemical analytes in either liquid or vapor phase.

  10. 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

  11. BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space.

    PubMed

    Hamdalla, Mai A; Mandoiu, Ion I; Hill, Dennis W; Rajasekaran, Sanguthevar; Grant, David F

    2013-03-25

    The structural identification of unknown biochemical compounds in complex biofluids continues to be a major challenge in metabolomics research. Using LC/MS, there are currently two major options for solving this problem: searching small biochemical databases, which often do not contain the unknown of interest or searching large chemical databases which include large numbers of nonbiochemical compounds. Searching larger chemical databases (larger chemical space) increases the odds of identifying an unknown biochemical compound, but only if nonbiochemical structures can be eliminated from consideration. In this paper we present BioSM; a cheminformatics tool that uses known endogenous mammalian biochemical compounds (as scaffolds) and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space. The results of a comprehensive set of empirical experiments suggest that BioSM identifies endogenous mammalian biochemical structures with high accuracy. In a leave-one-out cross validation experiment, BioSM correctly predicted 95% of 1388 Kyoto Encyclopedia of Genes and Genomes (KEGG) compounds as endogenous mammalian biochemicals using 1565 scaffolds. Analysis of two additional biological data sets containing 2330 human metabolites (HMDB) and 2416 plant secondary metabolites (KEGG) resulted in biochemical annotations of 89% and 72% of the compounds, respectively. When a data set of 3895 drugs (DrugBank and USAN) was tested, 48% of these structures were predicted to be biochemical. However, when a set of synthetic chemical compounds (Chembridge and Chemsynthesis databases) were examined, only 29% of the 458,207 structures were predicted to be biochemical. Moreover, BioSM predicted that 34% of 883,199 randomly selected compounds from PubChem were biochemical. We then expanded the scaffold list to 3927 biochemical compounds and reevaluated the above data sets to determine whether scaffold number influenced model performance

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

    SciTech Connect

    None

    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.

  13. 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.

  14. The role of thermodynamics in biochemical engineering

    NASA Astrophysics Data System (ADS)

    von Stockar, Urs

    2013-09-01

    This article is an adapted version of the introductory chapter of a book whose publication is imminent. It bears the title "Biothermodynamics - The role of thermodynamics in biochemical engineering." The aim of the paper is to give a very short overview of the state of biothermodynamics in an engineering context as reflected in this book. Seen from this perspective, biothermodynamics may be subdivided according to the scale used to formalize the description of the biological system into three large areas: (i) biomolecular thermodynamics (most fundamental scale), (ii) thermodynamics of metabolism (intermediary scale), and (iii) whole-cell thermodynamics ("black-box" description of living entities). In each of these subareas, the main available theoretical approaches and the current and the potential applications are discussed. Biomolecular thermodynamics (i) is especially well developed and is obviously highly pertinent for the development of downstream processing. Its use ought to be encouraged as much as possible. The subarea of thermodynamics of live cells (iii), although scarcely applied in practice, is also expected to enhance bioprocess research and development, particularly in predicting culture performances, for understanding the driving forces for cellular growth, and in developing, monitoring, and controlling cellular cultures. Finally, there is no question that thermodynamic analysis of cellular metabolism (ii) is a promising tool for systems biology and for many other applications, but quite a large research effort is still needed before it may be put to practical use.

  15. 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)

  16. 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.

  17. 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. Plant Biotechnology Journal © 2013 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

  18. Reaction networks and kinetics of biochemical systems.

    PubMed

    Arceo, Carlene Perpetua P; Jose, Editha C; Lao, Angelyn R; Mendoza, Eduardo R

    2017-01-01

    This paper further develops the connection between Chemical Reaction Network Theory (CRNT) and Biochemical Systems Theory (BST) that we recently introduced [1]. We first use algebraic properties of kinetic sets to study the set of complex factorizable kinetics CFK(N) on a CRN, which shares many characteristics with its subset of mass action kinetics. In particular, we extend the Theorem of Feinberg-Horn [9] on the coincidence of the kinetic and stoichiometric subsets of a mass action system to CF kinetics, using the concept of span surjectivity. We also introduce the branching type of a network, which determines the availability of kinetics on it and allows us to characterize the networks for which all kinetics are complex factorizable: A "Kinetics Landscape" provides an overview of kinetics sets, their algebraic properties and containment relationships. We then apply our results and those (of other CRNT researchers) reviewed in [1] to fifteen BST models of complex biological systems and discover novel network and kinetic properties that so far have not been widely studied in CRNT. In our view, these findings show an important benefit of connecting CRNT and BST modeling efforts. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Biochemical engineering aspects of solid state bioprocessing.

    PubMed

    Mitchell, D A; Berovic, M; Krieger, N

    2000-01-01

    Despite centuries of use and renewed interest over the last 20 years in solid-state fermentation (SSF) technology, and despite its good potential for a range of products, there are currently relatively few large-scale commercial applications. This situation can be attributed to the complexity of the system: Macroscale and microscale heat and mass transfer limitations are intrinsic to the system, and it is only over the last decade or so that we have begun to understand them. This review presents the current state of understanding of biochemical engineering aspects of SSF processing, including not only the fermentation itself, but also the auxiliary steps of substrate and inoculum preparation and downstream processing and waste disposal. The fermentation step has received most research attention. Significant advances have been made over the last decade in understanding how the performance of SSF bioreactors can be controlled either by the intraparticle processes of enzyme and oxygen diffusion or by the macroscale heat transfer processes of conduction, convection, and evaporation. Mathematical modeling has played an important role in suggesting how SSF bioreactors should be designed and operated. However, these models have been developed on the basis of laboratory-scale data and there is an urgent need to test these models with data obtained in large-scale bioreactors.

  20. A new dynamical layout algorithm for complex biochemical reaction networks

    PubMed Central

    Wegner, Katja; Kummer, Ursula

    2005-01-01

    Background To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every kind of pathway in biochemical research. This is mainly due to certain conventions to which biochemists/biologists are used to and which are not in accordance to conventional layout algorithms. A number of approaches has been developed to improve this situation. Some of these are used in the context of biochemical databases and make more or less use of the information in these databases to aid the layout process. However, visualisation becomes also more and more important in modelling and simulation tools which mostly do not offer additional connections to databases. Therefore, layout algorithms used in these tools have to work independently of any databases. In addition, all of the existing algorithms face some limitations with respect to the number of edge crossings when it comes to larger biochemical systems due to the interconnectivity of these. Last but not least, in some cases, biochemical conventions are not met properly. Results Out of these reasons we have developed a new algorithm which tackles these problems by reducing the number of edge crossings in complex systems, taking further biological conventions into account to identify and visualise cycles. Furthermore the algorithm is independent from database information in order to be easily adopted in any application. It can also be tested as part of the SimWiz package (free to download for academic users at [1]). Conclusion The new algorithm reduces the complexity of pathways, as well as edge crossings and edge length in the

  1. A new dynamical layout algorithm for complex biochemical reaction networks.

    PubMed

    Wegner, Katja; Kummer, Ursula

    2005-08-26

    To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every kind of pathway in biochemical research. This is mainly due to certain conventions to which biochemists/biologists are used to and which are not in accordance to conventional layout algorithms. A number of approaches has been developed to improve this situation. Some of these are used in the context of biochemical databases and make more or less use of the information in these databases to aid the layout process. However, visualisation becomes also more and more important in modelling and simulation tools which mostly do not offer additional connections to databases. Therefore, layout algorithms used in these tools have to work independently of any databases. In addition, all of the existing algorithms face some limitations with respect to the number of edge crossings when it comes to larger biochemical systems due to the interconnectivity of these. Last but not least, in some cases, biochemical conventions are not met properly. Out of these reasons we have developed a new algorithm which tackles these problems by reducing the number of edge crossings in complex systems, taking further biological conventions into account to identify and visualise cycles. Furthermore the algorithm is independent from database information in order to be easily adopted in any application. It can also be tested as part of the SimWiz package (free to download for academic users at 1). The new algorithm reduces the complexity of pathways, as well as edge crossings and edge length in the resulting graphical representation

  2. Cariporide and other new and powerful NHE1 inhibitors as potentially selective anticancer drugs--an integral molecular/biochemical/metabolic/clinical approach after one hundred years of cancer research.

    PubMed

    Harguindey, Salvador; Arranz, Jose Luis; Polo Orozco, Julian David; Rauch, Cyril; Fais, Stefano; Cardone, Rosa Angela; Reshkin, Stephan J

    2013-11-06

    In recent years an increasing number of publications have emphasized the growing importance of hydrogen ion dynamics in modern cancer research, from etiopathogenesis and treatment. A proton [H+]-related mechanism underlying the initiation and progression of the neoplastic process has been recently described by different research groups as a new paradigm in which all cancer cells and tissues, regardless of their origin and genetic background, have a pivotal energetic and homeostatic disturbance of their metabolism that is completely different from all normal tissues: an aberrant regulation of hydrogen ion dynamics leading to a reversal of the pH gradient in cancer cells and tissues (↑pHi/↓pHe, or "proton reversal"). Tumor cells survive their hostile microenvironment due to membrane-bound proton pumps and transporters, and their main defensive strategy is to never allow internal acidification because that could lead to their death through apoptosis. In this context, one of the primary and best studied regulators of both pHi and pHe in tumors is the Na+/H+ exchanger isoform 1 (NHE1). An elevated NHE1 activity can be correlated with both an increase in cell pH and a decrease in the extracellular pH of tumors, and such proton reversal is associated with the origin, local growth, activation and further progression of the metastatic process. Consequently, NHE1 pharmaceutical inhibition by new and potent NHE1 inhibitors represents a potential and highly selective target in anticancer therapy. Cariporide, being one of the better studied specific and powerful NHE1 inhibitors, has proven to be well tolerated by humans in the cardiological context, however some side-effects, mainly related to drug accumulation and cerebrovascular complications were reported. Thus, cariporide could become a new, slightly toxic and effective anticancer agent in different human malignancies.

  3. One gram of soil: a microbial biochemical gene library.

    PubMed

    Trevors, J T

    2010-02-01

    One gram of soil is an immense biochemical gene library producing diverse genetic instructions, which have been present for almost 4 billion years on the Earth. There is sufficient DNA in 1 g of soil to extend 1,598 km. However, this is certainly an underestimate for fertile soils. Can the amount of genetic information contained in one g of soil be accurately estimated? The answer is not always definitive as the estimate depends on the particular g of soil being researched and the methods for DNA extraction, purification and quantification. Moreover, there is no such entity as a typical or average g of soil. Extraction of DNA from soil samples is never 100% efficient and can vary from a few microg to almost 200 microg DNA per g dry weight soil. However, estimates can be made that lead to a better understanding of the immense biochemical gene library and gene expression (combined transcription and translation) in microorganisms within a single g of soil. Accurate estimates of genes expressed in a single g of soil under a multitude of changing, environmental, conditions still requires considerable research. In this article, soil as a biochemical gene library, gene expression, and the minimal number of genes for the first bacteria in the environment will be examined.

  4. 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)

  5. Raman spectroscopic biochemical mapping of tissues

    NASA Astrophysics Data System (ADS)

    Stone, Nicholas; Hart Prieto, Maria C.; Kendall, Catherine A.; Shetty, Geeta; Barr, Hugh

    2006-02-01

    Advances in technologies have brought us closer to routine spectroscopic diagnosis of early malignant disease. However, there is still a poor understanding of the carcinogenesis process. For example it is not known whether many cancers follow a logical sequence from dysplasia, to carcinoma in situ, to invasion. Biochemical tissue changes, triggered by genetic mutations, precede morphological and structural changes. These can be probed using Raman or FTIR microspectroscopy and the spectra analysed for biochemical constituents. Local microscopic distribution of various constituents can then be visualised. Raman mapping has been performed on a number of tissues including oesophagus, breast, bladder and prostate. The biochemical constituents have been calculated at each point using basis spectra and least squares analysis. The residual of the least squares fit indicates any unfit spectral components. The biochemical distribution will be compared with the defined histopathological boundaries. The distribution of nucleic acids, glycogen, actin, collagen I, III, IV, lipids and others appear to follow expected patterns.

  6. [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.

  7. Improving Marine Ecosystem Models with Biochemical Tracers

    NASA Astrophysics Data System (ADS)

    Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

    2018-01-01

    Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

  8. Illuminating the Cell's Biochemical Activity Architecture.

    PubMed

    Mehta, Sohum; Zhang, Jin

    2017-10-03

    All cellular behaviors arise through the coordinated actions of numerous intracellular biochemical pathways. Over the past 20 years, efforts to probe intracellular biochemical processes have undergone a fundamental transformation brought about by advances in fluorescence imaging, such as the development of genetically encoded fluorescent reporters and new imaging technologies; the impact of these approaches on our understanding of the molecular underpinnings of biological function cannot be understated. In particular, the ability to obtain information on the spatiotemporal regulation of biochemical processes unfolding in real time in the native context of a living cell has crystallized the view, long a matter of speculation, that cells achieve specific biological outcomes through the imposition of spatial control over the distribution of various biomolecules, and their associated biochemical activities, within the cellular environment. Indeed, the compartmentalization of biochemical activities by cells is now known to be pervasive and to span a multitude of spatial scales, from the length of a cell to just a few enzymes. In this Perspective, part of this special issue on "Seeing into cells", we highlight several recent imaging studies that provide detailed insights into not just where molecules are but where molecules are active within cells, offering a glimpse into the emerging view of biochemical activity architecture as a complement to the physical architecture of a cell.

  9. 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.

  10. 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

  11. Complete integrability of information processing by biochemical reactions

    PubMed Central

    Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

    2016-01-01

    Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling – based on spin systems – has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis–Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy – based on completely integrable hydrodynamic-type systems of PDEs – which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions. PMID:27812018

  12. Complete integrability of information processing by biochemical reactions

    NASA Astrophysics Data System (ADS)

    Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

    2016-11-01

    Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling - based on spin systems - has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis-Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy - based on completely integrable hydrodynamic-type systems of PDEs - which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions.

  13. 40 CFR 158.2010 - Biochemical pesticides 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 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 the...

  14. A molecular structure matching approach to efficient identification of endogenous mammalian biochemical structures.

    PubMed

    Hamdalla, Mai A; Ammar, Reda A; Rajasekaran, Sanguthevar

    2015-01-01

    Metabolomics is the study of small molecules, called metabolites, of a cell, tissue or organism. It is of particular interest as endogenous metabolites represent the phenotype resulting from gene expression. A major challenge in metabolomics research is the structural identification of unknown biochemical compounds in complex biofluids. In this paper we present an efficient cheminformatics tool, BioSMXpress that uses known endogenous mammalian biochemicals and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space. The results of a comprehensive set of empirical experiments suggest that BioSMXpress identifies endogenous mammalian biochemical structures with high accuracy. BioSMXpress is 8 times faster than our previous work BioSM without compromising the accuracy of the predictions made. BioSMXpress is freely available at http://engr.uconn.edu/~rajasek/BioSMXpress.zip.

  15. Biochemical and serological properties of Streptococcus uberis.

    PubMed

    Lämmler, C

    1991-12-01

    The Strep-Zym identification system, a combination of 23 enzymatic tests, allowed a rapid biochemical characterization of Streptococcus uberis. The biochemical profiles of the S. uberis cultures clearly differed from those of S. agalactiae and S. dysgalactiae. Serological grouping of S. uberis revealed polysaccharide antigens of groups E, G, P and U. Some cultures of S. uberis demonstrated CAMP-like synergistic hemolytic activities on sheep blood agar and reacted specifically with the lectins of Helix pomatia and Dolichos biflorus. The occurrence of group polysaccharides, CAMP-like reactivities, and the lectin agglutination reactions were obviously not related to each other or to any of the biochemical properties. These reactions, possibly of importance as virulence factors, might serve as epidemiological markers.

  16. Dynamical fluctuations in biochemical reactions and cycles

    NASA Astrophysics Data System (ADS)

    Pressé, S.; Ghosh, K.; Phillips, R.; Dill, K. A.

    2010-09-01

    We develop theory for the dynamics and fluctuations in some cyclic and linear biochemical reactions. We use the approach of maximum caliber, which computes the ensemble of paths taken by the system, given a few experimental observables. This approach may be useful for interpreting single-molecule or few-particle experiments on molecular motors, enzyme reactions, ion-channels, and phosphorylation-driven biological clocks. We consider cycles where all biochemical states are observable. Our method shows how: (1) the noise in cycles increases with cycle size and decreases with the driving force that spins the cycle and (2) provides a recipe for estimating small-number features, such as probability of backward spin in small cycles, from experimental data. The back-spin probability diminishes exponentially with the deviation from equilibrium. We believe this method may also be useful for other few-particle nonequilibrium biochemical reaction systems.

  17. eQuilibrator—the biochemical thermodynamics calculator

    PubMed Central

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

    2012-01-01

    The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. PMID:22064852

  18. 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

  19. 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.

  20. [Dimorphic fungi: biochemical approach to their dimorphism].

    PubMed

    San-Blas, G

    1995-01-01

    Dimorphism in pathogenic fungi is reviewed. The phenomenon is divided into four interwoven events: (a) perception of external stimuli by cellular sensors; (b) translation into a biochemical message; (c) alteration of the genomic expression, and (d) structural reorganization towards the morphological change. Experimental evidence is provided. Finally, the possibility that fungal dimorphism may have arisen multiple times throughout evolution, is discussed.

  1. 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…

  2. Biochemical reactions of ozone in plants

    Treesearch

    J. Brian Mudd

    1998-01-01

    Plants react biochemically to ozone in three phases: with constitutive chemicals in the apoplastic fluid and cell membranes; by forming messenger molecules by the affected constitutive materials (ethylene); and by responding to the messenger molecules with pathogenic RNAs and proteins. For instance, plant reactions with ozone result in constitutive molecules such as...

  3. 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.

  4. Biochemical Approaches to Improved Nitrogen Fixation

    USDA-ARS?s Scientific Manuscript database

    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...

  5. Probabilistic sensitivity analysis of biochemical reaction systems.

    PubMed

    Zhang, Hong-Xuan; Dempsey, William P; Goutsias, John

    2009-09-07

    Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. We develop here a probabilistic approach to sensitivity analysis of biochemical reaction systems. The proposed technique employs a biophysically derived model for parameter fluctuations and, by using a recently suggested variance-based approach to sensitivity analysis [Saltelli et al., Chem. Rev. (Washington, D.C.) 105, 2811 (2005)], it leads to a powerful sensitivity analysis methodology for biochemical reaction systems. The approach presented in this paper addresses many problems associated with derivative-based sensitivity analysis techniques. Most importantly, it produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of high-order interaction effects. By employing a computational model of the mitogen-activated protein kinase signaling cascade, we demonstrate that our approach is well suited for sensitivity analysis of biochemical reaction systems and can produce a wealth of information about the sensitivity properties of such systems. The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical.

  6. 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…

  7. 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)

  8. 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…

  9. Biochemical validation of smoking status: pros, cons, and data from four low-intensity intervention trials.

    PubMed

    Glasgow, R E; Mullooly, J P; Vogt, T M; Stevens, V J; Lichtenstein, E; Hollis, J F; Lando, H A; Severson, H H; Pearson, K A; Vogt, M R

    1993-01-01

    Biochemical validation of smoking status has long been considered essential, but recent reports have questioned its utility in certain kinds of field trials. We describe efforts to biochemically validate self-reports of smoking cessation from participants in four large-scale randomized trials in outpatient clinics, hospitals, worksites, and dental clinics. These studies included over 5,000 adults smokers who participated in the population-based low-intensity intervention evaluations. At a 1-year follow-up, 798 subjects reported no tobacco use. We attempted to verify these reports using saliva continine/carbon monoxide validation procedures. Overall, there was a moderately high nonparticipation rate (27%), a low disconfirmation rate (4%), and a high self-reported relapse rate (12%) in the interval between survey and biochemical validation. There were no differences between intervention and control conditions on any of the above variables. Longer durations of self-reported abstinence were strongly related to increased probability of biochemical confirmation. Differences in results across projects were related to how biochemical validation was conducted. These results, as well as statistical power considerations, raise questions about whether biochemical validation procedures are practical, informative, or cost-effective in such population-based, low-intensity intervention research.

  10. 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

  11. Kombucha tea fermentation: Microbial and biochemical dynamics.

    PubMed

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

    2016-03-02

    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

  12. 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.

  13. Thermodynamics of Computational Copying in Biochemical Systems

    NASA Astrophysics Data System (ADS)

    Ouldridge, Thomas E.; Govern, Christopher C.; ten Wolde, Pieter Rein

    2017-04-01

    Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that, as in computation, a canonical biochemical readout network generates correlations; extracting no work from these correlations sets a lower bound on dissipation. For general input, the biochemical network cannot reach this bound, even with arbitrarily slow reactions or weak thermodynamic driving. It faces an accuracy-dissipation trade-off that is qualitatively distinct from and worse than implied by the bound, and more complex steady-state copy processes cannot perform better. Nonetheless, the cost remains close to the thermodynamic bound unless accuracy is extremely high. Additionally, we show that biomolecular reactions could be used in thermodynamically optimal devices under exogenous manipulation of chemical fuels, suggesting an experimental system for testing computational thermodynamics.

  14. Advances in Biochemical Indices of Zooplankton Production.

    PubMed

    Yebra, L; Kobari, T; Sastri, A R; Gusmão, F; Hernández-León, S

    Several new approaches for measuring zooplankton growth and production rates have been developed since the publication of the ICES (International Council for the Exploration of the Sea) Zooplankton Methodology Manual (Harris et al., 2000). In this review, we summarize the advances in biochemical methods made in recent years. Our approach explores the rationale behind each method, the design of calibration experiments, the advantages and limitations of each method and their suitability as proxies for in situ rates of zooplankton community growth and production. We also provide detailed protocols for the existing methods and information relevant to scientists wanting to apply, calibrate or develop these biochemical indices for zooplankton production. © 2017 Elsevier Ltd. All rights reserved.

  15. 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.

  16. Self-organizing ontology of biochemically relevant small molecules.

    PubMed

    Chepelev, Leonid L; Hastings, Janna; Ennis, Marcus; Steinbeck, Christoph; Dumontier, Michel

    2012-01-06

    The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. We conclude that the proposed methodology can ease the burden of chemical data annotators and

  17. Numerical Simulation of Bubbly Flows in an Aeration Tank with Biochemical Reactions

    NASA Astrophysics Data System (ADS)

    Noor Ul Huda, Khateeb; Shimizu, Kazuya; Gong, Xiaobo; Takagi, Shu

    2016-11-01

    For bubbly flow with biochemical reactions, all the analyses including overall fluid flow, bubble motion, bubble dissolution at local level and bacterial reactions/consumption of substrates are important. The developed system is provided by mixed Eulerian-Lagrangian formulation in which liquid media is represented in Eulerian system and bubbles are tracked individually. Murai and Matsumoto developed a model to track bubbles to predict plume structure in finely dispersed domain. Gong et al. developed the model further to include mass transfer, gas dissolution and mixing phenomenon entrained in this model. In this research we are using the model to include simulation of bacterial biochemical reactions for the purification of water and make it resemble as the wastewater purification tank. The gas bubble dissolution and mass transfer from gas to liquid phase is linked with biochemical reactions for an overall comprehensive study. The main area associated with this research is to incorporate all biochemical reactions in this bubbly flow based on situation of water and demand. In this particular study, various kinds of biomass and substrates are considered. A detailed model for biological wastewater purification involving reactions using bacteria's is developed and primary validation has been carried out based on experimental study. Finally, we tried to achieve physical optimization for this biochemical reactions.

  18. Biochemical IC Chips Fabricated by Hybrid Microstereolithography

    DTIC Science & Technology

    2003-04-01

    fabricate functional polymer microdevices such as the biochemical IC chips as well as micro/nano machines such as microgears and nanotweezers. We have...microstructures Fig. 8 Microgear made by Super-IH process Fig. 6 shows a schematic diagram of our fabrication system, which consists of an He-Cd laser...photopolymer as shown in Fig. 7. Fig. 8 shows an SEM image of movable microgear fabricated by the Super-IH process. A microgear (diameter: 47 Vm

  19. 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.

  20. 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.

  1. Biochemical assessment of acute myocardial ischaemia.

    PubMed Central

    Perez-Cárceles, M D; Osuna, E; Vieira, D N; Martínez, A; Luna, A

    1995-01-01

    AIMS--To evaluate the efficacy of biochemical parameters in different fluids in the diagnosis of myocardial infarction of different causes, analysed after death. METHODS--The myoglobin concentration and total creatine kinase (CK) and creatine kinase MB isoenzyme (CK-MB) activities were measured in serum, pericardial fluid, and vitreous humour from seven diagnostic groups of cadavers classified according to the severity of myocardial ischaemia and cause of death. Lactate dehydrogenase (LDH) and myosin were measured only in serum and pericardial fluid, and cathepsin D only in pericardial fluid. Routine haematoxylin and eosin and acridine orange staining were used for microscopy studies of heart tissue. RESULTS--In pericardial fluid there were substantial differences between the different groups with respect to CK, CK-MB, and LDH activities and myosin concentrations. The highest values were found in cases with morphological evidence of myocardial ischaemia. CONCLUSIONS--Biochemical parameters, which reach the pericardial fluid via passive diffusion and ultrafiltration due to a pressure gradient, were thus detectable in this fluid earlier than in serum in cases with myocardial ischaemia. These biochemical parameters may be of use for ruling out myocardial ischaemia in those controversial cases in which reliable morphological findings are lacking. PMID:7745110

  2. 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.

  3. Multidimensional biochemical information processing of dynamical patterns.

    PubMed

    Hasegawa, Yoshihiko

    2018-02-01

    Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

  4. Multidimensional biochemical information processing of dynamical patterns

    NASA Astrophysics Data System (ADS)

    Hasegawa, Yoshihiko

    2018-02-01

    Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

  5. The Use of Item Analysis for Improvement of Biochemical Teaching

    ERIC Educational Resources Information Center

    Nagata, Ryoichi

    2004-01-01

    Item analysis was used to find out which biochemical explanations need to be improved in biochemical teaching, not which items are to be discarded, improved, or reusable in biochemical examinations. The analysis revealed the basic facts of which less able students had more misunderstanding than able students. Identifying these basic facts helps…

  6. [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.

  7. Ultra-Sensitive Biochemical Optical Detection Using Distributed Feedback Nanolasers

    NASA Astrophysics Data System (ADS)

    Scheuer, Jacob

    Circular resonators are promising candidates for a wide range of applications, ranging from research involving highly confined fields and strong photon-atom interactions such as cavity QED to optical communication systems and biochemical sensing. For sensing applications, circular cavities exhibit a great potential for achieving ultra-high sensitivity while retaining compact dimensions. The main characteristics of circular resonators are the Q-factor, the free spectral range (FSR), and the modal volume, where the last two are primarily determined by the resonator radius. The total-internal-reflection mechanism employed in “conventional” resonators couples between these characteristics and limits the ability to realize compact devices exhibiting large FSR, small modal volume, and high Q. Recently, a new class of annular resonator, based on a single defect surrounded by radial Bragg reflectors, has been proposed and analyzed. The radial Bragg confinement decouples the modal volume and the Q and paves a new way for the realization of compact and low loss resonators. Such properties as well as the unique mode profile of these circular Bragg nanolasers make this class of devices an excellent tool for ultra-sensitive biochemical detection as well as for studies in nonlinear optics.

  8. 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 ...

  9. [Biochemical risk factors for cardiovascular disease in children].

    PubMed

    Kowalewski, Wieslaw; Hebel, Kazimiera; Góral-Kubasik, Aleksandra

    2013-01-01

    The problem of finding the biochemical markers for determining cardiovascular risk is complex, difficult and multidisciplinary. Even in a simple biochemical blood test the number of possible variables significant for indicating the negative changes in the cardiovascular system is high. The image created from a variety of factors is fuzzy, inconclusive and sometimes difficult to define and explain. Contemporary cardiology uses fixed operative levels and the presence of biochemical factors as the basis for patient diagnosis. Even a thorough and multi-biochemical analysis can not give conclusive results. Many precautions are needed in using the results of biochemical analysis. Ambiguous results may be misleading, disrupt the analytical process, or suggest probable, but not necessarily the correct, solutions. This biochemical analysis presented points to the most important prognostic factors and biochemical information used in the cardiological treatment of children and adolescents.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Kasprzak, Cezary; Damijan, Zbigniew; Panuszka, Ryszard

    2004-05-01

    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.

  12. 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.

  13. [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

  14. The biochemical womb of schizophrenia: A review.

    PubMed

    Gaur, N; Gautam, S; Gaur, M; Sharma, P; Dadheech, G; Mishra, S

    2008-10-01

    The conclusive identification of specific etiological factors or pathogenic processes in the illness of schizophrenia has remained elusive despite great technological progress. The convergence of state-of-art scientific studies in molecular genetics, molecular neuropathophysiology, in vivo brain imaging and psychopharmacology, however, indicates that we may be coming much closer to understanding the genesis of schizophrenia. In near future, the diagnosis and assessment of schizophrenia using biochemical markers may become a "dream come true" for the medical community as well as for the general population. An understanding of the biochemistry/ visa vis pathophysiology of schizophrenia is essential to the discovery of preventive measures and therapeutic intervention.

  15. [Chronic fatigue syndrome: biochemical examination of blood].

    PubMed

    Hakariya, Yukiko; Kuratsune, Hirohiko

    2007-06-01

    Though patients with chronic fatigue syndrome (CFS) have lots of complaints, abnormal findings cannot be detected by biochemical screening tests. However, some specialized blood tests have revealed neuroendocrine immune axis abnormalities, which is closely associated with each other. Recent studies indicate that CFS can be understood as a special condition based on abnormality of the psycho-neuro-endocrino-immunological system, with the distinguishing feature of CFS seeming to be the secondary brain dysfunction caused by several cytokines and/or autoantibodies. In this paper, we summarize these abnormalities found in CFS and show the neuro-molecular mechanism leading to chronic fatigue.

  16. Guiding lights: recent developments in optogenetic control of biochemical signals.

    PubMed

    Yin, Taofei; Wu, Yi I

    2013-03-01

    Optogenetics arises from the innovative application of microbial opsins in mammalian neurons and has since been a powerful technology that fuels the advance of our knowledge in neuroscience. In recent years, there has been growing interest in designing optogenetic tools extendable to broader cell types and biochemical signals. To date, a variety of photoactivatable proteins (refers to induction of protein activity in contrast to fluorescence) have been developed based on the understanding of plant and microbial photoreceptors including phototropins, blue light sensors using flavin adenine dinucleotide proteins, cryptochromes, and phytochromes. Such tools offered researchers reversible, quantitative, and precise spatiotemporal control of enzymatic activity, protein-protein interaction, protein translocation, as well as gene transcription in cells and in whole animals. In this review, we will briefly introduce these photosensory proteins, describe recent developments in optogenetics, and compare and contrast different methods based on their advantages and limitations.

  17. Preterm labour. Biochemical and endocrinological preparation for parturition.

    PubMed

    Terzidou, Vasso

    2007-10-01

    Preterm delivery is a common obstetric problem occurring in about 1 in 10 of all births. Preterm babies have a high risk of morbidity and mortality. Such births account for 75% of all major neonatal problems. At the other end of the spectrum, prolonged pregnancy is also a subject of concern because it too is associated with increased fetal morbidity and mortality. Despite extensive research, the mechanisms that control the length of human pregnancy and signal the onset of labour have not been fully determined. This chapter will discuss basic principles in the biology of parturition and the regulation of contraction-associated proteins including the oxytocin receptor. The major pathways regulating contractions and the transcriptional regulation of the main genes that are known to be involved in the onset of labour and parturition will be examined. Some new potentially therapeutic strategies for the biochemical management of preterm labour will be discussed.

  18. 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.

  19. Biochemical markers of neonatal myocardial dysfunction.

    PubMed

    Almeida, Cristina Maria; Carrapato, Manuel R G; Pinto, Fernando; Pinto, Mariana; Ferreira, Sofia; Schmitt, Denise; Marinho, Luis

    2011-04-01

    Cardiac ultrasounds (US) are not always available at the bedside. Cardiac Troponin I (cTnI), CK-MB and NT-proBNP may be an alternative or complementary to influence evaluation and treatment. To determine reference ranges of biochemical markers cTnI, CK-MB and NT-proBNP in normal neonates. Cord and blood samples were collected from neonates and the above biochemical markers were determined. Ultrasounds were performed blindly. CK-MB remains constant from cord blood to the first day, declining thereafter to almost half the values (81.5 vs 52.0 U/l); cTnI increases from 0.004 to 0.058 ng/ml by 72 h falling to 0.030 by day 10; NT-proBNP peaks by 24 h (5085.5 pg/ml), subsiding to 3388.5 pg/ml by day 3, falling to 1316.0 pg/ml by day 10. CK-MB, mostly of muscle origin and reflecting labor stress or injury, is not to recommend as a measure of myocardial damage in the neonate. The rise in cTnI may be explained by a degree of myocardial involvement, albeit physiological. The initial rise and subsequent fall of NT-proBNP represents the physiological ventricular overload of transient birth adaptation.

  20. Biochemical and exoenzymatic properties of Aeromonas species.

    PubMed

    Janda, J M

    1985-05-01

    One hundred twenty-seven isolates of Aeromonas comprising the three currently recognizable species (A. hydrophila, A. sobria, and A. caviae) were evaluated for biochemical and exoenzymatic properties. Aeromonas species were generally (greater than 90%) characterized as gram-negative fermentative rods that were oxidase-, catalase-, and beta-galactosidase-positive, produced arginine dihydrolase, and failed to decarboxylate ornithine. More than 95% of all isolates tested failed to grow on 6.5% salt or thiosulfate-citrate bile salts agar and were resistant to the vibriostatic agent 0/129. Most Aeromonas species produced acid from hexoses while failing to ferment alcoholic sugars or trisaccharides. In exoenzymatic studies, Aeromonas species were uniformly found to produce several exoenzymes, including amylase, DNase, RNase, esterase, lipase, gelatinase, protease, fibrinolysin, and chitinase. Within the genus, a number of biochemical and enzymatic properties were found to be associated with one or more of the taxonomically recognizable species. These properties included glycoside utilization, Heiberg grouping based upon fermentation of arabinose, sucrose, and mannose, and the elaboration of several extracellular enzymes (elastase, hemolysin, lecithinase, phosphatase). In addition, phenotypic markers previously associated with enterotoxigenic Aeromonas isolates were almost exclusively found among A. hydrophila and A. sobria species, suggesting that these species are the major enteric pathogens.

  1. Biochemical Manifestation of HIV Lipodystrophy Syndrome.

    PubMed

    Ihenetu, Kenneth; Mason, Darius

    2012-01-01

    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. 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. 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). 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.

  2. Reference values of biochemical and hematological parameters for Guizhou minipigs.

    PubMed

    Chen, Younan; Qin, Shengfang; Ding, Yang; Li, Shengfu; Yang, Guang; Zhang, Jie; Li, Youping; Cheng, Jingqiu; Lu, Yanrong

    2011-04-01

    The pig is not only an economically important livestock animal but is also a valuable model animal for biomedical research and xenotransplantation. Reference values for clinical biochemical and hematological parameters are required for accurate data interpretation while using a pig model. In this study, whole blood samples were collected from 54 healthy Chinese Guizhou minipigs. We analyzed routine biochemical and hematological parameters and special coagulation parameters, including thrombelastography and coagulation factor activities, and have presented the baseline values of these parameters. These data provide valuable information for investigators using minipigs as animal models in biomedical studies and useful physiological data for veterinarians and livestock producers. We also compared all the results for the minipigs with the corresponding data from healthy humans. The bilirubin, uric acid and cholesterol levels of minipigs were significantly lower than those of humans (14%, 0.086% and 48% of human levels, respectively), whereas the serum enzyme levels were much higher than those in humans (e.g. the hydroxybutyrate dehydrogenase and creatine kinase levels of the minipigs were 19- and 8.4-fold higher than the human reference values). The red blood cell counts, platelet counts and white blood cell counts of the minipigs were significantly higher than those of the humans. The coagulation activities of factor VII and factor X were higher in minipigs than in humans. The significant differences observed between minipigs and humans for many of these parameters suggest substantial interspecies disparities in organs and tissues. These differences merit greater attention in biomedical research involving minipigs, particularly in the area of pig-to-human transplantation.

  3. 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.

  4. Recent buzz in malaria research.

    PubMed

    Chenette, Emily J

    2017-08-01

    In this Commentary, we highlight the latest findings in three active areas of malaria research: Plasmodium biology; host response; and malaria control, prevention and treatment. © 2017 Federation of European Biochemical Societies.

  5. Highly valuable microalgae: biochemical and topological aspects.

    PubMed

    Pignolet, Olivier; Jubeau, Sébastien; Vaca-Garcia, Carlos; Michaud, Philippe

    2013-08-01

    The past decade has seen a surge in the interest in microalgae culture for biodiesel production and other applications as renewable biofuels as an alternative to petroleum transport fuels. The development of new technologies for the culture of these photosynthetic microorganisms and improved knowledge of their biochemical composition has spurred innovation in the field of high-value biomolecules. These developments are only economically viable if all the microalgae fractions are valorized in a biorefinery strategy. Achieving this objective requires an understanding of microalgae content and the cellular localization of the main biomolecular families in order to develop efficient harvest and sequential recovery technologies. This review summarizes the state of the art in microalgae compositions and topologies using some examples of the main industrially farmed microalgae.

  6. Biochemical engineering aspects of expanded bed adsorption.

    PubMed

    Hubbuch, Jürgen; Thömmes, Jörg; Kula, Maria-Regina

    2005-01-01

    The economic feasibility of a biotechnological production process is directly linked to the number and efficiency of the processes required during purification in order to reach the requested product specifications. Expanded bed adsorption is an integrated process that combines solid-liquid separation and product recovery into a single unit operation. This approach suggests an increased overall yield, lower requirements for capital investments and consumables and most importantly a reduced process time. The success of an integrative process is, however, closely linked to a detailed understanding of the biochemical principles involved and the constraints arising from feedstock complexity. This paper reviews the hydrodynamic principles that expanded bed adsorption is based on, discusses current developments in resin and column design, and finally presents a methodology for targeted process development in expanded bed adsorption.

  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. Biochemical Basis of Sestrin Physiological Activities

    SciTech Connect

    Ho, Allison; Cho, Chun-Seok; Namkoong, Sim

    2016-05-10

    Excessive accumulation of reactive oxygen species (ROS) and chronic activation of mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) are well-characterized promoters of aging and age-associated degenerative pathologies. Sestrins, a family of highly conserved stress-inducible proteins, are important negative regulators of both ROS and mTORC1 signaling pathways; however, the mechanistic basis of how Sestrins suppress these pathways remains elusive. In the past couple of years, breakthrough discoveries about Sestrin signaling and its molecular nature have markedly increased our biochemical understanding of Sestrin function. These discoveries have also uncovered new potential therapeutic strategies that may eventually enable us to attenuate agingmore » and age-associated diseases.« less

  9. 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.

  10. 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

  11. Biochemical processes of oligotrophic peat deposits of Vasyugan Mire

    NASA Astrophysics Data System (ADS)

    Inisheva, L. I.; Sergeeva, M. A.

    2009-04-01

    The problem of peat and mire ecosystems functioning and their rational use is the main problem of biosphere study. This problem also refers to forecasting of biosphere changes results which are global and anthropogenic. According to many scientists' research the portion of mires in earth carbon balance is about 15% of world's stock. The aim of this study is to investigate biochemical processes in oligotrophic deposits in North-eastern part of Vasyugan Mire. The investigations were made on the territory of scientific-research ground (56˚ 03´ and 56˚ 57´ NL, 82˚ 22´ and 82˚ 42´ EL). It is situated between two rivers Bakchar and Iksa (in outskirts of the village Polynyanka, Bakchar region, Tomsk oblast). Evolution of investigated mire massif began with the domination of eutrophic phytocenosis - Filicinae, then sedge. Later transfer into oligotrophic phase was accompanied by formation of meter high-moor peat deposit. The age of three-meter peat deposit reaches four thousand years. Biochemical processes of carbon cycle cover the whole peat deposit, but the process activity and its direction in different layers are defined by genesis and duration of peat formation. So, the number of cellulose-fermenting aerobes in researched peat deposits ranges from 16.8 to 75.5 million CFU/g, and anaerobic bacteria from 9.6 to 48.6 million CFU/g. The high number of aerobes is characteristic for high water levels, organizing by raised bog peats. Their number decreases along the profile in 1.7 - 2 times. The number of microflora in peat deposit is defined by the position in the landscape profile (different geneses), by the depth, by hydrothermic conditions of years and individual months. But microflora activity shows along all depth of peat deposit. We found the same in the process of studying of micromycete complex structure. There was revealed either active component micromycete complex - mycelium, or inert one - spores in a meter layer of peat deposit. If mushrooms

  12. Developments in commercially produced microbials at Biochem Products

    Treesearch

    John Lublinkhof; Douglas H. Ross

    1985-01-01

    Biochem Products is part of a large industrial and scientific family - the Solvay Group. Solvay, headquartered in Brussels, Belgium is a multinational company with 46,000 employees worldwide. In the U.S., our working partners include a large polymer manufacturer, a peroxygen producer and a leading poultry and animal health products company. Biochem Products is a...

  13. 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)

  14. 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.

  15. Physiological, Biochemical, and Molecular Mechanisms of Heat Stress Tolerance in Plants

    PubMed Central

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

    2013-01-01

    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. PMID:23644891

  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. The need for combined inorganic, biochemical, and nutritional studies of chromium(III).

    PubMed

    Vincent, John B; Love, Sharifa T

    2012-09-01

    The history of biochemical and nutritional studies of the element is unfortunately full of twists and turns, most leading to dead ends. Chromium (Cr), as the trivalent ion, has been proposed to be an essential element, a body mass and muscle development agent, and, in the form of the most popular Cr-containing nutritional supplement, to be toxic when given orally to mammals. None of these proposals, despite significant attention in the popular media, has proven to be correct. Trivalent chromium has also been proposed as a therapeutic agent to increase insulin sensitivity and affect lipid metabolism, although a molecular mechanism for such actions has not been elucidated. Greater cooperative research interactions between nutritionists, biochemists, and chemists might have avoided the earlier issues in nutritional and biochemical Cr research and is necessary to establish the potential role of Cr as a therapeutic agent at a molecular level. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

  18. Muriel Wheldale Onslow and early biochemical genetics.

    PubMed

    Richmond, Marsha L

    2007-01-01

    Muriel Whedale, a distinguished graduate of Newnham College, Cambridge, was a member of William Bateson's school of genetics at Cambridge University from 1903. Her investigation of flower color inheritance in snapdragons (Antirrhinum), a topic of particular interest to botanists, contributed to establishing Mendelism as a powerful new tool in studying heredity. Her understanding of the genetics of pigment formation led her to do cutting-edge work in biochemistry, culminating in the publication of her landmark work, The Anthocyanin Pigments of Plants (1916). In 1915, she joined Frederick Gowland Hopkin's Department of Biochemistry as assistant and in 1926 became one of the first women to be appointed university lecturer. In 1919 she married the biochemist Huia Onslow, with whom she collaborated until his death in 1922. This paper examines Whedale's work in genetics and especially focuses on the early linkage of Mendelian methodology with new techniques in biochemistry that eventually led to the founding of biochemical genetics. It highlights significant issues in the early history of women in genetics, including the critical role of mentors, funding opportunities, and career strategies.

  19. 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.

  20. 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.

  1. Liver in Leprosy: Histological and Biochemical Findings

    PubMed Central

    Karat, A. B. A.; Job, C. K.; Rao, P. S. S.

    1971-01-01

    The histological findings and their correlation with biochemical functions of the liver in 240 leprosy patients are presented. In 21% with tuberculoid leprosy and in 62% with lepromatous leprosy leprous granulomata were found in the liver. A significant prevalence of granulomatous lesions in the liver among patients with tuberculoid and borderline-tuberculoid leprosy of less than one year's duration suggests that bacillaemia occurs early in all forms of leprosy. There was a direct correlation between bacterial index and the presence of acid-fast bacilli in the liver. Of 50 patients with negative skin smears seven had acid-fast bacilli at liver biopsy. From none of these liver homogenates were acid-fast bacilli grown on culture in Löwenstein-Jensen medium. The alterations in liver functions were more consistently seen when acid-fast bacilli were associated with the presence of leprous granulomatous lesions. The acid-fast bacilli were found to persist even after one to five years of specific antileprosy therapy and after the bacilli in the skin had cleared up. This may explain the relatively frequent recrudescence or relapse of the bacillated types of leprosy when specific antileprosy therapy is stopped soon after bacterial negativity is attained on skin smears. PMID:5541723

  2. 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. Copyright © 2013 Wiley Periodicals, Inc.

  3. 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).

  4. Validation of artificial neural network models for predicting biochemical markers associated with male infertility.

    PubMed

    Vickram, A S; Kamini, A Rao; Das, Raja; Pathy, M Ramesh; Parameswari, R; Archana, K; Sridharan, T B

    2016-08-01

    Seminal fluid is the secretion from many glands comprised of several organic and inorganic compounds including free amino acids, proteins, fructose, glucosidase, zinc, and other scavenging elements like Mg(2+), Ca(2+), K(+), and Na(+). Therefore, in the view of development of novel approaches and proper diagnosis to male infertility, overall understanding of the biochemical and molecular composition and its role in regulation of sperm quality is highly desirable. Perhaps this can be achieved through artificial intelligence. This study was aimed to elucidate and predict various biochemical markers present in human seminal plasma with three different neural network models. A total of 177 semen samples were collected for this research (both fertile and infertile samples) and immediately processed to prepare a semen analysis report, based on the protocol of the World Health Organization (WHO [2010]). The semen samples were then categorized into oligoasthenospermia (n=35), asthenospermia (n=35), azoospermia (n=22), normospermia (n=34), oligospermia (n=34), and control (n=17). The major biochemical parameters like total protein content, fructose, glucosidase, and zinc content were elucidated by standard protocols. All the biochemical markers were predicted by using three different artificial neural network (ANN) models with semen parameters as inputs. Of the three models, the back propagation neural network model (BPNN) yielded the best results with mean absolute error 0.025, -0.080, 0.166, and -0.057 for protein, fructose, glucosidase, and zinc, respectively. This suggests that BPNN can be used to predict biochemical parameters for the proper diagnosis of male infertility in assisted reproductive technology (ART) centres. AAS: absorption spectroscopy; AI: artificial intelligence; ANN: artificial neural networks; ART: assisted reproductive technology; BPNN: back propagation neural network model; DT: decision tress; MLP: multilayer perceptron; PESA: percutaneous

  5. [Clinical and biochemical characterization of childhood urolithiasis].

    PubMed

    Giraudon, A; Richard, E; Godron, A; Bouty, A; Dobremez, E; Barat, P; Blouin, J-M; Llanas, B; Harambat, J

    2014-12-01

    Urolithiasis is rare in children, but the incidence has increased over the past few decades. This study aims at describing the clinical and biochemical characteristics, etiology, and treatment of urolithiasis in children. This was a retrospective study of all children under 16 years of age seen at the Bordeaux University Children's Hospital with a diagnosis of urolithiasis. The diagnosis was confirmed either radiologically or clinically by the expulsion of the stone. A total of 186 children with a diagnosis of urolithiasis between 1994 and 2012 were included. The median age at diagnosis was 7.4 years. The male-to-female ratio was 1.9. The estimated annual incidence was around 5.5/100,000 children under 15 years of age in the past 5 years. The main presenting feature was nonspecific abdominal pain (71%). Metabolic calculi accounted for 48% of the patients with idiopathic hypercalciuria as the main cause. Genetic diseases accounted for 15% of cases. The proportion of infectious calculi was estimated at 33% and decreased in the past two decades. Stone fragments were sent for analysis in 86 children, and calcium oxalate was the major component (37%), followed by calcium phosphate (33%), purine (9%), and struvite (8%). At least 26% of patients experienced recurrence of stone passage. This retrospective study highlighted changes in characteristics of pediatric urolithiasis over time. Childhood-onset urolithiasis requires complete etiological work-up so that a metabolic cause with a high risk of recurrence does not go unrecognized. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  6. A chemiluminescence biochemical oxygen demand measuring method.

    PubMed

    Nakamura, Hideaki; Abe, Yuta; Koizumi, Rui; Suzuki, Kyota; Mogi, Yotaro; Hirayama, Takumi; Karube, Isao

    2007-10-17

    A new chemiluminescence biochemical oxygen demand (BOD(CL)) determining method was studied by employing redox reaction between quinone and Baker's yeast. The measurement was carried out by utilizing luminol chemiluminescence (CL) reaction catalyzed by ferricyanide with oxidized quinone of menadione, and Saccharomyces cerevisiae using a batch-type luminometer. In this study, dimethyl sulfoxide was used as a solvent for menadione. After optimization of the measuring conditions, the CL response to hydrogen peroxide in the incubation mixture had a linear response between 0.1 and 100 microM H2O2 (r2=0.9999, 8 points, n=3, average of relative standard deviation; R.S.D.(av)=4.22%). Next, a practical relationship between the BOD(CL) response and the glucose glutamic acid concentration was obtained over a range of 11-220 mg O2 L(-1) (6 points, n=3, R.S.D.(av) 3.71%) with a detection limit of 5.5 mg O2 L(-1) when using a reaction mixture and incubating for only 5 min. Subsequently, the characterization of this method was studied. First, the BOD(CL) responses to 16 pure organic substances were examined. Second, the influences of chloride ions, artificial seawater, and heavy metal ions on the BOD(CL) response were investigated. Real sample measurements using river water were performed. Finally, BOD(CL) responses were obtained for at least 8 days when the S. cerevisiae suspension was stored at 4 degrees C (response reduction, 69.9%; R.S.D. for 5 testing days, 18.7%). BOD(CL) responses after 8 days and 24 days were decreased to 69.9% and 35.8%, respectively, from their original values (R.S.D. for 8 days involving 5 testing days, 18.7%).

  7. Arsenic Uptake, Toxicity, Detoxification, and Speciation in Plants: Physiological, Biochemical, and Molecular Aspects

    PubMed Central

    Abbas, Ghulam; Murtaza, Behzad; Bibi, Irshad; Shahid, Muhammad; Khan, Muhammad Imran; Amjad, Muhammad; Hussain, Munawar; Natasha

    2018-01-01

    Environmental contamination with arsenic (As) is a global environmental, agricultural and health issue due to the highly toxic and carcinogenic nature of As. Exposure of plants to As, even at very low concentration, can cause many morphological, physiological, and biochemical changes. The recent research on As in the soil-plant system indicates that As toxicity to plants varies with its speciation in plants (e.g., arsenite, As(III); arsenate, As(V)), with the type of plant species, and with other soil factors controlling As accumulation in plants. Various plant species have different mechanisms of As(III) or As(V) uptake, toxicity, and detoxification. This review briefly describes the sources and global extent of As contamination and As speciation in soil. We discuss different mechanisms responsible for As(III) and As(V) uptake, toxicity, and detoxification in plants, at physiological, biochemical, and molecular levels. This review highlights the importance of the As-induced generation of reactive oxygen species (ROS), as well as their damaging impacts on plants at biochemical, genetic, and molecular levels. The role of different enzymatic (superoxide dismutase, catalase, glutathione reductase, and ascorbate peroxidase) and non-enzymatic (salicylic acid, proline, phytochelatins, glutathione, nitric oxide, and phosphorous) substances under As(III/V) stress have been delineated via conceptual models showing As translocation and toxicity pathways in plant species. Significantly, this review addresses the current, albeit partially understood, emerging aspects on (i) As-induced physiological, biochemical, and genotoxic mechanisms and responses in plants and (ii) the roles of different molecules in modulation of As-induced toxicities in plants. We also provide insight on some important research gaps that need to be filled to advance our scientific understanding in this area of research on As in soil-plant systems. PMID:29301332

  8. Arsenic Uptake, Toxicity, Detoxification, and Speciation in Plants: Physiological, Biochemical, and Molecular Aspects.

    PubMed

    Abbas, Ghulam; Murtaza, Behzad; Bibi, Irshad; Shahid, Muhammad; Niazi, Nabeel Khan; Khan, Muhammad Imran; Amjad, Muhammad; Hussain, Munawar

    2018-01-02

    Environmental contamination with arsenic (As) is a global environmental, agricultural and health issue due to the highly toxic and carcinogenic nature of As. Exposure of plants to As, even at very low concentration, can cause many morphological, physiological, and biochemical changes. The recent research on As in the soil-plant system indicates that As toxicity to plants varies with its speciation in plants (e.g., arsenite, As(III); arsenate, As(V)), with the type of plant species, and with other soil factors controlling As accumulation in plants. Various plant species have different mechanisms of As(III) or As(V) uptake, toxicity, and detoxification. This review briefly describes the sources and global extent of As contamination and As speciation in soil. We discuss different mechanisms responsible for As(III) and As(V) uptake, toxicity, and detoxification in plants, at physiological, biochemical, and molecular levels. This review highlights the importance of the As-induced generation of reactive oxygen species (ROS), as well as their damaging impacts on plants at biochemical, genetic, and molecular levels. The role of different enzymatic (superoxide dismutase, catalase, glutathione reductase, and ascorbate peroxidase) and non-enzymatic (salicylic acid, proline, phytochelatins, glutathione, nitric oxide, and phosphorous) substances under As(III/V) stress have been delineated via conceptual models showing As translocation and toxicity pathways in plant species. Significantly, this review addresses the current, albeit partially understood, emerging aspects on (i) As-induced physiological, biochemical, and genotoxic mechanisms and responses in plants and (ii) the roles of different molecules in modulation of As-induced toxicities in plants. We also provide insight on some important research gaps that need to be filled to advance our scientific understanding in this area of research on As in soil-plant systems.

  9. Biochemical mediator demand--a novel rapid alternative for measuring biochemical oxygen demand.

    PubMed

    Pasco, N; Baronian, K; Jeffries, C; Hay, J

    2000-05-01

    The biochemical oxygen demand (BOD) test (BOD5) is a crucial environmental index for monitoring organic pollutants in waste water but is limited by the 5-day requirement for completing the test. We have optimised a rapid microbial technique for measuring the BOD of a standard BOD5 substrate (150 mg glucose/l, 150 mg glutamic acid/l) by quantifying an equivalent biochemical mediator demand in the absence of oxygen. Elevated concentrations of Escherichia coli were incubated with an excess of redox mediator, potassium hexacyanoferrate(III), and a known substrate for 1 h at 37 degrees C without oxygen. The addition of substrate increased the respiratory activity of the microorganisms and the accumulation of reduced mediator; the mediator was subsequently re-oxidised at a working electrode generating a current quantifiable by a coulometric transducer. Catabolic conversion efficiencies exceeding 75% were observed for the oxidation of the standard substrate. The inclusion of a mediator allowed a higher co-substrate concentration compared to oxygen and substantially reduced the incubation time from 5 days to 1 h. The technique replicates the traditional BOD5 method, except that a mediator is substituted for oxygen, and we aim to apply the principle to measure the BOD of real waste streams in future work.

  10. Biochemical assays for the discovery of TDP1 inhibitors.

    PubMed

    Marchand, Christophe; Huang, Shar-yin N; Dexheimer, Thomas S; Lea, Wendy A; Mott, Bryan T; Chergui, Adel; Naumova, Alena; Stephen, Andrew G; Rosenthal, Andrew S; Rai, Ganesha; Murai, Junko; Gao, Rui; Maloney, David J; Jadhav, Ajit; Jorgensen, William L; Simeonov, Anton; Pommier, Yves

    2014-08-01

    Drug screening against novel targets is warranted to generate biochemical probes and new therapeutic drug leads. TDP1 and TDP2 are two DNA repair enzymes that have yet to be successfully targeted. TDP1 repairs topoisomerase I-, alkylation-, and chain terminator-induced DNA damage, whereas TDP2 repairs topoisomerase II-induced DNA damage. Here, we report the quantitative high-throughput screening (qHTS) of the NIH Molecular Libraries Small Molecule Repository using recombinant human TDP1. We also developed a secondary screening method using a multiple loading gel-based assay where recombinant TDP1 is replaced by whole cell extract (WCE) from genetically engineered DT40 cells. While developing this assay, we determined the importance of buffer conditions for testing TDP1, and most notably the possible interference of phosphate-based buffers. The high specificity of endogenous TDP1 in WCE allowed the evaluation of a large number of hits with up to 600 samples analyzed per gel via multiple loadings. The increased stringency of the WCE assay eliminated a large fraction of the initial hits collected from the qHTS. Finally, inclusion of a TDP2 counter-screening assay allowed the identification of two novel series of selective TDP1 inhibitors. ©2014 American Association for Cancer Research.

  11. 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

  12. Dietary intakes and biochemical profiles of nutritional status of ultramarathoners.

    PubMed

    Singh, A; Evans, P; Gallagher, K L; Deuster, P A

    1993-03-01

    Nutritional status was determined in 17 ultramarathoners registered to participate in the Old Dominion 100-Miler. They had a mean age of 40 +/- 2 yr and ran 67.7 +/- 9.0 miles.wk-1. Subjects maintained 4-d dietary records on two occasions: usual and prerace. Fasting blood samples and 24-h urine collections were also obtained, and concentrations of selected vitamins and minerals were analyzed. Usual and prerace energy, carbohydrate and fat intakes of the ultramarathoners were not significantly different, but usual protein and alcohol intakes were significantly (P < 0.05) higher than prerace intakes. The amount of energy supplied by carbohydrates rose from a usual intake of 54.2 +/- 2.3% to 60.1 +/- 2.4% in the prerace period. Twelve subjects reported taking vitamin/mineral supplements and mean usual and prerace intakes of vitamin and minerals from food and supplements combined met the current recommendations. Biochemical indices of vitamin and mineral status were normal. However, our findings suggest that vitamin B12 metabolism may be altered in ultraendurance runners. Further research is required to determine whether ultraendurance athletes have special nutrition needs.

  13. Homo sapiens ascorbicus, a biochemically corrected robust human mutant.

    PubMed

    Stone, I

    1979-06-01

    Homo sapiens' gene pool contains a defective gene for the synthesis of the active enzyme protein, L-gulonolactone oxidase(GLO). The absence of GLO in the human liver blocks the normal mammalian conversion of blood sugar into ascorbate, leading to the potentially-fatal "inborn error of carbohydrate metabolism", the genetic disease, Hypoascorbemia (in the older nomenclature- scurvy). To survive, humans need exogenous sources of daily ascorbate. Most mammals have the intact gene for GLO synthesis and produce generous daily amounts of the liver metabolite, ascorbate; for instance, an unstressed 70 Kg goat is capable of producing over 13 grams of ascorbate daily and much more under stress. The recommended dietary allowance of 45 milligrams of ascorbate a day for human adults, now proposed and used by nutritionists, is grossly inadequate to restore Homo sapiens to a normal mammalian ascorbate physiology. To correct fully this human genetic defect and banish epidemic chronic subclinical scurvy requires daily intakes of ascorbate equivalent to, at least, the amounts synthesized by the other mammals. Humans kept on a long term regime of full correction of this birth defect show great salutary benefits in health maintenance, disease therapy and slowing of the aging process. This can be regarded as the creation of a new and more robust, longer-living, tough human sub-species, Homo sapiens ascorbicus, by the biochemical reversal of a primate mutation occurring some 60 million years ago. Some of the practical benefits and pathways of future clinical research are discussed.

  14. Positron emission mammography: high-resolution biochemical breast imaging.

    PubMed

    Weinberg, Irving N; Beylin, David; Zavarzin, Valera; Yarnall, Steve; Stepanov, Pavel Y; Anashkin, Edward; Narayanan, Deepa; Dolinsky, Sergei; Lauckner, Kathrin; Adler, Lee P

    2005-02-01

    Positron emission mammography (PEM) provides images of biochemical activity in the breast with spatial resolution matching individual ducts (1.5 mm full-width at half-maximum). This spatial resolution, supported by count efficiency that results in high signal-to-noise ratio, allows confident visualization of intraductal as well as invasive breast cancers. Clinical trials with a full-breast PEM device have shown high clinical accuracy in characterizing lesions identified as suspicious on the basis of conventional imaging or physical examination (sensitivity 93%, specificity 83%, area under the ROC curve of 0.93), with high sensitivity preserved (91%) for intraductal cancers. Increased sensitivity did not come at a cost of reduced specificity. Considering that intraductal cancer represents more than 30% of reported cancers, and is the form of cancer with the highest probability of achieving surgical cure, it is likely that the use of PEM will complement anatomic imaging modalities in the areas of surgical planning, high-risk monitoring, and minimally invasive therapy. The quantitative nature of PET promises to assist researchers interested studying the response of putative cancer precursors (e.g., atypical ductal hyperplasia) to candidate prevention agents.

  15. 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 activemore » 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.« less

  16. [Application of chemiluminescent methods in biochemical investigations].

    PubMed

    Druzhina, N A; Moiseev, A Iu

    2005-01-01

    The review of modern luminescent methods of research, their prospects and potentialities of practical application in biological researches is presented. Special attention is given to the study of dynamics of the processes of peroxide oxidation and to activity of the enzymes of antioxidant protection in biological systems using the chemiluminescent methods, and also to their use in experimental oncology and radiobiology.

  17. Biochemical investigation of cypermethrin toxicity in rabbits.

    PubMed

    Dahamna, S; Harzallah, D; Guemache, A; Sekfali, N

    2009-01-01

    cypermethrin on the erythropoiesis. An increase of plasma enzyme activities in GOT, GPT and CPK were recorded, explain a high energy-generating product. An increase, in the plasma enzyme activity in Alkaline phosphatase, related to their role in the cell permeability. The histopathological results showed lesions and morphological changes of hepato-cellular, fibrosis and appearance of inflammatory infiltrate, confirmed disturbances of the biochemical parameters. These changes were much underlines during the animal toxicity.

  18. 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

  19. 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.

  20. 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)

  1. [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.

  2. Organic solvent pretreatment of lignocellulosic biomass for biofuels and biochemicals: A review.

    PubMed

    Zhang, Ke; Pei, Zhijian; Wang, Donghai

    2016-01-01

    Lignocellulosic biomass represents the largest potential volume and lowest cost for biofuel and biochemical production. Pretreatment is an essential component of biomass conversion process, affecting a majority of downstream processes, including enzymatic hydrolysis, fermentation, and final product separation. Organic solvent pretreatment is recognized as an emerging way ahead because of its inherent advantages, such as the ability to fractionate lignocellulosic biomass into cellulose, lignin, and hemicellulose components with high purity, as well as easy solvent recovery and solvent reuse. Objectives of this review were to update and extend previous works on pretreatment of lignocellulosic biomass for biofuels and biochemicals using organic solvents, especially on ethanol, methanol, ethylene glycol, glycerol, acetic acid, and formic acid. Perspectives and recommendations were given to fully describe implementation of proper organic solvent pretreatment for future research. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Laetrile: A Study of Its Physicochemical and Biochemical Properties

    PubMed Central

    Levi, Leo; French, W. N.; Bickis, I. J.; Henderson, I. W. D.

    1965-01-01

    A study was made of the composition and biochemical behaviour of the drug, Laetrile, distributed for clinical trial in the United States and Canada. It was established that the Canadian and the American product are different pharmaceutical formulations, displaying different physicochemical and biochemical properties. The investigation demonstrated, furthermore, that neither preparation can be considered as a palliative in cancer therapy on the basis of the biological rationale advanced by their manufacturers. ImagesFig. 3 PMID:14281087

  4. ALX receptor ligands define a biochemical endotype for severe asthma

    PubMed Central

    Ricklefs, Isabell; Barkas, Ioanna; Duvall, Melody G.; Grossman, Nicole L.; Israel, Elliot; Bleecker, Eugene R.; Castro, Mario; Erzurum, Serpil C.; Fahy, John V.; Gaston, Benjamin M.; Denlinger, Loren C.; Mauger, David T.; Wenzel, Sally E.; Comhair, Suzy A.; Coverstone, Andrea M.; Fajt, Merritt L.; Hastie, Annette T.; Johansson, Mats W.; Peters, Michael C.; Phillips, Brenda R.; Levy, Bruce D.

    2017-01-01

    BACKGROUND. In health, inflammation resolution is an active process governed by specialized proresolving mediators and receptors. ALX/FPR2 receptors (ALX) are targeted by both proresolving and proinflammatory ligands for opposing signaling events, suggesting pivotal roles for ALX in the fate of inflammatory responses. Here, we determined if ALX expression and ligands were linked to severe asthma (SA). METHODS. ALX expression and levels of proresolving ligands (lipoxin A4 [LXA4], 15-epi-LXA4, and annexin A1 [ANXA1]), and a proinflammatory ligand (serum amyloid A [SAA]) were measured in bronchoscopy samples collected in Severe Asthma Research Program-3 (SA [n = 69], non-SA [NSA, n = 51] or healthy donors [HDs, n = 47]). RESULTS. Bronchoalveolar lavage (BAL) fluid LXA4 and 15-epi-LXA4 were decreased and SAA was increased in SA relative to NSA. BAL macrophage ALX expression was increased in SA. Subjects with LXA4loSAAhi levels had increased BAL neutrophils, more asthma symptoms, lower lung function, increased relative risk for asthma exacerbation, sinusitis, and gastroesophageal reflux disease, and were assigned more frequently to SA clinical clusters. SAA and aliquots of LXA4loSAAhi BAL fluid induced IL-8 production by lung epithelial cells expressing ALX receptors, which was inhibited by coincubation with 15-epi-LXA4. CONCLUSIONS. Together, these findings have established an association between select ALX receptor ligands and asthma severity that define a potentially new biochemical endotype for asthma and support a pivotal functional role for ALX signaling in the fate of lung inflammation. TRIAL REGISTRATION. Severe Asthma Research Program-3 (SARP-3; ClinicalTrials.gov NCT01606826) FUNDING Sources. National Heart, Lung and Blood Institute, the NIH, and the German Society of Pediatric Pneumology. PMID:28724795

  5. 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

  6. [NUTRITIONAL STATUS BY ANTHROPOMETRIC AND BIOCHEMICAL PARAMETERS OF COLLEGE BASKETBALL PLAYERS].

    PubMed

    Godoy-Cumillaf, Andrés Esteban Roberto; Cárcamo-Araneda, Cristian Rodolfo; Hermosilla-Rodríguez, Freddy Patricio; Oyarzún-Ruiz, Jean Pierre; Viveros-Herrera, José Francisco Javier

    2015-12-01

    in relation to the student population, their class schedules, hours of study, budget shortages, among others, do not allow them to have good eating habits and sedentary ago. Within this context are the sports teams, which must deal with the above. knowing the nutritional status of a group of college basketball players (BU) by anthropometric and biochemical parameters. the research provides a non-experimental, descriptive, transversal, with a quantitative approach The sample was selected on a non-probabilistic approach. which included 12 players design. Anthropometric parameters for body mass index (BMI), somatotype and body composition was assessed. For biochemical glucose, triglycerides and cholesterol. have a BMI of 24.6 (kg/m2), are classified as endomesomorfas (5,5-4,3-1,2) have a fat mass 39.9% and 37.8% of muscle mass, glucose values are 68.7 (mg/dl), triglycerides 128 (mg/dl) and 189 cholesterol (mg/dl). the BU have normal values for BMI and biochemical parameters, but dig deeper greater amount of adipose tissue is found as reported by body composition and somatotype, a situation that could be related to poor eating habits, however is required further study to reach a categorical conclusion. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

  7. Development of web based database on biochemical characteristics of rapeseed-mustard.

    PubMed

    Kumar, Vinod; Bala, Manju

    2013-01-01

    Rapeseed-mustard oil is an essential dietary component, in India. The modification of rapeseed- mustard for fatty acid composition of seed oil to develop new genotypes having alternative oil and meal characteristics has been an important objective in quality breeding. Moreover, Breeding efforts in India are in progress to develop double low varieties to meet the internationally acceptable standards of oil and seed meal. So, information on the nutritional and anti-nutritional make-up of rapeseed-mustard oil and seed meal of the existing germplasm would be quite useful for the researchers especially breeders involved in the quality improvement programmes. In the present study database on biochemical characteristics of rapeseed-mustard has been developed using open source technology LAMP. The database provides the information on 14 important biochemical characters such as oil, saturated fatty acids, oleic, linoleic, linolenic, eicosenoic, erucic acid, monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), ω6/ω3 ratio, protein, glucosinolate, phenol, and fiber content. It offers web interface to submit and search data in the database. The database presently comprises biochemical characteristics of germplasm accessions, advance breeding lines and notified varieties of rapeseed-mustard. The database developed will be useful to the breeders in the selection of desired genotype with specific traits.

  8. 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.

  9. Effect of menthol cigarettes on biochemical markers of smoke exposure among black and white smokers.

    PubMed

    Clark, P I; Gautam, S; Gerson, L W

    1996-11-01

    Black smokers have been reported to have higher serum cotinine levels than do white smokers, and have higher rates of most smoking-related diseases, despite smoking fewer cigarettes per day. Another striking racial difference is the preference for mentholated cigarettes among black smokers. The contribution of menthol to variability in biochemical markers of cigarette smoke exposure (end-expiratory carbon monoxide and serum cotinine) was evaluated in a biracial sample. Descriptive cross-sectional. A university smoking research laboratory. Sixty-five black and 96 white adult established smokers who were paid for their participation. Information was obtained through direct observation, self-report (interview and self-administered questionnaires), measurement of butts collected for a week, and laboratory analyses of the biochemical markers of exposure. Compared with the white smokers, the black smokers had significantly higher cotinine and carbon monoxide levels per cigarette smoked and per millimeter of smoked tobacco rod (both p < 0.001). After adjusting for race, cigarettes per day, and mean amount of each cigarette smoked, menthol was associated with higher cotinine levels (p = 0.03) and carbon monoxide concentrations (p = 0.02). The use of menthol may be associated with increased health risks of smoking. Menthol use should be considered when biochemical markers of smoke exposure are used as quantitative measures of smoking intensity or as indicators of compliance with smoking reduction programs. In addition, the effect of menthol on total "dose" should be considered in any efforts to regulate the amount of nicotine in cigarettes.

  10. [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.

  11. Experimental evidence for interfacial biochemical bonding in osseointegrated titanium implants.

    PubMed

    Sul, Young-Taeg; Kwon, David H; Kang, Byung-Soo; Oh, Se-Jung; Johansson, Carina

    2013-08-01

    (i) To identify and quantify an interfacial biochemical bond and the bonding strength of osseointegrated implants with bioactive titanium oxide chemistry, ATiO(x)B (A, metal cations; TiO(x) , titanium oxides/hydroxides; B, non-metal anions) and (ii) to provide quantitative evidence for the biochemical bond theory of osseointegration proposed by Sul et al. for description and explanation of why and how the implants with ATiO(x) B surface oxide chemistry may exhibit a significantly stronger bone response, in spite of the fact that the roughness values approached zero, or were equivalent to or significantly lower than those of the control implants. We applied a newly developed biochemical bond measurement (BBM) method to model implant surfaces that were "perfectly" smooth nanotopography near-zero roughness as the constant parameter, and used the bioactive surface chemistry of titanium oxide, ATiOx B chemistry as a variable parameter in rabbit tibiae for 10 weeks. In this manner, we determined an interfacial biochemical bond and quantified its bonding strength. The increase in biochemical bond strengths of the test implant relative to the control implant was determined to be 0.018 (±0.008) MPa (0.031 vs 0.021 MPa, n = 10) for tensile strength and 8.9 (±6.1) Ncm (33.0 vs 24.1 Ncm, n = 10) for removal torque. Tensile and removal torque show strong correlation in the Pearson test (r = 0.901, P ≤ 0.001). In addition, histomorphometric measurements including bone-to-metal-contact (BMC, P = 0.007), bone area and newly formed bone showed significant increases in the mean values for ATiO(x) B chemistry (P = 0.007, n = 10). Biochemical bond theory states that the surface oxide chemistry, ATiO(x) B must have more electrical and chemical molecular polarity that fractionally charges the surfaces denoted as δ(+) and δ(-) and leads to electrostatic and electrodynamic interactions with the bone healing cascade, eventually leading to the formation of biochemical bonding at the

  12. Biochemical Characterization of Rift Valley Fever Virus

    DTIC Science & Technology

    1980-01-01

    disease with virus as a member of the family of Bunya- numerous fatalities was reported in the Nile viridae. Delta (6). The causative agent of this...Radiolabeled virus preparations were ob- epizootic. Rift Valley fever virus (RVFV) tained in the following manner. Viruses has been shown to be...J. S. Walker, pH 7.4) and layered onto a continuous 15-40% Plum Island Animal Research Laboratory, (w/v) Renografin (E. R. Squibb and Sons, and

  13. Diabetes mellitus: biochemical, histological and microbiological aspects in periodontal disease.

    PubMed

    Marigo, L; Cerreto, R; Giuliani, M; Somma, F; Lajolo, C; Cordaro, M

    2011-07-01

    Relationship between diabetes mellitus (DM) and periodontal disease has been the subject of many studies that underline that diabetic patients are two/three times more susceptible to have an increased risk of periodontal disease, especially when metabolic control is inadequate. In this review the authors analyze, in diabetic patient, biochemical, histological and microbiological aspects of periodontal disease. Recent studies reported the results obtained in not diabetic patients, both periodontopatic and not: in periodontopatic subjects, the value of glycated hemoglobin was higher. As regards type 2 DM has a positive relationship between periodontal inflammation and glycemia, with good probabilities of disease development. Some Authors showed how the hygiene and the professional/domiciliary control could support a reduction of the glycate hemoglobin and, therefore, of the periodontal disease. The glucose accumulation in the crevicular fluid, noticed in pockets with a depth >4 mm, causes an increase of spirochetes and bacteria. Some research reported that scarcely controlled patients show high levels of interleukin-1beta (IL-1beta). This alteration together with the prolonged expression of tumor necrosis factor (TNF) could represent a mechanism used by bacteria to cause a major damage during the inflammation process, sometimes favoured by immunological defects, due to the mobilization of lymphocytes subpopulations. By measuring the values of TNF-a, fibrinogen, high sensitive capsule reactive protein (hs-CRP), IL-4, IL-6, IL-8, IL-10, at the beginning of non-surgical periodontal therapy and it has been after 3 months of treatment, noticed a relevant reduction only of TNF-a and fibrinogen. Concerning vascular alteration, vascular endothelium growing factor (VEGF) could play a major role in the tissues ischemia. The VEGF should determine the tissue ischemia, the angiogenesis and the alteration of glucose haematic level, in patients affected by microvasculopathies due

  14. Conditions for duality between fluxes and concentrations in biochemical networks

    SciTech Connect

    Fleming, Ronan M. T.; Vlassis, Nikos; Thiele, Ines

    2016-06-23

    Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We alsomore » provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality.The condition prescribes that, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes« less

  15. Varenicline in Autism: Theory and Case Report of Clinical and Biochemical Changes.

    PubMed

    Mostafavi, Mojdeh; Hardy, Paul; Arnold, L Eugene

    2016-11-01

    To explore the potential benefits of varenicline (CHANTIX ® ), a highly specific partial agonist of neuronal α4β2 nicotinic acetylcholine receptors (nAChR), for autistic symptoms, and present resulting biochemical changes in light of dopamine-related genotype. The clinical and biochemical changes exhibited by a 19-year-old severely autistic man following the use of low-dose varenicline in an ABA experiment of nature, and his genotype, were extracted from chart review. Clinical outcome was measured by the Ohio Autism Clinical Impression Scale and 12 relevant urine and saliva metabolites were measured by Neuroscience Laboratory. With varenicline, this patient improved clinically and autonomic biochemical indicators in saliva and urine normalized, including dopamine, 3,4-dihydroxyphenylacetic acid (DOPAC), epinephrine, norepinephrine, taurine, and histamine levels. In addition, with varenicline, the dopamine D1 receptor (DRD1) antibody titer as well as the percent of baseline calmodulin-dependent protein kinase II (CaM KII) activity dropped significantly. When varenicline stopped, he deteriorated; when it was resumed, he again improved. Doses of 0.5, 1, and 2 mg daily were tried before settling on a dose of 1.5 mg daily. He has remained on varenicline for over a year with no noticeable side effects. This report is, to the best of our knowledge, only the second to demonstrate positive effects of varenicline in autism, the first to show it in a severe case, and the first to show normalization of biochemical parameters related to genotype. As with the previous report, these encouraging results warrant further controlled research before clinical recommendations can be made.

  16. Effect of season on physiological, biochemical, hormonal, and oxidative stress parameters of indigenous sheep.

    PubMed

    Rathwa, Sawankumar D; Vasava, A A; Pathan, M M; Madhira, S P; Patel, Y G; Pande, A M

    2017-06-01

    This study was conducted to evaluate the impact of summer and winter season on physiological, biochemical, hormonal, and antioxidant parameters in Indigenous sheep. The research was carried out during summer and winter season. 8 adult apparently healthy female sheep (aged 2-4 years) of similar physiological status were selected. Daily ambient temperature and relative humidity were recorded to calculate the temperature-humidity index (THI). The THI value of summer and winter season were 82.55 and 59.36, respectively, which indicate extreme hot condition during summer season and extreme cold condition during winter season. Physiological parameters were recorded daily during the experimental periods. Blood samples were collected at weekly interval and analyzed for biochemical, hormonal, and antioxidant parameters. The results were analyzed using completely randomized design. From data obtained in this study, we found that higher THI during summer have significant effect over various physiological, biochemical, hormonal, and enzymatic indices of indigenous sheep. The physiological response such as rectal temperature, respiration rate (RR), pulse rate (PR), and skin temperature (ST) was increased significantly. We also found a significant increase in some biochemical parameters such as blood urea nitrogen (BUN), uric acid, creatinine (Cr), alanine transaminase (ALT), aspartate transaminase (AST), sodium (Na), and potassium (K). The level of cortisol hormone and superoxide dismutase (SOD), glutathione peroxidase (GPx), and lipid peroxidase (LPO) antioxidants increased significantly during summer. Whereas, some parameters such as glucose, cholesterol, calcium (Ca), inorganic phosphorus (IP), triiodothyronine (T 3 ), and thyroxine (T 4 ) were decreased significantly during summer season. It was concluded that the THI is a sensitive indicator of heat stress and is impacted by ambient temperature more than the relative humidity in Indigenous sheep. Higher THI is associated

  17. Raman Spectroscopy Analysis of the Biochemical Characteristics of Experimental Keratomycosis.

    PubMed

    Hu, Jianzhang; Wu, Fujin; Huang, Zufang; Ma, Shuting; Zhang, Jingjin; Yang, Juan; Han, Xiaoli; Xu, Guoxing

    2016-11-01

    To investigate the biochemical characteristics in experimental keratomycosis by Raman spectroscopy analysis in vitro and in vivo. Raman spectroscopy was used to analyze the biochemical characteristics of cultured mouse keratocytes stimulated by Fusarium solani suspension in vitro, and the infected cornea of Fusarium solani keratitis of mice. The peak intensities at 1005, 1186, 1311, 1449 and 1657 cm -1 , which represented phenylalanine, tyrosine, nucleic acid bases, phospholipids and α-helix, were decreased in the infected keratocytes compared with the control keratocytes. The consistency of Raman spectra between the infected cornea tissue and the control cornea tissue was high. However, the intensity of some peaks declined, especially at 853, 940 and 1244 cm -1 , which represent the tyrosine, proline and collagen content, respectively. After infection with Fusarium solani, the biochemical characteristics of keratocyte and cornea showed a decrease of amino acids, nucleic acid phospholipids and collagen, which may closely relate to the pathophysiology of keratomycosis.

  18. 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.

  19. Optical fibre gratings as tools for chemical and biochemical sensing.

    PubMed

    Baldini, F; Brenci, M; Chiavaioli, F; Giannetti, A; Trono, C

    2012-01-01

    Optical fibre gratings have recently been suggested as optical platforms for chemical and biochemical sensing. On the basis of the measurement of refractive index changes induced by a chemical and biochemical interaction in the transmission spectrum along the fibres, they are proposed as a possible alternative to the other label-free optical approaches, such as surface plasmon resonance and optical resonators. The combination of the use of optical fibres with the fact that the signal modulation is spectrally encoded offers multiplexing and remote measurement capabilities which the other technology platforms are not able to or can hardly offer. The fundamentals of the different types of optical fibre gratings are described and the performances of the chemical and biochemical sensors based on this approach are reviewed. Advantages and limitations of optical fibre gratings are considered, with a look at new perspectives for their utilization in the field.

  20. [Biochemical study of unusual cases of Fabry disease].

    PubMed

    Beĭer, E M; Karpova, E A; Udalova, O V; Tsvetkova, I V

    1998-01-01

    Fourteen members of family P. and four members of family N. were clinico-biochemically examined. Among twelve adult children (19-32 years old) of family P. five sons manifested angiokeratotic skin lesions and other clinical signs of Fabry disease. Three of the probands had additional symptoms not generally found in Fabry disease. Biochemical studies including an enzyme assay, analysis of storage products and alpha-galactosidase multiple forms, allowed us to confirm the diagnosis of Fabry disease in four affected brothers and to establish the heterozygous status of their mother. The data of biochemical investigation of patient N. with atypical variant of Fabry disease are also presented. The patient N. with strong skin lesions had a high residual alpha-galactosidase activity and unusual composition of alpha-galactosidase multiple forms.

  1. Measurement of biochemical oxygen demand of the leachates.

    PubMed

    Fulazzaky, Mohamad Ali

    2013-06-01

    Biochemical oxygen demand (BOD) of the leachates originally from the different types of landfill sites was studied based on the data measured using the two manometric methods. The measurements of BOD using the dilution method were carried out to assess the typical physicochemical and biological characteristics of the leachates together with some other parameters. The linear regression analysis was used to predict rate constants for biochemical reactions and ultimate BOD values of the different leachates. The rate of a biochemical reaction implicated in microbial biodegradation of pollutants depends on the leachate characteristics, mass of contaminant in the leachate, and nature of the leachate. Character of leachate samples for BOD analysis of using the different methods may differ significantly during the experimental period, resulting in different BOD values. This work intends to verify effect of the different dilutions for the manometric method tests on the BOD concentrations of the leachate samples to contribute to the assessment of reaction rate and microbial consumption of oxygen.

  2. The origin recognition complex: a biochemical and structural view

    PubMed Central

    Li, Huilin; Stillman, Bruce

    2013-01-01

    The origin recognition complex (ORC) was first discovered in the baker’s yeast in 1992. Identification of ORC opened up a path for subsequent molecular level investigations on how eukaryotic cells initiate and control genome duplication each cell cycle. Twenty years after the first biochemical isolation, ORC is now taking on a three-dimensional shape, although a very blurry shape at the moment, thanks to the recent electron microscopy and image reconstruction efforts. In this chapter, we outline the current biochemical knowledge about ORC from several eukaryotic systems, with emphasis on the most recent structural and biochemical studies. Despite many species-specific properties, an emerging consensus is that ORC is a ATP-dependent machine that recruits other key proteins to form pre-Replicative Complexes (pre-RCs) at many origins of DNA replication, enabling the subsequent initiation of DNA replication in S phase. PMID:22918579

  3. 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

  4. Constructive effects of fluctuations in genetic and biochemical regulatory systems.

    PubMed

    Steuer, Ralf; Zhou, Changsong; Kurths, Jürgen

    2003-12-01

    Biochemical and genetic regulatory systems that involve low concentrations of molecules are inherently noisy. This intrinsic stochasticity has received considerable interest recently, leading to new insights about the sources and consequences of noise in complex systems of genetic regulation. However, most prior work was devoted to the reduction of fluctuation and the robustness of cellular function with respect to intrinsic noise. Here, we focus on several scenarios in which the inherent molecular fluctuations are not merely a nuisance, but act constructively and bring about qualitative changes in the dynamics of the system. It will be demonstrated that in many typical situations biochemical and genetic regulatory systems may utilize intrinsic noise to their advantage.

  5. Human milk as a carrier of biochemical messages.

    PubMed

    Bernt, K M; Walker, W A

    1999-08-01

    Not only does breast milk provides an ideal nutrient composition for the newborn, but it also contains a variety of substances that may actively influence growth and development of the infant and stimulate neonatal protection against gastrointestinal diseases. Hormones, growth factors, cytokines and even whole cells are present in breast milk and act to establish biochemical and immunological communication between mother and child. In addition, milk nutrients such as nucleotides, glutamine and lactoferrin have been shown to influence gastrointestinal development and host defense. The unique properties of milk as a mediator of biochemical messages will be presented and the clinical significance of breastfeeding in the prevention of neonatal gastrointestinal diseases will be discussed.

  6. Biotinidase deficiency: Genotype-biochemical phenotype association in Brazilian patients

    PubMed Central

    Borsatto, Taciane; Sperb-Ludwig, Fernanda; Lima, Samyra E.; S. Carvalho, Maria R.; S. Fonseca, Pablo A.; S. Camelo, José; M. Ribeiro, Erlane; F. V. de Medeiros, Paula; M. Lourenço, Charles; F. M. de Souza, Carolina; Boy, Raquel; Félix, Têmis M.; M. Bittar, Camila; L. C. Pinto, Louise; C. Neto, Eurico; J. Blom, Henk; D. Schwartz, Ida V.

    2017-01-01

    Introduction The association between the BTD genotype and biochemical phenotype [profound biotinidase deficiency (BD), partial BD or heterozygous activity] is not always consistent. This study aimed to investigate the genotype-biochemical phenotype association in patients with low biotinidase activity. Methods All exons, the 5'UTR and the promoter of the BTD gene were sequenced in 72 Brazilian individuals who exhibited low biotinidase activity. For each patient, the expected biochemical phenotype based on the known genotype was compared with the observed biochemical phenotype. Additional non-genetic factors that could affect the biotinidase activity were also analysed. Results Most individuals were identified by neonatal screening (n = 66/72). When consecutive results for the same patient were compared, age, prematurity and neonatal jaundice appeared to affect the level of biotinidase activity. The biochemical phenotype at the time of the second blood collection changed in 11/22 patients compared to results from the first sample. Three novel variants were found: c.1337T>C (p.L446P), c.1466A>G (p.N489S) and c.962G>A (p.W321*). Some patients with the same genotype presented different biochemical phenotypes. The expected and observed biochemical phenotypes agreed in 68.5% of cases (concordant patients). The non-coding variants c.-183G>A, c.-315A>G and c.-514C>T were present in heterozygosis in 5/17 discordant patients. In addition, c.-183G>A and c.-514C>T were also present in 10/37 concordant patients. Conclusions The variants found in the promoter region do not appear to have a strong impact on biotinidase activity. Since there is a disparity between the BTD genotype and biochemical phenotype, and biotinidase activity may be affected by both genetic and non-genetic factors, we suggest that the diagnosis of BD should be based on more than one measurement of plasma biotinidase activity. DNA analysis can be of additional relevance to differentiate between partial BD and

  7. Biotinidase deficiency: Genotype-biochemical phenotype association in Brazilian patients.

    PubMed

    Borsatto, Taciane; Sperb-Ludwig, Fernanda; Lima, Samyra E; S Carvalho, Maria R; S Fonseca, Pablo A; S Camelo, José; M Ribeiro, Erlane; F V de Medeiros, Paula; M Lourenço, Charles; F M de Souza, Carolina; Boy, Raquel; Félix, Têmis M; M Bittar, Camila; L C Pinto, Louise; C Neto, Eurico; J Blom, Henk; D Schwartz, Ida V

    2017-01-01

    The association between the BTD genotype and biochemical phenotype [profound biotinidase deficiency (BD), partial BD or heterozygous activity] is not always consistent. This study aimed to investigate the genotype-biochemical phenotype association in patients with low biotinidase activity. All exons, the 5'UTR and the promoter of the BTD gene were sequenced in 72 Brazilian individuals who exhibited low biotinidase activity. For each patient, the expected biochemical phenotype based on the known genotype was compared with the observed biochemical phenotype. Additional non-genetic factors that could affect the biotinidase activity were also analysed. Most individuals were identified by neonatal screening (n = 66/72). When consecutive results for the same patient were compared, age, prematurity and neonatal jaundice appeared to affect the level of biotinidase activity. The biochemical phenotype at the time of the second blood collection changed in 11/22 patients compared to results from the first sample. Three novel variants were found: c.1337T>C (p.L446P), c.1466A>G (p.N489S) and c.962G>A (p.W321*). Some patients with the same genotype presented different biochemical phenotypes. The expected and observed biochemical phenotypes agreed in 68.5% of cases (concordant patients). The non-coding variants c.-183G>A, c.-315A>G and c.-514C>T were present in heterozygosis in 5/17 discordant patients. In addition, c.-183G>A and c.-514C>T were also present in 10/37 concordant patients. The variants found in the promoter region do not appear to have a strong impact on biotinidase activity. Since there is a disparity between the BTD genotype and biochemical phenotype, and biotinidase activity may be affected by both genetic and non-genetic factors, we suggest that the diagnosis of BD should be based on more than one measurement of plasma biotinidase activity. DNA analysis can be of additional relevance to differentiate between partial BD and heterozygosity.

  8. 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

  9. Biochemical characterisation of Murray Valley encephalitis virus proteinase.

    PubMed

    Joy, Joma; Mee, Ng Fui; Kuan, Wee Liang; Perlyn, Kwek Zekui; Wen, Then Siew; Hill, Jeffrey

    2010-07-16

    Murray Valley encephalitis virus (MVEV) is a member of the flavivirus group, a large family of single stranded RNA viruses, which cause serious disease in all regions of the world. Its genome encodes a large polyprotein which is processed by both host proteinases and a virally encoded serine proteinase, non-structural protein 3 (NS3). NS3, an essential viral enzyme, requires another virally encoded protein cofactor, NS2B, for proteolytic activity. The cloning, expression and biochemical characterisation of a stable MVEV NS2B-NS3 fusion protein is described. Copyright 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  10. 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

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

    SciTech Connect

    NONE

    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. 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.

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

    SciTech Connect

    Fei, Q.; Tao, L.; Pienkos, P .T.

    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.

  14. 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.

  15. 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 atmore » 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.« less

  16. 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

  17. Molecular and Biochemical Characterization of Postharvest Senescence in Broccoli

    PubMed Central

    Page, Tania; Griffiths, Gareth; Buchanan-Wollaston, Vicky

    2001-01-01

    Postharvest senescence in broccoli (Brassica oleracea L. var Italica) florets results in phenotypic changes similar to those seen in developmental leaf senescence. To compare these two processes in more detail, we investigated molecular and biochemical changes in broccoli florets stored at two different temperatures after harvest. We found that storage at cooler temperatures delayed the symptoms of senescence at both the biochemical and gene expression levels. Changes in key biochemical components (lipids, protein, and chlorophyll) and in gene expression patterns occurred in the harvested tissue well before any visible signs of senescence were detected. Using previously identified senescence-enhanced genes and also newly isolated, differentially expressed genes, we found that the majority of these showed a similar enhancement of expression in postharvest broccoli as in developmental leaf senescence. At the biochemical level, a rapid loss of membrane fatty acids was detected after harvest, when stored at room temperature. However, there was no corresponding increase in levels of lipid peroxidation products. This, together with an increased expression of protective antioxidant genes, indicated that, in the initial stages of postharvest senescence, an orderly dismantling of the cellular constituents occurs, using the available lipid as an energy source. Postharvest changes in broccoli florets, therefore, show many similarities to the processes of developmental leaf senescence. PMID:11161029

  18. 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…

  19. 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.more » 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.« less

  20. 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.

  1. 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…

  2. Haematological and biochemical values of 10 green iguanas (Iguana iguana).

    PubMed

    Divers, S J; Redmayne, G; Aves, E K

    1996-03-02

    Ten clinically healthy green iguanas (Iguana iguana) imported from South America were examined, and haematological and biochemical measurements were made on samples of blood. This paper describes the methods of blood sampling, handling and laboratory analysis, and presents the results as a set of normal blood ranges for the green iguana.

  3. The biochemical properties of antibodies and their fragments

    USDA-ARS?s Scientific Manuscript database

    Immunoglobulins (Ig) or antibodies are a 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 c...

  4. 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.

  5. 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...

  6. Biochemical basis of heterogeneity in acute presentations of propionic acidemia.

    PubMed

    Sindgikar, Seema Pavaman; Rao, Suchetha; Shenoy, Rathika D; Kamath, Nutan

    2013-01-01

    Propionic acidemia (PA), an uncommon organic acidemia has varied clinical and metabolic presentation causing difficulty and delay in the diagnosis. We report a case of PA in an infant who presented with failure to thrive, acute encephalopathy due to severe hyperammonemia without acidosis and fungal sepsis. The biochemical basis of severe hyperammonemia is discussed.

  7. 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…

  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. 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…

  10. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Chemical and biochemical thermodynamics: Is it time for a reunification?

    PubMed

    Iotti, Stefano; Raff, Lionel; Sabatini, Antonio

    2017-02-01

    The thermodynamics of chemical reactions in which all species are explicitly considered with atoms and charge balanced is compared with the transformed thermodynamics generally used to treat biochemical reactions where atoms and charges are not balanced. The transformed thermodynamic quantities suggested by Alberty are obtained by execution of Legendre transformation of the usual thermodynamic potentials. The present analysis demonstrates that the transformed values for Δ r G' 0 and Δ r H' 0 can be obtained directly without performing Legendre transformations by simply writing the chemical reactions with all the pseudoisomers explicitly included and charges balanced. The appropriate procedures for computing the stoichiometric coefficients for the pseudoisomers are fully explained by means of an example calculation for the biochemical ATP hydrolysis reaction. It is concluded that the analysis has reunited the "two separate worlds" of conventional thermodynamics and transformed thermodynamics. In addition, it is also shown that the value of the conditional Gibbs energy of reaction, Δ r G', for a biochemical reaction is the same of the value of Δ r G for any chemical reaction involving pseudoisomers of the biochemical reagents. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. 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 ...

  13. Opium and heroin alter biochemical parameters of human's serum.

    PubMed

    Kouros, Divsalar; Tahereh, Haghpanah; Mohammadreza, Afarinesh; Minoo, Mahmoudi Zarandi

    2010-05-01

    Iran is a significant consumer of opium, and, generally, of opioids, in the world. Addiction is one of the important issues of the 21st century and is an imperative issue in Iran. Long-term consumption of opioids affects homeostasis. To determine the effects of opium and heroin consumption on serum biochemical parameters. In a cross-sectional study, subjects who had consumed heroin (n = 35) or opium (n = 42) for more than two years and 35 nonaddict volunteers as the control group were compared in regard to various biochemical parameters such as fasting blood sugar (FBS), Na(+), K(+), Ca(2+), blood urea nitrogen (BUN), uric acid (UA), triglyceride (TG), cholesterol, creatinine, and total protein. Chromatography was used to confirm opioid consumption, and the concentration of biochemical parameters was determined by laboratory diagnostic tests on serum. No significant differences were found in Na(+), Ca(2+), BUN, UA, TG, creatinine, and total protein concentrations among the three groups. FBS, K(+), and UA levels were significantly lower in opium addicts compared to the control group. Serum Ca(2+) concentration of heroin addicts showed a significant decrease compared to that of the control group. Both addict groups showed a significant decrease in serum cholesterol levels. Chronic use of opium and heroin can change serum FBS, K(+), Ca(2+), UA, and cholesterol. This study, one of few on the effects of opium on serum biochemical parameters in human subjects, has the potential to contribute to the investigation of new approaches for further basic studies.

  14. 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…

  15. 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<...

  16. Variation of biochemical gene markers in the population of Tomsk

    SciTech Connect

    Kucher, A.N.; Ivanova, O.F.; Puzyrev, V.P.

    1994-11-01

    Variation of seven biochemical gene markers (Tf, Gc, Hp, ACP1, PGM1, PGD, and EsD) in the population of Tomsk was examined. The genetic structure of this population is compared to that of other urban populations from different regions of Russia. 13 refs., 4 tabs.

  17. 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.

  18. 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…

  19. Serum biochemical reference intervals for wild dwarf ornate wobbegong sharks (Orectolobus ornatus).

    PubMed

    Otway, Nicholas M; Ellis, Megan T; Starr, Rod

    2011-09-01

    Sharks are important to sport and commercial fishing, public aquaria, and research institutions. However, serum biochemical reference values have been established for few species. The aim of this study was to establish serum biochemical reference intervals for wild-caught dwarf ornate wobbegong sharks (Orectolobus ornatus). Fifty wobbegongs were caught, and their health status, sex, length, and weight were evaluated and recorded. Following collection of blood, serum biochemical analytes were measured and analyzed using standard analytical and statistical methods. Combined samples generated means, medians, and reference intervals. For the measured analytes, means (reference intervals) were as follows: sodium 287 (284-289) mmol/L, chloride 277 (274-280) mmol/L, potassium 5.2 (5.0-5.3) mmol/L, total calcium 4.6 (4.5-4.7) mmol/L, magnesium 1.9 (1.7-2.0) mmol/L, inorganic phosphate 1.8 (1.7-1.9) mmol/L, glucose 2.6 (2.4-2.8) mmol/L, total protein 46 (45-47) g/L, urea 396 (392-401) mmol/L, creatinine ≤ 0.02 mmol/L, total bilirubin 2.0 (1.9-2.1) μmol/L, cholesterol 1.3 (1.2-1.4) mmol/L, triglyceride 0.5 (0.4-0.6) mmol/L, alkaline phosphatase 24 (21-28) U/L, alanine aminotransferase 3 U/L, aspartate aminotransferase 28 (25-31) U/L, creatine kinase 49 (38-59) U/L, and osmolarity 1104 (1094-1114) mmol/L. Serum values were not affected by sex, length, or weight. Established reference values will assist with clinical evaluation and treatment of dwarf ornate wobbegongs in aquaria, research institutions, and the wild. ©2011 American Society for Veterinary Clinical Pathology.

  20. Aspects on the Physiological and Biochemical Foundations of Neurocritical Care

    PubMed Central

    Nordström, Carl-Henrik; Koskinen, Lars-Owe; Olivecrona, Magnus

    2017-01-01

    Neurocritical care (NCC) is a branch of intensive care medicine characterized by specific physiological and biochemical monitoring techniques necessary for identifying cerebral adverse events and for evaluating specific therapies. Information is primarily obtained from physiological variables related to intracranial pressure (ICP) and cerebral blood flow (CBF) and from physiological and biochemical variables related to cerebral energy metabolism. Non-surgical therapies developed for treating increased ICP are based on knowledge regarding transport of water across the intact and injured blood–brain barrier (BBB) and the regulation of CBF. Brain volume is strictly controlled as the BBB permeability to crystalloids is very low restricting net transport of water across the capillary wall. Cerebral pressure autoregulation prevents changes in intracranial blood volume and intracapillary hydrostatic pressure at variations in arterial blood pressure. Information regarding cerebral oxidative metabolism is obtained from measurements of brain tissue oxygen tension (PbtO2) and biochemical data obtained from intracerebral microdialysis. As interstitial lactate/pyruvate (LP) ratio instantaneously reflects shifts in intracellular cytoplasmatic redox state, it is an important indicator of compromised cerebral oxidative metabolism. The combined information obtained from PbtO2, LP ratio, and the pattern of biochemical variables reveals whether impaired oxidative metabolism is due to insufficient perfusion (ischemia) or mitochondrial dysfunction. Intracerebral microdialysis and PbtO2 give information from a very small volume of tissue. Accordingly, clinical interpretation of the data must be based on information of the probe location in relation to focal brain damage. Attempts to evaluate global cerebral energy state from microdialysis of intraventricular fluid and from the LP ratio of the draining venous blood have recently been presented. To be of clinical relevance, the

  1. Bias due to Preanalytical Dilution of Rodent Serum for Biochemical Analysis on the Siemens Dimension Xpand Plus

    PubMed Central

    Johns, Jennifer L.; Moorhead, Kaitlin A.; Hu, Jing; Moorhead, Roberta C.

    2018-01-01

    Clinical pathology testing of rodents is often challenging due to insufficient sample volume. One solution in clinical veterinary and exploratory research environments is dilution of samples prior to analysis. However, published information on the impact of preanalytical sample dilution on rodent biochemical data is incomplete. The objective of this study was to evaluate the effects of preanalytical sample dilution on biochemical analysis of mouse and rat serum samples utilizing the Siemens Dimension Xpand Plus. Rats were obtained from end of study research projects. Mice were obtained from sentinel testing programs. For both, whole blood was collected via terminal cardiocentesis into empty tubes and serum was harvested. Biochemical parameters were measured on fresh and thawed frozen samples run straight and at dilution factors 2–10. Dilutions were performed manually, utilizing either ultrapure water or enzyme diluent per manufacturer recommendations. All diluted samples were generated directly from the undiluted sample. Preanalytical dilution caused clinically unacceptable bias in most analytes at dilution factors four and above. Dilution-induced bias in total calcium, creatinine, total bilirubin, and uric acid was considered unacceptable with any degree of dilution, based on the more conservative of two definitions of acceptability. Dilution often caused electrolyte values to fall below assay range precluding evaluation of bias. Dilution-induced bias occurred in most biochemical parameters to varying degrees and may render dilution unacceptable in the exploratory research and clinical veterinary environments. Additionally, differences between results obtained at different dilution factors may confound statistical comparisons in research settings. Comparison of data obtained at a single dilution factor is highly recommended. PMID:29497614

  2. 40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... pesticides nontarget organisms and environmental fate data requirements table. 158.2084 Section 158.2084 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical pesticides...

  3. 40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... pesticides nontarget organisms and environmental fate data requirements table. 158.2084 Section 158.2084 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical pesticides...

  4. 40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... pesticides nontarget organisms and environmental fate data requirements table. 158.2084 Section 158.2084 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical pesticides...

  5. 40 CFR 158.2084 - Experimental use permit biochemical pesticides nontarget organisms and environmental fate data...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... pesticides nontarget organisms and environmental fate data requirements table. 158.2084 Section 158.2084 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2084 Experimental use permit biochemical pesticides...

  6. 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...

  7. Hematological and Biochemical Reference Values for the Endangered Kiso Horse

    PubMed Central

    TAKASU, Masaki; NAGATANI, Nana; TOZAKI, Teruaki; KAKOI, Hironaga; MAEDA, Masami; MURASE, Tetsuma; MUKOYAMA, Harutaka

    2013-01-01

    To establish blood and biochemical references for the endangered Kiso horse, blood samples were collected from 111 adult Kiso horses, 74.5% of the existing breed. The samples were analyzed for 23 hematological and biochemical parameters to determine their means and standard deviations (SD). We compared the mean ± 2SD with the reference values cited in one of the most commonly used veterinary textbooks in Japan. The hematology of Kiso horses is characterized by lower erythrocyte count and hematocrit and hemoglobin levels. In addition, their serum biochemistry showed lower levels of aspartate transaminase, alkaline phosphatase, and γ-glutamyl transferase. Whether these propensities are attributed to breed-specific factors or are acquired factors remains unclear. Nevertheless, this study provides useful diagnostic indices for the endangered Kiso horse. PMID:24834006

  8. 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.

  9. Label-free optical resonant sensors for biochemical applications

    NASA Astrophysics Data System (ADS)

    Ciminelli, Caterina; Campanella, Clarissa Martina; Dell'Olio, Francesco; Campanella, Carlo Edoardo; Armenise, Mario Nicola

    2013-03-01

    For a number of years, the scientific community has been paying growing attention to the monitoring and enhancement of public health and the quality of life through the detection of all dangerous agents for the human body, including gases, proteins, virus, and bacterial agents. When these agents are detected through label-free biochemical sensors, the molecules are not modified structurally or functionally by adding fluorescent or radioactive dyes. This work focuses on label-free optical ring resonator-based configurations suited for bio-chemical sensing, highlighting their physical aspects and specific applications. Resonant wavelength shift and the modal splitting occurring when the analyte interacts with microresonant structures are the two major physical aspects analyzed in this paper. Competitive optical platforms proposed in the literature are also illustrated together with their properties and performance.

  10. Tunable release of multiplex biochemicals by plasmonically active rotary nanomotors.

    PubMed

    Xu, Xiaobin; Kim, Kwanoh; Fan, Donglei

    2015-02-16

    It is highly desirable to precisely tune the molecule release rate from the surfaces of nanoparticles (NPs) that are relevant to cancer therapy and single-cell biology. An innovative mechanism is reported to actively tune the biochemical release rate by rotation of NPs. Plasmonic nanomotors were assembled from NPs and applied in multiplex biochemical release and detection. Both single and multiplex biosignals can be released in a tunable fashion by controlling the rotation speed of the nanomotors. The chemistry and release rate of individual chemicals can be revealed by Raman spectroscopy. The fundamental mechanism was modeled quantitatively and attributed to the fluidic boundary-layer reduction owing to the liquid convection. This work, which explored the synergistic attributes of surface enhanced Raman scattering and nanoelectromechanical systems, could inspire new sensors that are potentially interesting for various bio-applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Microscopic and Biochemical Visualization of Auxins in Plant Tissues.

    PubMed

    Blakeslee, Joshua J; Murphy, Angus S

    2016-01-01

    Auxins are a particularly notable class of phytohormones in that they regulate plant growth and development at sites of synthesis, and via a regulated polar transport system comprising PIN, ABCB, and AUX/LAX transport proteins. In order to fully understand auxin-regulated physiological processes, it is therefore essential to be able to determine where indole-3-acetic acid and related compounds are being synthesized, where they are transported to, and how much IAA is accumulating in any given tissue. Auxin may be visualized either indirectly, through the use of auxin responsive promoters; directly, through the use of radiolabelled auxin or fluorescent auxin analogs; or biochemically through extraction and mass-spectrometric quantification of auxin and auxin metabolites from target cells or tissues. Here we focus on the use of the DR5::GUS synthetic auxin promoter reporter construct, fluorescent auxin analogs, and confirmatory biochemical (high-pressure liquid chromatography tandem mass-spectrometry) visualization of auxin and auxin metabolites.

  12. 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.

  13. Massively parallel and multiparameter titration of biochemical assays with droplet microfluidics.

    PubMed

    Baccouche, Alexandre; Okumura, Shu; Sieskind, Rémi; Henry, Elia; Aubert-Kato, Nathanaël; Bredeche, Nicolas; Bartolo, Jean-François; Taly, Valérie; Rondelez, Yannick; Fujii, Teruo; Genot, Anthony J

    2017-09-01

    Biochemical systems in which multiple components take part in a given reaction are of increasing interest. Because the interactions between these different components are complex and difficult to predict from basic reaction kinetics, it is important to test for the effect of variations in the concentration for each reagent in a combinatorial manner. For example, in PCR, an increase in the concentration of primers initially increases template amplification, but large amounts of primers result in primer-dimer by-products that inhibit the amplification of the template. Manual titration of biochemical mixtures rapidly becomes costly and laborious, forcing scientists to settle for suboptimal concentrations. Here we present a droplet-based microfluidics platform for mapping of the concentration space of up to three reaction components followed by detection with a fluorescent readout. The concentration of each reaction component is read through its internal standard (barcode), which is fluorescent but chemically orthogonal. We describe in detail the workflow, which comprises the following: (i) production of the microfluidics chips, (ii) preparation of the biochemical mixes, (iii) their mixing and compartmentalization into water-in-oil emulsion droplets via microfluidics, (iv) incubation and imaging of the fluorescent barcode and reporter signals by fluorescence microscopy and (v) image processing and data analysis. We also provide recommendations for choosing the appropriate fluorescent markers, programming the pressure profiles and analyzing the generated data. Overall, this platform allows a researcher with a few weeks of training to acquire ∼10,000 data points (in a 1D, 2D or 3D concentration space) over the course of a day from as little as 100-1,000 μl of reaction mix.

  14. Metabolic and biochemical effects of low-to-moderate alcohol consumption.

    PubMed

    Whitfield, John B; Heath, Andrew C; Madden, Pamela A F; Pergadia, Michele L; Montgomery, Grant W; Martin, Nicholas G

    2013-04-01

    Alcohol consumption has multiple biochemical consequences. Only a few of these are useful as diagnostic markers, but many reflect potentially harmful or beneficial effects of alcohol. Average consumption of 2 to 4 drinks per day is associated with lower overall or cardiovascular mortality risk than either lower or higher intake. We have analyzed the dose-response relationships between reported alcohol consumption and 17 biomarkers, with emphasis on intake of up to 3 drinks per day. Biochemical tests were performed on serum from 8,396 study participants (3,750 men and 4,646 women, aged 51 ± 13 years, range 18 to 93) who had provided information on alcohol consumption in the week preceding blood collection. Gamma glutamyl transferase, alanine aminotransferase, aspartate aminotransferase, carbohydrate-deficient transferrin, urate, ferritin, and bilirubin showed little or no change with alcohol consumption below 2 to 3 drinks per day, but increased with higher intake. High-density lipoprotein cholesterol and albumin showed increasing results, and insulin showed decreasing results, across the entire range of alcohol use. Biphasic responses, where subjects reporting 1 to 2 drinks per day had lower results than those reporting either more or less alcohol use, occurred for triglycerides, glucose, C-reactive protein, alkaline phosphatase, and butyrylcholinesterase. Increasing alcohol use was associated with decreasing low-density lipoprotein cholesterol (LDL-C) in younger women, but higher LDL-C in older men. Some markers show threshold relationships with alcohol, others show continuous ones, and a third group show biphasic or U-shaped relationships. Overall, the biochemical sequelae of low-to-moderate alcohol use are consistent with the epidemiological evidence on morbidity and mortality. Copyright © 2012 by the Research Society on Alcoholism.

  15. 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.

  16. Behavioral and Biochemical Interaction Between Nicotine and Chronic Unpredictable Mild Stress in Mice.

    PubMed

    Biala, G; Pekala, K; Boguszewska-Czubara, A; Michalak, A; Kruk-Slomka, M; Budzynska, B

    2017-03-01

    Nicotine, the main component of tobacco smoke, exerts influence on mood, and contributes to physical and psychological dependence. Taking into account frequent concomitance of nicotine abuse and stress, we aimed to research behavioral and biochemical effects associated with nicotine administration in combination with chronic unpredictable mild stress (CUMS). Mice were submitted to the procedure of CUMS for 4 weeks, 2 h per day. Our results revealed that CUMS-exposed animals exhibited behavioral alteration like anxiety disorders in the elevated plus maze (EPM) test, the disturbances in memory in the passive avoidance (PA) test and depressive effects in the forced swim test (FST). Moreover, nicotine (0.05-0.5 mg/kg), after an acute or subchronic administration decreased stress-induced depression- and anxiety-like effect as well as memory deficit. Administration of metyrapone (50 mg/kg), a glucocorticosteroid antagonist, alleviated the depressive effect induced by the CUMS. The biochemical experiments showed decreased values of the total antioxidant status (TAS), activities of superoxide dismutase (SOD) and glutathione peroxidase (GPx) with simultaneously increased in malondialdehyde (MDA) concentration in mice submitted to the CUMS. The same effects were observed after an acute and subchronic nicotine administration within all examined brain structures (i.e., hippocampus, cortex, and cerebellum) and in the whole brain in non-stressed and stressed mice confirming pro-oxidative effect of nicotine. Our study contributes to the understanding of behavioral and biochemical mechanisms involved in stress-induced disorders such as depression, anxiety and memory disturbances as well as dual nicotine-stress interactions on the basis of the development of nicotine dependence.

  17. 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 aceticmore » 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.« less

  18. Special investigations in COCM: biochemical analysis of cardiac biopsies.

    PubMed Central

    Torp, A.

    1978-01-01

    The introduction of the endomyocardial biopsy method has permitted unique possibilities to investigate the myocardium. Compared to several other methods described, it is superior for taking serial biopsies on one or more occasions. With already available methods, examination of heart muscle biopsies can be extended to a wide variety of biochemical analyses. The ultimate application of repeated or periodic tissue sampling is the potential of combining static and dynamic studies. PMID:212727

  19. Intermittency route to chaos in a biochemical system.

    PubMed

    De la Fuente, I M; Martinez, L; Veguillas, J

    1996-01-01

    The numerical analysis of a glycolytic model performed through the construction of a system of three differential-delay equations reveals a phenomenon of intermittency route to chaos. In our biochemical system, the consideration of delay time variations under constant input flux as well as frequency variations of the periodic substrate input flux allows us, in both cases, to observe a type of transition to chaos different from the 'Feigenbaum route'.

  20. State-of-the-art of (bio)chemical sensor developments in analytical Spanish groups.

    PubMed

    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.

  1. 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

  2. Biochemical principle of Limulus test for detecting bacterial endotoxins

    PubMed Central

    Iwanaga, Sadaaki

    2007-01-01

    A hemocyte lysate from horseshoe crab (Limulus) produced a gel, when exposed to Gram-negative bacterial endotoxins, lipopolysaccharides (LPS). This gelation reaction of the lysate, so-called Limulus test, has been widely employed as a simple and very sensitive assay method for endotoxins. Recent biochemical studies on the principle of Limulus test indicate that the hemocytes contain several serine protease zymogens, which constitute a coagulation cascade triggered by endotoxins, and that there is a (1,3)-β-D-glucan-mediated coagulation pathway which also results in the formation of gel. Up to now, six protein components, designated coagulogen, proclotting enzyme, factor B, factor C, and factor G, all of which are closely associated with the endotoxin-mediated coagulation pathway, have been purified and biochemically characterized. The molecular structures of these proteins have also been elucidated. Moreover, the reconstitution experiments using the isolated clotting factors, factor C, factor B, proclotting enzyme and coagulogen in the presence of endotoxin, leads to the formation of coagulin gel. Here, I will focus on the biochemical principle of Limulus test for detecting bacterial endotoxins, and its activation and regulation mechanism on the LPS-mediated coagulation cascade. PMID:24019589

  3. Biochemical principle of Limulus test for detecting bacterial endotoxins.

    PubMed

    Iwanaga, Sadaaki

    2007-05-01

    A hemocyte lysate from horseshoe crab (Limulus) produced a gel, when exposed to Gram-negative bacterial endotoxins, lipopolysaccharides (LPS). This gelation reaction of the lysate, so-called Limulus test, has been widely employed as a simple and very sensitive assay method for endotoxins. Recent biochemical studies on the principle of Limulus test indicate that the hemocytes contain several serine protease zymogens, which constitute a coagulation cascade triggered by endotoxins, and that there is a (1,3)-β-D-glucan-mediated coagulation pathway which also results in the formation of gel. Up to now, six protein components, designated coagulogen, proclotting enzyme, factor B, factor C, and factor G, all of which are closely associated with the endotoxin-mediated coagulation pathway, have been purified and biochemically characterized. The molecular structures of these proteins have also been elucidated. Moreover, the reconstitution experiments using the isolated clotting factors, factor C, factor B, proclotting enzyme and coagulogen in the presence of endotoxin, leads to the formation of coagulin gel. Here, I will focus on the biochemical principle of Limulus test for detecting bacterial endotoxins, and its activation and regulation mechanism on the LPS-mediated coagulation cascade.

  4. Biochemical and functional alterations in macrophages after thermal injury.

    PubMed Central

    Loose, L D; Megirian, R; Turinsky, J

    1984-01-01

    Biochemical and functional measurements of rat pulmonary alveolar macrophages were measured 4 h after 1 10-s, 26 to 28% total body surface area, full-thickness scald burn induced under ether anesthesia. Both phagocytic activity and capacity were significantly decreased to a comparable extent, whereas microbicidal activity was increased almost twofold in macrophages from the burned animals. Concurrent with the decreased phagocytic function was a marked impairment in chemotaxis and random migration of these cells when zymosan-activated serum was used as the chemoattractant. When biochemical parameters were examined, it was demonstrated that, on a per-cell but not total-protein basis, alveolar macrophages from burned animals had elevated levels of RNA, total protein beta-glucuronidase, acid phosphatase, and 5'-nucleotidase. These results raise the possibility that the increased pneumonitis in burned individuals may be due to more complex macrophage dysfunctions than impaired microbicidal activity, as was once thought. Alternatively, the biochemical and functional changes observed may be a reflection of a new population of macrophages appearing in the lungs after thermal injury. PMID:6202638

  5. Biochemical nutritional profile of liver cirrhosis patients with hepatocellular carcinoma.

    PubMed

    Port, Gabriela Zanatta; Oliveira, Kalinca; Soldera, Jonathan; Tovo, Cristiane Valle

    2014-01-01

    Liver cirrhosis patients with hepatocellular carcinoma present nutritional alterations and metabolic disorders that negatively impact the prognosis. The objective is to identify alterations in the metabolism of macro and micronutrients among liver cirrhosis patients with and without hepatocellular carcinoma and their relation to the Child-Turcote-Pugh score and Barcelona Clinic Liver Cancer staging. Analytical transversal study, with 31 hepatocellular carcinoma patients and 48 liver cirrhosis patients. Laboratorial exams were carried out. The existence of an association between the biochemical parameters and the disease severity as well as the presence of hepatocellular carcinoma was assessed. The metabolic-nutritional profile of liver cirrhosis patients caused by the hepatitis C virus and hepatocellular carcinoma showed alterations, specifically the lipid (total cholesterol, HDL and triglycerides), protein (albumin, creatinine and uric acid), iron (transferrin, iron and ferritin saturation), hematocrit and hemoglobin, zinc and B12 vitamin profiles. There is a relation between nutritional biochemical markers and the Child-Turcote-Pugh, as well as Barcelona Clinic Liver Cancer staging. Considering the existence of alterations in the metabolism of nutrients in liver cirrhosis patients with and without hepatocellular carcinoma, and also that conventional nutritional assessment methods present limitations for this population, the biochemical laboratorial exams are valid to complement the diagnosis of the nutritional state in a quick and practical manner.

  6. Biochemical comparison of osteoarthritic knees with and without effusion

    PubMed Central

    2011-01-01

    Background Several symptom-relieving interventions have been shown to be efficacious among osteoarthritis (OA) patients with knee effusion; however, not every symptomatic knee OA patient has clinical effusion. Results may be over-generalized since it is unclear if effused knees represent a unique pathological condition or subset compared to knees without effusion. The primary purpose of this study was to determine if biochemical differences existed between OA knees with and without effusion. Methods The present cross-sectional study consisted of 22 volunteers (11 with knee effusion, 11 without knee effusion) with confirmed late-stage radiographic knee OA (Kellgren-Lawrence score ≥ 3). Synovial fluid samples were collected and analyzed using a custom multiplex enzyme-linked immunosorbent assay to determine eight specific biomarker concentrations (e.g., catabolic, anabolic). Results Matrix metalloproteinase (MMP)-3, tissue inhibitor of MMPs (TIMP)-1, TIMP-2, and interleukin-10 were significantly higher in the knees with effusion than in the knees without effusion. Conclusions The biochemical differences that existed between knees with and without effusion provide support that OA subsets may exist, characterized by distinct biochemical characteristics and clinical findings (e.g., effusion). PMID:22122951

  7. Identification of biochemical features of defective Coffea arabica L. beans.

    PubMed

    Casas, María I; Vaughan, Michael J; Bonello, Pierluigi; McSpadden Gardener, Brian; Grotewold, Erich; Alonso, Ana P

    2017-05-01

    Coffee organoleptic properties are based in part on the quality and chemical composition of coffee beans. The presence of defective beans during processing and roasting contribute to off flavors and reduce overall cup quality. A multipronged approach was undertaken to identify specific biochemical markers for defective beans. To this end, beans were split into defective and non-defective fractions and biochemically profiled in both green and roasted states. A set of 17 compounds in green beans, including organic acids, amino acids and reducing sugars; and 35 compounds in roasted beans, dominated by volatile compounds, organic acids, sugars and sugar alcohols, were sufficient to separate the defective and non-defective fractions. Unsorted coffee was examined for the presence of the biochemical markers to test their utility in detecting defective beans. Although the green coffee marker compounds were found in all fractions, three of the roasted coffee marker compounds (1-methylpyrrole, 5-methyl- 2-furfurylfuran, and 2-methylfuran) were uniquely present in defective fractions. Published by Elsevier Ltd.

  8. Mechanical and biochemical properties of human cervical tissue.

    PubMed

    Myers, K M; Paskaleva, A P; House, M; Socrate, S

    2008-01-01

    The mechanical integrity of cervical tissue is crucial for maintaining a healthy gestation. Altered tissue biochemistry can cause drastic changes in the mechanical properties of the cervix and contribute to premature cervical dilation and delivery. We present an investigation of the mechanical and biochemical properties of cervical samples from human hysterectomy specimens. Three clinical cases were investigated: nonpregnant hysterectomy patients with previous vaginal deliveries; nonpregnant hysterectomy patients with no previous vaginal deliveries; and pregnant hysterectomy patients at time of cesarean section. Tissue samples were tested in confined compression, unconfined compression and tension. Cervical tissue samples for the three clinical cases were also subjected to biochemical analysis. Biochemical assays measured cervical tissue hydration, collagen content, collagen extractability and sulfated glycosaminoglycan (GAG) content. Results from the mechanical tests indicate that cervical stroma has a nonlinear, time-dependent stress response with varying degrees of conditioning and hysteresis depending on its obstetric background. It was found that the nonpregnant tissue was significantly stiffer than the pregnant tissue in both tension and compression. Further, collagen extractability, sulfated GAG content and hydration were substantially higher in the pregnant tissue. This study is the first important step towards the attainment of an improved understanding of the complex interplay between the molecular structure of cervical tissue and its macroscopic mechanical properties.

  9. Smith-Lemli-Opitz syndrome: clinical and biochemical correlates.

    PubMed

    Donoghue, Sarah E; Pitt, James J; Boneh, Avihu; White, Susan M

    2018-03-28

    Smith-Lemli-Opitz syndrome (SLOS) is an autosomal recessive disorder caused by mutations in the DHCR7 gene that result in reduced cholesterol biosynthesis. The aim of the study was to examine the biochemical and clinical features of SLOS in the context of the emerging evidence of the importance of cholesterol in morphogenesis and steroidogenesis. We retrospectively reviewed the records of 18 patients (including four fetuses) with confirmed SLOS and documented their clinical and biochemical features. Seven patients had branchial arch abnormalities, including micrognathia, immune dysfunction and hypocalcemia. Thymic abnormalities were found in three fetuses. All four patients with a cholesterol level of ≤0.35 mmol/L died. They all had electrolyte abnormalities (hyperkalemia, hyponatremia, hypocalcemia), necrotizing enterocolitis, sepsis-like episodes and midline defects including the branchial and cardiac defects. Patients with cholesterol levels ≥1.7 mmol/L had milder features and were diagnosed at 9 months to 25 years of age. All 10 patients had intellectual disability. One patient was found to have a novel mutation, c.1220A>G (p.Asn407Ser). We suggest that screening for adrenal insufficiency and for hypoparathyroidism, hypothyroidism and immunodeficiency, should be done routinely in infants diagnosed early with SLOS. Early diagnosis and intervention to correct these biochemical consequences may decrease mortality and improve long-term outcome in these patients.

  10. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

    PubMed Central

    Kaltenbacher, Barbara; Hasenauer, Jan

    2017-01-01

    Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics. PMID:28114351

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

    PubMed

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-07

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. 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

  13. 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 158.2081...

  14. 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 158.2081...

  15. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 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 158.2081...

  16. 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 158.2081...

  17. 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 for...

  18. 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 158.2081...

  19. 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 for...

  20. 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 for...

  1. 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…

  2. 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

  3. BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform.

    PubMed

    Chowdhury, Saikat; Sinha, Noopur; Ganguli, Piyali; Bhowmick, Rupa; Singh, Vidhi; Nandi, Sutanu; Sarkar, Ram Rup

    2018-03-16

    BIOchemical PathwaY DataBase is developed as a manually curated, readily updatable, dynamic resource of human cell specific pathway information along with integrated computational platform to perform various pathway analyses. Presently, it comprises of 46 pathways, 3189 molecules, 5742 reactions and 6897 different types of diseases linked with pathway proteins, which are referred by 520 literatures and 17 other pathway databases. With its repertoire of biochemical pathway data, and computational tools for performing Topological, Logical and Dynamic analyses, BIOPYDB offers both the experimental and computational biologists to acquire a comprehensive understanding of signaling cascades in the cells. Automated pathway image reconstruction, cross referencing of pathway molecules and interactions with other databases and literature sources, complex search operations to extract information from other similar resources, integrated platform for pathway data sharing and computation, etc. are the novel and useful features included in this database to make it more acceptable and attractive to the users of pathway research communities. The RESTful API service is also made available to the advanced users and developers for accessing this database more conveniently through their own computer programmes.

  4. Production optimization for concentration and volume-limited fed-batch reactors in biochemical processes.

    PubMed

    Liu, Ping; Liu, Xinggao; Zhang, Zeyin; Wang, Yalin; Yang, Chunhua; Gui, Weihua

    2018-03-01

    Since a very slight violation of constraint could cause process safety and product quality problems in biochemical processes, an adaptive approach of fed-batch reactor production optimization that can strictly satisfy constraints over the entire operating time is presented. In this approach, an improved smooth function is proposed such that the inequality constraints can be transformed into smooth constraints. Based on this, only an auxiliary state is needed to monitor violations in the augmented performance index. Combined with control variable parameterization (CVP), the dynamic optimization is executed and constraint violations are examined by calculating the sensitivities of states to ensure that the inequality constraints are satisfied everywhere inside the time interval. Three biochemical production optimization problems, including the manufacturing of ethanol, penicillin and protein, are tested as illustrations. Meanwhile, comparisons with pure penalty CVP method, famous dynamic optimization toolbox DOTcvp and literature results are carried out. Research results show that the proposed method achieves better performances in terms of optimization accuracy and computation cost.

  5. Multiple freeze-thaw cycled meniscal allograft tissue: A biomechanical, biochemical, and histologic analysis.

    PubMed

    Lewis, Paul B; Williams, James M; Hallab, Nadim; Virdi, Amarjit; Yanke, Adam; Cole, Brian J

    2008-01-01

    Meniscus allografting has provided relief of meniscal injuries that were previously thought irreparable. However, meniscus allograft tissue remains limited and a significant problem. To improve allograft tissue yield, decrease processing costs, and increase graft availability, this study investigated the biomechanical changes of meniscal allograft tissue frozen and thawed multiple times. Specifically, our study compared the intrinsic compressive resistances of meniscus undergoing four Freeze-Thaw cycles versus tissue undergoing a single Freeze-Thaw cycle. Seven menisci that were originally procured and processed for allografting were donated for the study. Each meniscus was segmented and samples independently underwent novel constant slow-rate compression testing, and histological and biochemical evaluation. The menisci that underwent a single Freeze-Thaw cycle demonstrated a significantly higher Young's Modulus (14 megapascals) as compared to menisci undergoing multiple Freeze-Thaw cycles (10 megapascals, p = 0.03). These results were maintained when medial and lateral menisci were compared independently. Histological and biochemical analyses supported, but did not provide an explanation for the change in intrinsic compressive resistance. From these results, transplantation of meniscal allograft tissue frozen and thawed four times may be compromised in its ability to resist compression; and thus may undermine its role in replacing native meniscal tissue. (c) 2007 Orthopaedic Research Society.

  6. Characterization of physical and biochemical changes in plasma treated spinach seed during germination

    NASA Astrophysics Data System (ADS)

    Hye Ji, Sang; Ki, Se Hoon; Kang, Min Ho; Choi, Jin Sung; Park, Yeunsoo; Oh, Jaesung; Kim, Seong Bong; Yoo, Suk Jae; Choi, Eun Ha; Park, Gyungsoon

    2018-04-01

    Despite the accumulating data on the effect of plasma on seed germination, mechanisms of plasma action need more extensive research. In a previous study, we observed that high voltage nanosecond pulsed plasma enhanced the germination of spinach seeds and subsequent seedling growth. As a follow-up study, we investigated the physico-chemical, biochemical, and molecular changes in seed after plasma treatment, focusing on the early germination stage, to elucidate mechanism(s) for the stimulating effects of plasma on seed germination. The primary radicle protruded from seeds exposed to high voltage nanosecond pulsed plasma (one shot) slightly faster than the control seeds. The hydrophilicity of the seed surface significantly increased after treatment with high voltage nanosecond pulsed plasma (one shot). However, a very subtle increase in water uptake by plasma treated seeds was observed. Raman and FTIR spectroscopy analyses on chloroform extract of seed coats demonstrated no significant chemical etching on the surface of plasma treated seeds. This may be related to no dramatic increase in water absorption by seeds. The level of GA hormone and starch hydrolysis inside the plasma treated seeds was significantly elevated within 24 h. Taken together, our results suggest that high voltage nanosecond pulsed plasma may not only enhance hydrophilicity of the seed surface but also stimulate biochemical and molecular processes inside seed, leading to enhanced embryonic development.

  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. © 2015 Authors; published by Portland Press Limited.

  8. Proteins Annexin A2 and PSA in Prostate Cancer Biopsies Do Not Predict Biochemical Failure.

    PubMed

    Lamb, David S; Sondhauss, Sven; Dunne, Jonathan C; Woods, Lisa; Delahunt, Brett; Ferguson, Peter; Murray, Judith; Nacey, John N; Denham, James W; Jordan, T William

    2017-12-01

    We previously reported the use of mass spectrometry and western blotting to identify proteins from tumour regions of formalin-fixed paraffin-embedded biopsies from 16 men who presented with apparently localized prostate cancer, and found that annexin A2 (ANXA2) appeared to be a better predictor of subsequent biochemical failure than prostate-specific antigen (PSA). In this follow-up study, ANXA2 and PSA were measured using western blotting of proteins extracted from biopsies from 37 men from a subsequent prostate cancer trial. No significant differences in ANXA2 and PSA levels were observed between men with and without biochemical failure. The statistical effect sizes were small, d=0.116 for ANXA2, and 0.266 for PSA. ANXA2 and PSA proteins measured from biopsy tumour regions are unlikely to be good biomarkers for prediction of the clinical outcome of prostate cancer presenting with apparently localized disease. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  9. Annular Bragg resonators (ABR): the ideal tool for biochemical sensing, nonlinear optics, and cavity QED

    NASA Astrophysics Data System (ADS)

    Scheuer, Jacob; Green, William M. J.; Yariv, Amnon

    2006-02-01

    Circular resonators are fundamentally interesting elements that are essential for research involving highly confined fields and strong photon-atom interactions such as cavity QED, as well as for practical applications in optical communication systems as and biochemical sensing. The important characteristics of a ring resonator are the Q-factor, the free spectral range (FSR) and the modal volume, where the last two are primarily determined by the resonator dimensions. The Total-Internal-Reflection (TIR) mechanism employed in "conventional" resonators couples between these characteristics and limits the ability to realize compact devices with large FSR, small modal volume and high Q. Recently, we proposed and analyzed a new class of a resonator in an annular geometry that is based on a single defect surrounded by radial Bragg reflectors on both sides. The radial Bragg confinement breaks the link between the characteristics of the mode and paves a new way for the realization of compact and low loss resonators. Such properties as well as the unique mode profile of the ABRs make this class of devices an excellent tool for ultra-sensitive biochemical detection as well as for studies in nonlinear optics and cavity QED.

  10. Postmatch recovery of physical performance and biochemical markers in team ball sports: a systematic review.

    PubMed

    Doeven, Steven H; Brink, Michel S; Kosse, Silke J; Lemmink, Koen A P M

    2018-01-01

    Insufficient postmatch recovery in elite players may cause an increased risk of injuries, illnesses and non-functional over-reaching. To evaluate postmatch recovery time courses of physical performance and biochemical markers in team ball sport players. Systematic review. PubMed and Web of Science. This systematic review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The Critical Review Form for Quantitative Studies was used to evaluate quality. Studies were included if they met the following criteria: (1) original research evaluated players' physical recovery postmatch; (2) team/intermittent sports; and (3) at least two postmeasurements were compared with baseline values. Twenty-eight studies were eligible. Mean methodological quality was 11.2±1.11. Most used performance tests and biochemical markers were the countermovement jump test, sprint tests and creatine kinase (CK), cortisol (C) and testosterone (T), respectively. The current evidence demonstrates that underlying mechanisms of muscle recovery are still in progress while performance recovery is already reached. CK recovery time courses are up to ≥72 hours. Soccer and rugby players need more time to recover for sprint performance, CK and C in comparison to other team ball sports. There are more high-quality studies needed regarding recovery in various team sports and recovery strategies on an individual level should be evaluated. Ongoing insufficient recovery can be prevented by the use of the presented recovery time courses as specific practical recovery guidelines.

  11. 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)

  12. Network representations and methods for the analysis of chemical and biochemical pathways

    PubMed Central

    Sandefur, Conner I.; Mincheva, Maya; Schnell, Santiago

    2013-01-01

    Systems biologists increasingly use network representations to investigate biochemical pathways and their dynamic behaviours. In this critical review, we discuss four commonly used network representations of chemical and biochemical pathways. We illustrate how some of these representations reduce network complexity but result in the ambiguous representation of biochemical pathways. We also examine the current theoretical approaches available to investigate the dynamic behaviour of chemical and biochemical networks. Finally, we describe how the critical chemical and biochemical pathways responsible for emergent dynamic behaviour can be identified using network mining and functional mapping approaches. PMID:23857078

  13. Biochemical Benefits, Diagnosis, and Clinical Risks Evaluation of Kratom.

    PubMed

    Fluyau, Dimy; Revadigar, Neelambika

    2017-01-01

    Kratom ( Mitragyna speciosa ) is a tropical tree with a long history of traditional use in parts of Africa and Southeast Asia. Kratom is also known as Thom, Thang, and Biak. Its leaves and the teas brewed from them have long been used by people in that region to manage pain and opioid withdrawal and to stave off fatigue. Kratom is actually consumed throughout the world for its stimulant effects and as an opioid substitute (in form of tea, chewed, smoked, or ingested in capsules). Some case reports have associated kratom exposure with psychosis, seizures, intrahepatic cholestasis, other medical conditions, and deaths. The clinical manifestations of kratom effects are not well defined and the clinical studies are limited. Data research suggest that both stimulant and sedative dose-dependent effects do exist, in addition to antinociceptive, antidepressant activity, anxiolytic-like effects, and anorectic effects, but a growing concern for the drug's effects and safety of use has resulted in national and international attention primarily due to an increase in hospital visits and deaths in several countries that are believed to have been caused by extracts of the plant. There is a dearth of double blind controlled studies. In this study, we aim to use existing literature to clarify both benefits and risks of kratom as well as its diagnosis evaluation as kratom misuse is an emerging trend in the Western world. Literature review using databases such as Embase, Medline, PubMed, Cochrane Library, and Mendeley from 2007 to 2017 were evaluated by all authors to analyze current state on benefits, risks, and diagnosis evaluation of kratom ( M. speciosa ). Data analysis suggested that kratom possesses some benefits such as stimulant and sedative effects as wells as antinociceptive effects. It seems to inhibit pro-inflammatory mediator release and vascular permeability and can enhance immunity. In addition, it may be an antidepressant and anorectic. However, kratom can cause

  14. Age- and Sex-Based Hematological and Biochemical Parameters for Macaca fascicularis

    PubMed Central

    Zhou, Qinming; Wu, Qingyuan; Gong, Wei; Cheng, Ke; Li, Juan; Li, Leilei; Fang, Liang; Zhou, Linke; Xie, Peng

    2013-01-01

    Background The cynomolgus monkey (Macaca fascicularis) has been increasingly used in biomedical research, making knowledge of its blood-based parameters essential to support the selection of healthy subjects and its use in preclinical research. As age and sex affect these blood-based parameters, it is important to establish baseline indices for these parameters on an age and sex basis and determine the effects of age and sex on these indices. Methods A total of 917 cynomolgus monkeys (374 males and 543 females) were selected and segregated by age (five groups) and sex. A total of 30 hematological and 22 biochemical parameters were measured, and the effects of age and sex were analyzed. Results Baseline indices for hematological and biochemical parameters were separately established by age and sex. Significant effects by age, sex, and age-sex interaction were observed in a number of blood parameters. In the 49–60 months and 61–72 months age groups, red blood cell count, hemoglobulin, and hematocrit showed significantly lower values (P<0.01) in females than males. Serum alkaline phosphatase varied with age in both sexes (P<0.01) and was significantly higher in females than males (P<0.05) in the groups aged 13–24 months and 25–36 months; however, in the three groups aged over 25–36 months, serum alkaline phosphatase was significantly lower in females than males (P<0.01). Creatinine concentration increased with age (P<0.01) in all age groups; specifically in the groups aged 49–60 months and 61–72 months, creatinine was significantly higher (P<0.01) in males than females. Total protein and globulin both increased with age (P<0.01). Conclusion The baseline values of hematological and biochemical parameters reported herein establish reference indices of blood-based parameters in the cynomolgus monkey by age and sex, thereby aiding researchers in selecting healthy subjects and evaluating preclinical studies using this species. PMID:23762263

  15. 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

  16. Physiological and biochemical investigations on egg stickiness in common carp.

    PubMed

    Mansour, N; Lahnsteiner, F; Patzner, R A

    2009-08-01

    The properties and behaviour of common carp, Cyprinus carpio, eggs in water and in ovarian fluids were studied at different temperature, pH, and with divalent cation concentrations. The biochemical composition of zona radiata externa (ZRE) was analyzed qualitatively and quantitatively on amino acids, carbohydrates, uronic acid and sialic acids using chemical assays; on proteins using electrophoresis. Comparative biochemical studies were performed on the chub, Leuciscus cephalus, the vimba, Vimba vimba and the bleak, Chalcalburnus chalcoides. Eggs of common carp became sticky within seconds after mixing with water. Egg stickiness was not affected by water pH in a range of 6-9, by water temperatures between 4 and 30 degrees C, by divalent cations in concentrations < or =20 mmol/l, and by sodium chloride concentrations < or =50 mmol/l. Our investigations indicated that specific proteins of the cyprinid ovarian fluid are controlling (inhibiting) the initiation of egg stickiness: egg stickiness did not develop as long as the eggs were incubated in ovarian fluid. When however the ovarian fluid proteins were removed from the ovarian fluid by heat treatment, eggs developed stickiness within seconds, like they do in water. Biochemically, the ZRE consisted of nine types of proteins whereby four of them were glycoproteins. Glucose, fructose, galactose, and uronic acids were the major carbohydrates. Treatment of the egg membrane with invertase or amyloglucosidase did not affect the egg stickiness. Treatment with protease prevented stickiness. From these results and from additional histochemical results, we conclude that glycoproteins are likely to be the molecules responsible for stickiness.

  17. Identification and prioritization of novel uncharacterized peptidases for biochemical characterization

    PubMed Central

    Rawlings, Neil D.

    2013-01-01

    Genome sequencing projects are generating enormous amounts of biological data that require analysis, which in turn identifies genes and proteins that require characterization. Enzymes that act on proteins are especially difficult to characterize because of the time required to distinguish one from another. This is particularly true of peptidases, the enzymes that activate, inactivate and degrade proteins. This article aims to identify clusters of sequences each of which represents the species variants of a single putative peptidase that is widely distributed and is thus merits biochemical characterization. The MEROPS database maintains large collections of sequences, references, substrate cleavage positions and inhibitor interactions of peptidases and their homologues. MEROPS also maintains a hierarchical classification of peptidase homologues, in which sequences are clustered as species variants of a single peptidase; homologous sequences are assembled into a family; and families are clustered into a clan. For each family, an alignment and a phylogenetic tree are generated. By assigning an identifier to a peptidase that has been biochemically characterized from a particular species (called a holotype), the identifier can be automatically extended to sequences from other species that cluster with the holotype. This permits transference of annotation from the holotype to other members of the cluster. By extending this concept to all peptidase homologues (including those of unknown function that have not been characterized) from model organisms representing all the major divisions of cellular life, clusters of sequences representing putative peptidases can also be identified. The 42 most widely distributed of these putative peptidases have been identified and discussed here and are prioritized as ideal candidates for biochemical characterization. Database URL: http://merops.sanger.ac.uk PMID:23584835

  18. iVUN: interactive Visualization of Uncertain biochemical reaction Networks

    PubMed Central

    2013-01-01

    Background Mathematical models are nowadays widely used to describe biochemical reaction networks. One of the main reasons for this is that models facilitate the integration of a multitude of different data and data types using parameter estimation. Thereby, models allow for a holistic understanding of biological processes. However, due to measurement noise and the limited amount of data, uncertainties in the model parameters should be considered when conclusions are drawn from estimated model attributes, such as reaction fluxes or transient dynamics of biological species. Methods and results We developed the visual analytics system iVUN that supports uncertainty-aware analysis of static and dynamic attributes of biochemical reaction networks modeled by ordinary differential equations. The multivariate graph of the network is visualized as a node-link diagram, and statistics of the attributes are mapped to the color of nodes and links of the graph. In addition, the graph view is linked with several views, such as line plots, scatter plots, and correlation matrices, to support locating uncertainties and the analysis of their time dependencies. As demonstration, we use iVUN to quantitatively analyze the dynamics of a model for Epo-induced JAK2/STAT5 signaling. Conclusion Our case study showed that iVUN can be used to perform an in-depth study of biochemical reaction networks, including attribute uncertainties, correlations between these attributes and their uncertainties as well as the attribute dynamics. In particular, the linking of different visualization options turned out to be highly beneficial for the complex analysis tasks that come with the biological systems as presented here. PMID:24564335

  19. 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.

  20. [Salvage brachytherapy for prostate cancer biochemical recurrence after radiotherapy].

    PubMed

    Rubio, Alfredo Polo; López, Ivan J Henríquez

    2012-01-01

    The best treatment option for patients with prostate cancer who experience local relapse after external beam radiation therapy remains uncertain. Salvage brachytherapy, cryotherapy, HIFU and radical prostatectomy have shown varying biochemical and quality-of-life outcomes according to disease-related and patient-related factors, but follow-up data are still short. It seems clear that careful patient selection for salvage brachytherapy is essential for good clinical and quality-of-life outcomes. We present a review of the currently available experiences of brachytherapy as salvage treatment after failure to external beam radiotherapy.

  1. Biochemical Signaling Pathways for Memory T cell Recall

    PubMed Central

    Farber, Donna L.

    2009-01-01

    Memory T cells exhibit low activation thresholds and rapid effector responses following antigen stimulation, contrasting naive T cells with high activation thresholds and no effector responses. Signaling mechanisms for the distinct properties of naive and memory T cells remain poorly understood. Here, I will discuss new results on signal transduction in naive and memory T cells that suggest proximal control of activation threshold and a distinct biochemical pathway to rapid recall. The signaling and transcriptional pathways controlling immediate effector function in memory T cells closely resemble pathways for rapid effector cytokine production in innate immune cells, suggesting memory T cells use innate pathways for efficacious responses. PMID:19298946

  2. Biochemical signaling pathways for memory T cell recall.

    PubMed

    Farber, Donna L

    2009-04-01

    Memory T cells exhibit low activation thresholds and rapid effector responses following antigen stimulation, contrasting naive T cells with high activation thresholds and no effector responses. Signaling mechanisms for the distinct properties of naive and memory T cells remain poorly understood. Here, I will discuss new results on signal transduction in naive and memory T cells that suggest proximal control of activation threshold and a distinct biochemical pathway to rapid recall. The signaling and transcriptional pathways controlling immediate effector function in memory T cells closely resemble pathways for rapid effector cytokine production in innate immune cells, suggesting memory T cells use innate pathways for efficacious responses.

  3. Biochemical Reconstitution and Characterization of Multicomponent Drug Efflux Transporters.

    PubMed

    Picard, Martin; Tikhonova, Elena B; Broutin, Isabelle; Lu, Shuo; Verchère, Alice; Zgurskaya, Helen I

    2018-01-01

    Efflux pumps are the major determinants in bacterial multidrug resistance. In Gram-negative bacteria, efflux transporters are organized as macromolecular tripartite machineries that span the two-membrane cell envelope of the bacterium. Biochemical data on purified proteins are essential to draw a mechanistic picture of this highly dynamical, multicomponent, efflux system. We describe protocols for the reconstitution and the in vitro study of transporters belonging to RND and ABC superfamilies: the AcrAB-TolC and MacAB-TolC efflux systems from Escherichia coli and the MexAB-OprM efflux pump from Pseudomonas aeruginosa.

  4. 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.

  5. 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

  6. Accelerator mass spectrometry in biomedical research

    NASA Astrophysics Data System (ADS)

    Vogel, J. S.; Turteltaub, K. W.

    1994-06-01

    Biological effects occur in natural systems at chemical concentrations of parts per billion (1:10 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 13-15 on milligram-sized samples and is ideal for quantifying long-lived radioisotopic labels for tracing biochemical pathways in natural systems. 14C-AMS has now been coupled to a variety of organic separation and definition technologies. Our primary research investigates pharmacokinetics and genotoxicities of toxins and drugs at very low doses. Human subjects research using AMS includes nutrition, toxicity and elemental balance studies. 3H, 41Ca and 26Al 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.

  7. [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.

  8. 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

  9. Sensitivity-based adaptive mesh refinement collocation method for dynamic optimization of chemical and biochemical processes.

    PubMed

    Xiao, Long; Liu, Ping; Liu, Xinggao; Zhang, Zeyin; Wang, Yalin; Yang, Chunhua; Gui, Weihua; Chen, Xu; Zhu, Bochao

    2017-09-01

    Collocation on finite element (CFE) is an effective simultaneous method of dynamic optimization to increase the profitability or productivity of industrial process. The approach needs to select an optimal mesh of time interval to balance the computational cost with desired solution. A new CFE approach with non-uniform refinement procedure based on the sensitivity analysis for dynamic optimization problems is, therefore, proposed, where a subinterval is further refined if the obtained control parameters have significant effect on the performance index. To improve the efficiency, the sensitivities of state parameters with respect to control parameters are derived from the solution of the discretized dynamic system. The proposed method is illustrated by testing two classic dynamic optimization problems from chemical and biochemical engineering. The detailed comparisons among the proposed method, the CFE with uniform mesh, and other reported methods are also carried out. The research results reveal the effectiveness of the proposed approach.

  10. Renewable Biochemical Methane Potential through Anaerobic Co-digestion from Selective Feed Stocks

    NASA Astrophysics Data System (ADS)

    Thara, K.; Navis Karthika, Ignatius; Dheenadayalan, M. S., Dr

    2017-08-01

    Biochemical Methane Potential (BMP) analysis provides a measure of the anaerobic biodegradability of a given substrate. BMP test is also used to evaluate the potential biogas (methane) production between various Co-digestion substrates. This test is also used to determine the amount of organic carbon in a given material that can be an aerobically converted to methane-Biogas. Studies were carried out for the production of biogas from the leather solid waste. Co-digestion (simultaneous digestion of two or more substrates) studies were carried out in batch reactor using the fleshing (a solid waste generated during the processing of raw hides or skins into finished leather) along with the fruit and vegetable waste at mesophilic condition 35° C). The anaerobic methanogenic seed sludge prepared separately followed by standard BMP test, which was used as the seed inoculums. Recent research on this topic is reviewed in this current paper.

  11. A new trend to determine biochemical parameters by quantitative FRET assays.

    PubMed

    Liao, Jia-yu; Song, Yang; Liu, Yan

    2015-12-01

    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 (K(d)), enzymatic velocity (k(cat)) and K(m). 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.

  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 review on bio-electrochemical systems (BESs) for the syngas and value added biochemicals production.

    PubMed

    Kumar, Gopalakrishnan; Saratale, Rijuta Ganesh; Kadier, Abudukeremu; Sivagurunathan, Periyasamy; Zhen, Guangyin; Kim, Sang-Hyoun; Saratale, Ganesh Dattatraya

    2017-06-01

    Bio-electrochemical systems (BESs) are the microbial systems which are employed to produce electricity directly from organic wastes along with some valuable chemicals production such as medium chain fatty acids; acetate, butyrate and alcohols. In this review, recent updates about value-added chemicals production concomitantly with the production of gaseous fuels like hydrogen and methane which are considered as cleaner for the environment have been addressed. Additionally, the bottlenecks associated with the conversion rates, lower yields and other aspects have been mentioned. In spite of its infant stage development, this would be the future trend of energy, biochemicals and electricity production in greener and cleaner pathway with the win-win situation of organic waste remediation. Henceforth, this review intends to summarise and foster the progress made in the BESs and discusses its challenges and outlook on future research advances. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals.

    PubMed

    Su, Fei; Xu, Ping

    2014-01-29

    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.

  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. Biochemical toxicology and suicide in Ireland: a laboratory study.

    PubMed

    Tormey, W P; Srinivasan, R; Moore, T

    2013-06-01

    Biochemical toxicology in suicides provides a template to improve preventive interventions in cases of suicide. The menu for biochemical toxicological analysis in coroners' cases is not prescriptive in Ireland or in the United Kingdom. The aim of the study was to confirm that reliance on the results of an immunoassay screen for drugs of abuse and common analgesics in order to select samples for compound confirmation by gas chromatography-mass spectrometry is likely to understate the potential role of drugs in suicide. Blood and urine samples were analyzed using enzyme immunoassay, alcohols by gas chromatography and urines were screened by Bio-Rad's Rapid Emergency Drug Identification (REMEDi) system. Laboratory data from analysis of 132 cases of suicide, including 101 cases of hanging revealed that 83 % were male confirming suicide as a male epidemic. Overall, alcohol was a factor in 57 %, benzodiazepines in 26 %, cannabinoids in 11 %, opioids in 19.7 %, sympathomimetics in 7.5 %, cocaine in 4.5 %, antidepressants 22 %, antipsychotics in 10 %, hypnotics in 5 %, and antihistamines in 4 % of these cases. Screening compounds in cases of hanging and other suicides should extend beyond the narrow focus of alcohol and illicit drugs to include a wide spectrum of psychoactive and other compounds as a standard procedure. The wide range of licit and illicit compounds found in these cases reflects current experience and dictates the necessity for chromatographic screening with mass spectroscopy confirmation in all cases as best practice.

  17. Effects of Mad Honey on Some Biochemical Parameters in Rats.

    PubMed

    Sahin, Huseyin; Yildiz, Oktay; Kolayli, Sevgi

    2016-10-01

    The aims of this study were to determine grayanotoxin (GTX-III) toxin level in mad honey using liquid chromatography-tandem mass spectrometry and examine the dynamic changes of certain biochemical parameters in blood serum of rats that consumed mad honey. For the experimental animal study, 20 Sprague-Dawley female rats were divided into 5 groups of 4 rats each, with one group being the control group (Group 1) and the others being the experimental groups (Groups 2-5). Groups 2, 3, 4, and 5 were, respectively, given mad honey extract at doses of 0.3, 0.6, 1.2, and 2.4 mg/g body weight/day via oral gavage for 8 days. According to results, the quantity of GTX-III found in the honey sample as 39.949 ± 0.020 μg GTX-III/g honey, and the biochemical analysis of the tested parameters (aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, alkaline phosphatase, creatine kinase, and creatine kinase muscle and brain) showed a significant elevation with increasing concentration of honey. In conclusion, the use of increasing concentrations of Rhododendron honey was seen as a source of enzymatic symptoms. © The Author(s) 2015.

  18. 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.

  19. Biochemical characterization of the human copper transporter Ctr1.

    PubMed

    Lee, Jaekwon; Peña, Maria Marjorette O; Nose, Yasuhiro; Thiele, Dennis J

    2002-02-08

    The trace metal copper is an essential cofactor for a number of biological processes including mitochondrial oxidative phosphorylation, free radical detoxification, neurotransmitter synthesis and maturation, and iron metabolism. Consequently, copper transport at the cell surface and the delivery of copper to intracellular proteins are critical events in normal physiology. Little is known about the molecules and biochemical mechanisms responsible for copper uptake at the plasma membrane in mammals. Here, we demonstrate that human Ctr1 (hCtr1) is a component of the copper transport machinery at the plasma membrane. hCtr1 transports copper with high affinity in a time-dependent and saturable manner and is metal-specific. hCtr1-mediated (64)Cu transport is an energy-independent process and is stimulated by extracellular acidic pH and high K(+) concentrations. hCtr1 exists as a homomultimer at the plasma membrane in mammalian cells. This is the first report on the biochemical characterization of the human copper transporter hCtr1, which is important for understanding mechanisms for mammalian copper transport at the plasma membrane.

  20. 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

  1. Biochemical transformation of lignin for deriving valued commodities from lignocellulose.

    PubMed

    Gall, Daniel L; Ralph, John; Donohue, Timothy J; Noguera, Daniel R

    2017-06-01

    The biochemical properties of lignin present major obstacles to deriving societally beneficial entities from lignocellulosic biomass, an abundant and renewable feedstock. Similar to other biopolymers such as polysaccharides, polypeptides, and ribonucleic acids, lignin polymers are derived from multiple types of monomeric units. However, lignin's renowned recalcitrance is largely attributable to its racemic nature and the variety of covalent inter-unit linkages through which its aromatic monomers are linked. Indeed, unlike other biopolymers whose monomers are consistently inter-linked by a single type of covalent bond, the monomeric units in lignin are linked via non-enzymatic, combinatorial radical coupling reactions that give rise to a variety of inter-unit covalent bonds in mildly branched racemic polymers. Yet, despite the chemical complexity and stability of lignin, significant strides have been made in recent years to identify routes through which valued commodities can be derived from it. This paper discusses emerging biological and biochemical means through which degradation of lignin to aromatic monomers can lead to the derivation of commercially valuable products. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  2. Biochemical characters and antibiotic susceptibility of Staphylococcus aureus isolates.

    PubMed

    Chakraborty, Subhankari Prasad; Mahapatra, Santanu Kar; Roy, Somenath

    2011-06-01

    To observe the biochemical characters and antibiotic susceptibility of isolated Staphylococcus aureus (S. auerus) strains against some conventional and traditional antibiotics. Thirty post operative pathogenic isolated S. aureus strains were used in this study. Bacterial culture was done in Mueller-Hinton broth at 37 °C. Characters of these strains were determined by traditional biochemical tests such as hydrolysis test of gelatin, urea, galactose, starch and protein, and fermentation of lactose and sucrose. Antibiotic susceptibility were carried out by minimum inhibitory concentration test, minium bactericidal concentration test, disc agar diffusion test and brain heart infusion oxacillin screening agar. From this study, it was observed that 100% S. aureus isolates showed positive results in gelatin, urea and galactose hydrolysis test, 50% isolates were positive in starch hydrolysis test, 35% in protein hydrolysis test, 100% isolates in lactose fermenting test, but no isolate was positive in sucrose fermenting test. Antibiotic susceptibility testing suggested that 20% of isolates were resistant to kanamycin and 46.67% were resistant to oxacillin. These findings show that all these isolates have gelatin, urea, galactose hydrolysis and lactose fermenting activity. 20% of these isolates were resistant to kanamycin and 46.67% were resistant to oxacillin.

  3. Molecular and biochemical characterization of tomato farnesyl-protein transferase.

    PubMed Central

    Schmitt, D; Callan, K; Gruissem, W

    1996-01-01

    The prenylation of membrane-associated proteins involved in the regulation of eukaryotic cell growth and signal transduction is critically important for their subcellular localization and biological activity. In contrast to mammalian cells and yeast, however, the function of protein prenylation in plants is not well understood and only a few prenylated proteins have been identified. We partially purified and characterized farnesyl-protein transferase from tomato (Lycopersicon esculentum, LeFTase) to analyze its biochemical and molecular properties. Using Ras- and G gamma-specific peptide substrates and competition assays we showed that tomato protein extracts have both farnesyl-protein transferase and geranylgeranyl-protein transferase 1 activities. Compared with the heterologous synthetic peptide substrates, the plant-specific CaaX sequence of the ANJ1 protein is a less efficient substrate for LeFTase in vitro. LeFTase activity profiles and LeFTase beta-subunit protein (LeFTB) levels differ significantly in various tissues and are regulated during fruit development. Partially purified LeFTase requires Zn2+ and Mg2+ for enzymatic activity and has an apparent molecular mass of 100 kD Immunoprecipitation experiments using anti-alpha LeFTB antibodies confirmed that LeFTB is a component of LeFTase but not of tomato geranylgeranyl-protein transferase 1. Based on their conserved bio-chemical activities, we expect that prenyltransferases are likely integrated with the sterol biosynthesis pathway in the control of plant cell growth. PMID:8883388

  4. Biochemical markers for the assessment of aquatic environment contamination

    PubMed Central

    Havelková, Marcela; Randák, Tomáš; Blahová, Jana; Slatinská, Iveta; Svobodová, Zdeňka

    2008-01-01

    The need for assessment of aquatic ecosystem contamination and of its impact on water dwelling organisms was developed in response to rising aquatic environmental pollution. In this field study, liver enzymes of phase I and phase II of xenobiotic transformation, namely cytochrome P450, ethoxyresorufin-O-deethylase, glutathione-S-transferase and tripeptide glutathione were used to assess the contamination of the aquatic environment at different rivers in the Czech Republic. The indicator species selected was the male chub (Leuciscus cephalus L.) and male brown trout (Salmo trutta fario). Chemical analyses included also the assessment of the most important inductors of previously mentioned biochemical markers. The major inductors of monitored biomarkers are industrial contaminants which belong to a large group of organic pollutants (PCB, PAH, PCDD/F, DDT, HCH, HCB and OCS), persistent in the environment. Four different groups of river basins were assessed: the River Tichá Orlice and its tributary the Kralický brook; important tributaries of the River Elbe (the rivers Orlice, Chrudimka, Cidlina, Jizera, Vltava, Ohře and Bílina); major rivers in the Czech Republic (the rivers Lužnice, Otava, Sázava, Berounka, Vltava, Labe, Ohře, Svratka, Dyje, Morava and Odra) and the River Vltava. The use of the biochemical markers together with chemical analyses seems to be an effective way to monitor the quality of aquatic environment. PMID:21218108

  5. Estimating rare events in biochemical systems using conditional sampling

    NASA Astrophysics Data System (ADS)

    Sundar, V. S.

    2017-01-01

    The paper focuses on development of variance reduction strategies to estimate rare events in biochemical systems. Obtaining this probability using brute force Monte Carlo simulations in conjunction with the stochastic simulation algorithm (Gillespie's method) is computationally prohibitive. To circumvent this, important sampling tools such as the weighted stochastic simulation algorithm and the doubly weighted stochastic simulation algorithm have been proposed. However, these strategies require an additional step of determining the important region to sample from, which is not straightforward for most of the problems. In this paper, we apply the subset simulation method, developed as a variance reduction tool in the context of structural engineering, to the problem of rare event estimation in biochemical systems. The main idea is that the rare event probability is expressed as a product of more frequent conditional probabilities. These conditional probabilities are estimated with high accuracy using Monte Carlo simulations, specifically the Markov chain Monte Carlo method with the modified Metropolis-Hastings algorithm. Generating sample realizations of the state vector using the stochastic simulation algorithm is viewed as mapping the discrete-state continuous-time random process to the standard normal random variable vector. This viewpoint opens up the possibility of applying more sophisticated and efficient sampling schemes developed elsewhere to problems in stochastic chemical kinetics. The results obtained using the subset simulation method are compared with existing variance reduction strategies for a few benchmark problems, and a satisfactory improvement in computational time is demonstrated.

  6. 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.

  7. Biochemical clocks and molecular noise: Theoretical study of robustness factors

    NASA Astrophysics Data System (ADS)

    Gonze, D.; Halloy, J.; Gaspard, P.

    2002-06-01

    We report a study of the influence of molecular fluctuations on a limit-cycle model of circadian rhythms based on the regulatory network of a gene involved in a biochemical clock. The molecular fluctuations may become important because of the low number of molecules involved in such genetic regulatory networks at the subcellular level. The molecular fluctuations are described by a birth-and-death stochastic process ruled by the chemical master equation of Nicolis and co-workers and simulated by Gillespie's algorithm. The robustness of the oscillations is characterized, in particular, by the probability distribution of the first-return times and the autocorrelation functions of the noisy oscillations. The half-life of the autocorrelation functions is studied as a function of the size of the system which controls the magnitude of the molecular fluctuations and of the degree of cooperativity of some reaction steps of the biochemical clock. The role of the attractivity of the limit cycle is also discussed.

  8. Estimating rare events in biochemical systems using conditional sampling.

    PubMed

    Sundar, V S

    2017-01-28

    The paper focuses on development of variance reduction strategies to estimate rare events in biochemical systems. Obtaining this probability using brute force Monte Carlo simulations in conjunction with the stochastic simulation algorithm (Gillespie's method) is computationally prohibitive. To circumvent this, important sampling tools such as the weighted stochastic simulation algorithm and the doubly weighted stochastic simulation algorithm have been proposed. However, these strategies require an additional step of determining the important region to sample from, which is not straightforward for most of the problems. In this paper, we apply the subset simulation method, developed as a variance reduction tool in the context of structural engineering, to the problem of rare event estimation in biochemical systems. The main idea is that the rare event probability is expressed as a product of more frequent conditional probabilities. These conditional probabilities are estimated with high accuracy using Monte Carlo simulations, specifically the Markov chain Monte Carlo method with the modified Metropolis-Hastings algorithm. Generating sample realizations of the state vector using the stochastic simulation algorithm is viewed as mapping the discrete-state continuous-time random process to the standard normal random variable vector. This viewpoint opens up the possibility of applying more sophisticated and efficient sampling schemes developed elsewhere to problems in stochastic chemical kinetics. The results obtained using the subset simulation method are compared with existing variance reduction strategies for a few benchmark problems, and a satisfactory improvement in computational time is demonstrated.

  9. Anatomical, architectural, and biochemical diversity of the murine forelimb muscles

    PubMed Central

    Mathewson, Margie A; Chapman, Mark A; Hentzen, Eric R; Fridén, Jan; Lieber, Richard L

    2012-01-01

    We characterized the architecture, fiber type, titin isoform distribution, and collagen content of 27 portions of 22 muscles in the murine forelimb. The mouse forelimb was different from the human arm in that it had the extensor digitorum lateralis muscle and no brachioradialis muscle. Architecturally, the mouse forelimb differed from humans with regard to load bearing, having a much larger contribution from extensors than flexors. In mice, the extensor : flexor PCSA ratio is 2.7, whereas in humans it is only 1.4. When the architectural difference index was calculated, similarities became especially apparent between flexors and extensors of the distal forelimb, as well as pronators. Discriminant analysis revealed that biochemical measures of collagen, titin, and myosin heavy chain were all strong between-species discriminators. In terms of composition, when compared with similar muscles in humans, mice had, on average, faster muscles with higher collagen content and larger titin isoforms. This report establishes the anatomical and biochemical properties of mouse forelimb muscles. Given the prevalence of this species in biological studies, these data will be invaluable for studying the biological basis of mouse muscle structure and function. PMID:22938020

  10. Combination of biochemical and mechanical cues for tendon tissue engineering.

    PubMed

    Testa, Stefano; Costantini, Marco; Fornetti, Ersilia; Bernardini, Sergio; Trombetta, Marcella; Seliktar, Dror; Cannata, Stefano; Rainer, Alberto; Gargioli, Cesare

    2017-11-01

    Tendinopathies negatively affect the life quality of millions of people in occupational and athletic settings, as well as the general population. Tendon healing is a slow process, often with insufficient results to restore complete endurance and functionality of the tissue. Tissue engineering, using tendon progenitors, artificial matrices and bioreactors for mechanical stimulation, could be an important approach for treating rips, fraying and tissue rupture. In our work, C3H10T1/2 murine fibroblast cell line was exposed to a combination of stimuli: a biochemical stimulus provided by Transforming Growth Factor Beta (TGF-β) and Ascorbic Acid (AA); a three-dimensional environment represented by PEGylated-Fibrinogen (PEG-Fibrinogen) biomimetic matrix; and a mechanical induction exploiting a custom bioreactor applying uniaxial stretching. In vitro analyses by immunofluorescence and mechanical testing revealed that the proposed combined approach favours the organization of a three-dimensional tissue-like structure promoting a remarkable arrangement of the cells and the neo-extracellular matrix, reflecting into enhanced mechanical strength. The proposed method represents a novel approach for tendon tissue engineering, demonstrating how the combined effect of biochemical and mechanical stimuli ameliorates biological and mechanical properties of the artificial tissue compared to those obtained with single inducement. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  11. Biochemical and bioinformatic analysis of the MYO19 motor domain

    PubMed Central

    Adikes, Rebecca C.; Unrath, William C.; Yengo, Christopher M.; Quintero, Omar A.

    2014-01-01

    Mitochondrial dynamics are dependent on both the microtubule and actin cytoskeletal systems. Evidence for the involvement of myosin motors has been described in many systems, and until recently a candidate mitochondrial transport motor had not been described in vertebrates. Myosin-XIX (MYO19) was predicted to represent a novel class of myosin and had previously been shown to bind to mitochondria and increase mitochondrial network dynamics when ectopically expressed. Our analyses comparing ∼40 MYO19 orthologs to ∼2000 other myosin motor domain sequences identified instances of homology well-conserved within class XIX myosins that were not found in other myosin classes, suggesting MYO19-specific mechanochemistry. Steady-state biochemical analyses of the MYO19 motor domain indicate that Homo sapiens MYO19 is a functional motor. Insect cell-expressed constructs bound calmodulin as a light chain at the predicted stoichiometry and displayed actin-activated ATPase activity. MYO19 constructs demonstrated high actin affinity in the presence of ATP in actin-cosedimentation assays, and translocated actin filaments in gliding assays. Expression of GFP-MYO19 containing a mutation impairing ATPase activity did not enhance mitochondrial network dynamics, as occurs with wild-type MYO19, indicating that myosin motor activity is required for mitochondrial motility. The measured biochemical properties of MYO19 suggest it is a high-duty ratio motor that could serve to transport mitochondria or anchor mitochondria, depending upon the cellular microenvironment. PMID:23568824

  12. A biochemical basis for induction of retina regeneration by antioxidants.

    PubMed

    Echeverri-Ruiz, Nancy; Haynes, Tracy; Landers, Joseph; Woods, Justin; Gemma, Michael J; Hughes, Michael; Del Rio-Tsonis, Katia

    2018-01-15

    The use of antioxidants in tissue regeneration has been studied, but their mechanism of action is not well understood. Here, we analyze the role of the antioxidant N-acetylcysteine (NAC) in retina regeneration. Embryonic chicks are able to regenerate their retina after its complete removal from retinal stem/progenitor cells present in the ciliary margin (CM) of the eye only if a source of exogenous factors, such as FGF2, is present. This study shows that NAC modifies the redox status of the CM, initiates self-renewal of the stem/progenitor cells, and induces regeneration in the absence of FGF2. NAC works as an antioxidant by scavenging free radicals either independently or through the synthesis of glutathione (GSH), and/or by reducing oxidized proteins through a thiol disulfide exchange activity. We dissected the mechanism used by NAC to induce regeneration through the use of inhibitors of GSH synthesis and the use of other antioxidants with different biochemical structures and modes of action, and found that NAC induces regeneration through its thiol disulfide exchange activity. Thus, our results provide, for the first time, a biochemical basis for induction of retina regeneration. Furthermore, NAC induction was independent of FGF receptor signaling, but dependent on the MAPK (pErk1/2) pathway. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Functional and biochemical properties of proteins from safflower seed.

    PubMed

    Sagiroglu, Ayten; Ozcan, Hakki M; Satana, Aziz

    2009-01-01

    There are relatively few studies on the properties of proteins that comprise a major part of the safflower seed. The biochemical and functional properties of these proteins have not been fully discovered. In this study, safflower seed proteins were obtained by isoelectric precipitation in two fractions. One of the fractions (Fraction-1) was obtained at pH 10 and the other fraction was obtained, as the protein supernatant separate from the pH precipitate, by ultra filtration (Fraction-2). Functional and biochemical properties of both of fractions were investigated. Gel permeation chromatography (GPC) was applied to both fractions. GPC shows that high-molecular weight constituents are present only in fraction 1, whereas fraction 2 consists of proteins with lower molecular weights in comparison with protein standards. Sodium dodecyl sulfate polyacrylamide gel (SDS-PAGE) electrophoresis in the presence of mercaptoethanol and SDS with protein weight markers was applied to both of the fractions. The proteins in both of the fractions were separated and stained with Commassie Brillant blue R-250 dye on the PAGE gel. The molecular weight (M(w)) of each protein band was determined graphically by plotting Log M(w) and relative mobilities (R(f)) using GS-300 scanning densitometry and a suitable computer program.

  14. 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

  15. Dust Fertilization of the Western Atlantic Biota: a Biochemical Model

    NASA Astrophysics Data System (ADS)

    Holmes, C. W.

    2017-12-01

    Every year an estimated 50 million tons of African dust reaches the Western Atlantic. This dust is composed of quartz sand, clay, and a mixture of quartz and clay particles agglutinated with micronutrient enriched ferruginous cement. However, whether it is friend or foe to biochemical systems is a matter of conjecture. Corals are ideal recorders of changing conditions as the layers can be dated so that the record of chemical changes is easily assessed. There is extensive shallow-and deep water coral development bordering the Florida Straits. The changes in trace element chemistry within these corals show a positive relationship with the African dust record. Recently, it has been demonstrated that many of the metals contained within the dust are necessary micronutrients in the fertilization of plankton. Using the results of these studies, a biochemical model has been constructed. This model suggests a path from inorganic dust through microbial transformation to micronutrient enzymes (i.e. Cd-enriched carbonic anahydrase) and carbonate precipitation on the Bahamian Banks. It is estimated that more than ten million metric tons of this fine, metal-rich sediment is formed each year. However, for much of this sediment, its deposition is temporary, as it is transported into the Florida Straits yearly by tropical cyclones. This metal-enriched fine carbonate becomes nutrients for phytoplankton, providing food for the corals, both shallow and deep.

  16. Biochemical changes in heat exposed buffalo heifers supplemented with yeast.

    PubMed

    Singh, Shiv Pratap; Hooda, Om Kanwar; Kundu, Shivlal Singh; Singh, Sohanvir

    2012-10-01

    Serum electrolytes, minerals, blood biochemical and plasma enzymes were studied in heat exposed buffalo heifers supplemented with yeast powder in feed to alleviate the adverse effects of heat stress. Eighteen healthy Murrah buffalo heifers (270-280) kg were divided into three groups. Animals of group I were kept in shed and served as control, while group II and group III were exposed in a psychrometric chamber at 40°C for 4 hrs daily for 16 days continuously. The animals in group III were also supplemented with yeast powder at 10 g per animal per day. The serum sodium, potassium and chloride levels decreased significantly (P < 0.05) in group II and their levels tended to be maintained in group III. Serum calcium, magnesium, phosphorus, glucose and total cholesterol concentration decreased (P < 0.05) significantly whereas total protein increased in group II due to heat stress. The levels of these minerals tended to be normal in group III. The plasma concentration of SGOT and SGPT increased significantly (P < 0.05), whereas the concentration of plasma alkaline phosphatase and acid phosphatase decreased due to thermal exposure. The levels of these enzymes tended to be normal in group III. The results indicated significant deviations in blood biochemical due to thermal stress and their levels tended to be normal in yeast supplemented group of buffalo heifers.

  17. Efficient stochastic simulation of biochemical reactions with noise and delays

    NASA Astrophysics Data System (ADS)

    Thanh, Vo Hong; Zunino, Roberto; Priami, Corrado

    2017-02-01

    The stochastic simulation algorithm has been used to generate exact trajectories of biochemical reaction networks. For each simulation step, the simulation selects a reaction and its firing time according to a probability that is proportional to the reaction propensity. We investigate in this paper new efficient formulations of the stochastic simulation algorithm to improve its computational efficiency. We examine the selection of the next reaction firing and reduce its computational cost by reusing the computation in the previous step. For biochemical reactions with delays, we present a new method for computing the firing time of the next reaction. The principle for computing the firing time of our approach is based on recycling of random numbers. Our new approach for generating the firing time of the next reaction is not only computationally efficient but also easy to implement. We further analyze and reduce the number of propensity updates when a delayed reaction occurred. We demonstrate the applicability of our improvements by experimenting with concrete biological models.

  18. Biochemical transformation of lignin for deriving valued commodities from lignocellulose

    DOE PAGES

    Gall, Daniel L.; Ralph, John; Donohue, Timothy J.; ...

    2017-03-24

    The biochemical properties of lignin present major obstacles to deriving societally beneficial entities from lignocellulosic biomass, an abundant and renewable feedstock. Similar to other biopolymers such as polysaccharides, polypeptides, and ribonucleic acids, lignin polymers are derived from multiple types of monomeric units. However, lignin’s renowned recalcitrance is largely attributable to its racemic nature and the variety of covalent inter-unit linkages through which its aromatic monomers are linked. Indeed, unlike other biopolymers whose monomers are consistently inter-linked by a single type of covalent bond, the monomeric units in lignin are linked via non-enzymatic, combinatorial radical coupling reactions that give rise tomore » a variety of inter-unit covalent bonds in mildly branched racemic polymers. Yet, despite the chemical complexity and stability of lignin, significant strides have been made in recent years to identify routes through which valued commodities can be derived from it. This paper discusses emerging biological and biochemical means through which degradation of lignin to aromatic monomers can lead to the derivation of commercially valuable products.« less

  19. Xeroderma pigmentosum and Cockayne syndrome: overlapping clinical and biochemical phenotypes.

    PubMed Central

    Greenhaw, G A; Hebert, A; Duke-Woodside, M E; Butler, I J; Hecht, J T; Cleaver, J E; Thomas, G H; Horton, W A

    1992-01-01

    Two siblings are described whose clinical presentation of cutaneous photosensitivity and central nervous system dysfunction is strongly reminiscent of the DeSanctis-Cacchione syndrome (DCS) variant of xeroderma pigmentosum. An extensive clinical evaluation supported a diagnosis of DCS and documented previously unreported findings. In vitro fibroblast studies showed UV sensitivity that was two to three times that of normal controls. However, neither a post-UV-irradiation DNA excision-repair defect indicative of XP nor a semiconservative DNA replication defect indicative of XP variant was found. Rather, a failure of RNA synthesis to recover to normal levels after UV exposure was observed, a biochemical abnormality seen in Cockayne syndrome (CS), one of the premature-aging syndromes with clinical UV sensitivity. These patients, therefore, clinically have XP, but their biochemical characteristics suggest CS. The reason(s) for the severe neurologic disease, in light of the relatively mild cutaneous abnormalities, is unclear. Other cases with unusual fibroblast responses to irradiation have been noted in the literature and, along with the data from our patients, reinforce the notion of the complexity of DNA maintenance and repair. Images Figure 1 Figure 1 Figure 2 Figure 3 PMID:1372469

  20. [Development of a new biosensor for biochemical oxygen demand].

    PubMed

    Chang, Dong; Du, Xiao-yan; Pan, Hong-zhi; Jia, Jian-bo; Wang, Bing-quan; Cheng, Guang-jin; Dong, Shao-jun

    2003-03-01

    To use a new kind of fixing material, i.e. Sol-Gel organic-inorganic hybridized material to immobilize bacterium to detect Biochemical oxygen demand quickly. The biosensor was fabricated using a thin film in which Hansenula anomala was immobilized by sol-gel and an oxygen electrode. The optimum measurement for biochemical oxygen demand was at pH 7.0; 28 degrees C; response time 3 - 12 min. Pure organic compound, sewage and rate of recovery were detected with the biosensor. It shows that the BOD biosensor can be used to detect many organic compounds such as amino acid, glucide. It is suitable to monitor sewage and industrial waste water which has low level alcohols and phenols. The microbial membrane can work 3 months and remain its 70% activity. It is measured that the rate of recovery of BOD is between 90% to 105% in sewage. The study confirmed the effectiveness and usefulness of BOD sensor, which is quick, convenient, low cost and reliable with little interference.

  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. Metabolic network failures in Alzheimer’s disease: A biochemical road map

    PubMed Central

    Toledo, Jon B.; Arnold, Matthias; Kastenmüuller, Gabi; Chang, Rui; Baillie, Rebecca A.; Han, Xianlin; Thambisetty, Madhav; Tenenbaum, Jessica D.; Suhre, Karsten; Thompson, J. Will; St. John-Williams, Lisa; MahmoudianDehkordi, Siamak; Rotroff, Daniel M.; Jack, John R.; Motsinger-Reif, Alison; Risacher, Shannon L.; Blach, Colette; Lucas, Joseph E.; Massaro, Tyler; Louie, Gregory; Zhu, Hongjie; Dallmann, Guido; Klavins, Kristaps; Koal, Therese; Kim, Sungeun; Nho, Kwangsik; Shen, Li; Casanova, Ramon; Varma, Sudhir; Legido-Quigley, Cristina; Moseley, M. Arthur; Zhu, Kuixi; Henrion, Marc Y. R.; van der Lee, Sven J.; Harms, Amy C.; Demirkan, Ayse; Hankemeier, Thomas; van Duijn, Cornelia M.; Trojanowski, John Q.; Shaw, Leslie M.; Saykin, Andrew J.; Weiner, Michael W.; Doraiswamy, P. Murali; Kaddurah-Daouk, Rima

    2018-01-01

    Introduction The Alzheimer’s Disease Research Summits of 2012 and 2015 incorporated experts from academia, industry, and nonprofit organizations to develop new research directions to transform our understanding of Alzheimer’s disease (AD) and propel the development of critically needed therapies. In response to their recommendations, big data at multiple levels are being generated and integrated to study network failures in disease. We used metabolomics as a global biochemical approach to identify peripheral metabolic changes in AD patients and correlate them to cerebrospinal fluid pathology markers, imaging features, and cognitive performance. Methods Fasting serum samples from the Alzheimer’s Disease Neuroimaging Initiative (199 control, 356 mild cognitive impairment, and 175 AD participants) were analyzed using the AbsoluteIDQ-p180 kit. Performance was validated in blinded replicates, and values were medication adjusted. Results Multivariable-adjusted analyses showed that sphingomyelins and ether-containing phosphatidylcholines were altered in preclinical biomarker-defined AD stages, whereas acylcarnitines and several amines, including the branched-chain amino acid valine and α-aminoadipic acid, changed in symptomatic stages. Several of the analytes showed consistent associations in the Rotterdam, Erasmus Rucphen Family, and Indiana Memory and Aging Studies. Partial correlation networks constructed for Aβ1–42, tau, imaging, and cognitive changes provided initial biochemical insights for disease-related processes. Coexpression networks interconnected key metabolic effectors of disease. Discussion Metabolomics identified key disease-related metabolic changes and disease-progression-related changes. Defining metabolic changes during AD disease trajectory and its relationship to clinical phenotypes provides a powerful roadmap for drug and biomarker discovery. PMID:28341160

  3. Metabolic network failures in Alzheimer's disease: A biochemical road map.

    PubMed

    Toledo, Jon B; Arnold, Matthias; Kastenmüller, Gabi; Chang, Rui; Baillie, Rebecca A; Han, Xianlin; Thambisetty, Madhav; Tenenbaum, Jessica D; Suhre, Karsten; Thompson, J Will; John-Williams, Lisa St; MahmoudianDehkordi, Siamak; Rotroff, Daniel M; Jack, John R; Motsinger-Reif, Alison; Risacher, Shannon L; Blach, Colette; Lucas, Joseph E; Massaro, Tyler; Louie, Gregory; Zhu, Hongjie; Dallmann, Guido; Klavins, Kristaps; Koal, Therese; Kim, Sungeun; Nho, Kwangsik; Shen, Li; Casanova, Ramon; Varma, Sudhir; Legido-Quigley, Cristina; Moseley, M Arthur; Zhu, Kuixi; Henrion, Marc Y R; van der Lee, Sven J; Harms, Amy C; Demirkan, Ayse; Hankemeier, Thomas; van Duijn, Cornelia M; Trojanowski, John Q; Shaw, Leslie M; Saykin, Andrew J; Weiner, Michael W; Doraiswamy, P Murali; Kaddurah-Daouk, Rima

    2017-09-01

    The Alzheimer's Disease Research Summits of 2012 and 2015 incorporated experts from academia, industry, and nonprofit organizations to develop new research directions to transform our understanding of Alzheimer's disease (AD) and propel the development of critically needed therapies. In response to their recommendations, big data at multiple levels are being generated and integrated to study network failures in disease. We used metabolomics as a global biochemical approach to identify peripheral metabolic changes in AD patients and correlate them to cerebrospinal fluid pathology markers, imaging features, and cognitive performance. Fasting serum samples from the Alzheimer's Disease Neuroimaging Initiative (199 control, 356 mild cognitive impairment, and 175 AD participants) were analyzed using the AbsoluteIDQ-p180 kit. Performance was validated in blinded replicates, and values were medication adjusted. Multivariable-adjusted analyses showed that sphingomyelins and ether-containing phosphatidylcholines were altered in preclinical biomarker-defined AD stages, whereas acylcarnitines and several amines, including the branched-chain amino acid valine and α-aminoadipic acid, changed in symptomatic stages. Several of the analytes showed consistent associations in the Rotterdam, Erasmus Rucphen Family, and Indiana Memory and Aging Studies. Partial correlation networks constructed for Aβ 1-42 , tau, imaging, and cognitive changes provided initial biochemical insights for disease-related processes. Coexpression networks interconnected key metabolic effectors of disease. Metabolomics identified key disease-related metabolic changes and disease-progression-related changes. Defining metabolic changes during AD disease trajectory and its relationship to clinical phenotypes provides a powerful roadmap for drug and biomarker discovery. Copyright © 2017 the Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

  4. 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.

  5. Tank cultivation of the red algae Palmaria mollis: Effects of nutrients on growth rate, biochemical quality, and epiphytic growth

    NASA Astrophysics Data System (ADS)

    Ben, D.; Langdon, C. J.

    2016-02-01

    Pacific dulse (Palmaria mollis) is a candidate for aquaculture production in Oregon due to its high protein content, fast growth rate, and ability to fare in cold water conditions. Current cultivation methods use the F/2 medium to supply nutrients to macroalgae cultures. The F/2 medium is a costly mixture of nitrate, phosphate, trace metals and vitamins. The F/2 medium has been the standard for microalgae cultivation, but research has lacked on the necessity of all or part of this mixture for macroalgae cultivation. This study is designed to contribute to the development of Pacific dulse cultivation by measuring how different fertilizer regimens affect the growth, biochemical composition, and quality of Palmaria mollis (C-3 variety) in hopes to reduce the production cost. I hypothesis that dulse will not require additional nutrients during summer cultivation, due to summer upwelling conditions. Experiments were conducted in a flow-through water system, controlling for flow rate, stocking density, and nutrient supplementation. To test this, two replicates of four nutrient regimes were organized: no supplemental nutrients, all nutrients (standard F/2 medium), nitrate/phosphate only, and nitrate/phosphate with trace metals. Each tank was monitored weekly for color quality, epiphytic growth, specific growth rate, production and a final biochemical analysis. This study has preliminarily concluded that supplemental nutrients have no significant effect on production or biochemical quality, but does have an effect quality of epiphytic growth.

  6. [Research on Fenton treatment of the biochemical processes effluent of bamboo industry wastewater].

    PubMed

    Guo, Qing-Wen; Zhang, Min; Wang, Wei; Yang, Zhi-Zhong; Wu, Dong-Lei

    2013-06-01

    The decolorization and organic matter reduction of bamboo wastewater using Fenton oxidation was studied. Considering the cost and the removal efficiency, the optimal conditions were t = 30 degrees C, pH = 3.5, p(H2O2) = 1 665 mg x L(-1), c(Fe2+)/c(H2O2) = 0.072 and reaction time 3 h, with an initial COD and color concentration of wastewater of 430 mg x L(-1) and 1 500 times, under these conditions, the removal efficiency of COD and color could achieve 87.5% and 94.4%, respectively. It was found that the color reduction was higher than that of organics, and less affected by operation factors. The GC-MS analysis revealed that the chromophoric groups and auxochromic groups were greatly removed after Fenton treatment. The intermediates were mainly ester derivatives, and the by-products included 1-iodo-tridecane and 1,1'-oxybisoctane.

  7. Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways

    PubMed Central

    Vinnakota, Kalyan C.; Wu, Fan; Kushmerick, Martin J.; Beard, Daniel A.

    2009-01-01

    The operation of biochemical systems in vivo and in vitro is strongly influenced by complex interactions between biochemical reactants and ions such as H+, Mg2+, K+, and Ca2+. These are important second messengers in metabolic and signaling pathways that directly influence the kinetics and thermodynamics of biochemical systems. Herein we describe the biophysical theory and computational methods to account for multiple ion binding to biochemical reactants and demonstrate the crucial effects of ion binding on biochemical reaction kinetics and thermodynamics. In simulations of realistic systems, the concentrations of these ions change with time due to dynamic buffering and competitive binding. In turn, the effective thermodynamic properties vary as functions of cation concentrations and important environmental variables such as temperature and overall ionic strength. Physically realistic simulations of biochemical systems require incorporating all of these phenomena into a coherent mathematical description. Several applications to physiological systems are demonstrated based on this coherent simulation framework. PMID:19216922

  8. Molecular diversity in the context of leadlikeness: compound properties that enable effective biochemical screening.

    PubMed

    Rishton, Gilbert M

    2008-06-01

    Molecular diversity is of vital importance in drug screening in general and for the discovery and development of new pharmacophores in particular. Biochemical screening is a powerful tool for pharmacophore development given understanding of the properties of a good lead compound operating in the biochemical environment. The properties of leadlikeness have evolved to accommodate the artificial conditions of a biochemical assay. Accordingly, the properties of leadlikeness that are suited for screening at protein targets biochemically are different and complementary to the properties of druglikeness used to guide the selection of good compounds studied biologically in cellular studies and animal models. The benefits of leadlikeness in the biochemical screening arena (including fragment-based screening and co-crystallization studies) are described here and recommendations are forwarded for the generation of leadlike molecular diversity. Chemically stable low molecular weight 'minimalist' compounds (or fragments) with dense heteroatom substitution and variable conformational constraint are promoted as conceptually superior compounds for biochemical screening.

  9. Hematologic and biochemical profiles in Standardbred mares during peripartum.

    PubMed

    Mariella, Jole; Pirrone, Alessandro; Gentilini, Fabio; Castagnetti, Carolina

    2014-03-01

    The purposes of this study were to determine physiological changes occurring in hematologic and biochemical parameters in mares between the last month of gestation and the first week after parturition. If a significant change was observed with respect to the reference interval of an adult horse, a further aim of the study was to establish different reference intervals. Blood samples were collected from 62 healthy pregnant Standardbred mares. Seventeen nonpregnant and nonlactating mares were used as a control group. In pregnant mares, blood sampling was conducted every three days from 1 month before the expected foaling date (335 days after the last mating), at parturition, and 7 days after foaling. The barren mares in the control group were sampled once. Results from samples collected 20 and 10 days before parturition, at parturition, and 7 days after were considered in the statistical analysis. A parametric method for all the parameters studied was used to establish reference intervals. Results were compared by repeated measures ANOVA. When significant differences were observed in relation to sampling time, a post hoc analysis was performed (Tukey test). The one-way ANOVA test followed by Dunnett's test was performed to evaluate the presence of a significant difference between each sampling time and the control group. Any significant difference in the blood count parameters at different sampling times was observed by repeated measure ANOVA. Hemoglobin (P < 0.01) and hematocrit (P < 0.01) 7 days after parturition and white blood cell count (P < 0.01) at parturition were significantly different from the control group. Erythrocyte indices and platelet count were within the normal reference intervals as established in the control group. In the biochemical panel, gamma-glutamyltransferase, creatinine, glucose, biliar acids, total protein, albumin-to-globulin ratio, and calcium were significantly different at different sampling times. Moreover, serum concentration of

  10. Biochemical alterations in rat Thiry-Vella fistulas.

    PubMed

    Arcuni, J; Wang, L; Franson, R C; Sonnino, R E

    2000-01-01

    In order to obtain baseline information on the secretory function of normal rat bowel for our work on intestinal graft ischemia, we studied several biochemical parameters in rat Thiry-Vella fistulas (TVF). TVFs were created in 200-g male Lewis rats (n = 11) using the 25-cm segment of jejunum normally used as a graft in our intestinal transplant model. The stomas were matured primarily and the animals were allowed to recover. The TVFs were flushed at 0, 6, and 24 h and then daily for up to 21 days with 12 mL normal saline solution. The effluent was collected and analyzed for total protein (TP), secretory phospholipase A2 (sPLA2), intestinal fatty acid binding protein (I-FABP), lactate dehydrogenase (LDH), and N-acetylglucosamine (NAGA). TP content was 0.12 +/- 0.01 mg/mL up to 48 h, then gradually increased and stabilized at 0.39 +/- 0.05 mg/mL at day 21. By sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), one major protein band was identified in the low-molecular-mass range (15 kD), consistent with I-FABP and sPLA2. Secretory PLA2 levels decreased over the first 4 days to a low of 115 +/- 24.8% hydrolysis/min/fraction, then gradually rose to a plateau at approximately 529.76 +/- 88.36% hydrolysis/min/fraction by day 18. I-FABP levels rose rapidly from 0 ng/mL at 2 h to 900 +/- 250.0 ng/mL at 6 h and approximately 3000 +/- 304.9 ng/mL by day 14. LDH levels at 2 h and 48 h did not differ, with 0.03 +/- 0.004 and 0.03 +/- 0.005 optical density units (OD)/min/mL, respectively. NAGA levels were 0.07 +/- 0.05 OD/h/mL at 2 h and rose to 0.14 +/- 0.04 OD/h/mL at 48 h. These data suggest that after an early equilibration period, biochemical secretion into the lumen of normal rat bowel reaches a state of equilibrium, and therefore appears to reflect the baseline biochemical status of the bowel. Some of these levels are not negligible as one would expect in "normal" bowel. This information should prove extremely helpful as a baseline study of abnormal

  11. A combined model reduction algorithm for controlled biochemical systems.

    PubMed

    Snowden, Thomas J; van der Graaf, Piet H; Tindall, Marcus J

    2017-02-13

    Systems Biology continues to produce increasingly large models of complex biochemical reaction networks. In applications requiring, for example, parameter estimation, the use of agent-based modelling approaches, or real-time simulation, this growing model complexity can present a significant hurdle. Often, however, not all portions of a model are of equal interest in a given setting. In such situations methods of model reduction offer one possible approach for addressing the issue of complexity by seeking to eliminate those portions of a pathway that can be shown to have the least effect upon the properties of interest. In this paper a model reduction algorithm bringing together the complementary aspects of proper lumping and empirical balanced truncation is presented. Additional contributions include the development of a criterion for the selection of state-variable elimination via conservation analysis and use of an 'averaged' lumping inverse. This combined algorithm is highly automatable and of particular applicability in the context of 'controlled' biochemical networks. The algorithm is demonstrated here via application to two examples; an 11 dimensional model of bacterial chemotaxis in Escherichia coli and a 99 dimensional model of extracellular regulatory kinase activation (ERK) mediated via the epidermal growth factor (EGF) and nerve growth factor (NGF) receptor pathways. In the case of the chemotaxis model the algorithm was able to reduce the model to 2 state-variables producing a maximal relative error between the dynamics of the original and reduced models of only 2.8% whilst yielding a 26 fold speed up in simulation time. For the ERK activation model the algorithm was able to reduce the system to 7 state-variables, incurring a maximal relative error of 4.8%, and producing an approximately 10 fold speed up in the rate of simulation. Indices of controllability and observability are additionally developed and demonstrated throughout the paper. These provide

  12. Biochemical changes during the storage of high hydrostatic pressure processed avocado paste.

    PubMed

    Jacobo-Velázquez, D A; Hernández-Brenes, C

    2010-08-01

    High hydrostatic pressure (HHP) processing improves the shelf life of avocado paste without a significant impact on flavor; however, scarce information is available on biochemical modifications during its extended storage period. The present study focused on the changes in oxidative enzyme activities of pressurized avocado paste (600 MPa for 3 min) during refrigerated storage (45 d at 4 degrees C). Aerobic plate counts (APC), lactic acid bacteria counts (LAB), pH, and instrumental color were also evaluated during storage. Processing with HHP caused a decrease in polyphenol oxidase (PPO) and lipoxygenase (LOX) activities, resulting in residual enzyme levels of 50.72% and 55.16%, respectively. Although instrumental color values didn't change significantly during the evaluated storage period, both enzymes (PPO and LOX) recuperated their activities at 10 to 15 d of storage, reached the original values observed in the fresh paste, and then started a declining phase until the end of the storage period. Pulp pH presented a consistent decline during the first 20 d of storage. LAB counts were very low during storage, discarding lactic acid production as responsible for the observed pH decline. Enzyme reactivation, cell disruption, and a gradual migration of intracellular components such as organic acids are herein proposed as the main mechanisms for the deterioration of HHP treated avocado paste during its refrigerated storage. Practical Application: At the present, HHP is the most effective commercial nonthermal technology to process avocado paste when compared to thermal and chemical alternatives. Although it has proven to be an excellent product-technology match, little information is known on the biochemical changes that take place in the product during its refrigerated shelf life. Biochemical reactions during storage are important, since they can influence avocado paste nutritional and flavor qualities at the time of product consumption. The present study reports for

  13. [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.

  14. Structural and biochemical analysis of a bacterial glycosyltransferase.

    PubMed

    Zhu, Fan; Wu, Ren; Zhang, Hua; Wu, Hui

    2013-01-01

    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.

  15. Overview of the biochemical and genetic processes in malignant mesothelioma*

    PubMed Central

    de Assis, Leonardo Vinícius Monteiro; 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 erionite, as well as to simian virus 40. 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. PMID:25210967

  16. Complexity of generic biochemical circuits: topology versus strength of interactions

    NASA Astrophysics Data System (ADS)

    Tikhonov, Mikhail; Bialek, William

    2016-12-01

    The historical focus on network topology as a determinant of biological function is still largely maintained today, illustrated by the rise of structure-only approaches to network analysis. However, biochemical circuits and genetic regulatory networks are defined both by their topology and by a multitude of continuously adjustable parameters, such as the strength of interactions between nodes, also recognized as important. Here we present a class of simple perceptron-based Boolean models within which comparing the relative importance of topology versus interaction strengths becomes a quantitatively well-posed problem. We quantify the intuition that for generic networks, optimization of interaction strengths is a crucial ingredient of achieving high complexity, defined here as the number of fixed points the network can accommodate. We propose a new methodology for characterizing the relative role of parameter optimization for topologies of a given class.

  17. Polyphenol Oxidases in Crops: Biochemical, Physiological and Genetic Aspects

    PubMed Central

    Taranto, Francesca; Pasqualone, Antonella; Mangini, Giacomo; Tripodi, Pasquale; Miazzi, Monica Marilena; Pavan, Stefano; Montemurro, Cinzia

    2017-01-01

    Enzymatic browning is a colour reaction occurring in plants, including cereals, fruit and horticultural crops, due to oxidation during postharvest processing and storage. This has a negative impact on the colour, flavour, nutritional properties and shelf life of food products. Browning is usually caused by polyphenol oxidases (PPOs), following cell damage caused by senescence, wounding and the attack of pests and pathogens. Several studies indicated that PPOs play a role in plant immunity, and emerging evidence suggested that PPOs might also be involved in other physiological processes. Genomic investigations ultimately led to the isolation of PPO homologs in several crops, which will be possibly characterized at the functional level in the near future. Here, focusing on the botanic families of Poaceae and Solanaceae, we provide an overview on available scientific literature on PPOs, resulting in useful information on biochemical, physiological and genetic aspects. PMID:28208645

  18. Biochemical events in naturally occurring forms of cell death.

    PubMed

    Fesus, L

    1993-08-09

    Several molecular elements of programmed cell death and apoptosis have recently been revealed. The function of gene products which deliver the lethal 'hit' is still not known. Well-characterized and newly discovered cell surface structures (e.g. antigen receptors, FAS/APO-1), as well as transcriptional factors (steroid receptor, c-myc, P53, retinoblastoma protein and others), have been implicated in the initiation of the death pathway. Negative regulators of the process (ced-9 gene product in programmed death of cells in Caenorhabditis elegans and bcl-2 protein in apoptosis) have been described. Biochemical mechanisms responsible for the silent nature of natural deaths of cells include their rapid engulfment (mainly through integrin receptors), transglutaminase-catalyzed cross-linking of cellular proteins, and fragmentation of DNA. Several lines of evidence suggest that distinct molecular mechanisms may operate in various forms of natural cell death.

  19. SIMULATING BIOCHEMICAL SIGNALING NETWORKS IN COMPLEX MOVING GEOMETRIES

    PubMed Central

    STRYCHALSKI, WANDA; ADALSTEINSSON, DAVID; ELSTON, TIMOTHY C.

    2013-01-01

    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

  20. The biochemical basis for thermoregulation in heat-producing flowers.

    PubMed

    Umekawa, Yui; Seymour, Roger S; Ito, Kikukatsu

    2016-04-20

    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.

  1. The Biochemical Basis for Stereochemical Control in Polyketide Biosynthesis

    PubMed Central

    Valenzano, Chiara R.; Lawson, Rachel J.; Chen, Alice Y.; Khosla, Chaitan; Cane, David E.

    2013-01-01

    One of the most striking features of complex polyketides is the presence of numerous methyl- and hydroxyl-bearing stereogenic centers. In order to investigate the biochemical basis for the control of polyketide stereochemistry and to establish the timing and mechanism of the epimerization at methyl-bearing centers, a series of incubations was carried out using reconstituted components from a variety of modular polyketide synthases. In all cases the stereochemistry of the product was directly correlated with the intrinsic stereospecificity of the ketoreductase domain, independent of the particular chain elongation domains that were used, thereby establishing that methyl group epimerization, when it does occur, takes place after ketosynthase-catalyzed chain elongation. The finding that there were only minor differences in the rates of product formation observed for parallel incubations using an epimerizing ketoreductase domain and the non-epimerizing ketoreductase domain supports the proposal that the epimerization is catalyzed by the ketoreductase domain itself. PMID:19928853

  2. Biochemical and structural investigations on phosphoribosylpyrophosphate synthetase from Mycobacterium smegmatis

    PubMed Central

    Donini, Stefano; Garavaglia, Silvia; Ferraris, Davide M.; Miggiano, Riccardo; Mori, Shigetarou; Shibayama, Keigo

    2017-01-01

    Mycobacterium smegmatis represents one model for studying the biology of its pathogenic relative Mycobacterium tuberculosis. The structural characterization of a M. tuberculosis ortholog protein can serve as a valid tool for the development of molecules active against the M. tuberculosis target. In this context, we report the biochemical and structural characterization of M. smegmatis phosphoribosylpyrophosphate synthetase (PrsA), the ortholog of M. tuberculosis PrsA, the unique enzyme responsible for the synthesis of phosphoribosylpyrophosphate (PRPP). PRPP is a key metabolite involved in several biosynthetic pathways including those for histidine, tryptophan, nucleotides and decaprenylphosphoryl-arabinose, an essential precursor for the mycobacterial cell wall biosynthesis. Since M. tuberculosis PrsA has been validated as a drug target for the development of antitubercular agents, the data presented here will add to the knowledge of the mycobacterial enzyme and could contribute to the development of M. tuberculosis PrsA inhibitors of potential pharmacological interest. PMID:28419153

  3. Biochemical and morphological changes in dormant ("Nonculturable") Mycobacterium smegmatis cells.

    PubMed

    Salina, E G; Zhogina, Yu A; Shleeva, M O; Sorokoumova, G M; Selishcheva, A A; Kaprelyants, A S

    2010-01-01

    Biochemical and morphological changes have been studied during transition of Mycobacterium smegmatis cells into their dormant ("nonculturable") state. A significant fraction of the population of irreversibly "nonculturable" (NC) cells has a thicker cell wall, condensed cytoplasm, and a decreased number of ribosomes. The lipid contents in the NC cells are lower than in the metabolically active cells, with a relatively decreased amount of phospholipid and neutral lipid. Free mycolic acids, which are abundant in metabolically active cells, were not found in the NC cells. The NC forms are also characterized by decreased respiratory activity on endogenous substrates; however, the respiratory chain enzymes retain their activities in the isolated membranes. Activities of the Krebs cycle and glyoxylate cycle enzymes are markedly decreased. Despite a significant decrease in metabolic activity, NC cells possess membrane potential that seems to provide for reversibility of the NC state of mycobacteria, i.e. their capability of reactivating.

  4. Robustness of complex feedback systems: application to oncological biochemical networks

    NASA Astrophysics Data System (ADS)

    Bianconi, Fortunato; Baldelli, Elisa; Ludovini, Vienna; Crinò, Lucio; Perruccio, Katia; Valigi, Paolo

    2013-07-01

    Biochemical transduction networks can be modelled through a proper set of differential equations, and at the same time they can be experimentally analysed only by measuring a few signals at the end of the cascades. The study of those networks is of special importance in oncology. The approach proposed in this paper is aimed at characterising the network robustness with respect to both parameters and initial condition perturbations. The key idea is to introduce a robustness index, the proliferation index, and to study its behaviour over the parameter space. The index relates the measurable signals, and the shape of their time behaviour, to the model parameters and initial conditions. In addition, the paper will also provide specific results for a dynamic model of the EGFR-IGFR receptor pathway, which turns out to be relevant to the study of some specific pathologies, such as lung cancer. The connection between the proposed robustness index and the pathology will also be addressed.

  5. Gluconeogenesis: An ancient biochemical pathway with a new twist

    PubMed Central

    Miyamoto, Tetsuya; Amrein, Hubert

    2017-01-01

    ABSTRACT Synthesis of sugars from simple carbon sources is critical for survival of animals under limited nutrient availability. Thus, sugar-synthesizing enzymes should be present across the entire metazoan spectrum. Here, we explore the evolution of glucose and trehalose synthesis using a phylogenetic analysis of enzymes specific for the two pathways. Our analysis reveals that the production of trehalose is the more ancestral biochemical process, found in single cell organisms and primitive metazoans, but also in insects. The gluconeogenic-specific enzyme glucose-6-phosphatase (G6Pase) first appears in Cnidaria, but is also present in Echinodermata, Mollusca and Vertebrata. Intriguingly, some species of nematodes and arthropods possess the genes for both pathways. Moreover, expression data from Drosophila suggests that G6Pase and, hence, gluconeogenesis, initially had a neuronal function. We speculate that in insects—and possibly in some vertebrates—gluconeogenesis may be used as a means of neuronal signaling. PMID:28121487

  6. 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

  7. 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,more » we formulate a stochastic model reproducing very well single realizations of kinesin and rotary ATPases.« less

  8. Molecular and biochemical characterisation of Trypanosoma cruzi phosphofructokinase.

    PubMed

    Rodríguez, Evelyn; Lander, Noelia; Ramirez, Jose Luis

    2009-08-01

    The characterisation of the gene encoding Trypanosoma cruzi CL Brener phosphofructokinase (PFK) and the biochemical properties of the expressed enzyme are reported here. In contradiction with previous reports, the PFK genes of CL Brener and YBM strain T. cruzi were found to be similar to their Leishmania mexicana and Trypanosoma brucei homologs in terms of both kinetic properties and size, with open reading frames encoding polypeptides with a deduced molecular mass of 53,483. The predicted amino acid sequence contains the C-terminal glycosome-targeting tripeptide SKL; this localisation was confirmed by immunofluorescence assays. In sequence comparisons with the genes of other eukaryotes, it was found that, despite being an adenosine triphosphate-dependent enzyme, T. cruzi PFK shows significant sequence similarity with inorganic pyrophosphate-dependent PFKs.

  9. Rhea—a manually curated resource of biochemical reactions

    PubMed Central

    Alcántara, Rafael; Axelsen, Kristian B.; Morgat, Anne; Belda, Eugeni; Coudert, Elisabeth; Bridge, Alan; Cao, Hong; de Matos, Paula; Ennis, Marcus; Turner, Steve; Owen, Gareth; Bougueleret, Lydie; Xenarios, Ioannis; Steinbeck, Christoph

    2012-01-01

    Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive resource of expert-curated biochemical reactions. Rhea provides a non-redundant set of chemical transformations for use in a broad spectrum of applications, including metabolic network reconstruction and pathway inference. Rhea includes enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list), transport reactions and spontaneously occurring reactions. Rhea reactions are described using chemical species from the Chemical Entities of Biological Interest ontology (ChEBI) and are stoichiometrically balanced for mass and charge. They are extensively manually curated with links to source literature and other public resources on metabolism including enzyme and pathway databases. This cross-referencing facilitates the mapping and reconciliation of common reactions and compounds between distinct resources, which is a common first step in the reconstruction of genome scale metabolic networks and models. PMID:22135291

  10. Ultrasensitive biochemical sensing device and method of sensing analytes

    DOEpatents

    Pinchuk, Anatoliy

    2017-06-06

    Systems and methods biochemically sense a concentration of a ligand using a sensor having a substrate having a metallic nanoparticle array formed onto a surface of the substrate. A light source is incident on the surface. A matrix is deposited over the nanoparticle array and contains a protein adapted to binding the ligand. A detector detects s-polarized and p-polarized light from the reflective surface. Spacing of nanoparticles in the array and wavelength of light are selected such that plasmon resonance occurs with an isotropic point such that -s and -p polarizations of the incident light result in substantially identical surface Plasmon resonance, wherein binding of the ligand to the protein shifts the resonance such that differences between the -S and -P polarizations give in a signal indicative of presence of the ligand.

  11. 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.

  12. Microchip-based chemical and biochemical analysis systems.

    PubMed

    Sato, Kiichi; Hibara, Akihide; Tokeshi, Manabu; Hisamoto, Hideaki; Kitamori, Takehiko

    2003-02-24

    This review focuses on chemical and biochemical analysis systems using pressure-driven microfluidic devices or microchips. Liquid microspace in a microchip has several characteristic features, for example, short diffusion distances, high specific interfacial area and small heat capacity. These characteristics are the key to controlling micro unit operations and constructing new integrated chemical systems. By combining multiphase laminar flow and the micro unit operations, such as mixing, reaction, extraction and separation, continuous flow chemical processing systems are realized in the microchip format. By applying these concepts, several different analysis systems were successfully integrated on a microchip. In this paper, we introduce the microchip-based chemical systems for wet analysis of cobalt ion, multi-ion sensors, immunoassay, and cellular analysis.

  13. 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.

  14. The biochemical basis for thermoregulation in heat-producing flowers

    PubMed Central

    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

  15. [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.

  16. Methods for assessing biochemical oxygen demand (BOD): a review.

    PubMed

    Jouanneau, S; Recoules, L; Durand, M J; Boukabache, A; Picot, V; Primault, Y; Lakel, A; Sengelin, M; Barillon, B; Thouand, G

    2014-02-01

    The Biochemical Oxygen Demand (BOD) is one of the most widely used criteria for water quality assessment. It provides information about the ready biodegradable fraction of the organic load in water. However, this analytical method is time-consuming (generally 5 days, BOD5), and the results may vary according to the laboratory (20%), primarily due to fluctuations in the microbial diversity of the inoculum used. Work performed during the two last decades has resulted in several technologies that are less time-consuming and more reliable. This review is devoted to the analysis of the technical features of the principal methods described in the literature in order to compare their performances (measuring window, reliability, robustness) and to identify the pros and the cons of each method. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. The structural and biochemical foundations of thiamin biosynthesis.

    PubMed

    Jurgenson, Christopher T; Begley, Tadhg P; Ealick, Steven E

    2009-01-01

    Thiamin is synthesized by most prokaryotes and by eukaryotes such as yeast and plants. In all cases, the thiazole and pyrimidine moieties are synthesized in separate branches of the pathway and coupled to form thiamin phosphate. A final phosphorylation gives thiamin pyrophosphate, the active form of the cofactor. Over the past decade or so, biochemical and structural studies have elucidated most of the details of the thiamin biosynthetic pathway in bacteria. Formation of the thiazole requires six gene products, and formation of the pyrimidine requires two. In contrast, details of the thiamin biosynthetic pathway in yeast are only just beginning to emerge. Only one gene product is required for the biosynthesis of the thiazole and one for the biosynthesis of the pyrimidine. Thiamin can also be transported into the cell and can be salvaged through several routes. In addition, two thiamin degrading enzymes have been characterized, one of which is linked to a novel salvage pathway.

  18. Hybrid nanogenerator for concurrently harvesting biomechanical and biochemical energy.

    PubMed

    Hansen, Benjamin J; Liu, Ying; Yang, Rusen; Wang, Zhong Lin

    2010-07-27

    Harvesting energy from multiple sources available in our personal and daily environments is highly desirable, not only for powering personal electronics, but also for future implantable sensor-transmitter devices for biomedical and healthcare applications. Here we present a hybrid energy scavenging device for potential in vivo applications. The hybrid device consists of a piezoelectric poly(vinylidene fluoride) nanofiber nanogenerator for harvesting mechanical energy, such as from breathing or from the beat of a heart, and a flexible enzymatic biofuel cell for harvesting the biochemical (glucose/O2) energy in biofluid, which are two types of energy available in vivo. The two energy harvesting approaches can work simultaneously or individually, thereby boosting output and lifetime. Using the hybrid device, we demonstrate a "self-powered" nanosystem by powering a ZnO nanowire UV light sensor.

  19. Hematological, biochemical, and behavioral responses of Oncorhynchus mykiss to dimethoate.

    PubMed

    Dogan, Demet; Can, Canan

    2011-12-01

    The effects of dimethoate on hematological, biochemical parameters, and behavior were investigated in Oncorhynchus mykiss exposed to sublethal concentrations of 0.0735, 0.3675, and 0.7350 mg/l for 5, 15, and 30 days. Significant decrease was determined in erythrocyte and leukocyte counts, hemoglobin, hematocrit, MCV, and MCH, which was pronounced after prolonged exposure indicating the appearance of microcytic hypochromic anemia. There were no prominent changes in thrombocyte and MCHC. The glucose concentration showed an ascending pattern that proved to be positively correlated with duration. The protein concentration declined in higher dimethoate concentrations following 15 and 30 days. Negative and significant correlation was detected between glucose and protein concentrations. The fish showed remarkable behavioral abnormality such as loss of balance, erratic swimming, and convulsion. Present findings revealed that dimethoate exerts its toxic action even in sublethal concentrations and hematological parameters and abnormal behavior may be sensitive indicators to evaluate pesticide intoxication.

  20. Biochemical composition of the alligator pipefish, Syngnathoides biaculeatus (Bloch, 1785)

    NASA Astrophysics Data System (ADS)

    Sanaye, Sushant Vilas; Pawar, Ashwini Pandurang; Rivonker, Chandrasheker Umanath; Sreepada, Rayadurga Anantha; Ansari, Zakir Ali; Ram, Anirudh

    2017-11-01

    Considering the economic importance in traditional Chinese medicine (TCM) and lack of baseline information, we evaluated the proximate composition, fatty acid and amino acid profiles, trace element content and C:N ratio in the alligator pipefish, Syngnathoides biaculeatus. Amongst proximate principals, a crude protein formed the major biochemical component ((58.9±2.2)% dry weight). Mean percent concentrations (dry weight) of other components such as a total lipid (TL), ash and nitrogen-free extract measured were, (1.8±0.2)%, (19.2±2.2)% and (20.1±0.45)%, respectively. The fatty acid profile revealed the presence of 27 saturated fatty acids (SFA) with 13 straight-chained and 14 branched-chained, 28 unsaturated fatty acids (UFA) with 14 monounsaturated and 14 polyunsaturated and nine other minor fatty acids. Mean percent contributions of total SFAs and UFAs to TL were found to be (55.41±0.24)% and (44.05±0.25)%, respectively. Altogether, 16 different amino acids with an equal number of essential (EAA) and non-essential (NAA) ones were identified. Percent contributions by EAA and NAA to the total amino acid content were 38.11% and 61.89%, respectively. Trace metal concentrations in S. biaculeatus were generally low and their distribution followed the order, Mg>Fe>Zn>Mn>Cu>Cr>Ni>Hg>Co. The C:N ratio was (4.37±0.04)%. The profile of major biochemical constituents in alligator pipefish, S. biaculeatus revealed its potential use in TCM as well as a nutritional diet for human consumption. The results of the study would also form the basis for formulation and optimization of diets for the culture of S. biaculeatus.

  1. Biochemical characterization of the maltokinase from Mycobacterium bovis BCG

    PubMed Central

    2010-01-01

    Background Maltose-1-phosphate was detected in Mycobacterium bovis BCG extracts in the 1960's but a maltose-1-phosphate synthetase (maltokinase, Mak) was only much later purified from Actinoplanes missouriensis, allowing the identification of the mak gene. Recently, this metabolite was proposed to be the intermediate in a pathway linking trehalose with the synthesis of glycogen in M. smegmatis. Although the M. tuberculosis H37Rv mak gene (Rv0127) was considered essential for growth, no mycobacterial Mak has, to date, been characterized. Results The sequence of the Mak from M. bovis BCG was identical to that from M. tuberculosis strains (99-100% amino acid identity). The enzyme was dependent on maltose and ATP, although GTP and UTP could be used to produce maltose-1-phosphate, which we identified by TLC and characterized by NMR. The Km for maltose was 2.52 ± 0.40 mM and 0.74 ± 0.12 mM for ATP; the Vmax was 21.05 ± 0.89 μmol/min.mg-1. Divalent cations were required for activity and Mg2+ was the best activator. The enzyme was a monomer in solution, had maximal activity at 60°C, between pH 7 and 9 (at 37°C) and was unstable on ice and upon freeze/thawing. The addition of 50 mM NaCl markedly enhanced Mak stability. Conclusions The unknown role of maltokinases in mycobacterial metabolism and the lack of biochemical data led us to express the mak gene from M. bovis BCG for biochemical characterization. This is the first mycobacterial Mak to be characterized and its properties represent essential knowledge towards deeper understanding of mycobacterial physiology. Since Mak may be a potential drug target in M. tuberculosis, its high-level production and purification in bioactive form provide important tools for further functional and structural studies. PMID:20507595

  2. 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 25A?C and exposed to five air temperatures (15, 20, 25, 35 and 45A?C) for 15, 30 and 60 min. After emersion, mussels were returned to water at 25A?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 447a??615 mg/g dry wt) among the species, followed by protein (179a??289 mg/g dry wt) and lipids (26.7a??38.1 mg/g dry wt). These results have positive implications for conducting conservation activities, because emersion over the range of temperatures (15a??35A?C) and durations (15a??60 min) examined did not appear acutely harmful to mussels.

  3. Biochemical markers of bone turnover in benign paroxysmal positional vertigo

    PubMed Central

    Lee, Sun Bin; Lee, Chang Ho; Kim, Young Ju; Kim, Hyoung-Mi

    2017-01-01

    Objective Several studies have suggested a possible relationship between recurrent benign paroxysmal positional vertigo (BPPV) and altered calcium homeostasis in the endolymph of the inner ear. The present study aimed to evaluate the association between Ca2+ and vitamin D status and BPPV occurrence as well as the status of bone biochemical markers in osteoporotic patients who were diagnosed with idiopathic BPPV. Methods The study included total 132 patients who were referred to our clinic between August 2008 and October 2013. Based on the bone mineral density (BMD) results, the subjects were divided into three groups: normal BMD (n = 34), osteopenia (n = 40) and osteoporosis (n = 58). The biochemical markers of bone turnover including serum Carboxy-terminal telopeptide of type I collagen (s-CTX), osteocalcin, alkaline phosphatase (ALP) and urinary free deoxypyridinoline (u-DPD), were analyzed, along with the serum Ca2+ and vitamin D levels. Results The mean serum calcium, phosphate and creatinine clearance levels were within the standard laboratory reference range. The incidence of vitamin D deficiency was 11.8% (4/34) in the normal BMD group, 15% (6/40) in the osteopenia group and 43.1% (25/58) in the osteoporosis group. There was a positive correlation between the 25(OH)D and BMD results in the patients with BPPV. Among the bone turnover markers, the osteocalcin and u-DPD levels were significantly elevated in the osteoporotic patients with BPPV. Multiple logistic regression analyses showed that osteoporosis and vitamin D deficiency were associated with BPPV. Conclusion Our findings suggest that the prevalence of BPPV in osteoporotic patients is associated with vitamin D deficiency and high bone turnover rates at systemic level, which could disturb local Ca2+ homeostasis in the inner ear. PMID:28467451

  4. Soil Biochemical Responses to Nitrogen Addition in a Bamboo Forest

    PubMed Central

    Tu, Li-hua; Chen, Gang; Peng, Yong; Hu, Hong-ling; Hu, Ting-xing; Zhang, Jian; Li, Xian-wei; Liu, Li; Tang, Yi

    2014-01-01

    Many vital ecosystem processes take place in the soils and are greatly affected by the increasing active nitrogen (N) deposition observed globally. Nitrogen deposition generally affects ecosystem processes through the changes in soil biochemical properties such as soil nutrient availability, microbial properties and enzyme activities. In order to evaluate the soil biochemical responses to elevated atmospheric N deposition in bamboo forest ecosystems, a two-year field N addition experiment in a hybrid bamboo (Bambusa pervariabilis × Dendrocalamopsis daii) plantation was conducted. Four levels of N treatment were applied: (1) control (CK, without N added), (2) low-nitrogen (LN, 50 kg N ha−1 year−1), (3) medium-nitrogen (MN, 150 kg N ha−1 year−1), and (4) high-nitrogen (HN, 300 kg N ha−1 year−1). Results indicated that N addition significantly increased the concentrations of NH4 +, NO3 −, microbial biomass carbon, microbial biomass N, the rates of nitrification and denitrification; significantly decreased soil pH and the concentration of available phosphorus, and had no effect on the total organic carbon and total N concentration in the 0–20 cm soil depth. Nitrogen addition significantly stimulated activities of hydrolytic enzyme that acquiring N (urease) and phosphorus (acid phosphatase) and depressed the oxidative enzymes (phenol oxidase, peroxidase and catalase) activities. Results suggest that (1) this bamboo forest ecosystem is moving towards being limited by P or co-limited by P under elevated N deposition, (2) the expected progressive increases in N deposition may have a potential important effect on forest litter decomposition due to the interaction of inorganic N and oxidative enzyme activities, in such bamboo forests under high levels of ambient N deposition. PMID:25029346

  5. Soil biochemical responses to nitrogen addition in a bamboo forest.

    PubMed

    Tu, Li-hua; Chen, Gang; Peng, Yong; Hu, Hong-ling; Hu, Ting-xing; Zhang, Jian; Li, Xian-wei; Liu, Li; Tang, Yi

    2014-01-01

    Many vital ecosystem processes take place in the soils and are greatly affected by the increasing active nitrogen (N) deposition observed globally. Nitrogen deposition generally affects ecosystem processes through the changes in soil biochemical properties such as soil nutrient availability, microbial properties and enzyme activities. In order to evaluate the soil biochemical responses to elevated atmospheric N deposition in bamboo forest ecosystems, a two-year field N addition experiment in a hybrid bamboo (Bambusa pervariabilis × Dendrocalamopsis daii) plantation was conducted. Four levels of N treatment were applied: (1) control (CK, without N added), (2) low-nitrogen (LN, 50 kg N ha(-1) year(-1)), (3) medium-nitrogen (MN, 150 kg N ha(-1) year(-1)), and (4) high-nitrogen (HN, 300 kg N ha(-1) year(-1)). Results indicated that N addition significantly increased the concentrations of NH4(+), NO3(-), microbial biomass carbon, microbial biomass N, the rates of nitrification and denitrification; significantly decreased soil pH and the concentration of available phosphorus, and had no effect on the total organic carbon and total N concentration in the 0-20 cm soil depth. Nitrogen addition significantly stimulated activities of hydrolytic enzyme that acquiring N (urease) and phosphorus (acid phosphatase) and depressed the oxidative enzymes (phenol oxidase, peroxidase and catalase) activities. Results suggest that (1) this bamboo forest ecosystem is moving towards being limited by P or co-limited by P under elevated N deposition, (2) the expected progressive increases in N deposition may have a potential important effect on forest litter decomposition due to the interaction of inorganic N and oxidative enzyme activities, in such bamboo forests under high levels of ambient N deposition.

  6. Biochemical and molecular characterization of hazelnut (Corylus avellana) seed lipoxygenases.

    PubMed

    Santino, Angelo; De Paolis, Angelo; Gallo, Antonia; Quarta, Angela; Casey, Rod; Mita, Giovanni

    2003-11-01

    Plant lipoxygenases (LOXs) are a class of dioxygenases which display diverse functions in several physiological processes such as growth, development and response to biotic and abiotic stresses. Even though LOXs have been characterized from several plant species, the physiological role of seed LOXs is still unclear. With the aim to better clarify the occurrence of LOXs and their influence on hazelnut seed quality, we carried out the biochemical and molecular characterization of the main LOX isoforms expressed during seed development. A genomic clone containing a complete LOX gene was isolated and fully characterized. The 9887 bp sequence reported contains an open reading frame of 5334 bp encoding a putative polypeptide of 99 kDa. Semiquantitative RT-PCR carried out from RNAs extracted from seeds at different maturation stages showed that LOXs are mainly expressed at early developmental stages. These results were confirmed by LOX activity assays. Biochemical characterization of the reaction products of the hazelnut LOX indicated that it is a 9-LOX. Two cDNAs were isolated by RT-PCR carried out on total RNA from immature hazelnut seeds. Sequence analysis indicated that the two cDNAs are highly homologous (91.9% degree of identity) and one of these corresponded exactly to the genomic clone. The deduced amino acid sequences of the hazelnut LOXs showed that they are closely related to a previously reported almond LOX (79.5% identity) and, to a lesser extent, to some LOXs involved in plant responses to pathogens (cotton and tobacco LOXs, 75.5 and 74.6% identity, respectively). The physiological role of hazelnut LOXs and their role in influencing seed quality are also discussed.

  7. Performance, biochemical, and endocrine changes during a competitive football game.

    PubMed

    Hoffman, Jay R; Maresh, Carl M; Newton, Robert U; Rubin, Martyn R; French, Duncan N; Volek, Jeff S; Sutherland, Jason; Robertson, Michael; Gómez, Ana L; Ratamess, Nicholas A; Kang, Jie; Kraemer, William J

    2002-11-01

    This study represents the first time that anaerobic power performance was examined during an actual intercollegiate American football game. In addition, biochemical and endocrine responses also were examined to assess the physiological stress imposed by this competitive contest. Twenty-one members of a NCAA Division III football team were divided into two groups. Group one (ST) were starters (N = 11). The second group (RS) consisted of red-shirt players (N = 10). Blood samples were obtained 24 h (Pre1) and 2.5 h (Pre2) before the game and within 15 min of game conclusion (IP). Anaerobic power measures were recorded approximately 10 min before kickoff (pre) and following the first (Q1), second (Q2), third (Q3), and fourth (Q4) quarters. Peak force (PF) and power (PP) in both squat and countermovement jumps decreased (P < 0.05) from pre to Q2 in both ST and RS; however, all variables returned to baseline levels by Q4. When averaged across trials, PF and PP in both jumps were greater (P < 0.05) in ST than RS. No significant changes in testosterone concentrations with respect to time or between groups were seen. Cortisol concentrations were significantly higher for ST at IP than RS. No significant changes in creatine kinase, alanine aminotransferase, urea, or uric acid were observed in either group from Pre2 to IP. In addition, no between group differences were seen in these variables. Myoglobin and aspartate aminotransferase significantly increased from Pre2 to IP in ST, and a significant difference in myoglobin concentrations was seen between the groups at IP. Performance, biochemical, and endocrine changes in these NCAA Division III football players reflected the stress and muscle damage that occurs as a result of a competitive American football game.

  8. Postoperative sellar hematoma after pituitary surgery: clinical and biochemical characteristics.

    PubMed

    El-Asmar, Nadine; El-Sibai, Katia; Al-Aridi, Ribal; Selman, Warren R; Arafah, Baha M

    2016-05-01

    Postoperative sellar hematoma can develop following surgery for pituitary tumors and other sellar masses such a Rathke's cleft cyst (RCC) due to continued blood oozing. Though often mild sellar hematoma can create mass effects that might impair pituitary function. This study summarizes the clinical and biochemical characteristics of sellar hematoma and explores the potential mechanisms for the associated hypopituitarism. Sellar hematoma was suspected clinically (worsening headaches, visual impairment, and mental status alterations) and confirmed radiographically in 23 patients (18/279 with macroadenomas and in 5/92 with RCC). Postoperatively, patients were monitored without glucocorticoid therapy and all had appropriately normal HPA function before sellar hematoma diagnosis. The demographics of patients who had sellar hematoma were similar to those who did not. Biochemical changes at diagnosis included decreased plasma ACTH and its dependent steroids (cortisol, DHEA, and DHEA-S), concomitant mild hyperprolactinemia, and mild hyponatremia (P < 0.005 for all parameters). Treatment with glucocorticoids resulted in rapid clinical improvement in most patients. Glucocorticoid therapy was discontinued within 2 weeks and re-testing thereafter showed normal HPA function in 16/23. None of the patients without sellar hematoma had worsening in pituitary function, visual, or neurological symptoms. When large, sellar hematoma can lead to mass effect that causes headaches, visual symptoms, and acute and often reversible hypopituitarism manifesting initially as impaired HPA function. Rapid resolution is observed in most patients with glucocorticoid administration The rapid onset and reversibility of hypopituitarism associated with mild hyperprolactinemia suggest that compression of pituitary stalk/ portal vessels is likely the dominant mechanism of pituitary dysfunction in this setting. © 2016 European Society of Endocrinology.

  9. Biochemical and nutritional markers and antioxidant activity in metabolic syndrome.

    PubMed

    Bernabé García, Juana; Zafrilla Rentero, Pilar; Mulero Cánovas, Juana; Gómez Jara, Purificación; Leal Hernández, Mariano; Abellán Alemán, José

    2014-01-01

    1) Nutritional assessment of the diet followed by patients with metabolic syndrome, and 2) biochemical analysis of the oxidation-reduction level in patients with metabolic syndrome. A cross-sectional study was conducted in patients with metabolic syndrome in Murcia. Fifty-three patients, 33 with and 20 without (control group) metabolic syndrome, were selected. The intervention consisted of completion of a recall survey and a test to nutritionally assess dietary intake. Anthropometric and laboratory variables, including those related to antioxidant activity, were also tested. Antioxidant activity was within normal limits in both groups (1.7 ± 0.2 mmol/L in the control group and 1.8 ± 0.1 mmol/L in the metabolic syndrome group) (NS). Superoxide dismutase levels were not significantly different between the groups. Mean glutathione reductase levels (U/L) were higher in the control group as compared to patients with metabolic syndrome (P<.05). As regards oxidative stress biomarkers, mean isoprostane levels were higher in the control group (4.9 ± 6.2 ng/mL) than in metabolic syndrome patients (3.5 ± 3.9 ng/mL) (P<.05). Oxidized LDL values tended to be higher in metabolic syndrome patients (96 ± 23.2U/L) as compared to the control group (86.2 ± 17.3 U/L), but differences were not significant. There is a trend to a poorer nutritional and biochemical profile in patients with metabolic syndrome, who also tend to have a greater degree of oxidative stress. Copyright © 2013 SEEN. Published by Elsevier Espana. All rights reserved.

  10. Biochemical analysis of the 20 S proteasome of Trypanosoma brucei.

    PubMed

    Wang, Ching C; Bozdech, Zbynek; Liu, Chao-lin; Shipway, Aaron; Backes, Bradley J; Harris, Jennifer L; Bogyo, Matthew

    2003-05-02

    We describe here biochemical characterization of the 20 S proteasome from the parasitic protozoan Trypanosoma brucei. Similar to the mammalian proteasome, the T. brucei proteasome is made up of seven alpha- and seven beta-subunits. Of the seven beta-type subunits, five contain pro-sequences that are proteolytically removed during assembly, and three of them are predicted to be catalytic based on primary sequence. Affinity labeling studies revealed that, unlike the mammalian proteasome where three beta-subunits were labeled by the affinity reagents, only two beta-subunits of the T. brucei proteasome were labeled in the complex. These two subunits corresponded to beta2 and beta5 subunits responsible for the trypsin-like and chymotrypsin-like proteolytic activities, respectively. Screening of a library of 137,180 tetrapeptide fluorogenic substrates against the T. brucei 20 S proteasome confirmed the nominal beta1-subunit (caspase-like or PGPH) activity and identified an overall substrate preference for hydrophobic residues at the P1 to P4 positions in a substrate. This overall stringency is relaxed in the 11 S regulator (PA26)-20 S proteasome complex, which shows both appreciable activities for cleavage after acidic amino acids and a broadened activity for cleavage after basic amino acids. The 20 S proteasome from T. brucei also shows appreciable activity for cleavage after P1-Gln that is minimally observed in the human counterpart. These results demonstrate the importance of substrate sequence specificity of the T. brucei proteasome and highlight its biochemical divergence from the human enzyme.

  11. 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

  12. Adaptive response of rat pancreatic β-cells to insulin resistance induced by monocrotophos: Biochemical evidence.

    PubMed

    Nagaraju, Raju; Rajini, Padmanabhan Sharda

    2016-11-01

    Our previous findings clearly suggested the role of duration of exposure to monocrotophos (MCP) in the development of insulin resistance. Rats exposed chronically to MCP developed insulin resistance with hyperinsulinemia without overt diabetes. In continuation of this vital observation, we sought to delineate the biochemical mechanisms that mediate heightened pancreatic β-cell response in the wake of MCP-induced insulin resistance in rats. Adult rats were orally administered (0.9 and 1.8mg/kgb.w/d) MCP for 180days. Terminally, MCP-treated rats exhibited glucose intolerance, hyperinsulinemia, and potentiation of glucose-induced insulin secretion along with elevated levels of circulating IGF1, free fatty acids, corticosterone, and paraoxonase activity. Biochemical analysis of islet extracts revealed increased levels of insulin, malate, pyruvate and ATP with a concomitant increase in activities of cytosolic and mitochondrial enzymes that are known to facilitate insulin secretion and enhanced shuttle activities. Interestingly, islets from MCP-treated rats exhibited increased insulin secretory potential ex vivo compared to those isolated from control rats. Further, MCP-induced islet hypertrophy was associated with increased insulin-positive cells. Our study demonstrates the impact of the biological interaction between MCP and components of metabolic homeostasis on pancreatic beta cell function/s. We speculate that the heightened pancreatic beta cell function evidenced may be mediated by increased IGF1 and paraoxonase activity, which effectively counters insulin resistance induced by chronic exposure to MCP. Our findings emphasize the need for focused research to understand the confounding environmental risk factors which may modulate heightened beta cell functions in the case of organophosphorus insecticide-induced insulin resistance. Such an approach may help us to explain the sharp increase in the prevalence of type II diabetes worldwide. Copyright © 2016 Elsevier

  13. Increased cell hydration promotes both tumor growth and metastasis: a biochemical mechanism consistent with genetic signatures.

    PubMed

    McIntyre, G I

    2007-01-01

    It was postulated previously that a progressive increase in cell hydration, induced by successive genetic or epigenetic changes, is the basic mechanism of multistep carcinogenesis, and also that the degree of malignancy increases with the degree of cell hydration. These hypotheses implied that increased cell hydration is a common factor promoting both tumor growth and metastasis, and that metastatic potential increases with the degree of cell hydration. This paper discusses these implications in relation to current concepts of genetic mechanisms determining the acquisition of metastatic potential. It was also postulated previously that the enhancement of metabolic activity by increased cell hydration will increase the ability of tumor cells to compete for nutrients with their normal counterparts. This effect may favor the preferential selection of cells whose genotypes confer the greatest increase in cell hydration and which, on the present hypothesis, would be those with the greatest capacity for metastasis. An important feature of this "common factor" hypothesis is that it suggests a biochemical explanation for DNA-microarray data showing a similarity between the gene expression patterns associated with both tumor growth and metastasis, while the postulated role of genes causing increased cell hydration might explain the apparent acquisition of metastatic potential at an early stage of tumorigenesis. Previous investigations were consistent with the hypothesis that various factors promoting carcinogenesis may do so by increasing cell hydration. A survey of the literature showed that all of these factors also promote cell motility, migration or metastasis, and provided evidence that these effects could be attributed to the associated increase in cell hydration. Methods are suggested for testing the hypothesis, and the paper concludes by emphasizing the need for more research on the biochemistry of cancer, and on the role of water as a biochemical factor of

  14. Novel method of dual fiber Bragg gratings integrated in fiber ring laser for biochemical sensors

    NASA Astrophysics Data System (ADS)

    Bui, H.; Pham, T. B.; Nguyen, V. A.; Pham, V. D.; Do, T. C.; Nguyen, T. V.; Hoang, T. H. C.; Le, H. T.; Pham, V. H.

    2018-05-01

    Optical sensors have been shown to be very effective for measuring the toxic content in liquid and air environments. Optical sensors, which operate based on the wavelength shift of the optical signals, require an expensive spectrometer. In this paper, we propose a new configuration of the optical sensor device for measuring wavelength shift without using a spectrometer. This configuration has a large potential for application in biochemical sensing techniques, and comes with a low cost. This configuration uses dual fiber Bragg gratings (FBGs) integrated in a fiber ring laser structure of erbium-doped fiber, in which one FBG is used as a reference to sweep over the applicable spectrum of the etched-Bragg grating. The etched-FBG as a sensing probe is suitable for bio- and/or chemical sensors. The sensitivity and accuracy of the sensor system can be improved by the narrow linewidth of emission spectra from the laser, the best limit of detection of this sensor is 1.5  ×  10‑4 RIU (RIU: refractive index unit), as achieved by the optical sensor using a high resolution spectrometer. This sensor system has been experimentally investigated to detect different types of organic compounds, gasoline, mixing ratios of organic solvents in gasoline, and nitrate concentration in water samples. The experimental results show that this sensing method could determine different mixing ratios of organic solvents with good repeatability, high accuracy, and rapid response: e.g. for ethanol and/or methanol in gasoline RON 92 (RON: research octane number) of 0%–14% v/v, and nitrate in water samples at a low concentration range of 0–50 ppm. These results suggest that the proposed configuration can construct low-cost and accurate biochemical sensors.

  15. Postmatch recovery of physical performance and biochemical markers in team ball sports: a systematic review

    PubMed Central

    Brink, Michel S; Kosse, Silke J; Lemmink, Koen A P M

    2018-01-01

    Background Insufficient postmatch recovery in elite players may cause an increased risk of injuries, illnesses and non-functional over-reaching. Objective To evaluate postmatch recovery time courses of physical performance and biochemical markers in team ball sport players. Study design Systematic review. Data sources PubMed and Web of Science. Eligibility criteria for selecting studies This systematic review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The Critical Review Form for Quantitative Studies was used to evaluate quality. Studies were included if they met the following criteria: (1) original research evaluated players’ physical recovery postmatch; (2) team/intermittent sports; and (3) at least two postmeasurements were compared with baseline values. Results Twenty-eight studies were eligible. Mean methodological quality was 11.2±1.11. Most used performance tests and biochemical markers were the countermovement jump test, sprint tests and creatine kinase (CK), cortisol (C) and testosterone (T), respectively. Summary/conclusions The current evidence demonstrates that underlying mechanisms of muscle recovery are still in progress while performance recovery is already reached. CK recovery time courses are up to ≥72 hours. Soccer and rugby players need more time to recover for sprint performance, CK and C in comparison to other team ball sports. There are more high-quality studies needed regarding recovery in various team sports and recovery strategies on an individual level should be evaluated. Clinical relevance Ongoing insufficient recovery can be prevented by the use of the presented recovery time courses as specific practical recovery guidelines. PMID:29527320

  16. Integration and detection of biochemical assays in digital microfluidic LOC devices.

    PubMed

    Malic, Lidija; Brassard, Daniel; Veres, Teodor; Tabrizian, Maryam

    2010-02-21

    The ambition of lab-on-a-chip (LOC) systems to achieve chip-level integration of a complete analytical process capable of performing a complex set of biomedical protocols is hindered by the absence of standard fluidic components able to be assembled. As a result, most microfluidic platforms built to date are highly specialized and designed to fulfill the requirements of a single particular application within a limited set of operations. Electrowetting-on-dielectric (EWOD) digital microfluidic technology has been recently introduced as a new methodology in the quest for LOC systems. Herein, unit volume droplets are manipulated along electrode arrays, allowing a microfluidic function to be reduced to a set of basic operations. The highly reprogrammable architecture of these systems can satisfy the needs of a diverse set of biochemical assays and ensure reconfigurability, flexibility and portability between different categories of applications and requirements. While important progress was made over past years in the fabrication, miniaturization and function programming of the basic EWOD fluidic operations, the success of this technology will in great part depend on the ability of researchers to couple or integrate digital microfluidics to detection approaches that can make the system competitive for LOC applications. The detection techniques should be able to circumvent the limitations of hydrophobic surfaces and exploit the advantages of the array format, high droplet transport speeds and rapid mixing schemes. This review provides an in-depth look at recent developments for the coupling and integration of detection techniques with digital microfluidic platforms for bio-chemical applications.

  17. Cylindrospermopsin induces biochemical changes leading to programmed cell death in plants.

    PubMed

    M-Hamvas, Márta; Ajtay, Kitti; Beyer, Dániel; Jámbrik, Katalin; Vasas, Gábor; Surányi, Gyula; Máthé, Csaba

    2017-02-01

    In the present study we provide cytological and biochemical evidence that the cyanotoxin cylindrospermopsin (CYN) induces programmed cell death (PCD) symptoms in two model vascular plants: the dicot white mustard (Sinapis alba) and the monocot common reed (Phragmites australis). Cytological data include chromatin fragmentation and the increase of the ratio of TUNEL-positive cells in roots, the latter being detected in both model systems studied. The strongest biochemical evidence is the elevation of the activity of several single-stranded DNA preferring nucleases-among them enzymes active at both acidic and alkaline conditions and are probably directly related to DNA breaks occurring at the initial stages of plant PCD: 80 kDa nucleases and a 26 kDa nuclease, both having dual (single- and double-stranded nucleic acid) specificity. Moreover, the total protease activity and in particular, a 53-56 kDa alkaline protease activity increases. This protease could be inhibited by PMSF, thus regarded as serine protease. Serine proteases are detected in all organs of Brassicaceae (Arabidopsis) having importance in differentiation of specialized plant tissue through PCD, in protein degradation/processing during early germination and defense mechanisms induced by a variety of biotic and abiotic stresses. However, knowledge of the physiological roles of these proteases and nucleases in PCD still needs further research. It is concluded that CYN treatment induces chromatin fragmentation and PCD in plant cells by activating specific nucleases and proteases. CYN is proposed to be a suitable molecule to study the mechanism of plant apoptosis.

  18. The Role of Compost in Stabilizing the Microbiological and Biochemical Properties of Zinc-Stressed Soil.

    PubMed

    Strachel, Rafał; Wyszkowska, Jadwiga; Baćmaga, Małgorzata

    2017-01-01

    The progressive development of civilization and intensive industrialization has contributed to the global pollution of the natural environment by heavy metals, especially the soil. Degraded soils generally contain less organic matter, and thus, their homeostasis is more often disturbed, which in turn manifests in changes in biological and physicochemical properties of the soil. Therefore, new possibilities and solutions for possible neutralization of these contaminations are sought, inter alia, through reclamation of degraded land. At present, the use of additives supporting the reclamation process that exhibit heavy metal-sorbing properties is becoming increasingly important in soil recovery. Research was conducted to determine the role of compost in stabilizing the microbial and biochemical balance of the soil due to the significant problem of heavy metal-contaminated areas. The study was conducted on loamy sand, to which zinc was applied at the following doses: 0, 250, 500, 750, 1000, and 1250 mg Zn 2+  kg -1 DM of soil. Compost was introduced to the appropriate objects calculated on the basis of organic carbon content in the amount of 0, 10, and 20 g C org  kg -1 DM of soil. The study was conducted over a period of 20 weeks, maintaining soil moisture at 50% capillary water capacity. Zinc significantly modified soil microbiome status. The abundance of microorganisms and their biological diversity and the enzymatic activity of the soil were affected. The negative effects of contaminating zinc doses were alleviated by the introduction of compost into the soil. Organic fertilization led to microbial growth intensification and increased biochemical activity of the soil already 2 weeks after compost application. These effects persisted throughout the experiment. Therefore, it can be stated that the use of compost is an appropriate method for restoring normal functions of soil ecosystems contaminated with zinc.

  19. Analysis of gingival pocket microflora and biochemical blood parameters in dogs suffering from periodontal disease.

    PubMed

    Polkowska, Izabela; Sobczyńska-Rak, Aleksandra; Gołyńska, Magdalena

    2014-01-01

    Periodontal diseases in dogs are caused by bacteria colonising the oral cavity. The presence of plaque comprising accumulations of aerobic and anaerobic bacteria leads to the development of periodontitis. Due to the fact that in a large percentage of cases periodontal diseases remain undiagnosed, and consequently untreated, they tend to acquire a chronic character, lead to bacteraemia and negatively impact the health of internal organs. The aim of the present study was to perform a qualitative microbiological analysis of gingival pockets and determine the correlations between selected morphological and biochemical blood parameters and the extent periodontal diseases. Twenty-one dogs treated for periodontal diseases were qualified for the study and subsequently divided into two groups: with 3rd and 4th stage of periodontal disease. Swabs from the patients' gingival pockets were taken for bacteriological testing. Blood was tested for parameters including erythrocyte count, haemoglobin concentration, haematocrit values and leukocyte count. Blood serum was analyzed with respect to the concentrations of alanine transaminase (ALT), aspartate transaminase (AspAT/AST) and urea. The microbiological analysis of gingival pockets indicated the presence of numerous pathogens with a growth tendency in bacterial cultures observed in dogs with advanced-stage periodontal disease. The concentration of biochemical blood markers was significantly higher in dogs with 4th stage of periodontal disease, to compared to the 3rd-stage group. Morphological parameters were not significantly different with the exception of haemoglobin concentration, which was lower in dogs with 4th stage disease. In both groups, elevated leukocyte counts were observed. By conducting a detailed microbiological examination, it is possible to provide a better prognosis, plan adequate treatment and monitor dogs treated for peridontopathy. Copyright © 2014 International Institute of Anticancer Research (Dr. John G

  20. [Clinical and biochemical analysis of ligature-induced periodontitis in rats].

    PubMed

    Chumakova, Y; Vishnevskaya, A; Kakabadze, A; Karalashvili, L; Kakabadze, Z

    2014-10-01

    The most common experimental model of periodontitis is a "ligature" model. However due to the complexity connected with performing on rats, modification of existing model is proposed, which differs by fixture of cotton ligature around the central incisor and not around the second molar. The purpose of research - a comparative evaluation of "peroxide" and modified by us, "ligature" models of periodontitis in rats. 2 series of experiments on 36 white Wistar rats were conducted. The animals were divided into two groups: intact rats (control) and rats with a "peroxide" model of periodontitis, which was reproduced by the addition to the diet of rats overoxidized sunflower oil (5% by weight of the feed), daily, for 45 days. "Ligature" model in rats was reproduced by applying a cotton ligature on the central incisor of the upper jaw for 14 days. Elastase activity, malondialdehyde content and catalase activity in the gums and in the blood serum was measured by biochemical methods. The degree of atrophy of the alveolar bone of the mandible was determined by morphometric method. It is found that in both models of periodontitis in rats, changes in the periodontal tissues and in the organism as a whole, is common for periodontal disease in humans. Clinically apparent inflammation of the periodontal tissues is observed, metabolic disorders in the gums, change of biochemical parameters in serum and progressive decline in the alveolar bone are determined. A comparative analysis of the two models showed that the modified "ligature" model of periodontitis in rats has several advantages over the "peroxide" model: shorter term of modeling, more pronounced clinical inflammation of periodontal tissues and faster resorption of alveolar bone.

  1. 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

  2. Clinical and biochemical data of endothelial function in Women Consuming Combined Contraceptives.

    PubMed

    Lobysheva, Irina I; Eeckhoudt, Sandrine van; Zotti, Flavia Dei; Rifahi, Ahmad; Pothen, Lucie; Beauloye, Christophe; Balligand, Jean-Luc

    2017-08-01

    The data presented in this article are associated with the research article entitled "Heme-Nitrosylated Hemoglobin and Oxidative Stress in Women Consuming Combined Contraceptives. Clinical Application of the EPR Spectroscopy" (Lobysheva et al., 2017 [1]), and describe the characteristics of redox status in blood, as well as biochemical and clinical parameters of young female subjects consuming (or not) contraceptive pills (CP). Erythrocyte concentration of reduced thiols reflecting erythrocyte redox capacity was measured before and after sample deproteinization by electron paramagnetic resonance spectroscopy (EPR) using a nitroxide biradical spin probe specifically interacting with reduced thiols; additional data were obtained by a colorimetric method using Ellman׳s reagents in the same samples. The products of nitric oxide oxidation, nitrite and total NO x (in presence of nitrate reductase) were measured in the plasma of study subjects by a colorimetric assay based on the detection of red-violet colored azo dye after reaction of nitrite with the Griess reagent. Biochemical and clinical parameters reflective of cardiovascular risk factors (diastolic blood pressure, C-reactive protein, triglycerides and homocysteine concentrations in venous blood) were compared in subgroups of consumers of CP containing ethinyl estradiol and different types of synthetic progestogens. Parameters reflective of the integrity of the vasculature, - erythrocyte concentration of heme-nitrosylated hemoglobin (5-coordinate α-heme-Fe II -NO, HbNO) measured directly by the EPR subtraction method; index of reactive hyperemia response (FRHI) measured by digital pulse tonometry using EndoPAT; oxidative vascular stress measured as total plasma peroxide concentration were compared in subgroups of young women taking CP containing ethinyl estradiol at different concentrations and for various durations.

  3. Protecting impact of Jaft against carbendazim induced biochemical changes in male Wistar rats

    PubMed Central

    Mirzaei, A; Sepehri, S; Sadeghi, H; Alamdari, A

    2015-01-01

    Introduction: Pesticides are a critical tool for crop protection and control of different pests and insects. The present research conducted to evaluate the protective role of Jaft extract against oxidative pressure, biochemical variations because of limited time giveaway to carbendazim in Wistar mice males. Fresh fruits of quercus brantii were dried and the internal layer (Jaft) was collected for a hydroalcoholic extract by a maceration method at normal ambient condition. For the experimental study, twenty-four adult male rats (Wistar albino rats weighing 150-200 g) were randomized into 3 teams out of eight. Team I subserved like a vehicle treated group, received corn oil additionally to their food, while the animals in the second team got 0.1 ml carbendazim (50mg/ kg in corn oil) via oral path for nine days. Rats in group III received Jaft (500 mg/ kg orally + in carbendazim for 9 days. Blood samples were obtained by heart puncture to determine alkaline phosphatase (ALP), blood urea nitrogen (BUN), creatinine, alanine (ALT) and aspartate aminotransferases (AST); by using auto-analyzer in serum.Kidneys and liver separated from rats and provided for series of biochemical parameters homogenization like GSH and MDA stages. Result: The serum content of AST, ALT, ALP, BUN and creatinine were significantly elevated by in carbendazim treatment (group II) compared to the negative group (p<0.01).The liver enzymes operations, creatinine and BUN were significantly reduced in rats (p<0.05) when Jaft was received in a short period of time (group III). Hepatic and GSH and renal MDA stages in group (II) were clearly (p<0.05) enhanced and decreased consequently. The GSH and MDA stages content were significantly normalized in mice (p<0.05) when Jaft was received by group III. Conclusions: According to the present data, Jaft can neutralize carbendazim contain pressure of oxidative and recover the abnormal pathological injuries in Wistar mice males. PMID:28316673

  4. Protecting impact of Jaft against carbendazim induced biochemical changes in male Wistar rats.

    PubMed

    Mirzaei, A; Sepehri, S; Sadeghi, H; Alamdari, A

    2015-01-01

    Introduction: Pesticides are a critical tool for crop protection and control of different pests and insects. The present research conducted to evaluate the protective role of Jaft extract against oxidative pressure, biochemical variations because of limited time giveaway to carbendazim in Wistar mice males. Fresh fruits of quercus brantii were dried and the internal layer (Jaft) was collected for a hydroalcoholic extract by a maceration method at normal ambient condition. For the experimental study, twenty-four adult male rats (Wistar albino rats weighing 150-200 g) were randomized into 3 teams out of eight. Team I subserved like a vehicle treated group, received corn oil additionally to their food, while the animals in the second team got 0.1 ml carbendazim (50mg/ kg in corn oil) via oral path for nine days. Rats in group III received Jaft (500 mg/ kg orally + in carbendazim for 9 days. Blood samples were obtained by heart puncture to determine alkaline phosphatase (ALP), blood urea nitrogen (BUN), creatinine, alanine (ALT) and aspartate aminotransferases (AST); by using auto-analyzer in serum.Kidneys and liver separated from rats and provided for series of biochemical parameters homogenization like GSH and MDA stages. Result: The serum content of AST, ALT, ALP, BUN and creatinine were significantly elevated by in carbendazim treatment (group II) compared to the negative group (p<0.01).The liver enzymes operations, creatinine and BUN were significantly reduced in rats (p<0.05) when Jaft was received in a short period of time (group III). Hepatic and GSH and renal MDA stages in group (II) were clearly (p<0.05) enhanced and decreased consequently. The GSH and MDA stages content were significantly normalized in mice (p<0.05) when Jaft was received by group III. Conclusions: According to the present data, Jaft can neutralize carbendazim contain pressure of oxidative and recover the abnormal pathological injuries in Wistar mice males.

  5. Localized Modeling of Biochemical and Flow Interactions during Cancer Cell Adhesion.

    PubMed

    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.

  6. Whey Protein Improves Exercise Performance and Biochemical Profiles in Trained Mice

    PubMed Central

    CHEN, WEN-CHYUAN; HUANG, WEN-CHING; CHIU, CHIEN-CHAO; CHANG, YU-KAI; HUANG, CHI-CHANG

    2014-01-01

    ABSTRACT Purpose The objective of this study is to verify the beneficial effects of whey protein (WP) supplementation on health promotion and enhance exercise performance in an aerobic-exercise training protocol. Methods In total, 40 male Institute of Cancer Research mice (4 wk old) were divided into four groups (n = 10 per group): sedentary control with vehicle (SC) or WP supplementation (4.1 g·kg−1, SC + WP), and exercise training with vehicle (ET) or WP supplementation (4.1 g·kg−1, ET + WP). Animals in the ET and ET + WP groups underwent swimming endurance training for 6 wk, 5 d·wk−1. Exercise performance was evaluated by forelimb grip strength and exhaustive swimming time as well as by changes in body composition and biochemical parameters at the end of the experiment. Results ET significantly decreased final body and muscle weight and levels of albumin, total protein, blood urea nitrogen, creatinine, total cholesterol, and triacylglycerol. ET significantly increased grip strength; relative weight (%) of liver, heart, and brown adipose tissue (BAT); and levels of aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, lactate dehydrogenase, creatine kinase, and total bilirubin. WP supplementation significantly decreased final body, muscle, liver, BAT, and kidney weight and relative weight (%) of muscle, liver, and BAT as well as levels of aspartate aminotransferase, lactate dehydrogenase, creatine kinase, and uric acid. In addition, WP supplementation slightly increased endurance time and significantly increased grip strength and levels of albumin and total protein. Conclusion WP supplementation improved exercise performance, body composition, and biochemical assessments in mice and may be an effective ergogenic aid in aerobic exercise training. PMID:24504433

  7. Hematological and biochemical findings in pregnant, postfoaling, and lactating jennies.

    PubMed

    Bonelli, F; Rota, A; Corazza, M; Serio, D; Sgorbini, M

    2016-04-15

    The aims of this study were to (1) verify if significant changes occur in hematological and biochemical parameters in jennies during the last 2 months of pregnancy and the first 2 months of lactation, and (2) determine any differences with mares. Hematological and biochemical parameters were evaluated in jennies every 15 days during late pregnancy, parturition, and early lactation. The Kolmogorov-Smirnov test, analysis of variance for repeated measurements and Tukey's multiple comparison test as post hoc were applied. The significance level was set at P < 0.05. Statistical analysis showed differences related to time for Red Blood Cells (RBC) count and Hematocrit (HCT), White Blood Cells (WBC) count, platelet count (PLT), total proteins, blood urea, triglycerides and total cholesterol concentrations, aspartate aminotransferase, gamma-glutamyltransferase, creatine-phosphokinase activities, sodium (Na) and potassium (K). RBC and HCT were higher in late pregnancy than at foaling and during lactation. The relative anemia might be due to increased water ingestion because of fluid losses. The WBC count was higher at foaling than during late pregnancy and lactation. This could be related to the release of cortisol and catecholamine during delivery. The PLT trend showed lower values from delivery to the first 2 months of lactation compared to late gestation. Blood urea increased near parturition, and then remained constant during delivery and lactation, which might be due to the high energy demand at the beginning of lactation. Triglycerides and total cholesterol showed a decrease from delivery through the lactation period. Thus, jennies seem to have a similar metabolism of fats to ponies and draft horse mares, characterized by a greater fat content and mobilization than light breed horses. Aspartate aminotransferase activity decreased at parturition and early lactation, probably because of a predominance of anabolic over catabolic processes during pregnancy. Gamma

  8. Using the Biochemical Pathway Model To Teach the Concepts of Gene Interaction and Epistasis.

    ERIC Educational Resources Information Center

    Chinnici, Joseph P.

    1999-01-01

    Describes the successful use of giving examples of genes affecting various steps in biochemical pathways to teach gene interaction. Finds that once students grasp the notion that genes can interact because they control different steps within biochemical pathways, the reason why phenotypic ratios appear to be non-Mendelian becomes more obvious and…

  9. 40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides residue data requirements table. 158.2040 Section 158.2040 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... product and the substance that needs to be tested. These data requirements apply to all biochemical...

  10. 40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Biochemical pesticides residue data requirements table. 158.2040 Section 158.2040 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... product and the substance that needs to be tested. These data requirements apply to all biochemical...

  11. 40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticides residue data requirements table. 158.2040 Section 158.2040 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... product and the substance that needs to be tested. These data requirements apply to all biochemical...

  12. 40 CFR 158.2040 - Biochemical pesticides residue data requirements table.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Biochemical pesticides residue data requirements table. 158.2040 Section 158.2040 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... product and the substance that needs to be tested. These data requirements apply to all biochemical...

  13. 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 requirements table. 158.2040 Section 158.2040 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... product and the substance that needs to be tested. These data requirements apply to all biochemical...

  14. Biochemical contacts and collaborations between China and the U.K. since 1911.

    PubMed

    Dodson, Guy G

    2011-10-01

    Scientific contact lies at the heart of research and that between China and the U.K. is an important example of how it can come about. In 1911, when the Biochemical Society began, U.K. science was developing fast with profound discoveries in physics (the Rutherford atomic model) and biochemistry (the discovery of vitamins). In China, however, there was great social and political instability and a revolution. Since then, the turbulence of two world wars and a variety of deep global political tensions meant that the contacts between China and U.K. did not reflect the prodigious growth of biochemistry. There was, however, one particular and remarkable contact, that made by Joseph Needham, an outstanding biochemist. He visited China between 1943 and 1946, contacting many Chinese universities that were severely dislocated by war. Showing remarkable diplomatic abilities, Needham managed to arrange delivery of research and teaching equipment. His activities helped the universities to carry out their functions under near-impossible conditions and reminded them that they had friends abroad. Most remarkably, Joseph Needham developed an extraordinary grasp of Chinese culture, science and history and he opened the West to the extent and importance of Chinese science. Formal scientific and intellectual contacts between the scientific academic bodies in China and U.K., notably the Chinese Academy of Science and the Royal Society, resumed after British recognition of the Chinese Communist government in 1950. The delegations included outstanding scientists in biochemistry and related disciplines. Research activities, such as that concerning influenza, were soon established, whereas institutions, such as the Royal Society and the Wellcome Trust, acted a little later to support research. The outcomes have been long-term collaborations in such areas as insulin structure and function. There are now numerous joint activities in biochemistry and biomedicine supported by the MRC (Medical

  15. Research Visibility: Manpower Research.

    ERIC Educational Resources Information Center

    Brandon, George L., Ed.

    1969-01-01

    Thirteen research reviews in this issue pertain to manpower research organized under these topics: (1) Manpower and Youth, treating youth unemployment and the youth labor market, (2) Manpower Needs, including an analysis of manpower research since World War II, health manpower planning, the shortage of skilled and technical workers, a projection…

  16. Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics

    PubMed Central

    2012-01-01

    Background The representation of a biochemical system as a network is the precursor of any mathematical model of the processes driving the dynamics of that system. Pharmacokinetics uses mathematical models to describe the interactions between drug, and drug metabolites and targets and through the simulation of these models predicts drug levels and/or dynamic behaviors of drug entities in the body. Therefore, the development of computational techniques for inferring the interaction network of the drug entities and its kinetic parameters from observational data is raising great interest in the scientific community of pharmacologists. In fact, the network inference is a set of mathematical procedures deducing the structure of a model from the experimental data associated to the nodes of the network of interactions. In this paper, we deal with the inference of a pharmacokinetic network from the concentrations of the drug and its metabolites observed at discrete time points. Results The method of network inference presented in this paper is inspired by the theory of time-lagged correlation inference with regard to the deduction of the interaction network, and on a maximum likelihood approach with regard to the estimation of the kinetic parameters of the network. Both network inference and parameter estimation have been designed specifically to identify systems of biotransformations, at the biochemical level, from noisy time-resolved experimental data. We use our inference method to deduce the metabolic pathway of the gemcitabine. The inputs to our inference algorithm are the experimental time series of the concentration of gemcitabine and its metabolites. The output is the set of reactions of the metabolic network of the gemcitabine. Conclusions Time-lagged correlation based inference pairs up to a probabilistic model of parameter inference from metabolites time series allows the identification of the microscopic pharmacokinetics and pharmacodynamics of a drug with a

  17. Discerning the biochemical stability of pyrogenic C in soils

    NASA Astrophysics Data System (ADS)

    De la Rosa, José M.; Paneque, Marina; Contreras-Bernal, Lidia; Miller, Ana Z.; Knicker, Heike

    2016-04-01

    The soil organic matter (SOM) constitutes approximately 2/3 of the global terrestrial C pool, which corresponds to estimated 4000 Pg to a depth of 3 m [1] and therefore, the dynamics of organic carbon (OC) in soils control a large part of the terrestrial C cycle. The term Pyrogenic Carbon (PyC) comprises the whole range of pyrogenic organic materials, from partly charred material through charcoal to soot produced during fire, as well as technical chars (biochars) produced by pyrolysis of biomass. The previously common assumption of PyC being inert has long been proven wrong [2]. In theory, the pyrogenic process confers these materials a longer mean residence time in the soils than their precursors, thus the application of PyC in general and particularly biochar to soil is proposed as a valid approach to establish a significant, long-term sink for atmospheric carbon dioxide in terrestrial ecosystems [3]. Nevertheless, the knowledge concerning the biochemical recalcitrance of PyOM in soils is still limited. This study combines the analysis by 13C solid state Nuclear Magnetic Resonance Spectroscopy (13C NMR), Field Emission Scanning Electron Microscopy (FESEM), analytical pyrolysis (Py-GC/MS) and CO2 emissions in incubated pots of burned and unburned soils as well as in biochar amended and un-amended soils. By using this integrated approach we achieved a more complete understanding of the stability of different forms of PyC in the soil and the chemical changes occurring during aging. Significant differences are found between the stability of PyC. They depend on the nature of the source material, surficial properties of PyC, the pyrolysis process and the soil conditions during aging. Acknowledgements: The Marie Skłodowska-Curie actions (PCIG12-GA-2012-333784-Biocharisma project and PIEF-GA-2012-328689-DECAVE project), and the Spanish Ministry of Economy and Competitiveness (MINECO) (project PCGL2012-37041) are thanked for the financial support of the present study

  18. Cherenkov imaging and biochemical sensing in vivo during radiation therapy

    NASA Astrophysics Data System (ADS)

    Zhang, Rongxiao

    While Cherenkov emission was discovered more than eighty years ago, the potential applications of imaging this during radiation therapy have just recently been explored. With approximately half of all cancer patients being treated by radiation at some point during their cancer management, there is a constant challenge to ensure optimal treatment efficiency is achieved with maximal tumor to normal tissue therapeutic ratio. To achieve this, the treatment process as well as biological information affecting the treatment should ideally be effective and directly derived from the delivery of radiation to the patient. The value of Cherenkov emission imaging was examined here, primarily for visualization of treatment monitoring and then secondarily for Cherenkov-excited luminescence for tissue biochemical sensing within tissue. Through synchronized gating to the short radiation pulses of a linear accelerator (200Hz & 3 micros pulses), and applying a gated intensified camera for imaging, the Cherenkov radiation can be captured near video frame rates (30 frame per sec) with dim ambient room lighting. This procedure, sometimes termed Cherenkoscopy, is readily visualized without affecting the normal process of external beam radiation therapy. With simulation, phantoms and clinical trial data, each application of Cherenkoscopy was examined: i) for treatment monitoring, ii) for patient position monitoring and motion tracking, and iii) for superficial dose imaging. The temporal dynamics of delivered radiation fields can easily be directly imaged on the patient's surface. Image registration and edge detection of Cherenkov images were used to verify patient positioning during treatment. Inter-fraction setup accuracy and intra-fraction patient motion was detectable to better than 1 mm accuracy. Cherenkov emission in tissue opens up a new field of biochemical sensing within the tissue environment, using luminescent agents which can be activated by this light. In the first study of

  19. Research Links Nutrition to Behavior Disorders.

    ERIC Educational Resources Information Center

    Schauss, Alexander G.

    1985-01-01

    Social and medical research studies are examined that show the dramatic effects of biochemical and nutritional factors on antisocial behavior. They include studies of cobalt levels in hair samples of violent and nonviolent criminals, effects of diet on chronic delinquents, and effects of vitamin/mineral supplements on behaviorally disordered…

  20. Reye's Syndrome: A Review of Research Studies.

    ERIC Educational Resources Information Center

    Lopez, Thomas P.; And Others

    1982-01-01

    Clinical and pathological studies of Reye's syndrome indicate that symptoms range from influenza-related encephalitis-type disease to cranial pressure, cerebral edema, hemorrhage, and coma. Biochemical research on the blood, ammonia, and the liver is increasing in sophistication, and hopes for future insight into the etiology of Reye's syndrome…

  1. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

    PubMed

    Qian, Hong; Beard, Daniel A

    2005-04-22

    The principles of thermodynamics apply to both equilibrium and nonequilibrium biochemical systems. The mathematical machinery of the classic thermodynamics, however, mainly applies to systems in equilibrium. We introduce a thermodynamic formalism for the study of metabolic biochemical reaction (open, nonlinear) networks in both time-dependent and time-independent nonequilibrium states. Classical concepts in equilibrium thermodynamics-enthalpy, entropy, and Gibbs free energy of biochemical reaction systems-are generalized to nonequilibrium settings. Chemical motive force, heat dissipation rate, and entropy production (creation) rate, key concepts in nonequilibrium systems, are introduced. Dynamic equations for the thermodynamic quantities are presented in terms of the key observables of a biochemical network: stoichiometric matrix Q, reaction fluxes J, and chemical potentials of species mu without evoking empirical rate laws. Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms.

  2. Soil biochemical properties of grassland ecosystems under anthropogenic emission of nitrogen compounds

    NASA Astrophysics Data System (ADS)

    Kudrevatykh, Irina; Ivashchenko, Kristina; Ananyeva, Nadezhda

    2016-04-01

    Inflow of pollutants in terrestrial ecosystems nowadays increases dramatically, that might be led to disturbance of natural biogeochemical cycles and landscapes structure. Production of nitrogen fertilizers is one of the air pollution sources, namely by nitrogen compounds (NH4+, NO3-, NO2-). Air pollution by nitrogen compounds of terrestrial ecosystems might be affected on soil biochemical properties, which results increasing mineral nitrogen content in soil, changing soil P/N and Al/Ca ratios, and, finally, the deterioration of soil microbial community functioning. The research is focused on the assessment of anthropogenic emission of nitrogen compounds on soil properties of grassland ecosystems in European Russia. Soil samples (Voronic Chernozem Pachic, upper 10 cm mineral layer, totally 10) were taken from grassland ecosystem: near (5-10 m) nitrogen fertilizer factory (NFF), and far from it (20-30 km, served as a control) in Tula region. In soil samples the NH4+ and NO3- (Kudeyarov's photocolorimetric method), P, Ca, Al (X-ray fluorescence method) contents were measured. Soil microbial biomass carbon (Cmic) was analyzed by substrate-induced respiration method. Soil microbial respiration (MR) was assessed by CO2 rate production. Soil microbial metabolic quotient (qCO2) was calculated as MR/Cmic ratio. Near NFF the soil ammonium and nitrate nitrogen contents were a strongly varied, variation coefficient (CV) was 42 and 86This study was supported by Russian Foundation of Basic Research Grant No. 14-04-00098, 15-44-03220, 15-04-00915.

  3. (Bio)Chemical Tailoring of Biogenic 3-D Nanopatterned Templates with Energy-Relevant Functionalities

    SciTech Connect

    Sandhage, Kenneth H; Kroger, Nils

    2014-09-08

    The overall aim of this research has been to obtain fundamental understanding of (bio)chemical methodologies that will enable utilization of the unique 3-D nanopatterned architectures naturally produced by diatoms for the syntheses of advanced functional materials attractive for applications in energy harvesting/conversion and storage. This research has been conducted in three thrusts: Thrust 1 (In vivo immobilization of proteins in diatom biosilica) is directed towards elucidating the fundamental mechanism(s) underlying the cellular processes of in vivo immobilization of proteins in diatom silica. Thrust 2 (Shape-preserving reactive conversion of diatom biosilica into porous, high-surface area inorganic replicas) is aimed at understandingmore » the fundamental mechanisms of shape preservation and nanostructural evolution associated with the reactive conversion and/or coating-based conversion of diatom biosilica templates into porous inorganic replicas. Thrust 3 (Immobilization of energy-relevant enzymes in diatom biosilica and onto diatom biosilica-derived inorganic replicas) involves use of the results from both Thrust 1 and 2 to develop strategies for in vivo and in vitro immobilization of enzymes in/on diatom biosilica and diatom biosilica-derived inorganic replicas, respectively. This Final Report describes progress achieved in all 3 of these thrusts.« less

  4. Mars Molecular and Isotopic Analysis Research Study

    NASA Technical Reports Server (NTRS)

    Manning, Heidi L. K.

    1998-01-01

    Recently, the Martian atmosphere and surface constituents have become of great interest. The Viking in situ gas chromatograph mass spectrometer experiment contributed greatly to our knowledge of the composition of the Martian atmosphere. However, important questions remain such as the abundance of water on Mars. The Viking experiment employed solid reagents to enhance their carbon measurements. Techniques of chemical conversion using simple solid reagents have advanced considerably in the past 20 years. In this investigation we researched the advancements in techniques to reversibly adsorb and desorb water and focused on the techniques potentially useful for the temperatures and pressures on the Martian surface. During the granting period from June 15, 1998 to August 14, 1998, a literature study of the material appropriate for use in a chemical conversion device and the availability of these materials were undertaken. The focus of this investigation was searching for methods and materials potentially useful in enhancing the measurements of water. Three different methods were considered for the means to extract water from a given gas sample. These methods included adsorption in a desiccant, adsorption on a clean metal surface, and adsorption in a carbon molecular sieve or zeolite. Each method was evaluated with feasibility and reversibility in mind. By far the simplest and perhaps cheapest way to remove water from a gaseous sample is by means of a bulk desiccant. Desiccants are commercially available from many companies including those that supply chemicals. The main feature of a desiccant is its ability to rapidly bind or absorb water from the atmosphere. Calcium chloride, for example, is frequently incorporated into drying tubes by organic chemists when reactions require the absence of water. Other desiccants include sodium hydroxide, calcium hydride, and commercial products such as Drierite, available from Aldrich Chemical. The disadvantage to most desiccants is

  5. A data-integrated method for analyzing stochastic biochemical networks

    NASA Astrophysics Data System (ADS)

    Chevalier, Michael W.; El-Samad, Hana

    2011-12-01

    Variability and fluctuations among genetically identical cells under uniform experimental conditions stem from the stochastic nature of biochemical reactions. Understanding network function for endogenous biological systems or designing robust synthetic genetic circuits requires accounting for and analyzing this variability. Stochasticity in biological networks is usually represented using a continuous-time discrete-state Markov formalism, where the chemical master equation (CME) and its kinetic Monte Carlo equivalent, the stochastic simulation algorithm (SSA), are used. These two representations are computationally intractable for many realistic biological problems. Fitting parameters in the context of these stochastic models is particularly challenging and has not been accomplished for any but very simple systems. In this work, we propose that moment equations derived from the CME, when treated appropriately in terms of higher order moment contributions, represent a computationally efficient framework for estimating the kinetic rate constants of stochastic network models and subsequent analysis of their dynamics. To do so, we present a practical data-derived moment closure method for these equations. In contrast to previous work, this method does not rely on any assumptions about the shape of the stochastic distributions or a functional relationship among their moments. We use this method to analyze a stochastic model of a biological oscillator and demonstrate its accuracy through excellent agreement with CME/SSA calculations. By coupling this moment-closure method with a parameter search procedure, we further demonstrate how a model's kinetic parameters can be iteratively determined in order to fit measured distribution data.

  6. Biochemical assays for the discovery of TDP1 inhibitors

    PubMed Central

    Marchand, Christophe; Huang, Shar-yin N.; Dexheimer, Thomas S.; Lea, Wendy A.; Mott, Bryan T.; Chergui, Adel; Naumova, Alena; Stephen, Andrew G.; Rosenthal, Andrew S.; Rai, Ganesha; Murai, Junko; Gao, Rui; Maloney, David J.; Jadhav, Ajit; Jorgensen, William L.; Simeonov, Anton; Pommier, Yves

    2014-01-01

    Drug screening against novel targets is warranted to generate biochemical probes and new therapeutic drug leads. Tyrosyl-DNA-phosphodiesterases 1 and 2 (TDP1 and TDP2) are two DNA repair enzymes that have yet to be successfully targeted. TDP1 repairs topoisomerase I-, alkylation-, and chain terminator-induced DNA damage, while TDP2 repairs topoisomerase II-induced DNA damage. Here we report the quantitative high-throughput screening (qHTS) of the NIH Molecular Libraries Small Molecule Repository using recombinant human TDP1. We also developed a secondary screening method using a multiple loading gel-based assay where recombinant TDP1 is replaced by whole cell extract (WCE) from genetically engineered DT40 cells. While developing this assay, we determined the importance of buffer conditions for testing TDP1, and most notably the possible interference of phosphate-based buffers. The high specificity of endogenous TDP1 in WCE allowed the evaluation of a large number of hits with up to 600 samples analyzed per gel via multiple loadings. The increased stringency of the WCE assay eliminated a large fraction of the initial hits collected from the qHTS. Finally, inclusion of a TDP2 counter-screening assay allowed the identification of two novel series of selective TDP1 inhibitors. PMID:25024006

  7. Evaluating biochemical methane production from brewer's spent yeast.

    PubMed

    Sosa-Hernández, Ornella; Parameswaran, Prathap; Alemán-Nava, Gibrán Sidney; Torres, César I; Parra-Saldívar, Roberto

    2016-09-01

    Anaerobic digestion treatment of brewer's spent yeast (SY) is a viable option for bioenergy capture. The biochemical methane potential (BMP) assay was performed with three different samples (SY1, SY2, and SY3) and SY1 dilutions (75, 50, and 25 % on a v/v basis). Gompertz-equation parameters denoted slow degradability of SY1 with methane production rates of 14.59-4.63 mL/day and lag phases of 10.72-19.7 days. Performance and kinetic parameters were obtained with the Gompertz equation and the first-order hydrolysis model with SY2 and SY3 diluted 25 % and SY1 50 %. A SY2 25 % gave a 17 % of TCOD conversion to methane as well as shorter lag phase (<1 day). Average estimated hydrolysis constant for SY was 0.0141 (±0.003) day(-1), and SY2 25 % was more appropriate for faster methane production. Methane capture and biogas composition were dependent upon the SY source, and co-digestion (or dilution) can be advantageous.

  8. Biochemical modifications induced in human blood by oxygenation-ozonation.

    PubMed

    Bocci, Velio; Aldinucci, Carlo

    2006-01-01

    Some biochemical effects determined on human blood after addition of a gas mixture composed of oxygen (approximately 96%) and ozone (approximately 4%) have been evaluated. Ozone was used in a mild concentration ranging between 0.21 and 1.68 mM. Within few minutes after rapid mixing of the equal gas-liquid volumes, the ozone was consumed because by instantaneously reacting with biomolecules, generating reactive oxygen species (particularly hydrogen peroxide) having very short lifetime and lipid oxidation products. The following results are oxygen-ozone dose dependent: (1) The pO(2) values have risen from about 40 up to 400 mmHg. (2) By testing the highest ozone concentration, the total antioxidant capacity of blood decreased within 1 min from 1.35 to 0.91 mM but regained its normal values within 20 min owing to the rapid reduction of oxidized antioxidants operated by erythrocytes. (3) Similarly, intraerythrocytic reduced glutathione after ozonation decreased from the initial value of 5.71 to 4.56 micromol/g Hb. (4) Both hemolysis and methemoglobin showed a negligible increase. (c) 2006 Wiley Periodicals, Inc.

  9. Fasciola gigantica thioredoxin glutathione reductase: Biochemical properties and structural modeling.

    PubMed

    Gupta, Ankita; Kesherwani, Manish; Velmurugan, Devadasan; Tripathi, Timir

    2016-08-01

    Platyhelminth thioredoxin glutathione reductase (TGR) is a multifunctional enzyme that crosstalk between the conventional thioredoxin (Trx) and glutathione (GSH) system. It has been validated as a potential drug target in blood flukes. In the present study, we have performed a biochemical study on Fasciola gigantica TGR with substrates DTNB and GSSG. The Michaelis constant (Km) with DTNB was found to be 4.34±0.12μM while it was 61.15±1.50μM with GSSG. The kinetic results were compared with the TGR activities of other helminths. FgTGR showed typical hysteretic behavior with GSSG as other TGRs. We also described a homology-based structure of FgTGR. The cofactors (NADPH and FAD) and substrates (GSSG and DTNB) were docked, and two possible binding sites for substrates were identified in a single chain. The substrates were found to bind more favorably in the second site of TrxR domains. We also presented the first report on binding interaction of DTNB with a TGR. DTNB forms H-bond with His204 and Arg450 of chain A, Sec597, and Gly598 from chain B, salt-bridge with Lys124, and numerous other hydrophobic interactions. Helminth TGR represents an important enzyme in the redox and antioxidant system; hence, its inhibition can be used as an effective strategy against liver flukes. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Biochemical and molecular characteristics of citrin deficiency in Korean children.

    PubMed

    Oh, Seak Hee; Lee, Beom Hee; Kim, Gu-Hwan; Choi, Jin-Ho; Kim, Kyung Mo; Yoo, Han-Wook

    2017-02-01

    Mutations in SLC25A13 cause citrin deficiency, which has three phenotypes: neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD), failure to thrive and dyslipidemia caused by citrin deficiency (FTTDCD) and adult-onset type 2 citrullinemia (CTLN2). The purpose of this study was to determine the mutation spectrum and the clinical and biochemical characteristics of citrin deficiency in Korean patients. Thirty-four patients were diagnosed with citrin deficiency based on mutations in SLC25A13, as verified by direct sequencing and long PCR screening of a large transposon insertion. A total of 66 alleles from 33 unrelated families of 34 patients with citrin deficiency (27 NICCD, 2 FTTDCD and 5 CTLN2) were retrospectively identified. The common pathogenic alleles were IVS16ins3kb (33%), c.851_854del (30%) and c.1177+1G>A (12%), and three novel variants were identified. Levels of citrulline, threonine, methionine, tyrosine and arginine and the threonine-to-serine ratio were higher in children with neonatal intrahepatic cholestasis caused by NICCD compared with that in patients with idiopathic neonatal hepatitis (INH). We concluded that Korean patients with citrin deficiency showed the highest frequency of the IVS16ins3kb mutation and that plasma amino-acid profiles can be used to differentiate between NICCD and INH.

  11. Systems glycobiology: biochemical reaction networks regulating glycan structure and function

    PubMed Central

    Neelamegham, Sriram; Liu, Gang

    2011-01-01

    There is a growing use of bioinformatics based methods in the field of Glycobiology. These have been used largely to curate glycan structures, organize array-based experimental data and display existing knowledge of glycosylation-related pathways in silico. Although the cataloging of vast amounts of data is beneficial, it is often a challenge to gain meaningful mechanistic insight from this exercise alone. The development of specific analysis tools to query the database is necessary. If these queries can integrate existing knowledge of glycobiology, new insights may be gained. Such queries that couple biochemical knowledge and mathematics have been developed in the field of Systems Biology. The current review summarizes the current state of the art in the application of computational modeling in the field of Glycobiology. It provides (i) an overview of experimental and online resources that can be used to construct glycosylation reaction networks, (ii) mathematical methods to formulate the problem including a description of ordinary differential equation and logic-based reaction networks, (iii) optimization techniques that can be applied to fit experimental data for the purpose of model reconstruction and for evaluating unknown model parameters, (iv) post-simulation analysis methods that yield experimentally testable hypotheses and (v) a summary of available software tools that can be used by non-specialists to perform many of the above functions. PMID:21436236

  12. Plant nanobionics approach to augment photosynthesis and biochemical sensing

    NASA Astrophysics Data System (ADS)

    Giraldo, Juan Pablo; Landry, Markita P.; Faltermeier, Sean M.; McNicholas, Thomas P.; Iverson, Nicole M.; Boghossian, Ardemis A.; Reuel, Nigel F.; Hilmer, Andrew J.; Sen, Fatih; Brew, Jacqueline A.; Strano, Michael S.

    2014-04-01

    The interface between plant organelles and non-biological nanostructures has the potential to impart organelles with new and enhanced functions. Here, we show that single-walled carbon nanotubes (SWNTs) passively transport and irreversibly localize within the lipid envelope of extracted plant chloroplasts, promote over three times higher photosynthetic activity than that of controls, and enhance maximum electron transport rates. The SWNT-chloroplast assemblies also enable higher rates of leaf electron transport in vivo through a mechanism consistent with augmented photoabsorption. Concentrations of reactive oxygen species inside extracted chloroplasts are significantly suppressed by delivering poly(acrylic acid)-nanoceria or SWNT-nanoceria complexes. Moreover, we show that SWNTs enable near-infrared fluorescence monitoring of nitric oxide both ex vivo and in vivo, thus demonstrating that a plant can be augmented to function as a photonic chemical sensor. Nanobionics engineering of plant function may contribute to the development of biomimetic materials for light-harvesting and biochemical detection with regenerative properties and enhanced efficiency.

  13. Plant nanobionics approach to augment photosynthesis and biochemical sensing.

    PubMed

    Giraldo, Juan Pablo; Landry, Markita P; Faltermeier, Sean M; McNicholas, Thomas P; Iverson, Nicole M; Boghossian, Ardemis A; Reuel, Nigel F; Hilmer, Andrew J; Sen, Fatih; Brew, Jacqueline A; Strano, Michael S

    2014-04-01

    The interface between plant organelles and non-biological nanostructures has the potential to impart organelles with new and enhanced functions. Here, we show that single-walled carbon nanotubes (SWNTs) passively transport and irreversibly localize within the lipid envelope of extracted plant chloroplasts, promote over three times higher photosynthetic activity than that of controls, and enhance maximum electron transport rates. The SWNT-chloroplast assemblies also enable higher rates of leaf electron transport in vivo through a mechanism consistent with augmented photoabsorption. Concentrations of reactive oxygen species inside extracted chloroplasts are significantly suppressed by delivering poly(acrylic acid)-nanoceria or SWNT-nanoceria complexes. Moreover, we show that SWNTs enable near-infrared fluorescence monitoring of nitric oxide both ex vivo and in vivo, thus demonstrating that a plant can be augmented to function as a photonic chemical sensor. Nanobionics engineering of plant function may contribute to the development of biomimetic materials for light-harvesting and biochemical detection with regenerative properties and enhanced efficiency.

  14. Optical and biochemical properties of a southwest Florida whiting event

    NASA Astrophysics Data System (ADS)

    Long, Jacqueline S.; Hu, Chuanmin; Robbins, Lisa L.; Byrne, Robert H.; Paul, John H.; Wolny, Jennifer L.

    2017-09-01

    ;Whiting; in oceanography is a term used to describe a sharply defined patch of water that contains high levels of suspended, fine-grained calcium carbonate (CaCO3). Whitings have been reported in many oceanic and lake environments, and recently have been reported in southwest Florida coastal waters. Here, field and laboratory measurements were used to study optical, biological, and chemical properties of whiting waters off southwest Florida. No significant difference was found in chlorophyll a concentrations between whiting and outside waters (non-whiting water), but average particle backscattering coefficients in whiting waters were double those in outside waters, and remote sensing reflectance in whiting waters was higher at all wavelengths (400-700 nm). While other potential causes cannot be completely ruled out, particle composition and biochemical differences between sampled whiting water, contiguous water, and outside water indicate a biologically precipitated mode of whiting formation. Taxonomic examination of marine phytoplankton samples collected during a whiting event revealed a community dominated by autotrophic picoplankton and a small (<10 μm), centric diatom species, identified as Thalassiosira sp. through the use of scanning electron microscopy. Amorphous to fully formed crystals of CaCO3 were observed along the girdle bands of Thalassiosira sp. cells and autotrophic picoplankton cells. Although carbonate parameters differed from whiting and contiguous to outside water, more sampling is needed to determine if these results are statistically significant.

  15. Biochemical correlates of neuropsychiatric illness in maple syrup urine disease.

    PubMed

    Muelly, Emilie R; Moore, Gregory J; Bunce, Scott C; Mack, Julie; Bigler, Don C; Morton, D Holmes; Strauss, Kevin A

    2013-04-01

    Maple syrup urine disease (MSUD) is an inherited disorder of branched chain amino acid metabolism presenting with neonatal encephalopathy, episodic metabolic decompensation, and chronic amino acid imbalances. Dietary management enables survival and reduces risk of acute crises. Liver transplantation has emerged as an effective way to eliminate acute decompensation risk. Psychiatric illness is a reported MSUD complication, but has not been well characterized and remains poorly understood. We report the prevalence and characteristics of neuropsychiatric problems among 37 classical MSUD patients (ages 5-35 years, 26 on dietary therapy, 11 after liver transplantation) and explore their underlying mechanisms. Compared with 26 age-matched controls, MSUD patients were at higher risk for disorders of cognition, attention, and mood. Using quantitative proton magnetic resonance spectroscopy, we found lower brain glutamate, N-acetylaspartate (NAA), and creatine concentrations in MSUD patients, which correlated with specific neuropsychiatric outcomes. Asymptomatic neonatal course and stringent longitudinal biochemical control proved fundamental to optimizing long-term mental health. Neuropsychiatric morbidity and neurochemistry were similar among transplanted and nontransplanted MSUD patients. In conclusion, amino acid dysregulation results in aberrant neural networks with neurochemical deficiencies that persist after transplant and correlate with neuropsychiatric morbidities. These findings may provide insight into general mechanisms of psychiatric illness.

  16. Biochemical correlates of neuropsychiatric illness in maple syrup urine disease

    PubMed Central

    Muelly, Emilie R.; Moore, Gregory J.; Bunce, Scott C.; Mack, Julie; Bigler, Don C.; Morton, D. Holmes; Strauss, Kevin A.

    2013-01-01

    Maple syrup urine disease (MSUD) is an inherited disorder of branched chain amino acid metabolism presenting with neonatal encephalopathy, episodic metabolic decompensation, and chronic amino acid imbalances. Dietary management enables survival and reduces risk of acute crises. Liver transplantation has emerged as an effective way to eliminate acute decompensation risk. Psychiatric illness is a reported MSUD complication, but has not been well characterized and remains poorly understood. We report the prevalence and characteristics of neuropsychiatric problems among 37 classical MSUD patients (ages 5–35 years, 26 on dietary therapy, 11 after liver transplantation) and explore their underlying mechanisms. Compared with 26 age-matched controls, MSUD patients were at higher risk for disorders of cognition, attention, and mood. Using quantitative proton magnetic resonance spectroscopy, we found lower brain glutamate, N-acetylaspartate (NAA), and creatine concentrations in MSUD patients, which correlated with specific neuropsychiatric outcomes. Asymptomatic neonatal course and stringent longitudinal biochemical control proved fundamental to optimizing long-term mental health. Neuropsychiatric morbidity and neurochemistry were similar among transplanted and nontransplanted MSUD patients. In conclusion, amino acid dysregulation results in aberrant neural networks with neurochemical deficiencies that persist after transplant and correlate with neuropsychiatric morbidities. These findings may provide insight into general mechanisms of psychiatric illness. PMID:23478409

  17. Clinical and biochemical parameters of children and adolescents applying pesticides.

    PubMed

    Ismail, A A; Rohlman, D S; Abdel Rasoul, G M; Abou Salem, M E; Hendy, O M

    2010-07-01

    The primary agricultural product in Egypt is the cotton crop. Children and adolescents work seasonally in the cotton fields applying pesticides. To examine the effect of pesticide exposure on clinical and biochemical parameters in children and adolescents applying pesticides. Male children currently applying pesticides and aged between 9 and 19 years (n = 50) were recruited for this study. They were asked to complete work, health, and exposure questionnaires; examined for any medical and neurological problems with particular attention to sensory and motor functions including cranial nerves, sensory and motor system, and reflexes. From each participant, a blood sample was taken to measure acetylcholinesterase activity, and liver and kidney functions. Children who have never worked in agriculture (n = 50), matched on age, education, and socioeconomic status were also studied and served as controls. More neuromuscular disorders were identified in pesticide applicators than controls. A significant lower level of acetylcholinesterase was found in the applicator group compared to the controls. There was also a significant difference in hematological, renal and hepatic indices in the exposed children compared to the control children. Working more days in the current season and also working more years as a pesticide applicator were both associated with an increase in the prevalence of neuromuscular abnormalities and significant changes in the laboratory tests. Children and adolescent pesticide applicators working in farms of Egypt are at risk of developing serious health problems similar to those of adults.

  18. Biochemical oxygen demand measurement by mediator method in flow system.

    PubMed

    Liu, Ling; Bai, Lu; Yu, Dengbin; Zhai, Junfeng; Dong, Shaojun

    2015-06-01

    Using mediator as electron acceptor for biochemical oxygen demand (BOD) measurement was developed in the last decade (BODMed). However, until now, no BOD(Med) in a flow system has been reported. This work for the first time describes a flow system of BOD(Med) method (BOD(Med)-FS) by using potassium ferricyanide as mediator and carbon fiber felt as substrate material for microbial immobilization. The system can determine the BOD value within 30 min and possesses a wider analytical linear range for measuring glucose-glutamic acid (GGA) standard solution from 2 up to 200 mg L(-1) without the need of dilution. The analytical performance of the BOD(Med)-FS is comparable or better than that of the previously reported BOD(Med) method, especially its superior long-term stability up to 2 months under continuous operation. Moreover, the BOD(Med)-FS has same determination accuracy with the conventional BOD5 method by measuring real samples from a local wastewater treatment plant (WWTP). Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase.

    PubMed

    Cook, William J; Senkovich, Olga; Hernandez, Agustin; Speed, Haley; Chattopadhyay, Debasish

    2015-03-01

    The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis. This paper describes the biochemical characterization of C. parvum lactate dehydrogenase and high resolution crystal structures of the apo-enzyme and four ternary complexes. The ternary complexes capture the enzyme bound to NAD/NADH or its 3-acetylpyridine analog in the cofactor binding pocket, while the substrate binding site is occupied by one of the following ligands: lactate, pyruvate or oxamate. The results reveal distinctive features of the parasitic enzyme. For example, C. parvum lactate dehydrogenase prefers the acetylpyridine analog of NADH as a cofactor. Moreover, it is slightly less sensitive to gossypol inhibition compared with mammalian lactate dehydrogenases and not inhibited by excess pyruvate. The active site loop and the antigenic loop in C. parvum lactate dehydrogenase are considerably different from those in the human counterpart. Structural features and enzymatic properties of C. parvum lactate dehydrogenase are similar to enzymes from related parasites. Structural comparison with malate dehydrogenase supports a common ancestry for the two genes. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Contrast in the Photoelectric Effect of Organic and Biochemical Surfaces

    PubMed Central

    Birrell, G. B.; Burke, C.; Dehlinger, P.; Griffith, O. H.

    1973-01-01

    The photoelectric effect can provide the physical basis for a new method of mapping organic and biological surfaces. The technique, photoelectron microscopy, is similar to fluorescence microscopy using incident ultraviolet light except that photoejected electrons form the image of the specimen surface. In this work the minimum wavelengths of incident light required to produce an image were determined for the molecules 3,6-bis(dimethylamino)acridine (acridine orange) (I), benzo[a]pyrene (II), N,N,N′,N′-tetraphenylbenzidine (III), and copper phthalocyanine (IV). The photoelectron image thresholds for these compounds are 220 (I), 215 (II), 220 (III), and 240 nm (IV), all ±5 nm. Contrast of I-IV with respect to typical protein, lipid, nucleic acid, and polysaccharide surfaces was examined over the wavelength range 240-180 nm. The low magnification micrographs exhibited bright areas corresponding to I-IV but dark regions for the biochemical surfaces. The high contrast suggests the feasibility of performing extrinsic photoelectron microscopy experiments through selective labeling of sites on biological surfaces. ImagesFIGURE 3 PMID:4704486

  1. Biochemical characterization of predicted Precambrian RuBisCO

    PubMed Central

    Shih, Patrick M.; Occhialini, Alessandro; Cameron, Jeffrey C.; Andralojc, P John; Parry, Martin A. J.; Kerfeld, Cheryl A.

    2016-01-01

    The antiquity and global abundance of the enzyme, RuBisCO, attests to the crucial and longstanding role it has played in the biogeochemical cycles of Earth over billions of years. The counterproductive oxygenase activity of RuBisCO has persisted over billions of years of evolution, despite its competition with the carboxylase activity necessary for carbon fixation, yet hypotheses regarding the selective pressures governing RuBisCO evolution have been limited to speculation. Here we report the resurrection and biochemical characterization of ancestral RuBisCOs, dating back to over one billion years ago (Gyr ago). Our findings provide an ancient point of reference revealing divergent evolutionary paths taken by eukaryotic homologues towards improved specificity for CO2, versus the evolutionary emphasis on increased rates of carboxylation observed in bacterial homologues. Consistent with these distinctions, in vivo analysis reveals the propensity of ancestral RuBisCO to be encapsulated into modern-day carboxysomes, bacterial organelles central to the cyanobacterial CO2 concentrating mechanism. PMID:26790750

  2. Biochemical, structural, and physiological characteristics of vacuolar H+-pyrophosphatase.

    PubMed

    Segami, Shoji; Asaoka, Mariko; Kinoshita, Satoru; Fukuda, Mayu; Nakanishi, Yoichi; Maeshima, Masayoshi

    2018-03-09

    Proton-translocating inorganic pyrophosphatase (H+-PPase) actively translocates protons across membranes coupled with the hydrolysis of inorganic pyrophosphate (PPi). H+-PPase, which is composed of a single protein and uses a simple compound as a substrate, has been recognized as a new type of ion pump in addition to the P-, F-, and V-type ion translocating ATPases. H+- and Na+-PPases are distributed in various organisms including plants, parasitic protozoa, Archaebacteria, and bacteria, but are not present in animals or yeast. Vacuolar H+-PPase has dual functions in plant cells: hydrolysis of cytosolic PPi to maintain the levels of PPi and translocation of protons into vacuoles to maintain the acidity of the vacuolar lumen. Acidification performed with the vacuolar type H+-ATPase and H+-PPase is essential to maintain acidic conditions, which are necessary for vacuolar hydrolytic enzymes and for supplying energy to secondary active transporters. Recent studies using loss-of-function mutant lines of H+-PPase and complementation lines with soluble PPases have emphasized the physiological importance of the scavenging role of PPi. An overview of the main features of H+-PPases present in the vacuolar membrane is provided in terms of tissue distribution in plants, intracellular localization, structure-function relationship, biochemical potential as a proton pump, and functional stability.

  3. A Biochemical and Morphological Study of Rat Liver Microsomes

    PubMed Central

    Moulé, Y.; Rouiller, C.; Chauveau, J.

    1960-01-01

    Microsomes isolated by differential centrifugation from a rat liver homogenate in 0.88 M sucrose solution have been studied from the biochemical and morphological point of view. 1. Under these experimental conditions, the "total microsome" fraction was obtained by centrifuging the cytoplasmic extract free of nuclei and mitochondria, for 3 hours at 145,000 g. Morphologically, the total microsomes consist mainly of "rough-surfaced membranes" and "smooth" ones. 2. The total microsomes have been divided into 2 subfractions so that the 1st microsomal fraction contains the "rough" vesicles (2 hours centrifugation at 40,000 g) while the 2nd microsomal fraction consists essentially of smooth vesicles, free particles, and ferritin (centrifugation of the supernatant at 145,000 g for 3 hours). 3. By the action of 0.4 per cent sodium deoxycholate in 0.88 M sucrose, it was possible to obtain a pellet for each of the 2 fractions which consisted of dense particles, rich in RNA, poor in lipids, and which represented about 50 to 60 percent of the RNA and 10 to 15 per cent of the proteins. The results have been discussed taking into consideration the hypothesis of the presence of RNA in the membranes of microsomal vesicles. PMID:14424705

  4. New approaches to biochemical radioprotection: antioxidants and DNA repair enhancement

    NASA Astrophysics Data System (ADS)

    Riklis, E.; Emerit, I.; Setlow, R. B.

    Chemical repair may be provided by radioprotective compounds present during exposure to ionizing radiation. Considering DNA as the most sensitive target it is feasible to biochemically improve protection by enhancing DNA repair mechanisms. Protection of DNA by reducing the amount of damage (by radical scavenging and chemical repair) followed by enhanced repair of DNA will provide much improved protection and recovery. Furthermore, in cases of prolonged exposure, such as is possible in prolonged space missions, or of unexpected variations in the intensity of radiation, as is possible when encountering solar flares, it is important to provide long-acting protection, and this may be provided by antioxidants and well functioning DNA repair systems. It has also become important to provide protection from the potentially damaging action of long-lived clastogenic factors which have been found in plasma of exposed persons from Hiroshima & Nagasaki, radiation accidents, radiotherapy patients and recently in ``liquidators'' - persons involved in salvage operations at the Chernobyl reactor. The clastogenic factor, which causes chromatid breaks in non-exposed plasma, might account for late effects and is posing a potential carcinogenic hazard /1/. The enzyme superoxide dismutase (SOD) has been shown to eliminate the breakage factor from cultured plasma of exposed persons /2/. Several compounds have been shown to enhance DNA repair: WR-2721 /3/, nicotinamide /4/, glutathione monoester (Riklis et al., unpublished) and others. The right combination of such compounds may prove effective in providing protection from a wide range of radiation exposures over a long period of time.

  5. MORPHOLOGICAL AND BIOCHEMICAL CHARACTERIZATION OF GOLDFISH ERYTHROPHORES AND THEIR PTERINOSOMES

    PubMed Central

    Matsumoto, Jiro; Obika, Masataka

    1968-01-01

    The fine structure of integumental erythrophores and the intracellular location of pteridine and carotenoid pigments in adult goldfish, Carassius auratus, were studied by means of cytochemistry, paper and thin-layer chromatography, ionophoresis, density-gradient centrifugal fractionation, and electron microscopy. The ultrastructure of erythrophores is characterized by large numbers of somewhat ellipsoidal pigment granules and a well-developed system of tubules which resembles endoplasmic reticulum. The combined morphological and biochemical approaches show that pteridine pigments of erythrophores are located characteristically in pigment granules and are the primary yellow pigments of these organelles. Accordingly, this organelle is considered to be the "pterinosome" which was originally found in swordtail erythrophores. Major pteridines obtainable from goldfish pterinosomes are sepiapterin, 7-hydroxybiopterin, isoxanthopterin, and 6-carboxyisoxanthopterin. Density-gradient fractions indicate that carotenoids are mostly associated with the endoplasmic reticulum. Both tyrosinase and possibly a tyrosinase inhibitor containing sulfhydryl groups are present in the pterinosome. The possible existence of a tyrosinase inhibitor is suggested by the marked increase of tyrosinase activity upon the addition of iodoacetamide or p-chloromercuribenzoic acid. In the light of their fine structure, pigmentary composition, and enzymatic properties, the erythrophores and pterinosomes are discussed with respect to their probable functions and their relationship to melanophores. PMID:5692582

  6. Insecticides induced biochemical changes in freshwater microalga Chlamydomonas mexicana.

    PubMed

    Kumar, Muthukannan Satheesh; Kabra, Akhil N; Min, Booki; El-Dalatony, Marwa M; Xiong, Jiuqiang; Thajuddin, Nooruddin; Lee, Dae Sung; Jeon, Byong-Hun

    2016-01-01

    The effect of insecticides (acephate and imidacloprid) on a freshwater microalga Chlamydomonas mexicana was investigated with respect to photosynthetic pigments, carbohydrate and protein contents, fatty acids composition and induction of stress indicators including proline, superoxide dismutase (SOD) and catalase (CAT). C. mexicana was cultivated with 1, 5, 10, 15, 20 and 25 mg L(-1) of acephate and imidacloprid. The microalga growth increased with increasing concentrations of both insecticides up to 15 mg L(-1), beyond which the growth declined compared to control condition (without insecticides). C. mexicana cultivated with 15 mg L(-1) of both insecticides for 12 days was used for further analysis. The accumulation of photosynthetic pigments (chlorophyll and carotenoids), carbohydrates and protein was decreased in the presence of both insecticides. Acephate and imidacloprid induced the activities of superoxide dismutase (SOD) and catalase (CAT) and increased the concentration of proline in the microalga, which play a defensive role against various environmental stresses. Fatty acid analysis revealed that the fraction of polyunsaturated fatty acids decreased on exposure to both insecticides. C. mexicana also promoted 25 and 21% removal of acephate and imidacloprid, respectively. The biochemical changes in C. mexicana on exposure to acephate and imidacloprid indicate that the microalga undergoes an adaptive change in response to the insecticide-induced oxidative stress.

  7. Mercury-induced biochemical and proteomic changes in rice roots.

    PubMed

    Chen, Yun-An; Chi, Wen-Chang; Huang, Tsai-Lien; Lin, Chung-Yi; Quynh Nguyeh, Thi Thuy; Hsiung, Yu-Chywan; Chia, Li-Chiao; Huang, Hao-Jen

    2012-06-01

    Mercury (Hg) is a serious environmental pollution threats to the planet. Accumulation of Hg in plants disrupts many cellular-level functions and inhibits growth and development, but the mechanism is not fully understood. We investigated cellular, biochemical and proteomic changes in rice roots under Hg stress. Root growth rate was decreased and Hg, reactive oxygen species (ROS), and malondialdehyde (MDA) content and lipoxygenase activity were increased significantly with increasing Hg concentration in roots. We revealed a time-dependent alteration in total glutathione content and enzymatic activity of superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) and peroxidase (POD) during Hg stress. 2-D electrophoresis revealed differential expression of 25 spots with Hg treatment of roots: 14 spots were upregulated and 11 spots downregulated. These differentially expressed proteins were identified by ESI-MS/MS to be involved in cellular functions including redox and hormone homeostasis, chaperone activity, metabolism, and transcription regulation. These results may provide new insights into the molecular basis of the Hg stress response in plants. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  8. Adaptive moment closure for parameter inference of biochemical reaction networks.

    PubMed

    Schilling, Christian; Bogomolov, Sergiy; Henzinger, Thomas A; Podelski, Andreas; Ruess, Jakob

    2016-11-01

    Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  9. Biochemical properties of penicillin amidohydrolase from Micrococcus luteus.

    PubMed Central

    Nam, D H; Ryu, D D

    1979-01-01

    Some biochemical properties of whole-cell penicillin amidohydrolase from Micrococcus luteus have been studied. This whole-cell enzyme showed its maximal activity at 36 degrees C at pH 7.5. It was found that the activation energy of this enzyme was 8.03 kcal (ca. 33.6 kJ) per mol, and this amidohydrolase showed first-order decay at 36 degrees C. The penicillin amidohydrolase was deactivated rapidly at temperatures above 50 degrees C during storage or preincubation for 24 h. The Michaelis constant, Km, for penicillin G was determined as 2.26 mM, and the substrate inhibition constant, Kis, was 155 mM. The whole-cell penicillin amidohydrolase from M. luteus was capable of hydrolyzing penicillin G, penicillin V, ampicillin, and cephalexin, but not cephalosporin C and cloxacillin. This whole-cell enzyme also had synthetic activity for semisynthetic penicillins or cephalosporins from D-(--)-alpha-phenylglycine methyl ester and 6-alpha-aminopenicillanic acid or 7-amino-3-deacetoxycephalosporanic acid. PMID:39505

  10. Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems

    PubMed Central

    Lomnitz, Jason G.; Savageau, Michael A.

    2016-01-01

    An overarching goal in molecular biology is to gain an understanding of the mechanistic basis underlying biochemical systems. Success is critical if we are to predict effectively the outcome of drug treatments and the development of abnormal phenotypes. However, data from most experimental studies is typically noisy and sparse. This allows multiple potential mechanisms to account for experimental observations, and often devising experiments to test each is not feasible. Here, we introduce a novel strategy that discriminates among putative models based on their repertoire of qualitatively distinct phenotypes, without relying on knowledge of specific values for rate constants and binding constants. As an illustration, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors. Our results show that the conventional models, based on their well-characterized components, cannot account for the experimental observations. We examine a total of 40 alternative hypotheses and show that only 5 have the potential to reproduce the experimental data, and one can do so with biologically relevant parameter values. PMID:27578053

  11. Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems.

    PubMed

    Lomnitz, Jason G; Savageau, Michael A

    2016-08-31

    An overarching goal in molecular biology is to gain an understanding of the mechanistic basis underlying biochemical systems. Success is critical if we are to predict effectively the outcome of drug treatments and the development of abnormal phenotypes. However, data from most experimental studies is typically noisy and sparse. This allows multiple potential mechanisms to account for experimental observations, and often devising experiments to test each is not feasible. Here, we introduce a novel strategy that discriminates among putative models based on their repertoire of qualitatively distinct phenotypes, without relying on knowledge of specific values for rate constants and binding constants. As an illustration, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors. Our results show that the conventional models, based on their well-characterized components, cannot account for the experimental observations. We examine a total of 40 alternative hypotheses and show that only 5 have the potential to reproduce the experimental data, and one can do so with biologically relevant parameter values.

  12. Physical and biochemical properties of green banana flour.

    PubMed

    Suntharalingam, S; Ravindran, G

    1993-01-01

    Banana flour prepared from two cooking banana varieties, namely 'Alukehel' and 'Monthan', were evaluated for their physical and biochemical characteristics. The yields of flour averaged 31.3% for 'Alukehel' and 25.5% for 'Monthan'. The pH of the flour ranged from 5.4 to 5.7. The bulk density and particle size distribution were also measured. The average chemical composition (% dry matter) of the flours were as follows: crude protein, 3.2; crude fat, 1.3; ash, 3.7; neutral detergent fiber, 8.9; acid detergent fiber, 3.8; cellulose, 3.1; lignin, 1.0 and hemicellulose, 5.0. Carbohydrate composition indicated the flour to contain 2.8% soluble sugars, 70.0% starch and 12.0% non-starch polysaccharides. Potassium is the predominant mineral in banana flour. Fresh green banana is a good source of vitamin C, but almost 65% is lost during the preparation of flour. Oxalate content (1.1-1.6%) of banana flour is probably nutritionally insignificant. The overall results are suggestive of the potential of green bananas as a source of flour.

  13. Chlamydomonas reinhardtii produces a profilin with unusual biochemical properties.

    PubMed

    Kovar, D R; Yang, P; Sale, W S; Drobak, B K; Staiger, C J

    2001-12-01

    We report the characterization of a profilin orthologue from Chlamydomonas reinhardtii. CrPRF, probably the only profilin isoform, is present in both the cell body and flagella. Examination of vegetative and gametic cells by immunofluorescence microscopy using multiple fixation procedures also revealed enrichment of CrPRF at the anterior of the cell near the base of flagella and near the base of the fertilization tubule in mating type plus gametes. Purified, recombinant CrPRF binds to actin with a Kd value approximately 10(-7) and displaces nuclei in a live cell 'nuclear displacement' assay, consistent with profilin's ability to bind G-actin in vivo. However, when compared with other profilin isoforms, CrPRF has a relatively low affinity for poly-L-proline and for phosphatidylinositol (4,5) bisphosphate micelles. Furthermore, and surprisingly, CrPRF inhibits exchange of adenine nucleotide on G-actin in a manner similar to human ADF or DNase I. Thus, we postulate that a primary role for CrPRF is to sequester actin in Chlamydomonas. The unusual biochemical properties of CrPRF offer a new opportunity to distinguish specific functions for profilin isoforms.

  14. Structuring evolution: biochemical networks and metabolic diversification in birds.

    PubMed

    Morrison, Erin S; Badyaev, Alexander V

    2016-08-25

    Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network - compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

  15. Chlorpromazine and lithium interaction: a biochemical and histological study.

    PubMed

    Messiha, F S; Sproat, H F; Striegler, R L

    1983-08-01

    Biochemical and histological studies on the effect of separate and combined administration of LiCl and of chlorpromazine (CPZ) on female C57BL/6J mice were performed. Mice were divided into 4 groups. One group was given an intraperitoneal injection daily of CPZ HCl, 5 mg/kg for 4 days followed by 4 more days of a daily dosage of 10 mg/kg. A second group was maintained on 0.4% (w/v) LiCl solution as the sole drinking fluid for 8 consecutive days and a third group received the same LiCl solution but with daily CPZ injection as the initial group for 8 days. The fourth group served as saline-controls. Hepatic liver alcohol dehydrogenase was induced by combined drug treatment from respective controls. The Li-treatment inhibited mitochondrial liver aldehyde dehydrogenase, and coadministration of CPZ with LiCl antagonized this effect. Mice treated with CPZ showed corneal cellularity and mitotic figure appearance without inflammation. The LiCl treated mice displayed variations in base corneal cell size, shape and pigmentation with aggregation of the nuclei, and the presence of mitotic activity inflammation. Mice receiving combined drug treatment showed similar corneal alterations, but mitotic figures were found above base cell layer suggesting an enhanced corneal toxicity. The results suggest a drug-drug interaction phenomenon which may explain some of their adverse reaction when given concurrently.

  16. Spongiosa Primary Development: A Biochemical Hypothesis by Turing Patterns Formations

    PubMed Central

    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. PMID:23193429

  17. Predictive hypotheses are ineffectual in resolving complex biochemical systems.

    PubMed

    Fry, Michael

    2018-03-20

    Scientific hypotheses may either predict particular unknown facts or accommodate previously-known data. Although affirmed predictions are intuitively more rewarding than accommodations of established facts, opinions divide whether predictive hypotheses are also epistemically superior to accommodation hypotheses. This paper examines the contribution of predictive hypotheses to discoveries of several bio-molecular systems. Having all the necessary elements of the system known beforehand, an abstract predictive hypothesis of semiconservative mode of DNA replication was successfully affirmed. However, in defining the genetic code whose biochemical basis was unclear, hypotheses were only partially effective and supplementary experimentation was required for its conclusive definition. Markedly, hypotheses were entirely inept in predicting workings of complex systems that included unknown elements. Thus, hypotheses did not predict the existence and function of mRNA, the multiple unidentified components of the protein biosynthesis machinery, or the manifold unknown constituents of the ubiquitin-proteasome system of protein breakdown. Consequently, because of their inability to envision unknown entities, predictive hypotheses did not contribute to the elucidation of cation theories remained the sole instrument to explain complex bio-molecular systems, the philosophical question of alleged advantage of predictive over accommodative hypotheses became inconsequential.

  18. Biochemical principles and inhibitors to interfere with viral capping pathways.

    PubMed

    Decroly, Etienne; Canard, Bruno

    2017-06-01

    Messenger RNAs are decorated by a cap structure, which is essential for their translation into proteins. Many viruses have developed strategies in order to cap their mRNAs. The cap is either synthetized by a subset of viral or cellular enzymes, or stolen from capped cellular mRNAs by viral endonucleases ('cap-snatching'). Reverse genetic studies provide evidence that inhibition of viral enzymes belonging to the capping pathway leads to inhibition of virus replication. The replication defect results from reduced protein synthesis as well as from detection of incompletely capped RNAs by cellular innate immunity sensors. Thus, it is now admitted that capping enzymes are validated antiviral targets, as their inhibition will support an antiviral response in addition to the attenuation of viral mRNA translation. In this review, we describe the different viral enzymes involved in mRNA capping together with relevant inhibitors, and their biochemical features useful in inhibitor discovery. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Biochemical studies on the metabolic activation of halogenated alkanes.

    PubMed Central

    Cheeseman, K H; Albano, E F; Tomasi, A; Slater, T F

    1985-01-01

    This paper reviews recent investigations by Slater and colleagues into the metabolic activation of halogenated alkanes in general and carbon tetrachloride in particular. It is becoming increasingly accepted that free radical intermediates are involved in the toxicity of many such compounds through mechanisms including lipid peroxidation, covalent binding, and cofactor depletion. Here we describe the experimental approaches that are used to establish that halogenated alkanes are metabolized in animal tissues to reactive free radicals. Electron spin resonance spectroscopy is used to identify free-radical products, often using spin-trapping compounds. The generation of specific free radicals by radiolytic methods is useful in the determination of the precise reactivity of radical intermediates postulated to be injurious to the cell. The enzymic mechanism of the production of such free radicals and their subsequent reactions with biological molecules is studied with specific metabolic inhibitors and free-radical scavengers. These combined techniques provide considerable insight into the process of metabolic activation of halogenated compounds. It is readily apparent, for instance, that the local oxygen concentration at the site of activation is of crucial importance to the subsequent reactions; the formation of peroxy radical derivatives from the primary free-radical product is shown to be of great significance in relation to carbon tetrachloride and may be of general importance. However, while these studies have provided much information on the biochemical mechanisms of halogenated alkane toxicity, it is clear that many problems remain to be solved. PMID:3007102

  20. Haematological and serum biochemical values of southern chamois (Rupicapra pyrenaica).

    PubMed

    López-Olvera, J R; Marco, I; Montané, J; Lavín, S

    2006-04-08

    Blood samples were taken from 75 free-ranging southern chamois (Rupicapra pyrenaica) captured in drive-nets in Catalonia, north-eastern Spain, and 20 haematological and 24 serum biochemical variables were analysed. The values were similar to those of other species of the Caprinae subfamily, except for cortisol, the concentration of which was higher. The red blood cell count (RBC), platelets and leucocytes, and the concentrations of cortisol, lactate, muscular enzymes and gamma-globulins were higher in summer than in spring, whereas the mean corpuscular volume, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, and the concentrations of cholesterol, total bilirubin and creatinine were lower. Adult males had higher RBCs and haemoglobin values than females in summer, and lower leucocyte, lymphocyte and neutrophil counts than females and yearling males. The concentrations of triglycerides, total bilirubin, lactate, creatinine, urea, chloride and alpha2-globulins were higher in adult males than yearling males. In summer the adult females had higher values for platelets, lymphocytes, cortisol, sodium and muscular enzymes.

  1. [Contribution and role of important biochemic factors in cerebral ischemia].

    PubMed

    Miller, Elzbieta; Rutkowski, Maciej

    2006-03-01

    After an ischemic insult, a multi-faceted complex cascade of biochemical reactions occurs that ultimately causes neurons death. Above reactions exert an influence on: immunological changes (activation of the complement system and the generation of antibodies), increased inflammation (actions of proinflammatory cytokines and chemokines), the production of reactive oxygen species leading to oxidative stress, diminished mitochondrial function and activation of apoptotic pathways. There is also intensive release and wrong reversible escapement many of neurotransmitters. The last one throught oxidative desamination are one of the main sources most of free radicals. Central nervous system is particularly susceptible to ROS-induced damage due to the high oxygen demands of the brain and low concentration of endogenous antioxidants. lts refer both enzymatic antioxidants: catalase, glutathione peroxidase, glutathione reductase, superoxide dismutase and nonenzymatic antioxidants glutathione, vitamin a, c, e, coenzym Q, uric acid etc. Presently there are no neuroprotective treatments and prevention. One way of treatment testing in clinical trials is hypothermia inhibits above-mentioned processes.

  2. Biochemical events during somatic embryogenesis in Coffea arabica L.

    PubMed

    Bartos, Patrícia Monah Cunha; Gomes, Hugo Teixeira; do Amaral, Lourdes Isabel Velho; Teixeira, João Batista; Scherwinski-Pereira, Jonny Everson

    2018-04-01

    Several biochemical components associated with different stages of somatic embryogenesis in coffee ( Coffea arabica L.) are investigated using foliar explants. Soluble sugar, starch, free amino acids and total proteins were extracted and quantified at different stages of somatic embryogenesis, such as foliar segments (initial explants), primary calluses, embryogenic calluses, globular embryos, torpedoes, cotyledonary embryos and mature fruit zygotic embryos. Total soluble sugar levels increased sixfold at the initial stages of somatic embryogenesis induction. During this period, total soluble sugar in the cultures contained approximately 99.3% glucose and fructose. At 67.4 μg/mg MS, no significant changes were observed in total sugar content during the embryo's somatic maturation and regeneration. During this stage, total soluble sugar was composed of 60% sucrose. After primary callus formation, starch contents increased gradually until the culture's conclusion. Total free amino acids, particularly arginine, lysine, methionine, asparagine, glutamine and histidine, revealed a higher synthesis until the formation of the primary callus, after which they remain statistically constant up to the end of the process. During the induction of calluses, a gradual increase of total proteins occurred, which, in the differentiating and maturing of somatic embryos, did not differ statistically till the formation of a cotyledonary embryo, when rates decreased 21.8%.

  3. Hematologic and biochemical characteristics of stranded green sea turtles.

    PubMed

    March, Duane T; Vinette-Herrin, Kimberly; Peters, Andrew; Ariel, Ellen; Blyde, David; Hayward, Doug; Christidis, Les; Kelaher, Brendan P

    2018-02-01

    To improve understanding of pathophysiologic processes occurring in green sea turtles ( Chelonia mydas) stranded along the east coast of Australia, we retrospectively examined the hematologic and biochemical blood parameters of 127 green turtles admitted to 2 rehabilitation facilities, Dolphin Marine Magic (DMM) and Taronga Zoo (TZ), between 2002 and 2016. The predominant size class presented was small immature animals (SIM), comprising 88% and 69% of admissions to DMM and TZ, respectively. Significant differences in blood profiles were noted between facility, size, and outcome. Elevated levels of aspartate aminotransferase (AST) and heterophils were poor prognostic indicators in animals from TZ, but not DMM. SIM animals at both institutions had lower protein levels than large older (LO) animals. SIM animals at DMM also had lower hematocrit and monocyte concentration; SIM animals at TZ had lower heterophil counts. Urea was measured for 27 SIM animals from TZ, but the urea-to-uric acid ratio was not prognostically useful. Strong correlations were seen between AST and glutamate dehydrogenase (GDH; r = 0.68) and uric acid and bile acids ( r = 0.72) in the 45 SIM animals from DMM in which additional analytes were measured. χ 2 contingency tests showed that the most recently published reference intervals were not prognostically useful. A paired t-test showed that protein levels rose and heterophil numbers fell in the 15 SIM animals from TZ during the rehabilitation process. Our results indicate that further work is required to identify reliable prognostic biomarkers for green turtles.

  4. Biomechanical and biochemical outcomes of porcine temporomandibular joint disc deformation

    PubMed Central

    Matuska, Andrea M.; Muller, Stephen; Dolwick, M. Franklin; McFetridge, Peter S.

    2016-01-01

    Objective The structure-function relationship in the healthy temporomandibular joint (TMJ) disc has been well established, however the changes in dysfunctional joints has yet to be systematically evaluated. Due to the poor understanding of the etiology of temporomandibular disorders (TMDs) this study evaluated naturally occurring degenerative remodeling in aged female porcine temporomandibular joint (TMJ) discs in order to gain insight into the progression and effects on possible treatment strategies of TMDs. Design Surface and regional biomechanical and biochemical properties of discal tissues were determined in grossly deformed (≥ Wilkes Stage 3) and morphologically normal (≤ Wilkes Stage 2) TMJ discs. Results Compared to normal disc structure the deformed discs lacked a smooth biconcave shape and characteristic ECM organization. Reduction in tensile biomechanical integrity and increased compressive stiffness and cellularity was found in deformed discs. Regionally, the posterior and intermediate zones of the disc were most frequently affected along with the inferior surface. Conclusions The frequency of degeneration observed on the inferior surface of the disc (predominantly posterior), suggests that a disruption in the disc-condyle relationship likely contributes to the progression of joint dysfunction more than the temporodiscal relationship. As such, the inferior joint space may be an important consideration in early clinical diagnosis and treatment of TMDs, as it is overlooked in techniques performed in the upper joint space, including arthroscopy and arthrocentesis. Furthermore, permanent damage to the disc mechanical properties would limit the ability to successfully reposition deformed discs, highlighting the importance of emerging therapies such as tissue engineering. PMID:26774186

  5. Role of biochemical factors in the pathogenesis of keratoconus.

    PubMed

    Wojcik, Katarzyna A; Blasiak, Janusz; Szaflik, Jerzy; Szaflik, Jacek P

    2014-01-01

    Keratoconus (KC) is a corneal disease associated with structural abnormalities in the corneal epithelium, Bowman's layer and stroma and altered concentration of tear components. KC corneas show a different pattern of collagen lamellae than their normal counterparts. Also, a reduction of several collagen types in KC epithelium and stroma was observed. Altered expression and/or activity of lysyl oxidase, a critical enzyme of the biogenesis of connective tissue detected in KC corneas, may weaken covalent bonds between collagen and elastin fibrils, what may lead to biomechanical deterioration of the cornea. Increased activity of matrix metalloproteinases observed in KC may induce the degradation of the extracellular matrix causing damage to the cornea. Oxidative and nitrative stress play an important role in KC pathogenesis and KC corneas are characterized by the disturbed lipid peroxidation and nitric oxide pathways. Malfunctioning of these pathways may lead to accumulation of their toxic by-products inducing several detrimental effects, along with apoptosis of the corneal cells, which may result from the loss of β-actin or increased levels of cytokines, including interleukin-1 and -6. Change in the expression of genes associated with wound healing, including the nerve growth factor and the visual system homeobox 1, may contribute to increased susceptibility of KC corneas to injury. Consequently, biochemical changes may play an important role in KC pathophysiology and, therefore, can be considered in prevention, diagnosis, prognosis and in the therapy of this disease as well.

  6. Molecular and biochemical characterization of Paragonimus westermani tyrosinase.

    PubMed

    Bae, Y-A; Kim, S-H; Ahn, C-S; Kim, J-G; Kong, Y

    2015-05-01

    Trematode tyrosinases (TYRs) play a major role in the tanning process during eggshell formation. We investigated the molecular and biochemical features of Paragonimus westermani TYR (PwTYR). The PwTYR cDNA was composed of 1568-bp encompassing a 1422-bp-long open reading frame (474-amino acid polypeptide). A strong phylogenetic relationship with Platyhelminthes and Deuterostomian orthologues was evident. The recombinant PwTYR expressed in prokaryotic cells promptly oxidized diphenol substrates, with a preferential affinity toward ortho-positioned hydroxyl groups. It demonstrated fairly weak activity for monophenol compounds. Diphenol oxidase activity was augmented with an increase of pH from 5.0 to 8.0, while monophenol oxidase activity was highest at an acidic pH and gradually decreased as pH increased. Transcription profile of PwTYR was temporally upregulated along with worm development. PwTYR was specifically localized in vitellocytes and eggs. The results suggested that conversion of tyrosine to L-dihydroxyphenylalanine by PwTYR monophenol oxidase activity might be rate-limiting step during the sclerotization process of P. westermani eggs. The pH-dependent pattern of monophenol and diphenol oxidase activity further proposes that the initial hydroxylation might slowly but steadily progress in acidic secreted vesicles of vitellocytes and the second oxidation process might be rapidly accelerated by neural or weak alkaline pH environments within the ootype.

  7. Optimal experiment design for model selection in biochemical networks

    PubMed Central

    2014-01-01

    Background Mathematical modeling is often used to formalize hypotheses on how a biochemical network operates by discriminating between competing models. Bayesian model selection offers a way to determine the amount of evidence that data provides to support one model over the other while favoring simple models. In practice, the amount of experimental data is often insufficient to make a clear distinction between competing models. Often one would like to perform a new experiment which would discriminate between competing hypotheses. Results We developed a novel method to perform Optimal Experiment Design to predict which experiments would most effectively allow model selection. A Bayesian approach is applied to infer model parameter distributions. These distributions are sampled and used to simulate from multivariate predictive densities. The method is based on a k-Nearest Neighbor estimate of the Jensen Shannon divergence between the multivariate predictive densities of competing models. Conclusions We show that the method successfully uses predictive differences to enable model selection by applying it to several test cases. Because the design criterion is based on predictive distributions, which can be computed for a wide range of model quantities, the approach is very flexible. The method reveals specific combinations of experiments which improve discriminability even in cases where data is scarce. The proposed approach can be used in conjunction with existing Bayesian methodologies where (approximate) posteriors have been determined, making use of relations that exist within the inferred posteriors. PMID:24555498

  8. Optimal experiment design for model selection in biochemical networks.

    PubMed

    Vanlier, Joep; Tiemann, Christian A; Hilbers, Peter A J; van Riel, Natal A W

    2014-02-20

    Mathematical modeling is often used to formalize hypotheses on how a biochemical network operates by discriminating between competing models. Bayesian model selection offers a way to determine the amount of evidence that data provides to support one model over the other while favoring simple models. In practice, the amount of experimental data is often insufficient to make a clear distinction between competing models. Often one would like to perform a new experiment which would discriminate between competing hypotheses. We developed a novel method to perform Optimal Experiment Design to predict which experiments would most effectively allow model selection. A Bayesian approach is applied to infer model parameter distributions. These distributions are sampled and used to simulate from multivariate predictive densities. The method is based on a k-Nearest Neighbor estimate of the Jensen Shannon divergence between the multivariate predictive densities of competing models. We show that the method successfully uses predictive differences to enable model selection by applying it to several test cases. Because the design criterion is based on predictive distributions, which can be computed for a wide range of model quantities, the approach is very flexible. The method reveals specific combinations of experiments which improve discriminability even in cases where data is scarce. The proposed approach can be used in conjunction with existing Bayesian methodologies where (approximate) posteriors have been determined, making use of relations that exist within the inferred posteriors.

  9. Collective behaviours: from biochemical kinetics to electronic circuits

    NASA Astrophysics Data System (ADS)

    Agliari, Elena; Barra, Adriano; Burioni, Raffaella; di Biasio, Aldo; Uguzzoni, Guido

    2013-12-01

    In this work we aim to highlight a close analogy between cooperative behaviors in chemical kinetics and cybernetics; this is realized by using a common language for their description, that is mean-field statistical mechanics. First, we perform a one-to-one mapping between paradigmatic behaviors in chemical kinetics (i.e., non-cooperative, cooperative, ultra-sensitive, anti-cooperative) and in mean-field statistical mechanics (i.e., paramagnetic, high and low temperature ferromagnetic, anti-ferromagnetic). Interestingly, the statistical mechanics approach allows a unified, broad theory for all scenarios and, in particular, Michaelis-Menten, Hill and Adair equations are consistently recovered. This framework is then tested against experimental biological data with an overall excellent agreement. One step forward, we consistently read the whole mapping from a cybernetic perspective, highlighting deep structural analogies between the above-mentioned kinetics and fundamental bricks in electronics (i.e. operational amplifiers, flashes, flip-flops), so to build a clear bridge linking biochemical kinetics and cybernetics.

  10. The Toxicology and Biochemical Characterization of Cantharidin on Cydia pomonella.

    PubMed

    Wu, Zheng-Wei; Yang, Xue-Qing; Zhang, Ya-Lin

    2015-02-01

    Cantharidin, a natural toxin produced by beetles in the families Meloidae and Oedemeridae, reported to be toxic to some pests, is being developed as a biopesticide in China. This study evaluates the toxicity and biochemical characterization of cantharidin on the codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), an economically important fruit pest, under both laboratory and field conditions. Laboratory dose response bioassays showed that the LC50 value of cantharidin against neonate larvae was 0.057 mg ml(-1). Exposure of the larvae to 0.024 and 0.057 mg ml(-1) of cantharidin resulted in significant reduction in larval body weight. Neonate larvae exposed to LC10 of cantharidin showed increased glutathione S-transferase activity and significantly reduced the carboxylesterase and cytochrome P450-dependent mixed-function oxidase activities. Results also showed 16 and 25% ovicidal activity at concentrations of 0.057 and 0.14 mg ml(-1) of cantharidin, respectively. Field trials demonstrated cantharidin has a significant effect on both the first and second generations of C. pomonella larvae, but it exhibits a lower control efficiency than the chemical reference emamectin benzoate. Cantharidin may be considered a valuable tool for the control of codling moth. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Biochemical and genetic toxicity of dinotefuran on earthworms (Eisenia fetida).

    PubMed

    Liu, Tong; Wang, Xiuguo; Xu, Jinli; You, Xiangwei; Chen, Dan; Wang, Fenglong; Li, Yiqiang

    2017-06-01

    Dinotefuran is a third-generation neonicotinoid insecticide, that is considered promising due to its excellent properties. In the present work, the biochemical and genetic toxicity of dinotefuran on earthworms were evaluated at a series of environmental background concentrations. Meanwhile, the effective concentrations of dinotefuran in artificial soil during the entire exposure period were monitored. The present results showed that dinotefuran was stable in artificial soil, and its concentrations changed no more than 20% during the 28-d exposure. At 1.0 mg/kg and 2.0 mg/kg, dinotefuran induced excess generation of ROS, resulting in significant changes in antioxidant enzyme activities and functional gene expression. Moreover, lipids, proteins and nucleic acids were oxidized and damaged by the excess ROS induced by dinotefuran, resulting in serious destruction of the structure and function of cells. Additionally, the toxicity of dinotefuran showed obvious dose- and time-dependent effects. Therefore, we consider that dinotefuran may be a high-risk pollutant for earthworms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Biochemical biomarkers in algae and marine pollution: a review.

    PubMed

    Torres, Moacir A; Barros, Marcelo P; Campos, Sara C G; Pinto, Ernani; Rajamani, Satish; Sayre, Richard T; Colepicolo, Pio

    2008-09-01

    Environmental pollution by organic compounds and metals became extensive as mining and industrial activities increased in the 19th century and have intensified since then. Environmental pollutants originating from diverse anthropogenic sources have been known to possess adverse values capable of degrading the ecological integrity of marine environment. The consequences of anthropogenic contamination of marine environments have been ignored or poorly characterized with the possible exception of coastal and estuarine waters close to sewage outlets. Monitoring the impact of pollutants on aquatic life forms is challenging due to the differential sensitivities of organisms to a given pollutant, and the inability to assess the long-term effects of persistent pollutants on the ecosystem as they are bio-accumulated at higher trophic levels. Marine microalgae are particularly promising indicator species for organic and inorganic pollutants since they are typically the most abundant life forms in aquatic environments and occupy the base of the food chain. We review the effects of pollutants on the cellular biochemistry of microalgae and the biochemical mechanisms that microalgae use to detoxify or modify pollutants. In addition, we evaluate the potential uses of microalgae as bioindicator species as an early sentinel in polluted sites.

  13. Immobilised activated sludge based biosensor for biochemical oxygen demand measurement.

    PubMed

    Liu, J; Björnsson, L; Mattiasson, B

    2000-02-01

    A biochemical oxygen demand (BOD) sensor, based on an immobilised mixed culture of microorganisms in combination with a dissolved oxygen electrode, has been developed for the purpose of on-line monitoring of the biological treatment process for waste and wastewater. The sensor was designed for easy replacement of the biomembrane, thereby making it suitable for short-term use. The drawbacks of activated sludge based sensor, such as short sensor lifetime, were thereby circumvented. The sensor BOD measurements were carried out in the kinetic mode using a flow injection system, resulting in 25 s for one measurement followed by 4-8 min recovery time. Based on the results of normalised sensor responses, the OECD synthetic wastewater was considered to be a more suitable calibration solution in comparison with the GGA solution. Good agreement was achieved between the results of the sensor BOD measurement and those obtained from BOD5 analysis of a wastewater sample from a food-processing factory. Reproducibility of responses using one sensor was below +/- 5.6%, standard deviation. Reproducibility of responses using different sensors was within acceptable bias limits, viz. +/- 15% standard deviation.

  14. Achromobacter species (CDC group Vd): morphological and biochemical characterization.

    PubMed Central

    Chester, B; Cooper, L H

    1979-01-01

    Twenty-three isolates of Achromobacter species (CDC group Vd) were examined morphologically and biochemically. Gram stains revealed gram-variable bacilli frequently curved or hooked at one pole and often coryneform in shape and arrangement. Electron microscopy revealed the presence of extracellular material in polar accumulations and demonstrated the polar flagella arrangement seen by light microscopy to be lateral. Two colony types were produced; one was minute and watery at 24 h (35 degrees C) progressing to large, mucoid colonies at 48 h, and the other type was shiny, glistening, opaque but nonmucoid. All isolates grew on MacConkey agar and produced catalase, oxidase, and urease. Most grew on salmonella-shigella agar, reduced nitrate to nitrite and gas, hydrolyzed esculin, deaminated phenylalanine (2 to 4 days) and produced H2S in triple sugar iron agar (4 to 12 days). Oxidation of carbohydrates was weak, delayed, and limited to glucose and xylose. Two isolates also oxidized maltose, mannitol, and sucrose. The ability of miniaturized "nonfermenter" kits to identify Achromobacter species was tested. The Minitek (Baltimore Biological Laboratory, Cockeysville, Md.) and N/F (Corning, Roslyn, N.Y.) systems, respectively, identified 21 and 19 of the 23 isolates, whereas the Oxi/Ferm (Roche, Nutley, N.J.) identified 13 and the API 20E (Analytab Products, Plainview, N.Y.) identified only 3. Images PMID:379035

  15. Biochemical Analyses of Sorghum Varieties Reveal Differential Responses to Drought

    PubMed Central

    Ogbaga, Chukwuma C.; Stepien, Piotr; Dyson, Beth C.; Rattray, Nicholas J. W.; Ellis, David I.; Goodacre, Royston; Johnson, Giles N.

    2016-01-01

    We have examined the biochemical responses of two sorghum cultivars of differing drought tolerance, Samsorg 17 (more drought tolerant) and Samsorg 40 (less drought tolerant), to sustained drought. Plants were exposed to different degrees of drought and then maintained at that level for five days. Responses were examined in terms of metabolic changes and the expression of drought induced proteins—Heat Shock Proteins (HSPs) and dehydrins (DHNs). Generalised phenotypic changes were studied using Fourier transform infrared (FT-IR) Spectroscopy and non-targeted Gas Chromatography Mass Spectrometry (GC-MS) was employed to detect changes in metabolites, while changes in protein expression were examined using Western blot analysis. Different response profiles of metabolites, HSPs and DHNs were observed in the two cultivars. Metabolic changes involved variation in amino acids, polysaccharides and their derivatives. A total of 188 compounds, with 142 known metabolites and 46 unknown small molecules, were detected in the two sorghum varieties. Under water deficit conditions, Samsorg 17 accumulated sugars and sugar alcohols, while in Samsorg 40 amino acids increased in concentration. This study suggest that the two Sorghum varieties adopt distinct approaches in response to drought, with Samsorg 17 being better able to maintain leaf function under severe drought conditions. PMID:27153323

  16. Chemical reaction network approaches to Biochemical Systems Theory.

    PubMed

    Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R

    2015-11-01

    This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Marine biosurfaces research program

    NASA Astrophysics Data System (ADS)

    The Office of Naval Research (ONR) of the U.S. Navy is starting a basic research program to address the initial events that control colonization of surfaces by organisms in marine environments. The program “arises from the Navy's need to understand and ultimately control biofouling and biocorrosion in marine environments,” according to a Navy announcement.The program, “Biological Processes Controlling Surface Modification in the Marine Environment,” will emphasize the application of in situ techniques and modern molecular biological, biochemical, and biophysical approaches; it will also encourage the development of interdisciplinary projects. Specific areas of interest include sensing and response to environmental surface (physiology/physical chemistry), factors controlling movement to and retention at surfaces (behavior/hydrodynamics), genetic regulation of attachment (molecular genetics), and mechanisms of attachment (biochemistry/surface chemistry).

  18. Development of a system for characterizing biomass quality of lignocellulosic feedstocks for biochemical conversion

    NASA Astrophysics Data System (ADS)

    Murphy, Patrick Thomas

    The purpose of this research was twofold: (i) to develop a system for screening lignocellulosic biomass feedstocks for biochemical conversion to biofuels and (ii) to evaluate brown midrib corn stover as feedstock for ethanol production. In the first study (Chapter 2), we investigated the potential of corn stover from bm1-4 hybrids for increased ethanol production and reduced pretreatment intensity compared to corn stover from the isogenic normal hybrid. Corn stover from hybrid W64A X A619 and respective isogenic bm hybrids was pretreated by aqueous ammonia steeping using ammonium hydroxide concentrations from 0 to 30%, by weight, and the resulting residues underwent simultaneous saccharification and cofermentation (SSCF) to ethanol. Dry matter (DM) digested by SSCF increased with increasing ammonium hydroxide concentration across all genotypes (P>0.0001) from 277 g kg-1 DM in the control to 439 g kg-1 DM in the 30% ammonium hydroxide pretreatment. The bm corn stover materials averaged 373 g kg-1 DM of DM digested by SSCF compared with 335 g kg-1 DM for the normal corn stover (P<0.0001). Of the bm mutations, bm3 had (i) the greatest effect on cell-wall carbohydrate hydrolysis of corn stover, (ii) the lowest initial cell-wall carbohydrate concentration, (iii) the lowest dry matter remaining after pretreatment, and (iv) the highest amount of monosaccharides released during enzymatic hydrolysis. However, bm corn stover did not reduce the severity of aqueous ammonia steeping pretreatment needed to maximize DM hydrolysis during SSCF compared with normal corn stover. In the remaining studies (Chapters 3 thru 5), a system for analyzing the quality of lignocellulosic biomass feedstocks for biochemical conversion to biofuels (i.e., pretreatment, enzymatic hydrolysis, and fermentation) was developed. To accomplish this, a carbohydrate availability model was developed to characterize feedstock quality. The model partitions carbohydrates within a feedstock material into

  19. Biochemical process of low level radioactive liquid simulation waste containing detergent

    SciTech Connect

    Kundari, Noor Anis, E-mail: nooranis@batan.go.id; 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 elementmore » 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

  20. [Organ transplantation. One of the biochemical reasons for the race against the clock].

    PubMed

    Zénatti, M; Emeric-Blanchouin, N; Bitker, M O; Barrou, B; Lugagne, P M; Thallier, M; Aupetit-Faisant, B

    1991-11-27

    The authors have studied the subcellular functioning of human adrenal glands removed from subjects in a stage IV coma. The present study has a two-fold interest: on the one hand, it offers biochemical information on a key element in the intermediate metabolism (namely, the mitochondrial energetic metabolism, occurring in a fragile tissue which, under a state of shock, is primarily affected; the results obtained on such type of tissue may therefore be inferred to other organs); on the other hand, it allows a wider approach of the adrenal biochemical mechanisms during a stage IV coma. The mitochondrial fraction was obtained by differential centrifugation carried out immediately after organ removal. The steroid synthesis, studied using radioactive precursors, turned out to be similar to that found in other mammals. Respiratory characteristics, determined by polarography with a Clark oxygen electrode, at 37 degrees C, were satisfactory: respiratory intensity was 77.25 +/- 12.16 nanomoles O2/min/mg mitochondrial protein in the presence of succinate 15 mM and respiratory control was 1.93 +/- 0.15 in the presence of ADP 37 microM. The respiratory chain functioned in a classical manner: rotenone 25 microM did not inhibit respiration in the presence of succinate 15 mM, while it did with L-malate 15 mM. In the presence of succinate 15 mM, the respiratory intensity was inhibited at 87.4 percent and 76.7 percent by KCN 0.01 microM and antimycin A 0.09 microM respectively; with DNP 85 microM, it was multiplied by 5. However, the value of the P/O ratio was low (0.24 +/- 0.04). Under the present conditions, this may highlight the difficulty to synthetize ATP whenever neither the functioning nor the regulation of the multi-enzymatic complex accounting for oxygen consumption are affected. This result clearly confirms that the shortest possible delay between organ removal and transplantation is crucial, as the renewal of cell structures requires energy. These fundamental research

  1. [On necessity to modify biochemical methods for detecting organophosphorus componds in chemical weapons extinction objects (review of literature)].

    PubMed

    Prokofieva, D S; Shmurak, V I; Sadovnikov, S V; Gontcharov, N V

    2015-01-01

    The article covers problems of biochemical methods assessing organophosphorus toxic compounds in objects of chemical weapons extinction. The authors present results of works developing new, more specific and selective biochemical methods.

  2. Proinflammatory Cytokines, Enolase and S-100 as Early Biochemical Indicators of Hypoxic-Ischemic Encephalopathy Following Perinatal Asphyxia in Newborns.

    PubMed

    Chaparro-Huerta, Verónica; Flores-Soto, Mario Eduardo; Merin Sigala, Mario Ernesto; Barrera de León, Juan Carlos; Lemus-Varela, María de Lourdes; Torres-Mendoza, Blanca Miriam de Guadalupe; Beas-Zárate, Carlos

    2017-02-01

    Estimation of the neurological prognosis of infants suffering from perinatal asphyxia and signs of hypoxic-ischemic encephalopathy is of great clinical importance; however, it remains difficult to satisfactorily assess these signs with current standard medical practices. Prognoses are typically based on data obtained from clinical examinations and neurological tests, such as electroencephalography (EEG) and neuroimaging, but their sensitivities and specificities are far from optimal, and they do not always reliably predict future neurological sequelae. In an attempt to improve prognostic estimates, neurological research envisaged various biochemical markers detectable in the umbilical cord blood of newborns (NB). Few studies examining these biochemical factors in the whole blood of newborns exist. Thus, the aim of this study was to determine the expression and concentrations of proinflammatory cytokines (TNF-α, IL-1β and IL-6) and specific CNS enzymes (S-100 and enolase) in infants with perinatal asphyxia. These data were compared between the affected infants and controls and were related to the degree of HIE to determine their utilities as biochemical markers for early diagnosis and prognosis. The levels of the proinflammatory cytokines and enzymes were measured by enzyme-linked immunosorbent assay (ELISA) and Reverse Transcription polymerase chain reaction (RT-PCR). The expression and serum levels of the proinflammatory cytokines, enolase and S-100 were significantly increased in the children with asphyxia compared with the controls. The role of cytokines after hypoxic-ischemic insult has been determined in studies of transgenic mice that support the use of these molecules as candidate biomarkers. Similarly, S-100 and enolase are considered promising candidates because these markers have been correlated with tissue damage in different experimental models. Copyright © 2016. Published by Elsevier B.V.

  3. Study of interfacial phenomena for bio/chemical sensing applications

    NASA Astrophysics Data System (ADS)

    Min, Hwall

    This work presents the fundamental study of biological and chemical interfacial phenomena and (bio)chemical sensing applications using high frequency resonator arrays. To realize a versatile (bio)chemical sensing system for the fundamental study as well as their practical applications, the following three distinct components were studied and developed: i) detection platforms with high sensitivity, ii) novel innovative sensing materials with high selectivity, iii) analytical model for data interpretation. 8-pixel micromachined quartz crystal resonator (muQCR) arrays with a fundamental resonance frequency of 60 ¡V 90 MHz have been used to provide a reliable detection platform with high sensitivity. Room temperature ionic liquid (RTIL) has been explored and integrated into the sensing system as a smart chemical sensing material. The use of nanoporous gold (np-Au) enables the combination of the resonator and surface-enhanced Raman spectroscopy for both quantitative and qualitative measurement. A statistical model for the characterization of resonator behavior to study the protein adsorption kinetics is developed by random sequential adsorption (RSA) approach with the integration of an effective surface depletion theory. The investigation of the adsorption kinetics of blood proteins is reported as the fundamental study of biological phenomena using the proposed sensing system. The aim of this work is to study different aspects of protein adsorption and kinetics of adsorption process with blood proteins on different surfaces. We specifically focus on surface depletion effect in conjunction with the RSA model to explain the observed adsorption isotherm characteristics. A number of case studies on protein adsorption conducted using the proposed sensing system has been discussed. Effort is specifically made to understand adsorption kinetics, and the effect of surface on the adsorption process as well as the properties of the adsorbed protein layer. The second half of the

  4. Pathological and 3 Tesla Volumetric Magnetic Resonance Imaging Predictors of Biochemical Recurrence after Robotic Assisted Radical Prostatectomy: Correlation with Whole Mount Histopathology.

    PubMed

    Tan, Nelly; Shen, Luyao; Khoshnoodi, Pooria; Alcalá, Héctor E; Yu, Weixia; Hsu, William; Reiter, Robert E; Lu, David Y; Raman, Steven S

    2018-05-01

    , staging and positive surgical margins, significantly predicted biochemical recurrence. This suggests an important new imaging biomarker. Copyright © 2018 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  5. Radiological and biochemical resolution of nutritional rickets with calcium

    PubMed Central

    Oginni, L; Sharp, C; Badru, O; Risteli, J; Davie, M; Worsfold, M; Fischer, P; Oginni, L; Badru, O; Sharp, C; Davie, M; Worsfold, M; Risteli, J

    2003-01-01

    Aims: To determine the response to oral calcium in Nigerian children with rickets. Methods: In a teaching hospital in Western Nigeria, 26 children (13 boys, 13 girls, aged 2–5 years) with confirmed rickets received calcium lactate (2.7 g/day). Results: Within one month of treatment leg pain was relieved and the children were more active. The mean x ray score improved from 3.3 at baseline to 1.7 at three months and 0.9 at six months (arbitrary scoring system, 0–6). Twelve cases were healed radiologically after six months, 11 others improved considerably, two showed no significant improvement, and a non-compliant patient was worse. There was progressive reversal of biochemical features. Median plasma alkaline phosphatase fell from 519 (range 178–1078) to 283 (209–443) IU/l (p = 0.04) in four months, while mean 1,25-dihydroxyvitamin D fell from 473 (251–1057) to 281 (155–481) pmol/l (p = 0.04), and mean plasma calcium increased from 2.26 (1.63–2.54) to 2.37 (2.06–2.54) mmol/l (p = 0.13). Parathyroid hormone fell from 5.3 (0.4–21.5) to 1.7 (0.45–7.4) pmol/l. Type I collagen carboxy terminal cross linked telopeptide was very high at baseline (20 (7.2–103) to 14 (11–24) µg/l) (p = 0.03) and fell promptly to normal. Conclusion: Calcium supplementation alone effected healing of rickets in most of these Nigerian children and may provide sufficient treatment in this environment. PMID:12937108

  6. Analytical Interference by Contrast Agents in Biochemical Assays

    PubMed Central

    Fogh-Andersen, Niels; Rømsing, Janne

    2017-01-01

    Objective To provide a clinically relevant overview of the analytical interference by contrast agents (CA) in laboratory blood test measurements. Materials and Methods The effects of five CAs, gadobutrol, gadoterate meglumine, gadoxetate disodium, iodixanol, and iomeprol, were studied on the 29 most frequently performed biochemical assays. One-day-old plasma, serum, and whole blood were spiked with doses of each agent such that the gadolinium agents and the iodine agents reached concentrations of 0.5 mM and 12 mg iodine/mL, respectively. Subsequently, 12 assays were reexamined using 1/2 and 1/4 of these CA concentrations. The results were assessed statistically by a paired Student's t-test. Results Iodixanol produced a negative interference on the bicarbonate (p = 0.011), lactate dehydrogenase (p < 0.0001), and zinc (p = 0.0034) assays and a positive interference on the albumin (p = 0.0062), calcium (p < 0.0001), ionized calcium (p = 0.0086), iron (p < 0.0001), and potassium (p = 0.0003) assays. Iomeprol produced a negative interference on the bicarbonate (p = 0.0057) and magnesium (p = 0.0001) assays and a positive interference on the calcium (p < 0.0001) and potassium (p = 0.0012) assays. Gadoxetate disodium produced a negative interference on the iron (p < 0.0001) and zinc (p < 0.0001) assays and a positive interference on the sodium (p = 0.032) assay. Conclusion CAs cause analytical interference. Attention should be given to the above-mentioned analyte-CA combinations when assessing laboratory blood test results obtained after CA administration. PMID:29097910

  7. Megalencephalic leukoencephalopathy with subcortical cysts: A personal biochemical retrospective.

    PubMed

    Estévez, Raúl; Elorza-Vidal, Xabier; Gaitán-Peñas, Héctor; Pérez-Rius, Carla; Armand-Ugón, Mercedes; Alonso-Gardón, Marta; Xicoy-Espaulella, Efren; Sirisi, Sònia; Arnedo, Tanit; Capdevila-Nortes, Xavier; López-Hernández, Tania; Montolio, Marisol; Duarri, Anna; Teijido, Oscar; Barrallo-Gimeno, Alejandro; Palacín, Manuel; Nunes, Virginia

    2018-01-01

    Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a rare type of leukodystrophy characterized by dysfunction of the role of glial cells in controlling brain fluid and ion homeostasis. Patients affected by MLC present macrocephaly, cysts and white matter vacuolation, which lead to motor and cognitive impairments. To date, there is no treatment for MLC, only supportive care. MLC is caused by mutations in the MLC1 and GLIALCAM genes. MLC1 is a membrane protein with low identity to the Kv1.1 potassium channel and GlialCAM belongs to an adhesion molecule family. Both proteins form a complex with an as-yet-unknown function that is expressed mainly in the astrocytes surrounding the blood-brain barrier and in Bergmann glia. GlialCAM also acts as an auxiliary subunit of the chloride channel ClC-2, thus regulating its localization at cell-cell junctions and modifying its functional properties by affecting the common gate of ClC-2. Recent studies in Mlc1-, GlialCAM- and Clcn2-knockout mice or Mlc1-knockout zebrafish have provided fresh insight into the pathophysiology of MLC and further details about the molecular interactions between these three proteins. Additional studies have shown that GlialCAM/MLC1 also regulates other ion channels (TRPV4, VRAC) or transporters (Na + /K + -ATPase) in a not-understood manner. Furthermore, it has been shown that GlialCAM/MLC1 may influence signal transduction mechanisms, thereby affecting other proteins not related with transport such as the EGF receptor. Here, we offer a personal biochemical retrospective of the work that has been performed to gain knowledge of the pathophysiology of MLC, and we discuss future strategies that may be used to identify therapeutic solutions for MLC patients. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  8. Biochemical characterization of rice xylan O-acetyltransferases.

    PubMed

    Zhong, Ruiqin; Cui, Dongtao; Dasher, Robert L; Ye, Zheng-Hua

    2018-03-22

    Rice xylan is predominantly monoacetylated at O-2 and O-3, and 14 rice DUF231 proteins were demonstrated to be xylan acetyltransferases. Acetylated xylans are the principal hemicellulose in the cell walls of grass species. Because xylan acetylation impedes the conversion of cellulosic biomass into biofuels, knowledge on acetyltransferases catalyzing xylan acetylation in grass species will be instrumental for a better utilization of grass biomass for biofuel production. Xylan in rice (Oryza sativa) is predominantly monoacetylated at O-2 and O-3 with a total degree of acetylation of 0.19. In this report, we have characterized 14 rice DUF231 proteins (OsXOAT1 to OsXOAT14) that are phylogenetically grouped together with Arabidopsis xylan acetyltransferases ESK1 and its close homologs. Complementation analysis demonstrated that the expression of OsXOAT1 to OsXOAT7 in the Arabidopsis esk1 mutant was able to rescue its defects in 2-O- and 3-O-monoacetylation and 2,3-di-O-acetylation. Activity assay of recombinant proteins revealed that all 14 OsXOATs exhibited acetyltransferase activities capable of transferring acetyl groups from acetyl-CoA to the xylohexaose acceptor with 10 of them having high activities. Structural analysis of the OsXOAT-catalyzed products showed that the acetylated structural units consisted mainly of 2-O- and 3-O-monoacetylated xylosyl residues with a minor amount of 2,3-di-O-acetylated xylosyl units, which is consistent with the acetyl substitution pattern of rice xylan. Further kinetic studies revealed that OsXOAT1, OsXOAT2, OsXOAT5, OsXOAT6 and OsXOAT7 had high affinity toward the xylohexaose acceptor. Our results provide biochemical evidence indicating that OsXOATs are acetyltransferases involved in xylan acetylation in rice.

  9. Amish microcephaly: Long-term survival and biochemical characterization.

    PubMed

    Siu, Victoria Mok; Ratko, Suzanne; Prasad, Asuri N; Prasad, Chitra; Rupar, C Anthony

    2010-07-01

    Amish microcephaly (MCPHA, OMIM #607196) is a metabolic disorder that has been previously characterized by severe infantile lethal congenital microcephaly and alpha-ketoglutaric aciduria. All reported patients have been from the Pennsylvania Amish community and homozygous for a p.Gly177Ala mutation in SLC25A19. We present a further male patient with MCPHA born to distantly consanguineous parents in Ontario, Canada with Amish ancestors. Microcephaly was evident at 21 weeks gestation on ultrasound. At birth, the facial appearance and brain MRI scan were characteristic of MCPHA, with the additional features of partial agenesis of the corpus callosum and a closed spinal dysraphic state. Urine levels of alpha-ketoglutaric acid were normal at birth and during metabolic crisis, but were markedly elevated during a time of metabolic stability. A severe lactic acidosis was present during metabolic crises and responded to treatment with a high fat diet. At age 7 years, the child is healthy but has severe microcephaly and profound developmental delay. SLC25A19 has been described as a mitochondria inner membrane transporter for both deoxynucleotides and thiamine pyrophosphate (TPP). The biochemical phenotype of MCPHA may be attributable to decreased activity of the three mitochondrial enzymes that require TPP as a cofactor: pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, and branched chain amino acid dehydrogenase. We confirm that alpha-ketoglutaric aciduria is not a constant finding in MCPHA and suggest that a persistent lactic acidemia may be more common. The diagnosis should be considered in patients with severe congenital microcephaly, especially in association with lissencephaly, dysgenesis of the corpus callosum, or a spinal dysraphic state. (c) 2010 Wiley-Liss, Inc.

  10. Hierarchical graphs for rule-based modeling of biochemical systems.

    PubMed

    Lemons, Nathan W; Hu, Bin; Hlavacek, William S

    2011-02-02

    In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system. For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm. Hierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language

  11. Hierarchical graphs for rule-based modeling of biochemical systems

    PubMed Central

    2011-01-01

    Background In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system. Results For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm. Conclusions Hierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models

  12. Advanced nanoimprint patterning for functional electronics and biochemical sensing

    NASA Astrophysics Data System (ADS)

    Wang, Chao

    Nano-fabrication has been widely used for a variety of disciplines, including electronics, material science, nano-optics, and nano-biotechnology. This dissertation focuses on nanoimprint lithography (NIL) based novel nano-patterning techniques for fabricating functional structures, and discusses their applications in advanced electronics and high-sensitivity molecular sensing. In this dissertation, examples of using nano-fabricated structures for promising electronic applications are presented. For instance, 10 nm and 18 nm features are NIL-fabricated for Si/SiGe heterojunction tunneling transistors and graphene nano-ribbon transistors, using shadow evaporation and line-width shrinking techniques, respectively. An ultrafast laser melting based method is applied on flexible plastic substrates to correct defects of nano-features. Nano-texturing of sapphire substrate is developed to improve the light extraction of GaN light emitting diodes (LEDs) by 70 %. A novel multi-layer nano-patterned Si-mediated catalyst is discovered to grow straight and uniform Si nanowires with optimized properties in size, location, and crystallization on amorphous SiO2 substrate. Nano-structures are also functionalized into highly sensitive bio-chemical sensors. Plasmonic nano-bar antenna arrays are demonstrated to effectively sense infrared molecules >10 times better than conventional plasmonic sensors. As small as 20 nm wide nano-channel fluidic devices are developed to linearize and detect DNA molecules for potential DNA sequencing. An integrated fluidic system is built to incorporate plasmonic nano-structures for 30X-enhanced fluorescence detection of large DNA molecules.

  13. Isoprene synthase: From biochemical mechanism to emission algorithm

    NASA Astrophysics Data System (ADS)

    Fall, Ray; Wildermuth, Mary C.

    1998-10-01

    Interest in modeling isoprene emission from vegetation has led to the development and widespread use of an emission algorithm (referred to here as the G93 algorithm) that estimates instantaneous leaf isoprene emission as a function of basal isoprene emission rate with corrections for the effects of light and temperature. Here we address the question: Does the G93 algorithm reflect the biochemical and physiological processes responsible for leaf isoprene emission? In particular, the activity of the enzyme isoprene synthase, thought to be responsible for leaf isoprene emission, is examined. Recent findings show that isoprene synthase activity in willow leaves is located in chloroplasts, where both soluble and thylakoid-bound forms of the enzyme occur. Short-term changes in the activity of the isoprene synthases in response to temperature are consistent with the temperature correction term of the G93 algorithm. The light dependence term of the algorithm, which predicts light saturation of leaf isoprene emission, is consistent with the plastidic location of the isoprene synthases and light-driven processes responsible for activation of enzymes. However, the complete mechanism for the light activation of isoprene synthase(s) has not been determined. Long-term changes in the amount of active isoprene synthase(s) correlate with the variations in basal isoprene emission rate seen as leaves mature and adapt to differences in leaf growth environment. Despite these correlations, recent reports that the G93 algorithm can be used to model light-dependent formic acid, 2-methyl-3-buten-2-ol and monoterpene emissions raise questions about the algorithm's specificity and underlying assumptions.

  14. Life style and biochemical adaptation in Antarctic fishes

    NASA Astrophysics Data System (ADS)

    di Prisco, Guido

    2000-12-01

    Respiration and metabolism are under investigation in Antarctic fish, in an effort to understand the interplay between ecology and biochemical and physiological processes. Fish of the dominant suborder Notothenioidei are red-blooded, except Channichthyidae (the most phyletically derived family), whose genomes retain transcriptionally inactive DNA sequences closely related to the α-globin gene of red-blooded notothenioids and have lost the β-globin locus. Our structure/function studies on 38 of the 80 red-blooded species are aimed at correlating sequence, multiplicity and oxygen binding with ecological constraints and at obtaining phylogenetic information on evolution. For comparative purposes, this work has been extended to non-Antarctic notothenioids. All sluggish bottom dwellers have a single major hemoglobin (Hb) and often a minor, functionally similar one. Three species of the family Nototheniidae have different life styles. They have uniquely specialised oxygen-transport systems, adjusted to the mode of life of each species. Artedidraconidae have a single Hb, lacking oxygen-binding cooperativity, similar to the ancestral hemoproteins of primitive organisms. The amino acid sequences are currently used in the molecular modelling approach. The study of several enzymes with key roles in metabolism (e.g. glucose-6-phosphate dehydrogenase, L-glutamate dehydrogenase, phosphorylase b, carbonic anhydrase) indicate that some aspects of the molecular structure (e.g. molecular mass, number of subunits, amino acid sequence, temperature of irreversible heat inactivation) have been conserved during development of cold adaptation. However, high catalytic efficiency, possibly due to subtle molecular changes, is observed at low temperature.

  15. Biochemical evaluation of hyaluronic acid in breast cancer.

    PubMed

    Yahya, Raida S; El-Bindary, Ashraf A; El-Mezayen, Hatem A; Abdelmasseh, Hanaa M; Eissa, Mohammed A

    2014-01-01

    The latest experimental studies on human cancer diseases have observed the bioactive role of hyaluronic acid (HA) during carcinogenesis. HA is a component of the extra-cellular matrix (ECM). It is closely correlated with tumor cell growth, proliferation, and metastasis. The present study aimed to evaluate the biochemical role of HA and its degrading enzymes and products in breast cancer (BC) patients under therapy treatment. An ELISA method was used to determine HA levels and standard spectrophotometric techniques were used to estimate the activities of HA degrading enzymes hyaluronidase (HAS), N-acetyl-beta-D-glucosminidase (NAG), and beta-glucuronidase (beta-Glu) and the concentration of both glucoseamine (G-Amine) and glucuronic acid (GA) as degrading products in blood sera of 50 BC patients before and after chemotherapy treatment and in blood sera of 40 healthy women as controls. Statistical analyses were performed by a statistical package for social sciences (SPSS, version 15.0). Elevated serum HA levels, increased HAS, NAG, and beta-Glu activities and high concentrations of G-Amine and GA were significantly found (p < 0.001) in patients before treatment compared to controls. After all BC patients had received the first chemotherapy course, HA and its previous degrading parameters were significantly decreased (p < 0.001) in post-treated patients compared to pre-treated patients. Hyaluronic acid and its degrading enzymes and products can be considered a biomarker for early detection of recurrent disease and also for monitoring the effective therapeutic follow up of BC patients.

  16. Clinical, biochemical and molecular genetic correlations in adenylosuccinate lyase deficiency.

    PubMed

    Race, V; Marie, S; Vincent, M F; Van den Berghe, G

    2000-09-01

    Adenylosuccinate lyase (ADSL) deficiency (MIM 103050) is an autosomal recessive inborn error of purine synthesis characterized by the accumulation in body fluids of succinylaminoimidazolecarboxamide (SAICA) riboside and succinyladenosine (S-Ado), the dephosphorylated derivatives of the two substrates of the enzyme. Because ADSL-deficient patients display widely variable degrees of psychomotor retardation, we have expressed eight mutated ADSL enzymes as thioredoxin fusions and compared their properties with the clinical and biochemical characteristics of 10 patients. Three expressed mutated ADSL enzymes (M26L, R426H and T450S) were thermolabile, four (A2V, R141W, R303C and S395R) were thermostable and one (del206-218), was inactive. Thermolabile mutations decreased activities with SAICA ribotide (SAICAR) and adenylosuccinate (S-AMP) in parallel, or more with SAICAR than with S-AMP. Patients homozygous for one of these mutations, R426H, displayed similarly decreased ADSL activities in their fibroblasts, S-Ado:SAICA riboside ratios of approximately 1 in their cerebrospinal fluid and were profoundly retarded. With the exception of A2V, thermostable mutations decreased activity with S-AMP to a much more marked extent than with SAICAR. Two unrelated patients homozygous for one of the thermostable mutations, R303C, also displayed a much more marked decrease in the activity of fibroblast ADSL with S-AMP than with SAICAR, had S-Ado:SAICA riboside ratios between 3 and 4 in their cerebrospinal fluid and were mildly retarded. These results suggest that, in some cases, the genetic lesion of ADSL determines the ratio of its activities with S-AMP versus SAICAR, which in turn defines the S-Ado:SAICA riboside ratio and the patients' mental status.

  17. Economic evaluation of diagnostic localization following biochemical prostate cancer recurrence.

    PubMed

    Barocas, Daniel A; Bensink, Mark E; Berry, Kristin; Musa, Zahra; Bodnar, Carolyn; Dann, Robert; Ramsey, Scott D

    2014-10-01

    The aim of this study was to assess potential cost-effectiveness of using a prostate cancer specific functional imaging technology capable of identifying residual localized disease versus small volume metastatic disease for asymptomatic men with low but detectable prostate specific antigen (PSA) elevation following radical prostatectomy. Markov modeling was used to estimate the incremental impact on healthcare system costs (2012 USD) and quality-adjusted life-years (QALYs) of two alternative strategies: (i) using the new diagnostic to guide therapy versus (ii) current usual care-using a combination of computed tomography, magnetic resonance imaging, and bone scan to guide therapy. Costs were based on estimates from literature and Medicare reimbursement. Prostate cancer progression, survival, utilities, and background risk of all-cause mortality were obtained from literature. Base-case diagnostic sensitivity (75 percent), specificity (90 percent), and cost (USD 2,500) were provided by our industry partner GE Healthcare. The new diagnostic strategy provided an average gain of 1.83 (95 percent uncertainty interval [UI]: 1.24-2.64) QALYs with added costs of USD 15,595 (95 percent UI: USD -6,330-44,402) over 35 years. The resulting incremental cost-effectiveness ratio was USD 8,516/QALY (95 percent UI: USD -2,947-22,372). RESULTS were most influenced by the utility discounting rate and test performance characteristics; however, the new diagnostic provided clinical benefits over a wide range of sensitivity and specificity. This analysis suggests a diagnostic technology capable of identifying whether men with biochemical recurrence after radical prostatectomy have localized versus metastatic disease would be a cost-effective alternative to current standard work-up. The results support additional investment in development and validation of such a diagnostic.

  18. Biochemical and nutritional characterization of coconut (Cocos nucifera L.) haustorium.

    PubMed

    Manivannan, Arivalagan; Bhardwaj, Rakesh; Padmanabhan, Sugatha; Suneja, Poonam; Hebbar, K B; Kanade, Santosh R

    2018-01-01

    Study was conducted to determine the biochemical constituents in coconut (Cocos nucifera L.) haustorium, a spongy tissue formed during coconut germination. Results indicated that 100g of dried coconut haustorium contained 1.05±0.2% ash, 44.2±4.6% soluble sugar, 24.5±3.2% starch, 5.50±0.3% protein, 1.99±0.9% fat, 5.72±0.4% soluble dietary fibre, 20.3±1.9% insoluble dietary fibre, and 146±14.3mg phenolics. Mineral profiling showed that it contained 145±8.6, 104±9.6, 33.9±8.2, 30.9±1.9, 9.45±2.1, 0.292±0.1, 2.53±0.2 and 1.20±0.1mg of K, Mg, Ca, P, Mn, Cu, Fe and Zn, respectively. Antioxidant activity assay indicated that 100g haustorium was equivalent to 1918±173, 170±20.4, 72.8±14.7 and 860±116mg of Trolox as measured by CUPRAC, FRAP, DPPH and ABTS, respectively. Amino acid score indicated that methionine+cysteine (57.6%), phenylalanine+tyrosine (32.6%), leucine (45.7%) and isoleucine (68%) are found less in haustorium. Further studies needed in developing nutritionally balanced formulations using coconut haustorium, which will be useful for lactose intolerant children. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. A BIOCHEMICAL AND MORPHOLOGIC STUDY OF MYELINATION AND DEMYELINATION

    PubMed Central

    Majno, Guido; Karnovsky, Manfred L.

    1958-01-01

    Bilateral transection was performed on rat sciatics. At varying intervals after the operation, samples of nerve were taken both distal and proximal to the level of transection, as well as from the tissue which bridged the gap between the stumps. These samples were incubated in Warburg flasks, with glucose and a labelled lipide precursor (acetate or phosphate). The total lipides were then extracted and their radioactivity was measured. Normal rat sciatics served as controls, and the biochemical and histological findings were correlated. In the distal portion undergoing Wallerian degeneration, the lipide content began to fall before any removal of myelin could be detected histologically. It is suggested that there is a period of "non-cellular removal" prior to the physical breakdown of the myelin. Changes in respiration and in lipogenesis from acetate followed a triphasic course, and agreed with the histological findings in that after a period of predominantly passive changes (approximately 1 to 3 days) there follows a period of cellular reaction (4 to 50 days) and a period of atrophy (from 50 days onward). The incorporation of phosphate into the lipides was increased at all stages examined, even as early as 22 hours after section. This increased P32 incorporation could not be reproduced in nerves allowed to degenerate in vitro. It is suggested that the hypertrophying Schwann cells synthesize some lipide moieties at a considerably faster rate than others. Proximal to the level of transection, lipogenesis from acetate was depressed, for as long as 32 days postoperatively. It appears, therefore, that the maintenance of the myelin sheath is impaired also above the level of transection. In the "union tissue" which developed between the stumps, prior to the appearance of histologically visible myelin, lipogenesis was low; later it rose above levels for normal nerve. This pattern of lipogenesis in regenerating nerve is similar to that found in growing nerves. PMID:13563756

  20. A BIOCHEMICAL AND MORPHOLOGIC STUDY OF MYELINATION AND DEMYELINATION

    PubMed Central

    Majno, Guido; Karnovsky, Manfred L.

    1958-01-01

    Samples of normal grey matter, white matter, and peripheral nerves obtained from rats were incubated in Warburg vessels with glucose and a labelled lipide precursor (acetate, phosphate, choline, glycerol, glucose). The total lipides were then extracted and their radioactivity measured. The preparations were compared with respect to dry weight, lipide content, O2 uptake, and ability to incorporate the various substrates into the lipides. Grey matter was found to be the least damaged by incubation, white matter the most. Damage to the tissue depressed lipogenesis to a greater extent than respiration. Five substrates were compared with respect to their degree of incorporation into the lipides of the various preparations. White matter, which had a greater oxygen uptake than peripheral nerves, showed the lowest degree of incorporation for most of the substrates studied. The results suggest that there are considerable quantitative differences in the metabolism of central and peripheral myelin. In the sciatic preparations, oxygen uptake and lipogenesis from acetate were found to decrease from the proximal to the distal end of the nerve. This finding may be relevant to the pathogenesis of peripheral neuropathies. The growth and metabolic activity of peripheral nerves were studied in rats aged 1 to 500 days, and the biochemical and histological findings were correlated. The results indicated that the lipogenetic activity of the Schwann cell was lowest in the newborn animal, and reached its peak at about 20 days. Comparative data were also obtained from the cerebral cortex. The growth pattern of peripheral nerves was distinctly different from that of the brain. With respect to changes in tissue weight, respiration, and lipogenesis, growing peripheral nerve correlated with body weight, while the brain matured much more rapidly. PMID:13513913