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Sample records for bacterial dehalogenases biochemistry

  1. Role of Dehalogenases in Aerobic Bacterial Degradation of Chlorinated Aromatic Compounds

    Directory of Open Access Journals (Sweden)

    Pankaj Kumar Arora

    2014-01-01

    Full Text Available This review was conducted to provide an overview of dehalogenases involved in aerobic biodegradation of chlorinated aromatic compounds. Additionally, biochemical and molecular characterization of hydrolytic, reductive, and oxygenolytic dehalogenases was reviewed. This review will increase our understanding of the process of dehalogenation of chlorinated aromatic compounds.

  2. In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin

    Directory of Open Access Journals (Sweden)

    Raghunath Satpathy

    2016-01-01

    Full Text Available 2-Haloalkanoic acid dehalogenase enzymes have broad range of applications, starting from bioremediation to chemical synthesis of useful compounds that are widely distributed in fungi and bacteria. In the present study, a total of 81 full-length protein sequences of 2-haloalkanoic acid dehalogenase from bacteria and fungi were retrieved from NCBI database. Sequence analysis such as multiple sequence alignment (MSA, conserved motif identification, computation of amino acid composition, and phylogenetic tree construction were performed on these primary sequences. From MSA analysis, it was observed that the sequences share conserved lysine (K and aspartate (D residues in them. Also, phylogenetic tree indicated a subcluster comprised of both fungal and bacterial species. Due to nonavailability of experimental 3D structure for fungal 2-haloalkanoic acid dehalogenase in the PDB, molecular modelling study was performed for both fungal and bacterial sources of enzymes present in the subcluster. Further structural analysis revealed a common evolutionary topology shared between both fungal and bacterial enzymes. Studies on the buried amino acids showed highly conserved Leu and Ser in the core, despite variation in their amino acid percentage. Additionally, a surface exposed tryptophan was conserved in all of these selected models.

  3. A bacterial haloalkane dehalogenase gene as a negative selectable marker in Arabidopsis

    DEFF Research Database (Denmark)

    Næsted, Henrik; Fennema, M.; Hao, L.

    1999-01-01

    , including Arabidopsis, tobacco, oil seed rape and rice, do not express detectable haloalkane dehalogenase activities, and that wild-type Arabidopsis grows in the presence of DCE. In contrast, DCE applied as a volatile can be used to select on plates or in soil transgenic Arabidopsis which express dhl...

  4. Bacterial diversity and reductive dehalogenase redundancy in a 1,2-dichloroethane-degrading bacterial consortium enriched from a contaminated aquifer

    Directory of Open Access Journals (Sweden)

    Wittebolle Lieven

    2010-02-01

    Full Text Available Abstract Background Bacteria possess a reservoir of metabolic functionalities ready to be exploited for multiple purposes. The use of microorganisms to clean up xenobiotics from polluted ecosystems (e.g. soil and water represents an eco-sustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and accurate strategies for monitoring and identification of bacteria and catabolic genes involved in the degradation of xenobiotics, key processes to follow up the activities in situ. Results We report the characterization of the response of an enriched bacterial community of a 1,2-dichloroethane (1,2-DCA contaminated aquifer to the spiking with 5 mM lactate as electron donor in microcosm studies. After 15 days of incubation, the microbial community structure was analyzed. The bacterial 16S rRNA gene clone library showed that the most represented phylogenetic group within the consortium was affiliated with the phylum Firmicutes. Among them, known degraders of chlorinated compounds were identified. A reductive dehalogenase genes clone library showed that the community held four phylogenetically-distinct catalytic enzymes, all conserving signature residues previously shown to be linked to 1,2-DCA dehalogenation. Conclusions The overall data indicate that the enriched bacterial consortium shares the metabolic functionality between different members of the microbial community and is characterized by a high functional redundancy. These are fundamental features for the maintenance of the community's functionality, especially under stress conditions and suggest the feasibility of a bioremediation treatment with a potential prompt dehalogenation and a process stability over time.

  5. Biochemistry

    Science.gov (United States)

    Part of the framework for effective control or management of cyst nematodes depends upon the detailed understanding of their biology. This chapter summarizes fundamental knowledge and recent discoveries about the biochemistry of cyst nematodes, particularly areas related to lipids, carbohydrates and...

  6. Crystallization and preliminary X-ray analysis of an enantioselective halohydrin dehalogenase from Agrobacterium radiobacter AD1

    NARCIS (Netherlands)

    Jong, René M. de; Rozeboom, Henriëtte J.; Kalk, Kor H.; Tang, Lixia; Janssen, Dick B.; Dijkstra, Bauke W.

    2002-01-01

    Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. Crystals of the enantioselective halohydrin dehalogenase HheC from Agrobacterium radiobacter AD1 have been obtained at room temperature from hanging-drop

  7. Crystallization and preliminary X-ray analysis of an enantioselective halohydrin dehalogenase from Agrobacterium radiobacter AD1

    NARCIS (Netherlands)

    de Jong, RM; Rozeboom, HJ; Kalk, KH; Tang, Lixia; Janssen, DB; Dijkstra, BW

    Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. Crystals of the enantioselective halohydrin dehalogenase HheC from Agrobacterium radiobacter AD1 have been obtained at room temperature from hanging-drop

  8. Biochemistry

    International Nuclear Information System (INIS)

    Thomson, J.F.

    1975-01-01

    The contributions of the group consist of six reports. The first is concerned with recent developments in the isolation and characterization of subcellular components of mammalian cells: the inhibition by imipramine of digitonin-induced lysis of mitochondrial membranes; age-dependent changes in mitochondrial sedimentability; peroxisomal enzymes; and collaborative studies on near-uv effects on bacterial respiration, radiation effects on mouse heart mitochondria, and toxicity and distribution of liposome-encapsulated drugs. Plant physiology is the theme of the next two reports. The first describes progress in a NASA-supported program on the involvement of organelles, especially dictyosomes, in the georesponse of roots, and the second covers work principally supported by ERDA on the interaction of light and gravity on differential growth of corn roots. Progress in liposome encapsulation of drugs is presented in three contributions. The first deals with studies on the toxicity, distribution, therapeutic action, and mechanism of encapsulated cancer chemotherapeutic agents; the second with morphologic studies, based principally on electron microscopy; and the third with alteration of liposomal surface properties by varying the lipid composition, in order to modify tissue distribution

  9. Metagenome-derived haloalkane dehalogenases with novel catalytic properties

    Czech Academy of Sciences Publication Activity Database

    Kotík, Michael; Vaňáček, P.; Kuňka, A.; Prokop, Z.; Dambrovský, J.

    2017-01-01

    Roč. 101, č. 16 (2017), s. 6385-6397 ISSN 0175-7598 R&D Projects: GA ČR GAP504/10/0137; GA MŠk(CZ) LM2015047; GA MŠk(CZ) LM2015055 Institutional support: RVO:61388971 Keywords : Haloalkane dehalogenase * Metagenomic DNA * Heterologous production Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 3.420, year: 2016

  10. Design of a Comprehensive Biochemistry and Molecular Biology Experiment: Phase Variation Caused by Recombinational Regulation of Bacterial Gene Expression

    Science.gov (United States)

    Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

    2014-01-01

    Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about "Salmonella enterica" serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation,…

  11. A ten-week biochemistry lab project studying wild-type and mutant bacterial alkaline phosphatase.

    Science.gov (United States)

    Witherow, D Scott

    2016-11-12

    This work describes a 10-week laboratory project studying wild-type and mutant bacterial alkaline phosphatase, in which students purify, quantitate, and perform kinetic assays on wild-type and selected mutants of the enzyme. Students also perform plasmid DNA purification, digestion, and gel analysis. In addition to simply learning important techniques, students acquire novel biochemical data in their kinetic analysis of mutant enzymes. The experiments are designed to build on students' work from week to week in a way that requires them to apply quantitative analysis and reasoning skills, reinforcing traditional textbook biochemical concepts. Students are assessed through lab reports focused on journal style writing, quantitative and conceptual question sheets, and traditional exams. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):555-564, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

  12. Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

    Science.gov (United States)

    Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

    2017-03-01

    To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.

  13. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications

    Directory of Open Access Journals (Sweden)

    Thiau-Fu Ang

    2018-05-01

    Full Text Available The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.

  14. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications.

    Science.gov (United States)

    Ang, Thiau-Fu; Maiangwa, Jonathan; Salleh, Abu Bakar; Normi, Yahaya M; Leow, Thean Chor

    2018-05-07

    The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.

  15. Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation.

    Science.gov (United States)

    Payne, Karl Ap; Quezada, Carolina P; Fisher, Karl; Dunstan, Mark S; Collins, Fraser A; Sjuts, Hanno; Levy, Colin; Hay, Sam; Rigby, Stephen Ej; Leys, David

    2015-01-22

    Organohalide chemistry underpins many industrial and agricultural processes, and a large proportion of environmental pollutants are organohalides. Nevertheless, organohalide chemistry is not exclusively of anthropogenic origin, with natural abiotic and biological processes contributing to the global halide cycle. Reductive dehalogenases are responsible for biological dehalogenation in organohalide respiring bacteria, with substrates including polychlorinated biphenyls or dioxins. Reductive dehalogenases form a distinct subfamily of cobalamin (B12)-dependent enzymes that are usually membrane associated and oxygen sensitive, hindering detailed studies. Here we report the characterization of a soluble, oxygen-tolerant reductive dehalogenase and, by combining structure determination with EPR (electron paramagnetic resonance) spectroscopy and simulation, show that a direct interaction between the cobalamin cobalt and the substrate halogen underpins catalysis. In contrast to the carbon-cobalt bond chemistry catalysed by the other cobalamin-dependent subfamilies, we propose that reductive dehalogenases achieve reduction of the organohalide substrate via halogen-cobalt bond formation. This presents a new model in both organohalide and cobalamin (bio)chemistry that will guide future exploitation of these enzymes in bioremediation or biocatalysis.

  16. A Ten-Week Biochemistry Lab Project Studying Wild-Type and Mutant Bacterial Alkaline Phosphatase

    Science.gov (United States)

    Witherow, D. Scott

    2016-01-01

    This work describes a 10-week laboratory project studying wild-type and mutant bacterial alkaline phosphatase, in which students purify, quantitate, and perform kinetic assays on wild-type and selected mutants of the enzyme. Students also perform plasmid DNA purification, digestion, and gel analysis. In addition to simply learning important…

  17. Weak Activity of Haloalkane Dehalogenase LinB with 1,2,3-Trichloropropane Revealed by X-Ray Crystallography and Microcalorimetry▿

    OpenAIRE

    Monincová, Marta; Prokop, Zbyněk; Vévodová, Jitka; Nagata, Yuji; Damborský, Jiří

    2007-01-01

    1,2,3-Trichloropropane (TCP) is a highly toxic and recalcitrant compound. Haloalkane dehalogenases are bacterial enzymes that catalyze the cleavage of a carbon-halogen bond in a wide range of organic halogenated compounds. Haloalkane dehalogenase LinB from Sphingobium japonicum UT26 has, for a long time, been considered inactive with TCP, since the reaction cannot be easily detected by conventional analytical methods. Here we demonstrate detection of the weak activity (kcat = 0.005 s−1) of Li...

  18. Utilization of Glyphosate as Phosphate Source: Biochemistry and Genetics of Bacterial Carbon-Phosphorus Lyase

    Science.gov (United States)

    Zechel, David L.; Jochimsen, Bjarne

    2014-01-01

    SUMMARY After several decades of use of glyphosate, the active ingredient in weed killers such as Roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. Glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. This is in contrast to the general phosphorus compounds utilized and metabolized by microorganisms. Here phosphorus is found as phosphoric acid or phosphate ion, phosphoric acid esters, or phosphoric acid anhydrides. The latter compounds contain phosphorus that is bound only to oxygen. Hydrolytic, oxidative, and radical-based mechanisms for carbon-phosphorus bond cleavage have been described. This review deals with the radical-based mechanism employed by the carbon-phosphorus lyase of the carbon-phosphorus lyase pathway, which involves reactions for activation of phosphonate, carbon-phosphorus bond cleavage, and further chemical transformation before a useful phosphate ion is generated in a series of seven or eight enzyme-catalyzed reactions. The phn genes, encoding the enzymes for this pathway, are widespread among bacterial species. The processes are described with emphasis on glyphosate as a substrate. Additionally, the catabolism of glyphosate is intimately connected with that of aminomethylphosphonate, which is also treated in this review. Results of physiological and genetic analyses are combined with those of bioinformatics analyses. PMID:24600043

  19. A review on non-stereospecific haloalkanoic acid dehalogenases ...

    African Journals Online (AJOL)

    Haloalkanoic acid dehalogenases remove halides from organic haloacids and have potential as bioremediation agents. DehE from Rhizobium sp. RC1, DehI from Pseudomonas putida PP3 and D,LDEX 113 from Pseudomonas sp. 113 are non-stereospecific dehalogenases that invert the configurations of D- and L- ...

  20. Biochemistry Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Biochemistry Facility provides expert services and consultation in biochemical enzyme assays and protein purification. The facility currently features 1) Liquid...

  1. Haloalkane hydrolysis with an immobilized haloalkane dehalogenase.

    Science.gov (United States)

    Dravis, B C; Swanson, P E; Russell, A J

    2001-11-20

    Haloalkane dehalogenase from Rhodococcus rhodochrous was covalently immobilized onto a polyethyleneimine impregnated gamma-alumina support. The dehalogenating enzyme was found to retain greater than 40% of its original activity after immobilization, displaying an optimal loading (max. activity/supported protein) of 70 to 75 mg/g with an apparent maximum (max. protein/support) of 156 mg/g. The substrate, 1,2,3-trichloropropane, was found to favorably partition (adsorb) onto the inorganic alumina carrier (10 to 20 mg/g), thereby increasing the local reactant concentration with respect to the catalyst's environment, whereas the product, 2,3-dichloropropan-1-ol, demonstrated no affinity. Additionally, the inorganic alumina support exhibited no adverse effects because of solvent/component incompatibilities or deterioration due to pH variance (pH 7.0 to 10.5). As a result of the large surface area to volume ratio of the support matrix and the accessibility of the bound protein, the immobilized biocatalyst was not subject to internal mass transfer limitations. External diffusional restrictions could be eliminated with simple agitation (mixing speed: 50 rpm; flux: 4.22 cm/min). The pH-dependence of the immobilized dehalogenase was essentially the same as that for the native enzyme. Finally, both the thermostability and resistance toward inactivation by organic solvent were improved by more than an order of magnitude after immobilization. Copyright 2001 John Wiley & Sons, Inc.

  2. Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene

    OpenAIRE

    Bosma, Tjibbe; Damborský, Jiří; Stucki, Gerhard; Janssen, Dick B.

    2002-01-01

    Using a combined strategy of random mutagenesis of haloalkane dehalogenase and genetic engineering of a chloropropanol-utilizing bacterium, we constructed an organism that is capable of growth on 1,2,3-trichloropropane (TCP). This highly toxic and recalcitrant compound is a waste product generated from the manufacture of the industrial chemical epichlorohydrin. Attempts to select and enrich bacterial cultures that can degrade TCP from environmental samples have repeatedly been unsuccessful, p...

  3. Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene.

    Science.gov (United States)

    Bosma, Tjibbe; Damborský, Jirí; Stucki, Gerhard; Janssen, Dick B

    2002-07-01

    Using a combined strategy of random mutagenesis of haloalkane dehalogenase and genetic engineering of a chloropropanol-utilizing bacterium, we constructed an organism that is capable of growth on 1,2,3-trichloropropane (TCP). This highly toxic and recalcitrant compound is a waste product generated from the manufacture of the industrial chemical epichlorohydrin. Attempts to select and enrich bacterial cultures that can degrade TCP from environmental samples have repeatedly been unsuccessful, prohibiting the development of a biological process for groundwater treatment. The critical step in the aerobic degradation of TCP is the initial dehalogenation to 2,3-dichloro-1-propanol. We used random mutagenesis and screening on eosin-methylene blue agar plates to improve the activity on TCP of the haloalkane dehalogenase from Rhodococcus sp. m15-3 (DhaA). A second-generation mutant containing two amino acid substitutions, Cys176Tyr and Tyr273Phe, was nearly eight times more efficient in dehalogenating TCP than wild-type dehalogenase. Molecular modeling of the mutant dehalogenase indicated that the Cys176Tyr mutation has a global effect on the active-site structure, allowing a more productive binding of TCP within the active site, which was further fine tuned by Tyr273Phe. The evolved haloalkane dehalogenase was expressed under control of a constitutive promoter in the 2,3-dichloro-1-propanol-utilizing bacterium Agrobacterium radiobacter AD1, and the resulting strain was able to utilize TCP as the sole carbon and energy source. These results demonstrated that directed evolution of a key catabolic enzyme and its subsequent recruitment by a suitable host organism can be used for the construction of bacteria for the degradation of a toxic and environmentally recalcitrant chemical.

  4. Kinetic mechanism and enantioselectivity of halohydrin dehalogenase from Agrobacterium radiobacter

    NARCIS (Netherlands)

    Tang, Lixia; Lutje Spelberg, Jeffrey H.; Fraaije, Marco W.; Janssen, DB

    2003-01-01

    Halohydrin dehalogenase (HheC) from Agrobacterium radiobacter AD1 catalyzes the reversible intramolecular nucleophilic displacement of a halogen by a hydroxyl group in vicinal haloalcohols, producing the corresponding epoxides. The enzyme displays high enantioselectivity toward some aromatic

  5. Relationship of sediment-biochemistry, bacterial morphology, and activity to geotechnical properties in the central Indian Basin

    Digital Repository Service at National Institute of Oceanography (India)

    Naik, S.S.; Khadge, N.H.; Valsangkar, A.B.; Das, A.; Fernandes, C.E.G.; LokaBharathi, P.A.

    of bacterial community to artificially simulated disturbance (Nair et al., 2000; Raghukumar et al., 2001a, b) and long-term response to the same (Raghukumar et al., 2006). Specific observations of deep-sea cultures and their role in ammonia oxidation under... et al., 1990; Trueblood, 1993; Fukushima, 1995; Tkatchenko et al., 1996; Sharma, 2005). Earlier studies on the effect of artificial disturbance on microbiology of deep-sea sediments were restricted to culturable fraction and suggested the revival...

  6. Chloromuconolactone dehalogenase ClcF of actinobacteria.

    Science.gov (United States)

    Solyanikova, Inna P; Plotnikova, Elena G; Shumkova, Ekaterina S; Robota, Irina V; Prisyazhnaya, Natalya V; Golovleva, Ludmila A

    2014-01-01

    This work investigated the distribution of the clcF gene in actinobacteria isolated from different ecotopes. The gene encodes chloromuconolactone dehalogenase (CMLD) ClcF, the enzyme found to date in only one representative of Gram-positive bacteria, Rhodococcus opacus 1CP, adapted to 2-chlorophenol (2CP). Using primers specific to the clcF gene, from the DNA matrix of rhodococcal strains closely related to species Rhodococcus wratislaviensis (P1, P12, P13, P20, G10, KT112, KT723, BO1) we obtained PCR products whose nucleotide sequences were 100% identical to that of the clcF gene from strain R. opacus 1CP. CMLDs isolated from the biomass of strains Rhodococcus spp. G10 and P1 grown on 2CP did not differ by their subunit molecular mass deduced from the known amino acid sequence of the clcF gene from the ClcF of strain R. opacus 1CP. Matrix-assisted laser dissociation/ionization time-of-flight mass spectrometry showed the presence of a peak with m/z 11,194-11,196 Da both in whole cells and in protein solutions with a ClcF activity. Thus, we have first time shown the distribution of ClcF among actinobacteria isolated from geographically distant habitats.

  7. Nutritional Biochemistry

    Science.gov (United States)

    Smith, Scott M.

    2010-01-01

    This slide presentation reviews some of the effects that space flight has on humans nutritional biochemistry. Particular attention is devoted to the study of protein breakdown, inflammation, hypercatabolism, omega 3 fatty acids, vitamin D, calcium, urine, folate and nutrient stability of certain vitamins, the fluid shift and renal stone risk, acidosis, iron/hematology, and the effects on bone of dietary protein, potassium. inflammation, and omega-3 fatty acids

  8. Biochemistry engineering

    International Nuclear Information System (INIS)

    Jang, Ho Nam

    1993-01-01

    This deals with biochemistry engineering with nine chapters. It explains bionics on development and prospect, basics of life science on classification and structure, enzyme and metabolism, fundamentals of chemical engineering on viscosity, shear rate, PFR, CSTR, mixing, dispersion, measurement and response, Enzyme kinetics, competitive inhibition, pH profile, temperature profile, stoichiometry and fermentation kinetics, bio-reactor on Enzyme-reactor and microorganism-reactor, measurement and processing on data acquisition and data processing, separation and purification, waste water treatment and economics of bionics process.

  9. Conformational Changes Allow Processing of Bulky Substrates by a Haloalkane Dehalogenase with a Small and Buried Active Site.

    Science.gov (United States)

    Kokkonen, Piia; Bednar, David; Dockalova, Veronika; Prokop, Zbynek; Damborsky, Jiri

    2018-06-01

    Haloalkane dehalogenases catalyze the hydrolysis of halogen-carbon bonds in organic halogenated compounds and as such are of great utility as biocatalysts. The crystal structures of the haloalkane dehalogenase DhlA from the bacterium from Xanthobacter autotrophicus GJ10, specifically adapted for the conversion of the small 1,2-dichloroethane (DCE) molecule, display the smallest catalytic site (110 Å3) within this enzyme family. However, during a substrate-specificity screening, we noted that DhlA can catalyze the conversion of far bulkier substrates, such as the 4-(bromomethyl)-6,7-dimethoxy-coumarin (220 Å3). This large substrate cannot bind to DhlA without conformational alterations. These conformational changes have been previously inferred from kinetic analysis, but their structural basis has not been understood. Using molecular dynamic simulations, we demonstrate here the intrinsic flexibility of part of the cap domain that allows DhlA to accommodate bulky substrates. The simulations displayed two routes for transport of substrates to the active site, one of which requires the conformational change and which is likely the route for bulky substrates. These results provide insights into the structure-dynamics-function relationships in enzymes with deeply buried active sites. Moreover, understanding the structural basis for the molecular adaptation of DhlA to DCE introduced into the biosphere during the industrial revolution provides a valuable lesson in enzyme design by nature. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane

    KAUST Repository

    Merlino, Giuseppe

    2015-03-06

    The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales . Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community.

  11. Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane

    KAUST Repository

    Merlino, Giuseppe; Balloi, Annalisa; Marzorati, Massimo; Mapelli, Francesca; Rizzi, Aurora; Lavazza, Davide; de Ferra, Francesca; Carpani, Giovanna; Daffonchio, Daniele

    2015-01-01

    The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales . Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community.

  12. Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetry.

    Science.gov (United States)

    Monincová, Marta; Prokop, Zbynek; Vévodová, Jitka; Nagata, Yuji; Damborsky, Jirí

    2007-03-01

    1,2,3-Trichloropropane (TCP) is a highly toxic and recalcitrant compound. Haloalkane dehalogenases are bacterial enzymes that catalyze the cleavage of a carbon-halogen bond in a wide range of organic halogenated compounds. Haloalkane dehalogenase LinB from Sphingobium japonicum UT26 has, for a long time, been considered inactive with TCP, since the reaction cannot be easily detected by conventional analytical methods. Here we demonstrate detection of the weak activity (k(cat) = 0.005 s(-1)) of LinB with TCP using X-ray crystallography and microcalorimetry. This observation makes LinB a useful starting material for the development of a new biocatalyst toward TCP by protein engineering. Microcalorimetry is proposed to be a universal method for the detection of weak enzymatic activities. Detection of these activities is becoming increasingly important for engineering novel biocatalysts using the scaffolds of proteins with promiscuous activities.

  13. Weak Activity of Haloalkane Dehalogenase LinB with 1,2,3-Trichloropropane Revealed by X-Ray Crystallography and Microcalorimetry▿

    Science.gov (United States)

    Monincová, Marta; Prokop, Zbyněk; Vévodová, Jitka; Nagata, Yuji; Damborský, Jiří

    2007-01-01

    1,2,3-Trichloropropane (TCP) is a highly toxic and recalcitrant compound. Haloalkane dehalogenases are bacterial enzymes that catalyze the cleavage of a carbon-halogen bond in a wide range of organic halogenated compounds. Haloalkane dehalogenase LinB from Sphingobium japonicum UT26 has, for a long time, been considered inactive with TCP, since the reaction cannot be easily detected by conventional analytical methods. Here we demonstrate detection of the weak activity (kcat = 0.005 s−1) of LinB with TCP using X-ray crystallography and microcalorimetry. This observation makes LinB a useful starting material for the development of a new biocatalyst toward TCP by protein engineering. Microcalorimetry is proposed to be a universal method for the detection of weak enzymatic activities. Detection of these activities is becoming increasingly important for engineering novel biocatalysts using the scaffolds of proteins with promiscuous activities. PMID:17259360

  14. Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

    Science.gov (United States)

    Kuznetsova, Ekaterina; Nocek, Boguslaw; Brown, Greg; Makarova, Kira S; Flick, Robert; Wolf, Yuri I; Khusnutdinova, Anna; Evdokimova, Elena; Jin, Ke; Tan, Kemin; Hanson, Andrew D; Hasnain, Ghulam; Zallot, Rémi; de Crécy-Lagard, Valérie; Babu, Mohan; Savchenko, Alexei; Joachimiak, Andrzej; Edwards, Aled M; Koonin, Eugene V; Yakunin, Alexander F

    2015-07-24

    The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. A 13-week research-based biochemistry laboratory curriculum.

    Science.gov (United States)

    Lefurgy, Scott T; Mundorff, Emily C

    2017-09-01

    Here, we present a 13-week research-based biochemistry laboratory curriculum designed to provide the students with the experience of engaging in original research while introducing foundational biochemistry laboratory techniques. The laboratory experience has been developed around the directed evolution of an enzyme chosen by the instructor, with mutations designed by the students. Ideal enzymes for this curriculum are able to be structurally modeled, solubly expressed, and monitored for activity by UV/Vis spectroscopy, and an example curriculum for haloalkane dehalogenase is given. Unique to this curriculum is a successful implementation of saturation mutagenesis and high-throughput screening of enzyme function, along with bioinformatics analysis, homology modeling, structural analysis, protein expression and purification, polyacrylamide gel electrophoresis, UV/Vis spectroscopy, and enzyme kinetics. Each of these techniques is carried out using a novel student-designed mutant library or enzyme variant unique to the lab team and, importantly, not described previously in the literature. Use of a well-established set of protocols promotes student data quality. Publication may result from the original student-generated hypotheses and data, either from the class as a whole or individual students that continue their independent projects upon course completion. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):437-448, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  16. Biochemistry of Catabolic Reductive Dehalogenation.

    Science.gov (United States)

    Fincker, Maeva; Spormann, Alfred M

    2017-06-20

    A wide range of phylogenetically diverse microorganisms couple the reductive dehalogenation of organohalides to energy conservation. Key enzymes of such anaerobic catabolic pathways are corrinoid and Fe-S cluster-containing, membrane-associated reductive dehalogenases. These enzymes catalyze the reductive elimination of a halide and constitute the terminal reductases of a short electron transfer chain. Enzymatic and physiological studies revealed the existence of quinone-dependent and quinone-independent reductive dehalogenases that are distinguishable at the amino acid sequence level, implying different modes of energy conservation in the respective microorganisms. In this review, we summarize current knowledge about catabolic reductive dehalogenases and the electron transfer chain they are part of. We review reaction mechanisms and the role of the corrinoid and Fe-S cluster cofactors and discuss physiological implications.

  17. Macromolecular interactions of the bacterial division FtsZ protein: from quantitative biochemistry and crowding to reconstructing minimal divisomes in the test tube.

    Science.gov (United States)

    Rivas, Germán; Alfonso, Carlos; Jiménez, Mercedes; Monterroso, Begoña; Zorrilla, Silvia

    2013-06-01

    The division of Escherichia coli is an essential process strictly regulated in time and space. It requires the association of FtsZ with other proteins to assemble a dynamic ring during septation, forming part of the functionally active division machinery, the divisome. FtsZ reversibly interacts with FtsA and ZipA at the cytoplasmic membrane to form a proto-ring, the first molecular assembly of the divisome, which is ultimately joined by the rest of the division-specific proteins. In this review we summarize the quantitative approaches used to study the activity, interactions, and assembly properties of FtsZ under well-defined solution conditions, with the aim of furthering our understanding of how the behavior of FtsZ is controlled by nucleotides and physiological ligands. The modulation of the association and assembly properties of FtsZ by excluded-volume effects, reproducing in part the natural crowded environment in which this protein has evolved to function, will be described. The subsequent studies on the reactivity of FtsZ in membrane-like systems using biochemical, biophysical, and imaging technologies are reported. Finally, we discuss the experimental challenges to be met to achieve construction of the minimum protein set needed to initiate bacterial division, without cells, in a cell-like compartment. This integrated approach, combining quantitative and synthetic strategies, will help to support (or dismiss) conclusions already derived from cellular and molecular analysis and to complete our understanding on how bacterial division works.

  18. Identification of Multiple Dehalogenase Genes Involved in Tetrachloroethene-to-Ethene Dechlorination in a Dehalococcoides-Dominated Enrichment Culture

    Directory of Open Access Journals (Sweden)

    Mohamed Ismaeil

    2017-01-01

    Full Text Available Chloroethenes (CEs are widespread groundwater toxicants that are reductively dechlorinated to nontoxic ethene (ETH by members of Dehalococcoides. This study established a Dehalococcoides-dominated enrichment culture (designated “YN3” that dechlorinates tetrachloroethene (PCE to ETH with high dechlorination activity, that is, complete dechlorination of 800 μM PCE to ETH within 14 days in the presence of Dehalococcoides species at 5.7±1.9×107 copies of 16S rRNA gene/mL. The metagenome of YN3 harbored 18 rdhA genes (designated YN3rdhA1–18 encoding the catalytic subunit of reductive dehalogenase (RdhA, four of which were suggested to be involved in PCE-to-ETH dechlorination based on significant increases in their transcription in response to CE addition. The predicted proteins for two of these four genes, YN3RdhA8 and YN3RdhA16, showed 94% and 97% of amino acid similarity with PceA and VcrA, which are well known to dechlorinate PCE to trichloroethene (TCE and TCE to ETH, respectively. The other two rdhAs, YN3rdhA6 and YN3rdhA12, which were never proved as rdhA for CEs, showed particularly high transcription upon addition of vinyl chloride (VC, with 75±38 and 16±8.6 mRNA copies per gene, respectively, suggesting their possible functions as novel VC-reductive dehalogenases. Moreover, metagenome data indicated the presence of three coexisting bacterial species, including novel species of the genus Bacteroides, which might promote CE dechlorination by Dehalococcoides.

  19. Biochemistry Instrumentation Core Technology Center

    Data.gov (United States)

    Federal Laboratory Consortium — The UCLA-DOE Biochemistry Instrumentation Core Facility provides the UCLA biochemistry community with easy access to sophisticated instrumentation for a wide variety...

  20. Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining.

    Science.gov (United States)

    Schallmey, Marcus; Koopmeiners, Julia; Wells, Elizabeth; Wardenga, Rainer; Schallmey, Anett

    2014-12-01

    Halohydrin dehalogenases are very rare enzymes that are naturally involved in the mineralization of halogenated xenobiotics. Due to their catalytic potential and promiscuity, many biocatalytic reactions have been described that have led to several interesting and industrially important applications. Nevertheless, only a few of these enzymes have been made available through recombinant techniques; hence, it is of general interest to expand the repertoire of these enzymes so as to enable novel biocatalytic applications. After the identification of specific sequence motifs, 37 novel enzyme sequences were readily identified in public sequence databases. All enzymes that could be heterologously expressed also catalyzed typical halohydrin dehalogenase reactions. Phylogenetic inference for enzymes of the halohydrin dehalogenase enzyme family confirmed that all enzymes form a distinct monophyletic clade within the short-chain dehydrogenase/reductase superfamily. In addition, the majority of novel enzymes are substantially different from previously known phylogenetic subtypes. Consequently, four additional phylogenetic subtypes were defined, greatly expanding the halohydrin dehalogenase enzyme family. We show that the enormous wealth of environmental and genome sequences present in public databases can be tapped for in silico identification of very rare but biotechnologically important biocatalysts. Our findings help to readily identify halohydrin dehalogenases in ever-growing sequence databases and, as a consequence, make even more members of this interesting enzyme family available to the scientific and industrial community. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  1. Reproduction, physiology and biochemistry

    Science.gov (United States)

    This chapter summarizes fundamental knowledge and recent discoveries about the reproduction, physiology and biochemistry of plant-parasitic nematodes. Various types of reproduction are reviewed, including sexual reproduction and mitotic and meiotic parthenogenesis. Although much is known about the p...

  2. Purification and characterization of the 3-chloro-4-hydroxy-phenylacetate reductive dehalogenase of Desulfitobacterium hafniense

    DEFF Research Database (Denmark)

    Christensen, Nina; Ahring, Birgitte Kiær; Wohlfarth, Gert

    1998-01-01

    The membrane-bound 3-chloro-4-hydroxyphenylacetate (Cl-OHPA) reductive dehalogenase from the chlorophenol- educing anaerobe Desulfitobacterium hafniense was purified 11.3-fold to apparent homogeneity in the presence of the detergent CHAPS. The purified dehalogenase catalyzed the reductive...... dechlorination of Cl-OHPA to 4-hydroxyphenylacetate with reduced methyl viologen as the electron donor at a specific activity of 103.2 nkat/mg protein. SDS-PAGErevealed a single protein band with an apparent molecular mass of 46.5 kDa. The enzyme contained 0.68±0.2 mol corrinoid, 12.0±0.7 mol iron, and 13...

  3. Dynamics and hydration explain failed functional transformation in dehalogenase design

    Czech Academy of Sciences Publication Activity Database

    Sýkora, Jan; Brezovský, J.; Koudeláková, T.; Lahoda, M.; Fořtová, A.; Chernovets, Tatsiana; Chaloupková, R.; Štěpánková, V.; Prokop, Z.; Kutá-Smatanová, Ivana; Hof, Martin; Damborský, J.

    2014-01-01

    Roč. 10, č. 6 (2014), s. 428-430 ISSN 1552-4450 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388955 ; RVO:67179843 Keywords : fluorescence * dynamics * hydration Subject RIV: CF - Physical ; Theoretical Chemistry ; CE - Biochemistry (UEK-B) Impact factor: 12.996, year: 2014

  4. Characterization of the corrinoid iron-sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus

    NARCIS (Netherlands)

    Maillard, J.; Schumacher, W.; Vazquez, F.; Regeard, C.; Hagen, W.R.; Holliger, C.

    2003-01-01

    The membrane-bound tetrachloroethene reductive dehalogenase (PCE-RDase) (PceA; EC 1.97.1.8), the terminal component of the respiratory chain of Dehalobacter restrictus, was purified 25-fold to apparent electrophoretic homogeneity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a

  5. Directed Evolution Strategies for Enantiocomplementary Haloalkane Dehalogenases : From Chemical Waste to Enantiopure Building Blocks

    NARCIS (Netherlands)

    van Leeuwen, Jan G. E.; Wijma, Hein J.; Floor, Robert J.; van der Laan, Jan-Metske; Janssen, Dick B.

    2012-01-01

    We used directed evolution to obtain enantiocomplementary haloalkane dehalogenase variants that convert the toxic waste compound 1,2,3-trichloropropane (TCP) into highly enantioenriched (R)- or (S)-2,3-dichloropropan-1-ol, which can easily be converted into optically active

  6. Crystal Structures of Intermediates in the Dehalogenation of Haloalkanoates by L-2-Haloacid Dehalogenase

    NARCIS (Netherlands)

    Ridder, Ivo S.; Rozeboom, Henriëtte J.; Kalk, Kor H.; Dijkstra, Bauke W.

    1999-01-01

    The L-2-haloacid dehalogenase from the 1,2-dichloroethane-degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoates to their corresponding D-2-hydroxyalkanoates, with inversion of the configuration at the C2 atom. The structure of the

  7. Kinetics of halide release of haloalkane dehalogenase : Evidence for a slow conformational change

    NARCIS (Netherlands)

    Schanstra, JP; Janssen, DB; Schanstra, Joost P.

    1996-01-01

    Haloalkane dehalogenase converts haloalkanes to their corresponding alcohols and halides, The reaction mechanism involves the formation of a covalent alkyl-enzyme complex which is hydrolyzed by water. The active site is a hydrophobic cavity buried between the main domain and the cap domain of the

  8. REPLACEMENT OF TRYPTOPHAN RESIDUES IN HALOALKANE DEHALOGENASE REDUCES HALIDE BINDING AND CATALYTIC ACTIVITY

    NARCIS (Netherlands)

    KENNES, C; PRIES, F; KROOSHOF, GH; BOKMA, E; Kingma, Jacob; JANSSEN, DB

    1995-01-01

    Haloalkane dehalogenase catalyzes the hydrolytic cleavage of carbon-halogen bonds in short-chain haloalkanes. Two tryptophan residues of the enzyme (Trp125 and Trp175) form a halide-binding site in the active-site cavity, and were proposed to play a role in catalysis. The function of these residues

  9. Repositioning the catalytic triad aspartic acid of haloalkane dehalogenase : Effects on stability, kinetics, and structure

    NARCIS (Netherlands)

    Krooshof, Geja H.; Kwant, Edwin M.; Damborský, Jiří; Koča, Jaroslav; Janssen, Dick B.

    1997-01-01

    Haloalkane dehalogenase (DhlA) catalyzes the hydrolysis of haloalkanes via an alkyl-enzyme intermediate. The covalent intermediate, which is formed by nucleophilic substitution with Asp124, is hydrolyzed by a water molecule that is activated by His289. The role of Asp260, which is the third member

  10. Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with degenerate primer PCR screens.

    Directory of Open Access Journals (Sweden)

    Laura Audrey Hug

    2013-11-01

    Full Text Available Reductive dehalogenases are the critical enzymes for anaerobic organohalide respiration, a microbial metabolic process that has been harnessed for bioremediation efforts to resolve chlorinated solvent contamination in groundwater and is implicated in the global halogen cycle. Reductive dehalogenase sequence diversity is informative for the dechlorination potential of the site or enrichment culture. A suite of degenerate PCR primers targeting a comprehensive curated set of reductive dehalogenase genes was designed and applied to twelve DNA samples extracted from contaminated and pristine sites, as well as six enrichment cultures capable of reducing chlorinated compounds to non-toxic end-products. The amplified gene products from four environmental sites and two enrichment cultures were sequenced using Illumina HiSeq, and the reductive dehalogenase complement of each sample determined. The results indicate that the diversity of the reductive dehalogenase gene family is much deeper than is currently accounted for: one-third of the translated proteins have less than 70% pairwise amino acid identity to database sequences. Approximately 60% of the sequenced reductive dehalogenase genes were broadly distributed, being identified in four or more samples, and often in previously sequenced genomes as well. In contrast, 17% of the sequenced reductive dehalogenases were unique, present in only a single sample and bearing less than 90% pairwise amino acid identity to any previously identified proteins. Many of the broadly distributed reductive dehalogenases are uncharacterized in terms of their substrate specificity, making these intriguing targets for further biochemical experimentation. Finally, comparison of samples from a contaminated site and an enrichment culture derived from the same site eight years prior allowed examination of the effect of the enrichment process.

  11. Insights into the molecular mechanism of dehalogenation catalyzed by D-2-haloacid dehalogenase from crystal structures.

    Science.gov (United States)

    Wang, Yayue; Feng, Yanbin; Cao, Xupeng; Liu, Yinghui; Xue, Song

    2018-01-23

    D-2-haloacid dehalogenases (D-DEXs) catalyse the hydrolytic dehalogenation of D-2-haloacids, releasing halide ions and producing the corresponding 2-hydroxyacids. A structure-guided elucidation of the catalytic mechanism of this dehalogenation reaction has not been reported yet. Here, we report the catalytic mechanism of a D-DEX, HadD AJ1 from Pseudomonas putida AJ1/23, which was elucidated by X-ray crystallographic analysis and the H 2 18 O incorporation experiment. HadD AJ1 is an α-helical hydrolase that forms a homotetramer with its monomer including two structurally axisymmetric repeats. The product-bound complex structure was trapped with L-lactic acid in the active site, which is framed by the structurally related helices between two repeats. Site-directed mutagenesis confirmed the importance of the residues lining the binding pocket in stabilizing the enzyme-substrate complex. Asp205 acts as a key catalytic residue and is responsible for activating a water molecule along with Asn131. Then, the hydroxyl group of the water molecule directly attacks the C2 atom of the substrate to release the halogen ion instead of forming an enzyme-substrate ester intermediate as observed in L-2-haloacid dehalogenases. The newly revealed structural and mechanistic information on D-DEX may inspire structure-based mutagenesis to engineer highly efficient haloacid dehalogenases.

  12. Thiol biochemistry of prokaryotes

    Science.gov (United States)

    Fahey, Robert C.

    1986-01-01

    The present studies have shown that GSH metabolism arose in the purple bacteria and cyanobacteria where it functions to protect against oxygen toxicity. Evidence was obtained indicating that GSH metabolism was incorporated into eucaryotes via the endosymbiosis giving rise to mitochrondria and chloroplasts. Aerobic bacteria lacking GSH utilize other thiols for apparently similar functions, the thiol being coenzyme A in Gram positive bacteria and chi-glutamylcysteine in the halobacteria. The thiol biochemistry of prokaryotes is thus seen to be much more highly diversified than that of eucaryotes and much remains to be learned about this subject.

  13. The Biochemistry of Mitosis

    Science.gov (United States)

    Wieser, Samuel; Pines, Jonathon

    2015-01-01

    In this article, we will discuss the biochemistry of mitosis in eukaryotic cells. We will focus on conserved principles that, importantly, are adapted to the biology of the organism. It is vital to bear in mind that the structural requirements for division in a rapidly dividing syncytial Drosophila embryo, for example, are markedly different from those in a unicellular yeast cell. Nevertheless, division in both systems is driven by conserved modules of antagonistic protein kinases and phosphatases, underpinned by ubiquitin-mediated proteolysis, which create molecular switches to drive each stage of division forward. These conserved control modules combine with the self-organizing properties of the subcellular architecture to meet the specific needs of the cell. Our discussion will draw on discoveries in several model systems that have been important in the long history of research on mitosis, and we will try to point out those principles that appear to apply to all cells, compared with those in which the biochemistry has been specifically adapted in a particular organism. PMID:25663668

  14. Learning Biochemistry by Chocolate

    Directory of Open Access Journals (Sweden)

    M.C Guedes

    2006-07-01

    Full Text Available Both sensations and biochemical reactions taken place or promoted during ingestion of chocolate were the motivation for  investigating  the  organic  compounds  present  in  this  source.  Cocoa  and  chocolate  are  composed  by  several substances , among them, aminoacids and alkaloids.The objective of this investigation was to purpose a contextured approach  of  biochemistry  through  the  sensations  and  reactions  involving  aminoacids,  theobromine  and  hormones. Methodology: 1. Theoretical part:  constituted  by theoretical  and tutorial classes  about aminoacids, theobromine and hormones  involved  at  the  metabolism;  2.  Questionary:  ten  questions  based  upon  theoretical  classes,  personal sensations  and  general  aspects  of chocolate;  3.Lecture:  Cientific  articles  searched  in  periodics  by  own  students  as well  as  newspaper  reports;  4.  Experimental:  Laboratory  experiments  including  extraction,  characterization, spectrometric quantification  after  specific reactions  and identification by  Rf  comparison with  standards  on TLC  from cocoa  almonds  and  both  powder  cocoa  and  chocolate.  The  study  was  applied  in  30  students  from  a  chemistry college. Results: The results pointed out to a higher frequency of the students and to a increased interest  from them by   biochemistry  issues  and  cientific  lectures,  as  well  as  a  satisfactory  acquirement  of  theoretical  and  practice knowledge of aminoacids and hormones, spectrometry and chromatography. Conclusion: A contextured approach is quite positive for learning biochemistry to chemists.

  15. Chapter IV: ultrafast biochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Chergui, M. [Swiss Federal Institute of Technology (EPFL), Lausanne (Switzerland); Kjelstrup, S. [Norwegian University of Science and Technology (NTNU), Trondheim (Norway); Meuwly, M. [Universitaet Basel, Basel (Switzerland); Schuler, B. [University of Zuerich (ETH), Zurich (Switzerland); Thor, J. van [Imperial College London (IC), London (United Kingdom)

    2009-09-15

    The whole report issued by the Paul Scherrer Institute (PSI) in Switzerland takes a look at the scientific opportunities offered by the institute's SwissFEL X-ray Laser facility. In this sixth part, initial events and fluctuations in biochemical processes at the atomic scale are discussed. Sub-nanosecond processes are fundamental to biochemistry and will be accessible to the ultra-short pulses of the SwissFEL. Time and length scales of biochemical reactions are discussed, as is the photo-initiation of biochemical processes. Time-resolved measurement techniques are looked at. Fluorescence resonant energy transfer is discussed. As an example, the photo cycle of bacteriorhodopsin is examined. The dynamics of protein folding and catalytic action are also looked at. Mesoscopic non-equilibrium thermodynamics is discussed

  16. Biochemistry and radiopharmacy

    International Nuclear Information System (INIS)

    Mendoza de G, M.

    1989-01-01

    The article reviews the historical development of the nuclear medicine in Colombia and the primordial role of the IAN in this field. The main objective of the Biochemistry and Radiopharmacy Area is go to give technical support for the application of the nuclear energy in the human and veterinary medicine. The department has laboratories for the production of radiopharmaceuticals to be labelled with Tc-99m and quality control of the same human and veterinary RIA. Each one of the laboratories develops its work in three different areas: research and development, production, training and teaching. An actualization of the programs, results and publications are analyzed in this review also. Some of these programs have the support of the IAEA

  17. Characterization of the haloacid dehalogenase from Xanthobacter autotrophicus GJ10 and sequencing of the dhlB gene

    DEFF Research Database (Denmark)

    van der Ploeg, J; Van Hall, Gerrit; Janssen, D B

    1991-01-01

    B) was cloned and could be allocated to a 6.5-kb EcoRI-BglII fragment. Part of this fragment was sequenced, and the dhlB open reading frame was identified by comparison with the N-terminal amino acid sequence of the protein. The gene was found to encode a protein of 27,433 Da that showed considerable homology...... chromatography. The enzyme was active with 2-halogenated carboxylic acids and converted only the L-isomer of 2-chloropropionic acid with inversion of configuration to produce D-lactate. The activity of the enzyme was not readily influenced by thiol reagents. The gene encoding the haloacid dehalogenase (dhl...... (60.5 and 61.0% similarity) with the two other haloacid dehalogenases sequenced to date but not with the haloalkane dehalogenase from X. autotrophicus GJ10....

  18. American journal of biochemistry and biotechnology

    National Research Council Canada - National Science Library

    2005-01-01

    .... Areas covered include: general biochemistry, patho-biochemistry, evolutionary biology, structural biology, molecular and cellular biology, molecular medicine, cancer research, virology, immunology, plant molecular biology...

  19. Directed evolution strategies for enantiocomplementary haloalkane dehalogenases: from chemical waste to enantiopure building blocks.

    Science.gov (United States)

    van Leeuwen, Jan G E; Wijma, Hein J; Floor, Robert J; van der Laan, Jan-Metske; Janssen, Dick B

    2012-01-02

    We used directed evolution to obtain enantiocomplementary haloalkane dehalogenase variants that convert the toxic waste compound 1,2,3-trichloropropane (TCP) into highly enantioenriched (R)- or (S)-2,3-dichloropropan-1-ol, which can easily be converted into optically active epichlorohydrins-attractive intermediates for the synthesis of enantiopure fine chemicals. A dehalogenase with improved catalytic activity but very low enantioselectivity was used as the starting point. A strategy that made optimal use of the limited capacity of the screening assay, which was based on chiral gas chromatography, was developed. We used pair-wise site-saturation mutagenesis (SSM) of all 16 noncatalytic active-site residues during the initial two rounds of evolution. The resulting best R- and S-enantioselective variants were further improved in two rounds of site-restricted mutagenesis (SRM), with incorporation of carefully selected sets of amino acids at a larger number of positions, including sites that are more distant from the active site. Finally, the most promising mutations and positions were promoted to a combinatorial library by using a multi-site mutagenesis protocol with restricted codon sets. To guide the design of partly undefined (ambiguous) codon sets for these restricted libraries we employed structural information, the results of multiple sequence alignments, and knowledge from earlier rounds. After five rounds of evolution with screening of only 5500 clones, we obtained two strongly diverged haloalkane dehalogenase variants that give access to (R)-epichlorohydrin with 90 % ee and to (S)-epichlorohydrin with 97 % ee, containing 13 and 17 mutations, respectively, around their active sites. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Wanderings in biochemistry.

    Science.gov (United States)

    Lengyel, Peter

    2014-07-11

    My Ph.D. thesis in the laboratory of Severo Ochoa at New York University School of Medicine in 1962 included the determination of the nucleotide compositions of codons specifying amino acids. The experiments were based on the use of random copolyribonucleotides (synthesized by polynucleotide phosphorylase) as messenger RNA in a cell-free protein-synthesizing system. At Yale University, where I joined the faculty, my co-workers and I first studied the mechanisms of protein synthesis. Thereafter, we explored the interferons (IFNs), which were discovered as antiviral defense agents but were revealed to be components of a highly complex multifunctional system. We isolated pure IFNs and characterized IFN-activated genes, the proteins they encode, and their functions. We concentrated on a cluster of IFN-activated genes, the p200 cluster, which arose by repeated gene duplications and which encodes a large family of highly multifunctional proteins. For example, the murine protein p204 can be activated in numerous tissues by distinct transcription factors. It modulates cell proliferation and the differentiation of a variety of tissues by binding to many proteins. p204 also inhibits the activities of wild-type Ras proteins and Ras oncoproteins. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. [Research activity in clinical biochemistry

    DEFF Research Database (Denmark)

    Jorgensen, H.L.; Larsen, B.; Ingwersen, P.

    2008-01-01

    Clinical Biochemistry, 57 fulfilled the inclusion criteria. Each of these 57 was matched according to medical title with two randomly chosen specialists from other specialities, totaling 114. Using Medline and the Web of Science, the number of publications and the number of citations were then ascertained......BACKGROUND: Quantitative bibliometric measurements of research activity are frequently used, e.g. for evaluating applicants for academic positions. The purpose of this investigation is to assess research activity within the medical speciality of Clinical Biochemistry by comparing it with a matched....... RESULTS: 25% of the 11,691 specialists held a PhD degree or doctoral degree, DMSci, (Clinical Biochemistry: 61%). The 171 specialists included in the study had 9,823 papers in Medline and 10,140 papers in the Web of Science. The number of Medline papers per specialist was 71 for Clinical Biochemistry...

  2. [Research activity in clinical biochemistry

    DEFF Research Database (Denmark)

    Jorgensen, H.L.; Larsen, B.; Ingwersen, P.

    2008-01-01

    BACKGROUND: Quantitative bibliometric measurements of research activity are frequently used, e.g. for evaluating applicants for academic positions. The purpose of this investigation is to assess research activity within the medical speciality of Clinical Biochemistry by comparing it with a matched...... Clinical Biochemistry, 57 fulfilled the inclusion criteria. Each of these 57 was matched according to medical title with two randomly chosen specialists from other specialities, totaling 114. Using Medline and the Web of Science, the number of publications and the number of citations were then ascertained....... RESULTS: 25% of the 11,691 specialists held a PhD degree or doctoral degree, DMSci, (Clinical Biochemistry: 61%). The 171 specialists included in the study had 9,823 papers in Medline and 10,140 papers in the Web of Science. The number of Medline papers per specialist was 71 for Clinical Biochemistry...

  3. Postmortem Biochemistry and Toxicology

    Directory of Open Access Journals (Sweden)

    Robert Flanagan

    2017-04-01

    Full Text Available The aim of postmortem biochemistry and toxicology is either to help establish the cause of death, or to gain information on events immediately before death. If self-poisoning is suspected, the diagnosis may be straightforward and all that could be required is confirmation of the agents involved. However, if the cause of death is not immediately obvious then suspicion of possible poisoning or of conditions such as alcoholic ketoacidosis is of course crucial. On the other hand, it may be important to investigate adherence to prescribed therapy, for example with anticonvulsants or antipsychotics, hence sensitive methods are required. Blood sampling (needle aspiration, peripheral vein, for example femoral, ideally after proximal ligation before opening the body minimizes the risk of sample contamination with, for example, gut contents or urine. Other specimens (stomach contents, urine, liver, vitreous humor may also be valuable and may be needed to corroborate unexpected or unusual findings in the absence of other evidence. The site of sampling should always be recorded. The availability of antemortem specimens should not necessarily preclude postmortem sampling. Appropriate sample preservation, transport, and storage are mandatory. Interpretation of analytical toxicology results must take into account what is known of the pharmacokinetics and toxicology of the agent(s in question, the circumstances under which death occurred including the mechanism of exposure, and other factors such as the stability of the analyte(s and the analytical methods used. It is important to realise that changes may occur in the composition of body fluids, even peripheral blood, after death. Such changes are likely to be greater after attempted resuscitation, and with centrally-acting drugs with large volumes of distribution given chronically, and may perhaps be minimised by prompt refrigeration of the body and performing the autopsy quickly.

  4. Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity

    Energy Technology Data Exchange (ETDEWEB)

    Pegan, Scott D., E-mail: pegan@uic.edu [Center of Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago (United States); Serrano, Hector; Whitman, Christian P. [Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin (United States); Mesecar, Andrew D., E-mail: pegan@uic.edu [Center of Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago (United States)

    2008-12-01

    The X-ray structure of a noncovalently modified trans-3-chloroacrylic acid dehalogenase with a substrate-homolog acetate bound in the active site has been determined to 1.7 Å resolution. Elucidation of catalytically important water is reported and multiple conformations of the catalytic residue αGlu52 are observed. Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1, 3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon–halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic βPro1 residue. Here, the 1.7 Å resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain αGlu52 is observed in the structure, supporting its role in the catalytic mechanism.

  5. Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Klvana, M.; Pavlová, M.; Koudeláková, T.; Chaloupková, R.; Dvořák, P.; Prokop, Z.; Stsiapanava, A.; Kutý, Michal; Kutá-Smatanová, Ivana; Dohnálek, Jan; Kulhánek, P.; Damborský, J.

    2009-01-01

    Roč. 392, č. 5 (2009), s. 1339-1356 ISSN 0022-2836 R&D Projects: GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z60870520 Keywords : haloalkane dehalogenase * product release * random acceleration molecular dynamics Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.871, year: 2009

  6. Steady-state and pre-steady-state kinetic analysis of halopropane conversion by a Rhodococcus haloalkane dehalogenase

    NARCIS (Netherlands)

    Bosma, T; Pikkemaat, MG; Kingma, Jacob; Dijk, J; Janssen, DB

    2003-01-01

    Haloalkane dehalogenase from Rhodococcus rhodochrous NCIMB 13064 (DhaA) catalyzes the hydrolysis of carbon-halogen bonds in a wide range of haloalkanes. We examined the steady-state and pre-steady-state kinetics of halopropane conversion by DhaA to illuminate mechanistic details of the

  7. Activation of an Asp-124→Asn mutant of haloalkane dehalogenase by hydrolytic deamidation of asparagine

    NARCIS (Netherlands)

    Pries, Frens; Kingma, Jacob; JANSSEN, Dick B

    1995-01-01

    Haloalkane dehalogenase hydrolyses various 1-halon-alkanes to the corresponding alcohols by covalent catalysis with formation of an alkyl-enzyme intermediate. The carboxylate function of the nucleophilic aspartate (Asp-124) that displaces the halogen during formation of the intermediate was changed

  8. Kinetic resolution of α-bromoamides: Experimental and theoretical investigation of highly enantioselective reactions catalyzed by haloalkane dehalogenases

    NARCIS (Netherlands)

    Westerbeek, Alja; Szymanski, Wiktor; Wijma, Hein J.; Marrink, Siewert; Feringa, Ben L.; Janssen, Dick B.

    2011-01-01

    Haloalkane dehalogenases from five sources were heterologously expressed in Escherichia coli, isolated, and tested for their ability to achieve kinetic resolution of racemic alpha-bromoamides, which are important intermediates used in the preparation of bioactive compounds. To explore the substrate

  9. [Research activity in clinical biochemistry].

    Science.gov (United States)

    Jørgensen, Henrik L; Larsen, Birger; Ingwersen, Peter; Rehfeld, Jens F

    2008-09-01

    Quantitative bibliometric measurements of research activity are frequently used, e.g. for evaluating applicants for academic positions. The purpose of this investigation is to assess research activity within the medical speciality of Clinical Biochemistry by comparing it with a matched control group from other medical specialities in Denmark. A list of all physicians registered in Denmark (23,127 persons) was drawn from the database "Laeger.dk". Of these, 5,202 were generalists (not included) while 11,691 were from other specialities. Of the 126 specialists from Clinical Biochemistry, 57 fulfilled the inclusion criteria. Each of these 57 was matched according to medical title with two randomly chosen specialists from other specialities, totaling 114. Using Medline and the Web of Science, the number of publications and the number of citations were then ascertained. 25% of the 11,691 specialists held a PhD degree or doctoral degree, DMSci, (Clinical Biochemistry: 61%). The 171 specialists included in the study had 9,823 papers in Medline and 10,140 papers in the Web of Science. The number of Medline papers per specialist was 71 for Clinical Biochemistry compared to 51 for the control group. The number of citations per specialist was 1,844 for Clinical Biochemistry compared to 816 for the control group. The top ten H-indices (of which 8 were in Clinical Biochemistry) ranged from 30 to 69. Both the number of papers and the number of citations were higher for Clinical Biochemistry than for the control group. The difference was most pronounced among professors.

  10. [Changes of chlorine isotope composition characterize bacterial dehalogenation of dichloromethane].

    Science.gov (United States)

    Ziakun, A M; Firsova, Iu E; Torgonskaia, M L; Doronina, N V; Trotsenko, Iu A

    2007-01-01

    Fractionation of dichloromethane (DCM) molecules with different chlorine isotopes by aerobic methylobacteria Methylobacterium dichloromethanicum DM4 and Albibacter nethylovorans DM10; cell-free extract of strain DM4; and transconjugant Methylobacterium evtorquens Al1/pME 8220, expressing the dcmA gene for DCM dehalogenase but unable to grow on DCM, was studied. Kinetic indices of DCM isotopomers for chlorine during bacterial dehalogenation and diffusion were compared. A two-step model is proposed, which suggests diffusional DCM transport to bacterial cells.

  11. Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels.

    Science.gov (United States)

    Stsiapanava, A; Dohnalek, J; Gavira, J A; Kuty, M; Koudelakova, T; Damborsky, J; Kuta Smatanova, I

    2010-09-01

    The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 is a bacterial enzyme that shows catalytic activity for the hydrolytic degradation of the highly toxic industrial pollutant 1,2,3-trichloropropane (TCP). Mutagenesis focused on the access tunnels of DhaA produced protein variants with significantly improved activity towards TCP. Three mutants of DhaA named DhaA04 (C176Y), DhaA14 (I135F) and DhaA15 (C176Y + I135F) were constructed in order to study the functional relevance of the tunnels connecting the buried active site of the protein with the surrounding solvent. All three protein variants were crystallized using the sitting-drop vapour-diffusion technique. The crystals of DhaA04 belonged to the orthorhombic space group P2(1)2(1)2(1), while the crystals of DhaA14 and DhaA15 had triclinic symmetry in space group P1. The crystal structures of DhaA04, DhaA14 and DhaA15 with ligands present in the active site were solved and refined using diffraction data to 1.23, 0.95 and 1.22 A, resolution, respectively. Structural comparisons of the wild type and the three mutants suggest that the tunnels play a key role in the processes of ligand exchange between the buried active site and the surrounding solvent.

  12. Medical Biochemistry – Clinical Cases

    Directory of Open Access Journals (Sweden)

    Gustavo Henrique Cavalcante

    2017-10-01

    Full Text Available The presentation of situations that exemplifies the practical application of the biochemical concepts is one of the main challenges in the development of didactic materials for the teaching of biochemistry. So far, there are a small number of materials, especially in Portuguese language, that present practical situations exemplifying the application of the several biochemical concepts in the area of human health. The Medical Biochemistry-Clinical Cases app/ebook is intended to enable the integrated vision of the basic knowledge in biochemistry and its practical application in day-to-day situations of human health professionals. The biochemical concepts are presented as clinical cases, making possible the exercise of the analytical attitude and decision-making to solve problems based on real situations. The app is available on the internet for free, facilitating both, the access and the use of the material as a supplementary source.

  13. Environmental biochemistry of arsenic

    Energy Technology Data Exchange (ETDEWEB)

    Tamaki, S.; Frankenberger, W.T. Jr. (Department of Soil and Environmental Sciences, University of California, Riverside (United States))

    1992-01-01

    Microorganisms are involved in the redistribution and global cycling of arsenic. Arsenic can accumulate and can be subject to various biotransformations including reduction, oxidation, and methylation. Bacterial methylation of inorganic arsenic is coupled to the methane biosynthetic pathway in methanogenic bacteria under anaerobic conditions and may be a mechanism for arsenic detoxification. The pathway proceeds by reduction of arsenate to arsenite followed by methylation to dimethylarsine. Fungi are also able to transform inorganic and organic arsenic compounds into volatile methylarsines. The pathway proceeds aerobically by arsenate reduction to arsenite followed by several methylation steps producing trimethylarsine. Volatile arsine gases are very toxic to mammals because they destroy red blood cells (LD50 in rats; 3.0 mg kg-1). Further studies are needed on dimethylarsine and trimethylarsine toxicity tests through inhalation of target animals. Marine algae transform arsenate into non-volatile methylated arsenic compounds (methanearsonic and dimethylarsinic acids) in seawater. This is considered to be a beneficial step not only to the primary producers, but also to the higher trophic levels, since non-volatile methylated arsenic is much less toxic to marine invertebrates. Freshwater algae like marine algae synthesize lipid-soluble arsenic compounds and do not produce volatile methylarsines. Aquatic plants also synthesize similar lipid-soluble arsenic compounds. In terrestrial plants, arsenate is preferentially taken up 3 to 4 times the rate of arsenite. In the presence of phosphate, arsenate uptake is inhibited while in the presence of arsenate, phosphate uptake is only slightly inhibited. There is a competitive interaction between arsenate and phosphate for the same uptake system in terrestrial plants.

  14. Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments▿ †

    Science.gov (United States)

    Futagami, Taiki; Morono, Yuki; Terada, Takeshi; Kaksonen, Anna H.; Inagaki, Fumio

    2009-01-01

    Halogenated organic compounds serve as terminal electron acceptors for anaerobic respiration in a diverse range of microorganisms. Here, we report on the widespread distribution and diversity of reductive dehalogenase homologous (rdhA) genes in marine subsurface sediments. A total of 32 putative rdhA phylotypes were detected in sediments from the southeast Pacific off Peru, the eastern equatorial Pacific, the Juan de Fuca Ridge flank off Oregon, and the northwest Pacific off Japan, collected at a maximum depth of 358 m below the seafloor. In addition, significant dehalogenation activity involving 2,4,6-tribromophenol and trichloroethene was observed in sediment slurry from the Nankai Trough Forearc Basin. These results suggest that dehalorespiration is an important energy-yielding pathway in the subseafloor microbial ecosystem. PMID:19749069

  15. Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation

    Directory of Open Access Journals (Sweden)

    Bat-Erdene eJugder

    2016-03-01

    Full Text Available Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e. organohalide respiration. Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDase, which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses RDases, concentrating on those which have been purified (partially or wholly and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.

  16. Commentary: Biochemistry Re-Natured

    Science.gov (United States)

    White, Harold B.

    2010-01-01

    In his last commentary on "Biochemistry Denatured," this author dealt with his perception that college students today have spent too little of their childhood years playing outside in nature and as a consequence have not learned basic things about the world from personal experience. This "nature-deficit disorder" removes many opportunities for…

  17. Soil Microbiology, Ecology, and Biochemistry

    Science.gov (United States)

    The 4th edition of Soil Microbiology, Ecology, and Biochemistry Edited by Eldor Paul continues in the vein of the 3rd edition by providing an excellent, broad-reaching introduction to soil biology. The new edition improves on the previous by providing extensive supplementary materials, links to outs...

  18. Multitracers in chemistry and biochemistry

    International Nuclear Information System (INIS)

    Ambe, F.

    2000-01-01

    The multitracer technique using heavy-ion reactions has successfully developed in the last decade and is expected to widen its application in chemistry, biochemistry and other fields with technical improvement in future. Several examples of recent application are reviewed and development in the coming century is forecast. (author)

  19. Does breast-feeding influence liver biochemistry?

    DEFF Research Database (Denmark)

    Jørgensen, M. H.; Ott, P.; Juul, A.

    2003-01-01

    It is assumed that early feeding can affect liver biochemistry because breast-fed infants have a higher risk of hyperbilirubinemia than formula-fed infants. The authors sought to determine how feeding mode affected liver biochemistry in healthy term infants.......It is assumed that early feeding can affect liver biochemistry because breast-fed infants have a higher risk of hyperbilirubinemia than formula-fed infants. The authors sought to determine how feeding mode affected liver biochemistry in healthy term infants....

  20. Balancing the Stability–Activity Trade-Off by Fine-Tuning Dehalogenase Access Tunnels

    Czech Academy of Sciences Publication Activity Database

    Lišková, V.; Bednář, D.; Prudnikova, Tatyana; Řezáčová, P.; Koudeláková, T.; Šebestová, E.; Kutá-Smatanová, Ivana; Březovský, J.; Chaloupková, R.; Damborský, J.

    2015-01-01

    Roč. 7, č. 4 (2015), s. 648-659 ISSN 1867-3880 Institutional support: RVO:67179843 Keywords : alkanes * enzymes * catalysis * halogenation * molecular dynamics * protein engineering Subject RIV: CE - Biochemistry Impact factor: 4.724, year: 2015

  1. Crystallization and preliminary X-ray analysis of the haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58

    International Nuclear Information System (INIS)

    Mase, Tomoko; Yabuki, Hideya; Okai, Masahiko; Ohtsuka, Jun; Imai, Fabiana Lica; Nagata, Yuji; Tanokura, Masaru

    2012-01-01

    The haloalkane dehalogenase DatA from A. tumefaciens C58 was expressed, purified and crystallized by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 1.70 Å resolution. Haloalkane dehalogenases are enzymes that catalyze the hydrolytic reaction of a wide variety of haloalkyl substrates to form the corresponding alcohol and hydrogen halide products. DatA from Agrobacterium tumefaciens C58 is a haloalkane dehalogenase that has a unique pair of halide-binding residues, asparagine (Asn43) and tyrosine (Tyr109), instead of the asparagine and tryptophan that are conserved in other members of the subfamily. DatA was expressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method with a reservoir solution consisting of 0.1 M CHES pH 8.6, 1.0 M potassium sodium tartrate, 0.2 M lithium sulfate, 0.01 M barium chloride. X-ray diffraction data were collected to 1.70 Å resolution. The space group of the crystal was determined as the primitive tetragonal space group P422, with unit-cell parameters a = b = 123.7, c = 88.1 Å. The crystal contained two molecules in the asymmetric unit

  2. Clinical biochemistry education in Spain.

    Science.gov (United States)

    Queraltó, J M

    1994-12-31

    Clinical biochemistry in Spain was first established in 1978 as an independent specialty. It is one of several clinical laboratory sciences specialties, together with haematology, microbiology, immunology and general laboratory (Clinical analysis, análisis clinicos). Graduates in Medicine, Pharmacy, Chemistry and Biological Sciences can enter post-graduate training in Clinical Chemistry after a nation-wide examination. Training in an accredited Clinical Chemistry department is 4 years. A national committee for medical and pharmacist specialties advises the government on the number of trainees, program and educational units accreditation criteria. Technical staff includes nurses and specifically trained technologists. Accreditation of laboratories is developed at different regional levels. The Spanish Society for Clinical Biochemistry and Molecular Pathology (SECQ), the national representative in the IFCC, has 1600 members, currently publishes a scientific journal (Química Clinica) and a newsletter. It organizes a continuous education program, a quality control program and an annual Congress.

  3. Biochemistry: from supermarket to laboratory

    OpenAIRE

    F. R. Freitas-Rego; M. G. Pereira; S. O. Loureiro; M. T. de Santana; R.G. Garrido; F. de S.R.G Garrido

    2007-01-01

    After new campi as Instituto Multidisciplinar em Saúde (IMS/UFBA) startedworking, it was necessary to develop practical classes using domestic reagents atBiochemistry to Pharmacy (IMS078). Firstly, students visited a supermarket to readnutritional information at label and select possible products to be used in class. Moreover,chemical processes and fermentation were discussed as different foods and drinks wereanalysed. Some food were token to laboratories so that biomole cules qualitative ana...

  4. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.

    Science.gov (United States)

    Pavlova, Martina; Klvana, Martin; Prokop, Zbynek; Chaloupkova, Radka; Banas, Pavel; Otyepka, Michal; Wade, Rebecca C; Tsuda, Masataka; Nagata, Yuji; Damborsky, Jiri

    2009-10-01

    Engineering enzymes to degrade anthropogenic compounds efficiently is challenging. We obtained Rhodococcus rhodochrous haloalkane dehalogenase mutants with up to 32-fold higher activity than wild type toward the toxic, recalcitrant anthropogenic compound 1,2,3-trichloropropane (TCP) using a new strategy. We identified key residues in access tunnels connecting the buried active site with bulk solvent by rational design and randomized them by directed evolution. The most active mutant has large aromatic residues at two out of three randomized positions and two positions modified by site-directed mutagenesis. These changes apparently enhance activity with TCP by decreasing accessibility of the active site for water molecules, thereby promoting activated complex formation. Kinetic analyses confirmed that the mutations improved carbon-halogen bond cleavage and shifted the rate-limiting step to the release of products. Engineering access tunnels by combining computer-assisted protein design with directed evolution may be a valuable strategy for refining catalytic properties of enzymes with buried active sites.

  5. PCB dechlorination hotspots and reductive dehalogenase genes in sediments from a contaminated wastewater lagoon.

    Science.gov (United States)

    Mattes, Timothy E; Ewald, Jessica M; Liang, Yi; Martinez, Andres; Awad, Andrew; Richards, Patrick; Hornbuckle, Keri C; Schnoor, Jerald L

    2017-08-12

    Polychlorinated biphenyls (PCBs) are a class of persistent organic pollutants that are distributed worldwide. Although industrial PCB production has stopped, legacy contamination can be traced to several different commercial mixtures (e.g., Aroclors in the USA). Despite their persistence, PCBs are subject to naturally occurring biodegradation processes, although the microbes and enzymes involved are poorly understood. The biodegradation potential of PCB-contaminated sediments in a wastewater lagoon located in Virginia (USA) was studied. Total PCB concentrations in sediments ranged from 6.34 to 12,700 mg/kg. PCB congener profiles in sediment sample were similar to Aroclor 1248; however, PCB congener profiles at several locations showed evidence of dechlorination. The sediment microbial community structure varied among samples but was dominated by Proteobacteria and Firmicutes. The relative abundance of putative dechlorinating Chloroflexi (including Dehalococcoides sp.) was 0.01-0.19% among the sediment samples, with Dehalococcoides sp. representing 0.6-14.8% of this group. Other possible PCB dechlorinators present included the Clostridia and the Geobacteraceae. A PCR survey for potential PCB reductive dehalogenase genes (RDases) yielded 11 sequences related to RDase genes in PCB-respiring Dehalococcoides mccartyi strain CG5 and PCB-dechlorinating D. mccartyi strain CBDB1. This is the first study to retrieve potential PCB RDase genes from unenriched PCB-contaminated sediments.

  6. Teaching Biochemistry to Medical Technology Students.

    Science.gov (United States)

    Gomez-Silva, Benito; And Others

    1997-01-01

    Describes the biochemistry component of study to become a medical technologist in a Chilean university. Provides details of program structure, course content descriptions, and teaching strategies. (DDR)

  7. Identification of a multi-protein reductive dehalogenase complex in Dehalococcoides mccartyi strain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement

    DEFF Research Database (Denmark)

    Kublik, Anja; Deobald, Darja; Hartwig, Stefanie

    2016-01-01

    electrophoresis (BN-PAGE), gel filtration and ultrafiltration an active dehalogenating protein complex with a molecular mass of 250–270 kDa was identified. The active subunit of reductive dehalogenase (RdhA) colocalised with a complex iron-sulfur molybdoenzyme (CISM) subunit (CbdbA195) and an iron-sulfur cluster...... of the dehalogenating complex prior to membrane solubilisation. Taken together, the identification of the respiratory dehalogenase protein complex and the absence of indications for quinone participation in the respiration suggest a quinone-independent protein-based respiratory electron transfer chain in D. mccartyi....

  8. Teaching Biochemistry Online at Oregon State University

    Science.gov (United States)

    Ahern, Kevin

    2017-01-01

    A strategy for growing online biochemistry courses is presented based on successes in ecampus at Oregon State University. Four free drawing cards were key to the effort--YouTube videos, iTunes U online free course content, an Open Educational Resource textbook--Biochemistry Free and Easy, and a fun set of educational songs known as the Metabolic…

  9. Biochemical characterization of a haloalkane dehalogenase DadB from Alcanivorax dieselolei B-5.

    Directory of Open Access Journals (Sweden)

    Anzhang Li

    Full Text Available Recently, we found that Alcanivorax bacteria from various marine environments were capable of degrading halogenated alkanes. Genome sequencing of A. dieselolei B-5 revealed two putative haloalkane dehalogenase (HLD genes, which were supposed to be involved in degradation of halogenated compounds. In this report, we confirm for the first time that the Alcanivorax bacterium encodes a truly functional HLD named DadB. An activity assay with 46 halogenated substrates indicated that DadB possesses broad substrate range and has the highest overall activity among the identified HLDs. DadB prefers brominated substrates; chlorinated alkenes; and the C2-C3 substrates, including the persistent pollutants of 1,2-dichloroethane, 1,2-dichloropropane and 1,2,3-trichloropropane. As DadB displays no detectable activity toward long-chain haloalkanes such as 1-chlorohexadecane and 1-chlorooctadecane, the degradation of them in A. dieselolei B-5 might be attributed to other enzymes. Kinetic constants were determined with 6 substrates. DadB has highest affinity and largest k cat/K m value toward 1,3-dibromopropane (K(m = 0.82 mM, k(cat/K(m = 16.43 mM(-1 · s(-1. DadB aggregates fast in the buffers with pH ≤ 7.0, while keeps stable in monomer form when pH ≥ 7.5. According to homology modeling, DadB has an open active cavity with a large access tunnel, which is supposed important for larger molecules as opposed to C2-C3 substrates. Combined with the results for other HLDs, we deduce that residue I247 plays an important role in substrate selection. These results suggest that DadB and its host, A. dieselolei B-5, are of potential use for biocatalysis and bioremediation applications.

  10. Biochemical characterization of a haloalkane dehalogenase DadB from Alcanivorax dieselolei B-5.

    Science.gov (United States)

    Li, Anzhang; Shao, Zongze

    2014-01-01

    Recently, we found that Alcanivorax bacteria from various marine environments were capable of degrading halogenated alkanes. Genome sequencing of A. dieselolei B-5 revealed two putative haloalkane dehalogenase (HLD) genes, which were supposed to be involved in degradation of halogenated compounds. In this report, we confirm for the first time that the Alcanivorax bacterium encodes a truly functional HLD named DadB. An activity assay with 46 halogenated substrates indicated that DadB possesses broad substrate range and has the highest overall activity among the identified HLDs. DadB prefers brominated substrates; chlorinated alkenes; and the C2-C3 substrates, including the persistent pollutants of 1,2-dichloroethane, 1,2-dichloropropane and 1,2,3-trichloropropane. As DadB displays no detectable activity toward long-chain haloalkanes such as 1-chlorohexadecane and 1-chlorooctadecane, the degradation of them in A. dieselolei B-5 might be attributed to other enzymes. Kinetic constants were determined with 6 substrates. DadB has highest affinity and largest k cat/K m value toward 1,3-dibromopropane (K(m) = 0.82 mM, k(cat)/K(m) = 16.43 mM(-1) · s(-1)). DadB aggregates fast in the buffers with pH ≤ 7.0, while keeps stable in monomer form when pH ≥ 7.5. According to homology modeling, DadB has an open active cavity with a large access tunnel, which is supposed important for larger molecules as opposed to C2-C3 substrates. Combined with the results for other HLDs, we deduce that residue I247 plays an important role in substrate selection. These results suggest that DadB and its host, A. dieselolei B-5, are of potential use for biocatalysis and bioremediation applications.

  11. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

    Directory of Open Access Journals (Sweden)

    Mikihiko eKawai

    2014-03-01

    Full Text Available Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5 and 107.0 mbsf at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB, key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.

  12. Symposium 19: The contributions of the Department of Biochemistry/USP towards Biochemistry teaching

    Directory of Open Access Journals (Sweden)

    Bayardo Baptista Torres

    2014-08-01

    Full Text Available K-Education(Portuguese Chair: V. Trindade Bayardo Torres; Clovis Wannmacher; Denise MacedoThe contributions of the Department of Biochemistry/USP towards Biochemistry teaching.O ensino de Bioquímica nos últimos 20 anosBayardo B. TorresDepartamento de Bioquímica, Instituto de Química, USP. São Paulo, Brazil.Among the contributions of the Department of Biochemistry/USP one must recall:1. Winter school for graduate studentsThis course, now at the ninth edition, is intended for students in the final stage of their Masters or PhD in Biochemistry or related areas from any institution of higher education.Modern and important techniques are offered as possible support to help the student’s projects.2. Summer courses for undergraduate studentsThe Department offers every year, since 1999, complementary courses for undergraduate students to extend their knowledge in biochemical subjects not ordinarily treated in introductory courses. Some examples:Plant Molecular Biology, Biochemistry and Diseases, Biochemistry of Mind, Biochemistry of Ageing, Cancer Biochemistry, Nutrition and Sports, Biochemistry of Beauty, Biochemistry of the Envenomation Response, etc.3. Summer courses for high school teachers. Some examples:Biochemistry of Nutrition, DNA – Techniques and Applications, Biochemistry in the kitchen.4. Software developmentMany software for biochemistry teaching/learning were developed and are freely available at the Biblioteca Digital de Ciências [http://www.bdc.ib.unicamp.br/bdc/index.php]. Some examples:Oxygen consumption by mitochondria, Muscle contraction, Electron transport chain and oxidative phosphorylation, Free radicals, Enzyme kinetics, cAMP signalization, Interactive study of protein structure, Leptin, Insulin and Obesity.5. A Biochemistry textbook. 

  13. Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31.

    Science.gov (United States)

    Lahoda, Maryna; Mesters, Jeroen R; Stsiapanava, Alena; Chaloupkova, Radka; Kuty, Michal; Damborsky, Jiri; Kuta Smatanova, Ivana

    2014-02-01

    Haloalkane dehalogenases catalyze the hydrolytic cleavage of carbon-halogen bonds, which is a key step in the aerobic mineralization of many environmental pollutants. One important pollutant is the toxic and anthropogenic compound 1,2,3-trichloropropane (TCP). Rational design was combined with saturation mutagenesis to obtain the haloalkane dehalogenase variant DhaA31, which displays an increased catalytic activity towards TCP. Here, the 1.31 Å resolution crystal structure of substrate-free DhaA31, the 1.26 Å resolution structure of DhaA31 in complex with TCP and the 1.95 Å resolution structure of wild-type DhaA are reported. Crystals of the enzyme-substrate complex were successfully obtained by adding volatile TCP to the reservoir after crystallization at pH 6.5 and room temperature. Comparison of the substrate-free structure with that of the DhaA31 enzyme-substrate complex reveals that the nucleophilic Asp106 changes its conformation from an inactive to an active state during the catalytic cycle. The positions of three chloride ions found inside the active site of the enzyme indicate a possible pathway for halide release from the active site through the main tunnel. Comparison of the DhaA31 variant with wild-type DhaA revealed that the introduced substitutions reduce the volume and the solvent-accessibility of the active-site pocket.

  14. Expression, purification and preliminary X-ray characterization of dl-2-haloacid dehalogenase from Methylobacterium sp. CPA1

    Energy Technology Data Exchange (ETDEWEB)

    Omi, Rie [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585 (Japan); Jitsumori, Keiji; Yamauchi, Takahiro; Ichiyama, Susumu; Kurihara, Tatsuo; Esaki, Nobuyoshi [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Kamiya, Nobuo; Hirotsu, Ken, E-mail: hirotsu@sci.osaka-cu.ac.jp; Miyahara, Ikuko [Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585 (Japan); Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan)

    2007-07-01

    A recombinant form of dl-2-haloacid dehalogenase from Methylobacterium sp. CPA1 has been expressed in E. coli, purified and crystallized. The crystal belongs to space group P6{sub 3}. Diffraction data have been collected to 1.75 Å resolution. dl-2-Haloacid dehalogenase from Methylobacterium sp. CPA1 (dl-DEX Mb) is a unique enzyme that catalyzes the dehalogenation reaction without the formation of an ester intermediate. A recombinant form of dl-DEX Mb has been expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the hexagonal space group P6{sub 3}, with unit-cell parameters a = b = 186.2, c = 114.4 Å. The crystals are likely to contain between four and eight monomers in the asymmetric unit, with a V{sub M} value of 4.20–2.10 Å{sup 3} Da{sup −1}. A self-rotation function revealed peaks on the χ = 180° section. X-ray data have been collected to 1.75 Å resolution.

  15. Nitrite-mediated hydrolysis of epoxides catalyzed by halohydrin dehalogenase from Agrobacterium radiobacter AD1 : A new tool for the kinetic resolution of epoxides

    NARCIS (Netherlands)

    Hasnaoui, Ghania; Lutje Spelberg, Jeffrey H.; de Vries, Erik; Tang, Lixia; Hauer, Bernhard; Janssen, Dick B.

    2005-01-01

    Halohydrin dehalogenase obtained from Agrobacterium radiobacter AD1, has been tested for the nitrite-mediated ring opening of epoxides. This reaction mainly leads to the formation of unstable hydroxynitrite ester intermediates, which can be further hydrolyzed to the corresponding diols. This

  16. Biochemistry of epidermal stem cells.

    Science.gov (United States)

    Eckert, Richard L; Adhikary, Gautam; Balasubramanian, Sivaprakasam; Rorke, Ellen A; Vemuri, Mohan C; Boucher, Shayne E; Bickenbach, Jackie R; Kerr, Candace

    2013-02-01

    The epidermis is an important protective barrier that is essential for maintenance of life. Maintaining this barrier requires continuous cell proliferation and differentiation. Moreover, these processes must be balanced to produce a normal epidermis. The stem cells of the epidermis reside in specific locations in the basal epidermis, hair follicle and sebaceous glands and these cells are responsible for replenishment of this tissue. A great deal of effort has gone into identifying protein epitopes that mark stem cells, in identifying stem cell niche locations, and in understanding how stem cell populations are related. We discuss these studies as they apply to understanding normal epidermal homeostasis and skin cancer. An assortment of stem cell markers have been identified that permit assignment of stem cells to specific regions of the epidermis, and progress has been made in understanding the role of these cells in normal epidermal homeostasis and in conditions of tissue stress. A key finding is the multiple stem cell populations exist in epidermis that give rise to different structures, and that multiple stem cell types may contribute to repair in damaged epidermis. Understanding epidermal stem cell biology is likely to lead to important therapies for treating skin diseases and cancer, and will also contribute to our understanding of stem cells in other systems. This article is part of a Special Issue entitled Biochemistry of Stem Cells. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Biochemistry of epidermal stem cells☆

    Science.gov (United States)

    Eckert, Richard L.; Adhikary, Gautam; Balasubramanian, Sivaprakasam; Rorke, Ellen A.; Vemuri, Mohan C.; Boucher, Shayne E.; Bickenbach, Jackie R.; Kerr, Candace

    2014-01-01

    Background The epidermis is an important protective barrier that is essential for maintenance of life. Maintaining this barrier requires continuous cell proliferation and differentiation. Moreover, these processes must be balanced to produce a normal epidermis. The stem cells of the epidermis reside in specific locations in the basal epidermis, hair follicle and sebaceous glands and these cells are responsible for replenishment of this tissue. Scope of review A great deal of effort has gone into identifying protein epitopes that mark stem cells, in identifying stem cell niche locations, and in understanding how stem cell populations are related. We discuss these studies as they apply to understanding normal epidermal homeostasis and skin cancer. Major conclusions An assortment of stem cell markers have been identified that permit assignment of stem cells to specific regions of the epidermis, and progress has been made in understanding the role of these cells in normal epidermal homeostasis and in conditions of tissue stress. A key finding is the multiple stem cell populations exist in epidermis that give rise to different structures, and that multiple stem cell types may contribute to repair in damaged epidermis. General significance Understanding epidermal stem cell biology is likely to lead to important therapies for treating skin diseases and cancer, and will also contribute to our understanding of stem cells in other systems. This article is part of a Special Issue entitled Biochemistry of Stem Cells. PMID:22820019

  18. Purification, crystallization and preliminary crystallographic analysis of DehI, a group I α-haloacid dehalogenase from Pseudomonas putida strain PP3

    Energy Technology Data Exchange (ETDEWEB)

    Schmidberger, Jason W. [School of Pharmacology and Medicine, University of Western Australia, Crawley, Western Australia (Australia); Wilce, Jackie A. [Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria (Australia); Weightman, Andrew J. [School of Biosciences, Cardiff University, Cardiff,Wales (United Kingdom); Wilce, Matthew C. J., E-mail: matthew.wilce@med.monash.edu.au [Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria (Australia); School of Pharmacology and Medicine, University of Western Australia, Crawley, Western Australia (Australia)

    2008-07-01

    The α-haloacid dehalogenase DehI from P. putida strain PP3 was cloned into a vector with an N-terminal His tag and expressed in E. coli Nova Blue strain. Purified protein was crystallized in a primitive monoclinic form and a complete native data set was collected and analysed. Pseudomonas putida strain PP3 produces two dehalogenases, DehI and DehII, which belong to the group I and II α-haloacid dehalogenases, respectively. Group I dehalogenases catalyse the removal of halides from d-haloalkanoic acids and in some cases also the l-enantiomers, both substituted at their chiral centres. Studies of members of this group have resulted in the proposal of general catalytic mechanisms, although no structural information is available in order to better characterize their function. This work presents the initial stages of the structural investigation of the group I α-haloacid dehalogenase DehI. The DehI gene was cloned into a pET15b vector with an N-terminal His tag and expressed in Escherichia coli Nova Blue strain. Purified protein was crystallized in 25% PEG 3350, 0.4 M lithium sulfate and 0.1 M bis-tris buffer pH 6.0. The crystals were primitive monoclinic (space group P2{sub 1}), with unit-cell parameters a = 68.32, b = 111.86, c = 75.13 Å, α = 90, β = 93.7, γ = 90°, and a complete native data set was collected. Molecular replacement is not an option for structure determination, so further experimental phasing methods will be necessary.

  19. Purification, crystallization and preliminary crystallographic analysis of DehI, a group I α-haloacid dehalogenase from Pseudomonas putida strain PP3

    International Nuclear Information System (INIS)

    Schmidberger, Jason W.; Wilce, Jackie A.; Weightman, Andrew J.; Wilce, Matthew C. J.

    2008-01-01

    The α-haloacid dehalogenase DehI from P. putida strain PP3 was cloned into a vector with an N-terminal His tag and expressed in E. coli Nova Blue strain. Purified protein was crystallized in a primitive monoclinic form and a complete native data set was collected and analysed. Pseudomonas putida strain PP3 produces two dehalogenases, DehI and DehII, which belong to the group I and II α-haloacid dehalogenases, respectively. Group I dehalogenases catalyse the removal of halides from d-haloalkanoic acids and in some cases also the l-enantiomers, both substituted at their chiral centres. Studies of members of this group have resulted in the proposal of general catalytic mechanisms, although no structural information is available in order to better characterize their function. This work presents the initial stages of the structural investigation of the group I α-haloacid dehalogenase DehI. The DehI gene was cloned into a pET15b vector with an N-terminal His tag and expressed in Escherichia coli Nova Blue strain. Purified protein was crystallized in 25% PEG 3350, 0.4 M lithium sulfate and 0.1 M bis-tris buffer pH 6.0. The crystals were primitive monoclinic (space group P2 1 ), with unit-cell parameters a = 68.32, b = 111.86, c = 75.13 Å, α = 90, β = 93.7, γ = 90°, and a complete native data set was collected. Molecular replacement is not an option for structure determination, so further experimental phasing methods will be necessary

  20. Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling.

    Science.gov (United States)

    Marques, Sérgio M; Dunajova, Zuzana; Prokop, Zbynek; Chaloupkova, Radka; Brezovsky, Jan; Damborsky, Jiri

    2017-08-28

    The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution ( Pavlova, M. et al. Nat. Chem. Biol. 2009 , 5 , 727 - 733 ), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements. Using molecular dynamics and quantum mechanics approaches we have surveyed (i) the substrate binding, (ii) the formation of the reactive complex, (iii) the chemical step, and (iv) the release of the products. We showed that the binding of the substrate and its transport through the molecular tunnel to the active site is a relatively fast process. The cleavage of the carbon-halogen bond was previously identified as the rate-limiting step in the wild-type. Here we demonstrate that this step was enhanced in DhaA31 due to a significantly higher number of reactive configurations of the substrate and a decrease of the energy barrier to the S N 2 reaction. C176Y and V245F were identified as the key mutations responsible for most of those improvements. The release of the alcohol product was found to be the rate-limiting step in DhaA31 primarily due to the C176Y mutation. Mutational dissection of DhaA31 and kinetic analysis of the intermediate mutants confirmed the theoretical observations. Overall, our comprehensive computational approach has unveiled mechanistic details of the catalytic cycle which will enable a balanced design of more efficient enzymes. This approach is applicable to deepen the biochemical knowledge of a large number of other systems and may contribute to robust

  1. Improved catalytic properties of halohydrin dehalogenase by modification of the halide-binding site.

    Science.gov (United States)

    Tang, Lixia; Torres Pazmiño, Daniel E; Fraaije, Marco W; de Jong, René M; Dijkstra, Bauke W; Janssen, Dick B

    2005-05-03

    Halohydrin dehalogenase (HheC) from Agrobacterium radiobacter AD1 catalyzes the dehalogenation of vicinal haloalcohols by an intramolecular substitution reaction, resulting in the formation of the corresponding epoxide, a halide ion, and a proton. Halide release is rate-limiting during the catalytic cycle of the conversion of (R)-p-nitro-2-bromo-1-phenylethanol by the enzyme. The recent elucidation of the X-ray structure of HheC showed that hydrogen bonds between the OH group of Tyr187 and between the Odelta1 atom of Asn176 and Nepsilon1 atom of Trp249 could play a role in stabilizing the conformation of the halide-binding site. The possibility that these hydrogen bonds are important for halide binding and release was studied using site-directed mutagenesis. Steady-state kinetic studies revealed that mutant Y187F, which has lost both hydrogen bonds, has a higher catalytic activity (k(cat)) with two of the three tested substrates compared to the wild-type enzyme. Mutant W249F also shows an enhanced k(cat) value with these two substrates, as well as a remarkable increase in enantiopreference for (R)-p-nitro-2-bromo-1-phenylethanol. In case of a mutation at position 176 (N176A and N176D), a 1000-fold lower catalytic efficiency (k(cat)/K(m)) was obtained, which is mainly due to an increase of the K(m) value of the enzyme. Pre-steady-state kinetic studies showed that a burst of product formation precedes the steady state, indicating that halide release is still rate-limiting for mutants Y187F and W249F. Stopped-flow fluorescence experiments revealed that the rate of halide release is 5.6-fold higher for the Y187F mutant than for the wild-type enzyme and even higher for the W249F enzyme. Taken together, these results show that the disruption of two hydrogen bonds around the halide-binding site increases the rate of halide release and can enhance the overall catalytic activity of HheC.

  2. In vivo imaging of human biochemistry

    International Nuclear Information System (INIS)

    Hall, L.D.

    1983-01-01

    Positron Emission Tomography (PET) is an extremely powerful method for studying aspects of the biochemistry of defined regions of the human body, literally 'in-vivo' biochemistry. To place this technique in the broader perspective of medical diagnostic methods an introduction is given to some of the more important imaging methods which are already widely used clinically. A brief summary of the most recently developed imaging method, which is based on Nuclear Magnetic Resonance (NMR) Spectroscopy, is also included

  3. Nutritional Biochemistry of Space Flight

    Science.gov (United States)

    Smith, Scott M.

    2000-01-01

    Adequate nutrition is critical for maintenance of crew health during and after extended-duration space flight. The impact of weightlessness on human physiology is profound, with effects on many systems related to nutrition, including bone, muscle, hematology, fluid and electrolyte regulation. Additionally, we have much to learn regarding the impact of weightlessness on absorption, mtabolism , and excretion of nutrients, and this will ultimately determine the nutrient requirements for extended-duration space flight. Existing nutritional requirements for extended-duration space flight have been formulated based on limited flight research, and extrapolation from ground-based research. NASA's Nutritional Biochemistry Laboratory is charged with defining the nutritional requirements for space flight. This is accomplished through both operational and research projects. A nutritional status assessment program is included operationally for all International Space Station astronauts. This medical requirement includes biochemical and dietary assessments, and is completed before, during, and after the missions. This program will provide information about crew health and nutritional status, and will also provide assessments of countermeasure efficacy. Ongoing research projects include studies of calcium and bone metabolism, and iron absorption and metabolism. The calcium studies include measurements of endocrine regulation of calcium homeostasis, biochemical marker of bone metabolism, and tracer kinetic studies of calcium movement in the body. These calcium kinetic studies allow for estimation of intestinal absorption, urinary excretion, and perhaps most importantly - deposition and resorption of calcium from bone. The Calcium Kinetics experiment is currently being prepared for flight on the Space Shuttle in 2001, and potentially for subsequent Shuttle and International Space Station missions. The iron study is intended to assess whether iron absorption is down-regulated dUl1ng

  4. Education in Medical Biochemistry in Serbia.

    Science.gov (United States)

    Majkic-Sing, Nada

    2010-06-01

    Medical biochemistry is the usual name for clinical biochemistry or clinical chemistry in Serbia. Medical biochemistry laboratories and medical biochemists as a profession are part of Health Care System and are regulated through: the Health Care Law and rules issued by the Chamber of Medical Biochemists of Serbia. The first continuous and organized education for Medical Biochemists in Serbia dates from 1945, when Department of Medical Biochemistry was established at Pharmaceutical Faculty in Belgrade. In 1987 at the same Faculty a five years undergraduate branch was established, educating Medical Biochemists under a special program. Since 2006 the new five year undergraduate (according to Bologna Declaration) and postgraduate program of four-year specialization according to EC4 European Syllabus for Post-Graduate Training in Clinical Chemistry and Laboratory Medicine has been established. The Ministry of Education and Ministry of Public Health accredits the programs. There are four requirements for practicing medical biochemistry in the Health Care System: University Diploma of the Faculty of Pharmacy (Medical Biochemistry), successful completion of the profession exam at the Ministry of Health after completion of one additional year of obligatory practical training in medical laboratories, membership in the Serbian Chamber of Medical Biochemists and licence for skilled work issued by Serbian Chamber of Medical Biochemists.

  5. INTERNET ASSISTED LEARNING OF BIOCHEMISTRY

    Directory of Open Access Journals (Sweden)

    R.M. Lima

    2005-07-01

    Full Text Available The revolution  in information  technology  has included the INTERNET to the available  resources for biochemical  education.  There  is a great  deal of biochemical  information, and  the  amount is increas- ing rapidly,  indeed  exponentially.  The  aim of this work is to analyze  the  biochemical  issues cellular respiration, photosynthesis and membrane  transport available  in web pages, taking  into account con- tents  quality,  trustworthiness and effectiveness. Firstly  1st secondary level students were inquired by a questionnaire on their use of INTERNET resources.  More then 80 percent of them were regular users. The  results  confirm the  already  known  potential of INTERNET in education.  Fourteen sites  were analyzed  regarding  to contents, presence  of bibliographical, references,  authorship, titles  responsible and adequacy  to the target public.  In relation  to contents, presence of conceptual  errors, illustrations and other  stimulatory elements  were analyzed.  The great  majority  did not mention  bibliographic  ref- erences and target public.  Less than  half divulged responsible  names and/or their  graduation status. Some sites contained critical  conceptual  errors,  as the mention  of, as examples:  during  the cell active transport process, of energy (ATP waste (desperdício by the cell; the yeast is a pluricellular  fungal; and  the  oxygen is essential  for anaerobic  respiration.  However,  one of the  sites,  where  such  errors were found, was the only one to mention  enzymes and regulation  steps of cellular respiration. Half of the sites present identical  texts  and figures. None of the analyzed  sites thus  was considered excellent. Our data  strenghthen the need for rigorous evaluation concerning of scholarly research  of biochemical theme  on the web.INTERNET ASSISTED LEARNING OF  BIOCHEMISTRY

  6. Regio- and Enantioselective Sequential Dehalogenation of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB.

    Science.gov (United States)

    Gross, Johannes; Prokop, Zbyněk; Janssen, Dick; Faber, Kurt; Hall, Mélanie

    2016-08-03

    The hydrolytic dehalogenation of rac-1,3-dibromobutane catalyzed by the haloalkane dehalogenase LinB from Sphingobium japonicum UT26 proceeds in a sequential fashion: initial formation of intermediate haloalcohols followed by a second hydrolytic step to produce the final diol. Detailed investigation of the course of the reaction revealed favored nucleophilic displacement of the sec-halogen in the first hydrolytic event with pronounced R enantioselectivity. The second hydrolysis step proceeded with a regioselectivity switch at the primary position, with preference for the S enantiomer. Because of complex competition between all eight possible reactions, intermediate haloalcohols formed with moderate to good ee ((S)-4-bromobutan-2-ol: up to 87 %). Similarly, (S)-butane-1,3-diol was formed at a maximum ee of 35 % before full hydrolysis furnished the racemic diol product. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. BIOLUMINESCENCE: TEACHING BIOCHEMISTRY BEYOND THE UNIVERSITY WALLS

    Directory of Open Access Journals (Sweden)

    Ana Paula Jesus de Almeida

    2016-11-01

    Full Text Available INTRODUCTION: The use of video in teaching and learning processes provides a challenging environment, able to stimulate the intellect and facilitate understanding in life science studies. Videos can be of extraordinary importance in education and dissemination of knowledge, contributing to greater learning, but is rarely used and exploited properly, especially for teaching biochemistry. Biochemistry is considered complex because it involves many molecular structures and processes, especially considering the number of events and molecules involved in the metabolism. OBJECTIVES: This study aimed to introduce biochemistry for the students of basic education using the theme "Light, Science and Life" in a playful and fun way. MATERIALS AND METHODS: A video about bioluminescence was designed and prepared aiming to use it as a support for learning biochemistry by students of basic education of public schools located in Salvador, Bahia. In order to prepare the video, undergraduate students initially revised the literature in order to acquire proper knowledge, and along with their teacher advisor worked the elaboration of texts, textbook and questionnaire and applied at school. DISCUSSION AND RESULTS: Analysis the qualitative results of the experiment on the preparation and use of the video about "Bioluminescence" focused mainly on the content of biochemistry linked to theme Light, Science and Life, and demonstrated the importance of such work in the teaching-learning process. The dynamics used allowed greater interaction between students and teacher, and the teaching of biochemistry in a fun way beyond the university walls. CONCLUSION: The teaching through recreational resources, e.g. videos and other educational strategies that foster learning should be encouraged from basic education, always bearing in order to transmit through these teaching methods the main concepts covered in biochemistry.

  8. In-silico gene co-expression network analysis in Paracoccidioides brasiliensis with reference to haloacid dehalogenase superfamily hydrolase gene

    Directory of Open Access Journals (Sweden)

    Raghunath Satpathy

    2015-01-01

    Full Text Available Context: Paracoccidioides brasiliensis, a dimorphic fungus is the causative agent of paracoccidioidomycosis, a disease globally affecting millions of people. The haloacid dehalogenase (HAD superfamily hydrolases enzyme in the fungi, in particular, is known to be responsible in the pathogenesis by adhering to the tissue. Hence, identification of novel drug targets is essential. Aims: In-silico based identification of co-expressed genes along with HAD superfamily hydrolase in P. brasiliensis during the morphogenesis from mycelium to yeast to identify possible genes as drug targets. Materials and Methods: In total, four datasets were retrieved from the NCBI-gene expression omnibus (GEO database, each containing 4340 genes, followed by gene filtration expression of the data set. Further co-expression (CE study was performed individually and then a combination these genes were visualized in the Cytoscape 2. 8.3. Statistical Analysis Used: Mean and standard deviation value of the HAD superfamily hydrolase gene was obtained from the expression data and this value was subsequently used for the CE calculation purpose by selecting specific correlation power and filtering threshold. Results: The 23 genes that were thus obtained are common with respect to the HAD superfamily hydrolase gene. A significant network was selected from the Cytoscape network visualization that contains total 7 genes out of which 5 genes, which do not have significant protein hits, obtained from gene annotation of the expressed sequence tags by BLAST X. For all the protein PSI-BLAST was performed against human genome to find the homology. Conclusions: The gene co-expression network was obtained with respect to HAD superfamily dehalogenase gene in P. Brasiliensis.

  9. Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1

    Directory of Open Access Journals (Sweden)

    Ismaila Yada Sudi

    2012-11-01

    Full Text Available Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD simulation and docking of D-2-chloropropionate (D-2CP, D-2-bromopropionate (D-2BP, monochloroacetate (MCA, monobromoacetate (MBA, 2,2-dichloropropionate (2,2-DCP, d,l-2,3-dichloropropionate (d,l-2,3-DCP, and 3-chloropropionate (3-CP into the DehD active site. The sequences of DehD and D-2-haloacid dehalogenase (HadD from Pseudomonas putida AJ1 have 15% sequence similarity. The model had 80% of the amino acid residues in the most favored region when compared to the crystal structure of DehI from Pseudomonas putida PP3. Docking analysis revealed that Arg107, Arg134 and Tyr135 interacted with D-2CP, and Glu20 activated the water molecule for hydrolytic dehalogenation. Single residue substitutions at 25–30 °C showed that polar residues of DehD were stable when substituted with nonpolar residues and showed a decrease in activity within the same temperature range. The molecular dynamics simulation of DehD and its variants showed that in R134A variant, Arg107 interacted with D-2CP, while in Y135A, Gln221 and Arg231 interacted with D-2CP. It is our emphatic belief that the new model will be useful for the rational design of DehDs with enhanced potentials.

  10. The Biochemistry Tetrahedron and the Development of the Taxonomy of Biochemistry External Representations (TOBER)

    Science.gov (United States)

    Towns, Marcy H.; Raker, Jeffrey R.; Becker, Nicole; Harle, Marissa; Sutcliffe, Jonathan

    2012-01-01

    Visual literacy, the ability to interpret and create external representations (ERs), is essential to success in biochemistry. Studies have been conducted that describe students' abilities to use and interpret specific types of ERs. However, a framework for describing ERs derived through a naturalistic inquiry of biochemistry classrooms has not…

  11. Effects of intensive mariculture on sediment biochemistry

    DEFF Research Database (Denmark)

    Pusceddu, Antonio; Fraschetti, Simonetta; Mirto, Simone

    2007-01-01

    The exponential growth of off-shore mariculture that has occurred worldwide over the last 10 years has raised concern about the impact of the waste produced by this industry on the ecological integrity of the sea bottom. Investigations into this potential source of impact on the biochemistry...... of the sea floor have provided contrasting results, and no compelling explanations for these discrepancies have been provided to date. To quantify the impact of fish-farm activities on the biochemistry of sediments, we have investigated the quantity and biochemical composition of sediment organic matter...... regions, with the exception of seagrass sediments in Spain, the biochemistry of the sediments showed significant differences between the control and fish-farm locations. However, the variables explaining the differences observed varied among the regions and between habitats, suggesting idiosyncratic...

  12. BOREAS TE-9 NSA Canopy Biochemistry

    Science.gov (United States)

    Hall, Forrest G. (Editor); Curd, Shelaine (Editor); Margolis, Hank; Charest, Martin; Sy, Mikailou

    2000-01-01

    The BOREAS TE-9 team collected several data sets related to chemical and photosynthetic properties of leaves. This data set contains canopy biochemistry data collected in 1994 in the NSA at the YJP, OJR, OBS, UBS, and OA sites, including biochemistry lignin, nitrogen, cellulose, starch, and fiber concentrations. These data were collected to study the spatial and temporal changes in the canopy biochemistry of boreal forest cover types and how a high-resolution radiative transfer model in the mid-infrared could be applied in an effort to obtain better estimates of canopy biochemical properties using remote sensing. The data are available in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  13. Identification of functional residues essential for dehalogenation by the non-stereospecific α-haloalkanoic acid dehalogenase from Rhizobium sp. RC1.

    Science.gov (United States)

    Hamid, Azzmer Azzar Abdul; Hamid, Tengku Haziyamin Tengku Abdul; Wahab, Roswanira Abdul; Huyop, Fahrul

    2015-03-01

    The non-stereospecific α-haloalkanoic acid dehalogenase DehE from Rhizobium sp. RC1 catalyzes the removal of the halide from α-haloalkanoic acid D,L-stereoisomers and, by doing so, converts them into hydroxyalkanoic acid L,D-stereoisomers, respectively. DehE has been extensively studied to determine its potential to act as a bioremediation agent, but its structure/function relationship has not been characterized. For this study, we explored the functional relevance of several putative active-site amino acids by site-specific mutagenesis. Ten active-site residues were mutated individually, and the dehalogenase activity of each of the 10 resulting mutants in soluble cell lysates against D- and L-2-chloropropionic acid was assessed. Interestingly, the mutants W34→A,F37→A, and S188→A had diminished activity, suggesting that these residues are functionally relevant. Notably, the D189→N mutant had no activity, which strongly implies that it is a catalytically important residue. Given our data, we propose a dehalogenation mechanism for DehE, which is the same as that suggested for other non-stereospecific α-haloalkanoic acid dehalogenases. To the best of our knowledge, this is the first report detailing a functional aspect for DehE, and our results could help pave the way for the bioengineering of haloalkanoic acid dehalogenases with improved catalytic properties. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Release of Halide Ions from the Buried Active Site of the Haloalkane Dehalogenase LinB Revealed by Stopped-Flow Fluorescence Analysis and Free Energy Calculations

    Czech Academy of Sciences Publication Activity Database

    Hladílková, Jana; Prokop, Z.; Chaloupková, R.; Damborský, J.; Jungwirth, Pavel

    2013-01-01

    Roč. 117, č. 46 (2013), s. 14329-14335 ISSN 1520-6106 R&D Projects: GA ČR GBP208/12/G016 Grant - others:GA ČR(CZ) GAP207/12/0775 Program:GA Institutional support: RVO:61388963 Keywords : access tunnel * buried active site * catalytic activity * enzyme mechanism * haloalkane dehalogenase * halide ions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.377, year: 2013

  15. Purifying, cloning and characterizing a novel dehalogenase from Bacillus sp. GZT to enhance the biodegradation of 2,4,6-tribromophenol in water.

    Science.gov (United States)

    Liang, Zhishu; Li, Guiying; An, Taicheng

    2017-06-01

    2,4,6-Tribromophenol (TBP), an intermediate of brominated flame retardants, can easily release to environment and recalcitrant to degradation. Previously, Bacillus sp. GZT, a pure aerobic strain capable of simultaneously debrominating and mineralizing TBP, was successfully isolated by us. To further obtain a practical application and dig up its TBP degradation mechanism, a total of 46.7-fold purification of a novel dehalogenase with a final specific activity of 18.9 U mg -1 and a molecular mass of 63.4 kDa was achieved. Under optimal conditions (35 °C and 200 rpm), up to 80% degradation efficiencies were achieved within 120 min. Adding H 2 O 2 , NADPH, Mn 2+ and Mg 2+ promoted enzyme reaction effectively; while EDTA, methyl viologen, Ni 2+ , Cu 2+ , Ca 2+ and Fe 2+ strongly inhibited reaction activities. The debromination of TBP was catalyzed by the enzyme at a Km of 78 μM and a Vmax of 0.65 min -1  mg protein -1 , which indicated that this dehalogenase could specifically eliminate TBP with a high efficiency and stability. Based on MALDI-TOF/TOF analysis, the dehalogenase shared 98% identity with peptide ABC transporter substrate-binding protein. One open reading frame (ORF) encoding this peptide was found in Strain GZT genome, subjected to clone and expressed in Escherichia coli (E. coli) to characterize the encoding gene. Result showed that this recombinant strain could also remove as similar amount of TBP as Bacillus sp. GZT under the identical condition. Based on these results, we suggest that this newly-isolated TBP dehalogenase highlights a new approach for remediating TBP pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. THE BIOCHEMISTRY OF VITREOSCILLA HEMOGLOBIN

    Directory of Open Access Journals (Sweden)

    Benjamin C. Stark

    2012-10-01

    Full Text Available The hemoglobin (VHb from Vitreoscilla was the first bacterial hemoglobin discovered. Its structure and function have been extensively investigated, and engineering of a wide variety of heterologous organisms to express VHb has been performed to increase their growth and productivity. This strategy has shown promise in applications as far-ranging as the production of antibiotics and petrochemical replacements by microorganisms to increasing stress tolerance in plants. These applications of “VHb technology” have generally been of the “black box” variety, wherein the endpoint studied is an increase in the levels of a certain product or improved growth and survival. Their eventual optimization, however, will require a thorough understanding of the various functions and activities of VHb, and how VHb expression ripples to affect metabolism more generally. Here we review the current knowledge of these topics. VHb's functions all involve oxygen binding (and often delivery in one way or another. Several biochemical and structure-function studies have provided an insight into the molecular details of this binding and delivery. VHb activities are varied. They include supply of oxygen to oxygenases and the respiratory chain, particularly under low oxygen conditions; oxygen sensing and modulation of transcription factor activity; and detoxification of NO, and seem to require interactions of VHb with “partner proteins”. VHb expression affects the levels of ATP and NADH, although not enormously. VHb expression may affect the level of many compounds of intermediary metabolism, and, apparently, alters the levels of expression of many genes. Thus, the metabolic changes in organisms engineered to express VHb are likely to be numerous and complicated.

  17. Symposium 19: The contributions of the Department of Biochemistry/USP towards Biochemistry teaching

    OpenAIRE

    Baptista Torres, Bayardo; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP)

    2014-01-01

    K-Education(Portuguese) Chair: V. Trindade Bayardo Torres; Clovis Wannmacher; Denise MacedoThe contributions of the Department of Biochemistry/USP towards Biochemistry teaching.O ensino de Bioquímica nos últimos 20 anosBayardo B. TorresDepartamento de Bioquímica, Instituto de Química, USP. São Paulo, Brazil.Among the contributions of the Department of Biochemistry/USP one must recall:1. Winter school for graduate studentsThis course, now at the ninth edition, is intended for students in the f...

  18. Blood biochemistry responses of chickens experimentally infected ...

    African Journals Online (AJOL)

    This study investigated the blood biochemistry responses of cockerels experimentally infected with a velogenic Newcastle disease virus (NDV) strain, KUDU 113. One hundred Isa white cockerels were used for the study. The cockerels were obtained at day-old and randomly divided into groups A- vaccinated and infected, ...

  19. Jmol-Enhanced Biochemistry Research Projects

    Science.gov (United States)

    Saderholm, Matthew; Reynolds, Anthony

    2011-01-01

    We developed a protein research project for a one-semester biochemistry lecture class to enhance learning and more effectively train students to understand protein structure and function. During this semester-long process, students select a protein with known structure and then research its structure, sequence, and function. This project…

  20. Modern trends in biochemistry and biotechnology

    International Nuclear Information System (INIS)

    1996-01-01

    On the conference 'Modern trends in biochemistry and biotechnology' several lectures concerned influence of ionizing radiation on the animal cells. Changes in the cell division caused by radiation induced DNA damage were discussed. Application of single cell gel electrophoresis assay (comet assay) in assessment of DNA damages was the subject of dedicated session

  1. Haematology, serum biochemistry and growth performance of ...

    African Journals Online (AJOL)

    High performing does have the tendency of producing healthy kids with reasonable weight at birth compared to least performing does. A study was conducted to investigate the haematology, serum biochemistry and growth performance of grazing pregnant Kalahari Red does fed concentrate diets at three protein levels.

  2. Identification of Threshold Concepts for Biochemistry

    Science.gov (United States)

    Loertscher, Jennifer; Green, David; Lewis, Jennifer E.; Lin, Sara; Minderhout, Vicky

    2014-01-01

    Threshold concepts (TCs) are concepts that, when mastered, represent a transformed understanding of a discipline without which the learner cannot progress. We have undertaken a process involving more than 75 faculty members and 50 undergraduate students to identify a working list of TCs for biochemistry. The process of identifying TCs for…

  3. A Kinetic Experiment for the Biochemistry Laboratory.

    Science.gov (United States)

    Palmer, Richard E.

    1986-01-01

    Discusses the use of specific reactions of metabolic pathways to make measurements in the laboratory. Describes an adaptation of an experiment used in undergraduate biochemistry laboratories involving the induction of an enzyme in E. coli, as well as its partial purification and characterization. (TW)

  4. There is No Overkill in Biochemistry

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 17; Issue 12. There is No Overkill in Biochemistry - Har Gobind Khorana, a Pioneer in Membrane Biology. Sadashiva Karnik Sriram Subramaniam. General Article Volume 17 Issue 12 December 2012 pp 1157-1164 ...

  5. Biochemistry in the idea of graduation students

    Directory of Open Access Journals (Sweden)

    D. F. Escoto et al

    2015-08-01

    Full Text Available INTRODUCTION AND OBJECTIVE: Biochemistry is an interdisciplinary area that allows us to study chemical phenomena in live organisms. That way, its study is of extreme importance, in all levels, to enlarge the comprehension of natural phenomena. However, it is barely explored in the basic education and often fragmented in the higher education, or in graduation degrees that contemplate this area. Especially in the teacher training, where the fragmentation of knowledge can contribute to form wrong concepts. Based on that, this work aims to identify the concept of Biochemistry according to the future teachers of Natural Science. MATERIALS AND METHODS: The work was developed with 3º, 5º and 9º semesters students of the natural science degree on Universidade Federal do Pampa. 50 students, from 18 to 56 years old, were interviewed. The data was obtained through a semi-structured questionnaire. The methodology of categorization and analysis of content with emergent categories of speech was chosen for the analysis. RESULTS AND CONCLUSION: Initially, 11 categories were chosen by content similarity. In descending order: chemical reactions in organisms, chemistry area, chemistry of life, cell metabolism, the study of living beings, origin of life, biology area, organic balance, chemical-biological study. The reports made possible to identify that most students do understand with clarity the goal of studying biochemistry. Although, we can see that there are some students that fragment the area, what means, they try to discriminate chemistry from biology. This way, they demonstrate a difficulty to comprehend biochemistry as interdisciplinary, what makes it hard to contextualize the built knowledge. It is important to develop strategies to overcome the fragmentation of knowledge, so that biochemistry can be comprehended in its fullness and help on the teaching processes that will be developed by the future teachers.

  6. Commentary: PhDs in Biochemistry Education--5 Years Later

    Science.gov (United States)

    Offerdahl, Erika G.; Momsen, Jennifer L.; Osgood, Marcy

    2014-01-01

    In this commentary, the discussion of PhDs in biochemistry education research is expanded to explore a number of diverse pathways leading to a competitive research program in biochemistry education research.

  7. Exploring protein structure and dynamics through a project-oriented biochemistry laboratory module.

    Science.gov (United States)

    Lipchock, James M; Ginther, Patrick S; Douglas, Bonnie B; Bird, Kelly E; Patrick Loria, J

    2017-09-01

    Here, we present a 10-week project-oriented laboratory module designed to provide a course-based undergraduate research experience in biochemistry that emphasizes the importance of biomolecular structure and dynamics in enzyme function. This module explores the impact of mutagenesis on an important active site loop for a biomedically-relevant human enzyme, protein tyrosine phosphatase 1B (PTP1B). Over the course of the semester students guide their own mutant of PTP1B from conception to characterization in a cost-effective manner and gain exposure to fundamental techniques in biochemistry, including site-directed DNA mutagenesis, bacterial recombinant protein expression, affinity column purification, protein quantitation, SDS-PAGE, and enzyme kinetics. This project-based approach allows an instructor to simulate a research setting and prepare students for productive research beyond the classroom. Potential modifications to expand or contract this module are also provided. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):403-410, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  8. Television Medical Dramas as Case Studies in Biochemistry

    Science.gov (United States)

    Millard, Julie T.

    2009-01-01

    Several case studies from popular television medical dramas are described for use in an undergraduate biochemistry course. These cases, which illustrate fundamental principles of biochemistry, are used as the basis for problems that can be discussed further in small groups. Medical cases provide an interesting context for biochemistry with video…

  9. Commentary: PhDs in biochemistry education-5 years later.

    Science.gov (United States)

    Offerdahl, Erika G; Momsen, Jennifer L; Osgood, Marcy

    2014-01-01

    In this commentary, the discussion of PhDs in biochemistry education research is expanded to explore a number of diverse pathways leading to a competitive research program in biochemistry education research. © 2013 by The International Union of Biochemistry and Molecular Biology.

  10. [Scientific and practical activity of the Department of Muscle Biochemistry of the Palladin Institute of Biochemistry of NAS of Ukraine].

    Science.gov (United States)

    Vynogradova, R P; Danilova, V M; Yurasova, S P

    2017-01-01

    The article focuses on scientific and practical activity of the Department of Muscle Biochemistry of the Palladin Institute of Biochemistry of NAS of Ukraine in the context of its foundation and development. Main findings and practical achievements in the area of muscle biochemistry are summarized and discussed.

  11. Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling

    Science.gov (United States)

    Banáš, Pavel; Otyepka, Michal; Jeřábek, Petr; Petřek, Martin; Damborský, Jiří

    2006-06-01

    1,2,3-Trichloropropane (TCP) is a highly toxic, recalcitrant byproduct of epichlorohydrin manufacture. Haloalkane dehalogenase (DhaA) from Rhodococcus sp. hydrolyses the carbon-halogen bond in various halogenated compounds including TCP, but with low efficiency ( k cat/ K m = 36 s-1 M-1). A Cys176Tyr-DhaA mutant with a threefold higher catalytic efficiency for TCP dehalogenation has been previously obtained by error-prone PCR. We have used molecular simulations and quantum mechanical calculations to elucidate the molecular mechanisms involved in the improved catalysis of the mutant, and enantioselectivity of DhaA toward TCP. The Cys176Tyr mutation modifies the protein access and export routes. Substitution of the Cys residue by the bulkier Tyr narrows the upper tunnel, making the second tunnel "slot" the preferred route. TCP can adopt two major orientations in the DhaA enzyme, in one of which the halide-stabilizing residue Asn41 forms a hydrogen bond with the terminal halogen atom of the TCP molecule, while in the other it bonds with the central halogen atom. The differences in these binding patterns explain the preferential formation of the ( R)- over the ( S)-enantiomer of 2,3-dichloropropane-1-ol in the reaction catalyzed by the enzyme.

  12. How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase

    Directory of Open Access Journals (Sweden)

    Yanwei Li

    2016-08-01

    Full Text Available The quantum mechanics/molecular mechanics (QM/MM method (e.g., density functional theory (DFT/MM is important in elucidating enzymatic mechanisms. It is indispensable to study “multiple” conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case.

  13. Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents.

    Science.gov (United States)

    Stepankova, Veronika; Khabiri, Morteza; Brezovsky, Jan; Pavelka, Antonin; Sykora, Jan; Amaro, Mariana; Minofar, Babak; Prokop, Zbynek; Hof, Martin; Ettrich, Rudiger; Chaloupkova, Radka; Damborsky, Jiri

    2013-05-10

    The use of enzymes for biocatalysis can be significantly enhanced by using organic cosolvents in the reaction mixtures. Selection of the cosolvent type and concentration range for an enzymatic reaction is challenging and requires extensive empirical testing. An understanding of protein-solvent interaction could provide a theoretical framework for rationalising the selection process. Here, the behaviour of three model enzymes (haloalkane dehalogenases) was investigated in the presence of three representative organic cosolvents (acetone, formamide, and isopropanol). Steady-state kinetics assays, molecular dynamics simulations, and time-resolved fluorescence spectroscopy were used to elucidate the molecular mechanisms of enzyme-solvent interactions. Cosolvent molecules entered the enzymes' access tunnels and active sites, enlarged their volumes with no change in overall protein structure, but surprisingly did not act as competitive inhibitors. At low concentrations, the cosolvents either enhanced catalysis by lowering K(0.5) and increasing k(cat), or caused enzyme inactivation by promoting substrate inhibition and decreasing k(cat). The induced activation and inhibition of the enzymes correlated with expansion of the active-site pockets and their occupancy by cosolvent molecules. The study demonstrates that quantitative analysis of the proportions of the access tunnels and active-sites occupied by organic solvent molecules provides the valuable information for rational selection of appropriate protein-solvent pair and effective cosolvent concentration. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Production of chlorothalonil hydrolytic dehalogenase from agro-industrial wastewater and its application in raw food cleaning.

    Science.gov (United States)

    He, Qin; Xu, Xi-Hui; Zhang, Fan; Tai, Yu-Kai; Luo, Yan-Fei; He, Jian; Hong, Qing; Jiang, Jian-Dong; Yan, Xin

    2017-06-01

    To reduce the fermentation cost for industrialization of chlorothalonil hydrolytic dehalogenase (Chd), agro-industrial wastewaters including molasses, corn steep liquor (CSL) and fermentation wastewater were used to substitute for expensive carbon and nitrogen sources and fresh water for lab preparation. The results showed that molasses and CSL could replace 5% carbon source and 100% organic nitrogen source respectively to maintain the same fermentation level. Re-fermentation from raffinate of ultra-filtered fermentation wastewater could achieve 61.03% of initial Chd activity and reach 96.39% activity when cultured in a mixture of raffinate and 50% of original medium constituent. Typical raw foods were chosen to evaluate the chlorothalonil removal ability of Chd. After Chd treatment for 2 h at room temperature, 97.40 and 75.55% of 30 mg kg -1 chlorothalonil on cherry tomato and strawberry respectively and 60.29% of 50 mg kg -1 chlorothalonil on Chinese cabbage were removed. Furthermore, the residual activity of the enzyme remained at 78-82% after treatment, suggesting its potential for reuse. This study proved the cost-feasibility of large-scale production of Chd from agro-industrial wastewater and demonstrated the potential of Chd in raw food cleaning. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  15. Studies of biochemistry and clinical biochemistry. Studies at sample medical schools in 13 EU countries regarding biochemistry and clinical biochemistry teaching.

    Science.gov (United States)

    Stern, Petr; Sebesta, Ivan; Trnkova, Bohuslava; Zima, Tomas

    2008-07-01

    The study summarizes the results obtained during personal visits to 53 medical schools in the 13 original EU countries during 2004--2006. Data from the Czech Republic is shown for comparison. The possibilities of acquiring information from the websites of the medical schools in the local language and English are assessed. The admission process to medical schools and the organization of studies of medicine, dentistry, and non-medical healthcare fields are briefly characterized. Significant attention is paid to the forms of education in biochemistry and clinical (bio)chemistry in the medical study field. The position of these subjects in the studies of dentistry and non-medical healthcare fields is also noted. In addition, the course of subject exams is described. The methods of funding and postgraduate studies at the medical schools are also briefly addressed.

  16. Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31

    Czech Academy of Sciences Publication Activity Database

    Lahoda, M.; Mesters, J. R.; Stsiapanava, A.; Chaloupková, R.; Kutý, Michal; Damborský, J.; Kutá-Smatanová, Ivana

    2014-01-01

    Roč. 70, FEB 2014 (2014), s. 209-217 ISSN 0907-4449 Institutional support: RVO:67179843 Keywords : DhaA31 * substrate-free * 3rk4 * complex with TCP * 4fwb * wild-type DhaA * 4hzg Subject RIV: CE - Biochemistry Impact factor: 7.232, year: 2013

  17. Writing throughout the biochemistry curriculum: Synergistic inquiry-based writing projects for biochemistry students.

    Science.gov (United States)

    Mertz, Pamela; Streu, Craig

    2015-01-01

    This article describes a synergistic two-semester writing sequence for biochemistry courses. In the first semester, students select a putative protein and are tasked with researching their protein largely through bioinformatics resources. In the second semester, students develop original ideas and present them in the form of a research grant proposal. Both projects involve multiple drafts and peer review. The complementarity of the projects increases student exposure to bioinformatics and literature resources, fosters higher-order thinking skills, and develops teamwork and communication skills. Student feedback and responses on perception surveys demonstrated that the students viewed both projects as favorable learning experiences. © 2015 The International Union of Biochemistry and Molecular Biology.

  18. BIOCHEMISTRY TEACHING WITH VIRTUAL DYNAMIC METABOLIC DIAGRAMS

    Directory of Open Access Journals (Sweden)

    G. B. Lazzarotto

    2004-05-01

    Full Text Available This work presents a game like educational software (courseware to study metabolic pathways, calledDiagrama Metabolico Din^amico Virtual (DMDV of Krebs Cycle. The experience acquired teachingwith the logical sequence tray games in the FFFCMPAs Biochemistry Course provides the beddingswith the use of this model as education method. With DMDV, students can assembly the sequenceof reactions that describe the desired metabolic pathway, create situational models which can guidehis/her choices, reduce the subject complexity of the scheme in knowledge construction presentingin a graphical way the current interrelations. Biochemistry teachers can use the present software inclassroom as well as distance classes. This product integrates multimedia resources extensively andis distributed in CD-ROM format. The virtual environment will make possible interaction of thestudent with the environment and with colleagues and teachers, through tools as chats and forum.Experience with the use of this method was carried through with two distinct groups of students.The rst group was composed by 11 students, who were more familiar with the content and answereda specic questionnaire to previously evaluate the software. The second group was formed by 24students regularly registered in the FFFCMPAs Biochemistry Course, who used the software as astudy method. The rst group considered DMDV of easy and pleasant navigation. The knowledgeevaluation of the second group students was made by a written test and the analysis of three conceptualmaps constructed by each one of them: one map before initiating the study with the DMDV, thesecond just after the study and the third one two months later. Every conceptual maps producedafter DMDV method showed an expansion of valid concepts if compared with the rst maps. Simplevisual comparison of maps shows that new elements where added. All students who passed throughthe experiment reached a greater than ve grade in the subjects written

  19. Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.

    Science.gov (United States)

    Klvana, Martin; Pavlova, Martina; Koudelakova, Tana; Chaloupkova, Radka; Dvorak, Pavel; Prokop, Zbynek; Stsiapanava, Alena; Kuty, Michal; Kuta-Smatanova, Ivana; Dohnalek, Jan; Kulhanek, Petr; Wade, Rebecca C; Damborsky, Jiri

    2009-10-09

    Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein X-ray crystallography, were constructed and biochemically characterized. The mutants showed distinct catalytic efficiencies with the halogenated substrate 1,2,3-trichloropropane. Release pathways for the two dehalogenation products, 2,3-dichloropropane-1-ol and the chloride ion, and exchange pathways for water molecules, were studied using classical and random acceleration molecular dynamics simulations. Five different pathways, denoted p1, p2a, p2b, p2c, and p3, were identified. The individual pathways showed differing selectivity for the products: the chloride ion releases solely through p1, whereas the alcohol releases through all five pathways. Water molecules play a crucial role for release of both products by breakage of their hydrogen-bonding interactions with the active-site residues and shielding the charged chloride ion during its passage through a hydrophobic tunnel. Exchange of the chloride ions, the alcohol product, and the waters between the buried active site and the bulk solvent can be realized by three different mechanisms: (i) passage through a permanent tunnel, (ii) passage through a transient tunnel, and (iii) migration through a protein matrix. We demonstrate that the accessibility of the pathways and the mechanisms of ligand exchange were modified by mutations. Insertion of bulky aromatic residues in the tunnel corresponding to pathway p1 leads to reduced accessibility to the ligands and a change in mechanism of opening from permanent to transient. We propose that engineering the accessibility of tunnels and the mechanisms of ligand exchange is a powerful strategy for modification of the functional properties of enzymes with buried active sites.

  20. Radioactive isotopes in biochemistry (historical essay)

    International Nuclear Information System (INIS)

    Blanko, M.A.; Shamin, A.N.

    1988-01-01

    A large volume of facts, including little-known biobibliographic data on the the first reserchers who applied the method, are used in the study. The main attention is paid to the use of the method of labelled atoms, when considering intermediate exchange of substances and creating metabolic ways maps (the end of 30-ies - beginning of 50-ies). Using as an example the history of creation of the labelled atom method and its introduction into biochemistry, the problem of the research methods transfer from one branch of science to another is considered

  1. The biochemistry of hematopoietic stem cell development.

    Science.gov (United States)

    Kaimakis, P; Crisan, M; Dzierzak, E

    2013-02-01

    The cornerstone of the adult hematopoietic system and clinical treatments for blood-related disease is the cohort of hematopoietic stem cells (HSC) that is harbored in the adult bone marrow microenvironment. Interestingly, this cohort of HSCs is generated only during a short window of developmental time. In mammalian embryos, hematopoietic progenitor and HSC generation occurs within several extra- and intraembryonic microenvironments, most notably from 'hemogenic' endothelial cells lining the major vasculature. HSCs are made through a remarkable transdifferentiation of endothelial cells to a hematopoietic fate that is long-lived and self-renewable. Recent studies are beginning to provide an understanding of the biochemical signaling pathways and transcription factors/complexes that promote their generation. The focus of this review is on the biochemistry behind the generation of these potent long-lived self-renewing stem cells of the blood system. Both the intrinsic (master transcription factors) and extrinsic regulators (morphogens and growth factors) that affect the generation, maintenance and expansion of HSCs in the embryo will be discussed. The generation of HSCs is a stepwise process involving many developmental signaling pathways, morphogens and cytokines. Pivotal hematopoietic transcription factors are required for their generation. Interestingly, whereas these factors are necessary for HSC generation, their expression in adult bone marrow HSCs is oftentimes not required. Thus, the biochemistry and molecular regulation of HSC development in the embryo are overlapping, but differ significantly from the regulation of HSCs in the adult. HSC numbers for clinical use are limiting, and despite much research into the molecular basis of HSC regulation in the adult bone marrow, no panel of growth factors, interleukins and/or morphogens has been found to sufficiently increase the number of these important stem cells. An understanding of the biochemistry of HSC

  2. Writing throughout the Biochemistry Curriculum: Synergistic Inquiry-Based Writing Projects for Biochemistry Students

    Science.gov (United States)

    Mertz, Pamela; Streu, Craig

    2015-01-01

    This article describes a synergistic two-semester writing sequence for biochemistry courses. In the first semester, students select a putative protein and are tasked with researching their protein largely through bioinformatics resources. In the second semester, students develop original ideas and present them in the form of a research grant…

  3. Site-Directed Mutagenesis Study of an Antibiotic-Sensing Noncoding RNA Integrated into a One-Semester Project-Based Biochemistry Lab Course

    Science.gov (United States)

    Gerczei, Timea

    2017-01-01

    A laboratory sequence is described that is suitable for upper-level biochemistry or molecular biology laboratories that combines project-based and traditional laboratory experiments. In the project-based sequence, the individual laboratory experiments are thematically linked and aim to show how a bacterial antibiotic sensing noncoding RNA (the…

  4. Concept mapping enhances learning of biochemistry.

    Science.gov (United States)

    Surapaneni, Krishna M; Tekian, Ara

    2013-03-05

    Teaching basic science courses is challenging in undergraduate medical education because of the ubiquitous use of didactic lectures and reward for recall of factual information during examinations. The purpose of this study is to introduce concept maps with clinical cases (the innovative program) to improve learning of biochemistry course content. Participants were first year medical students (n=150) from Saveetha Medical College and Hospital (India); they were randomly divided into two groups of 75, one group attending the traditional program, the other the innovative program. Student performance was measured using three written knowledge tests (each with a maximum score of 20). The students also evaluated the relevance of the learning process using a 12-item questionnaire. Students in the innovative program using concept mapping outperformed those in the traditional didactic program (means of 7.13-8.28 vs. 12.33-13.93, pbiochemistry to clinical practice, and to enhance their reasoning and learning skills, as well as their deeper understanding for biochemistry.

  5. Concept mapping enhances learning of biochemistry.

    Science.gov (United States)

    Surapaneni, KrishnaM; Tekian, Ara

    2013-01-01

    Teaching basic science courses is challenging in undergraduate medical education because of the ubiquitous use of didactic lectures and reward for recall of factual information during examinations. The purpose of this study is to introduce concept maps with clinical cases (the innovative program) to improve learning of biochemistry course content. Participants were first year medical students (n=150) from Saveetha Medical College and Hospital (India); they were randomly divided into two groups of 75, one group attending the traditional program, the other the innovative program. Student performance was measured using three written knowledge tests (each with a maximum score of 20). The students also evaluated the relevance of the learning process using a 12-item questionnaire. Students in the innovative program using concept mapping outperformed those in the traditional didactic program (means of 7.13-8.28 vs. 12.33-13.93, pbiochemistry to clinical practice, and to enhance their reasoning and learning skills, as well as their deeper understanding for biochemistry.

  6. Bacterial meningitis

    NARCIS (Netherlands)

    Roos, Karen L.; van de Beek, Diederik

    2010-01-01

    Bacterial meningitis is a neurological emergency. Empiric antimicrobial and adjunctive therapy should be initiated as soon as a single set of blood cultures has been obtained. Clinical signs suggestive of bacterial meningitis include fever, headache, meningismus, vomiting, photophobia, and an

  7. Crystallization and preliminary X-ray studies of TON-1713 from Thermococcus onnurineus NA1, a putative member of the haloacid dehalogenase superfamily

    International Nuclear Information System (INIS)

    Le, Binh Van; Lee, Hyun Sook; Cho, Yona; Kang, Sung Gyun; Kim, Dong Young; Kim, Yang-Gyun; Kim, Kyeong Kyu

    2007-01-01

    A putative member of the haloacid dehalogenase superfamily from T. onnurineus has been expressed, purified and crystallized using 1.6 M magnesium sulfate as a precipitant. The crystals belonged to the triclinic space group P1 and diffracted to 1.8 Å resolution. The haloacid dehalogenase (HAD) protein superfamily is one of the largest enzyme families and shows hydrolytic activity towards diverse substrates. Structural analyses of enzymes belonging to the HAD family are required to elucidate the molecular basis underlying their broad substrate specificity and reaction mechanism. For this purpose, TON-1713, a hypothetical protein from Thermococcus onnurineus that is a member of the HAD superfamily, was expressed in Escherichia coli, purified and crystallized at 295 K using 1.6 M magnesium sulfate as a precipitant. X-ray diffraction data were collected to 1.8 Å resolution using a synchrotron-radiation source. The crystals belong to the triclinic space group P1, with unit-cell parameters a = 52.5, b = 65.8, c = 203.4 Å, α = 71.1, β = 79.9, γ = 74.3°

  8. Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models

    Science.gov (United States)

    Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher

    2014-01-01

    Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

  9. Nuclear magnetic resonance spectroscopy in biochemistry

    International Nuclear Information System (INIS)

    Roberts, J.K.M.; Jardetzky, O.

    1985-01-01

    This chapter aims to provide an orienting overview of the main directions in which the field of biological application of NMR has developed, the kinds of biochemical or biological questions which can be studied by NMR, and the major specific NMR techniques useful for this purpose. This discussion is preceded by a brief exposition of the elementary concepts of NMR and supplemented by references to the literature that treats each topic in greater depth. Applications of NMR of interest in biochemistry are treated in three major categories: (1) determination of the structure of biologically active compounds - especially new natural products; (2) studies of biochemical reactions, or processes, especially in vivo; and (3) studies of macromolecular structure and dynamics. 122 refs.; 35 figs.; 3 tabs

  10. Biochemistry for dietetic students: course content and format.

    Science.gov (United States)

    Sirota, L H

    1984-12-01

    This article presents the results of a survey of the 251 undergraduate dietetic programs for course content and level of the biochemistry course most frequently used to satisfy competencies in biochemistry under Plan IV of the ADA in 1979-80. It showed that a common core of information was stressed by all biochemistry instructors, but there was great variability in content and level of material covered and the textbook chosen, depending on whether the biochemistry course was offered to dietetic majors only, in classes with other nonchemistry majors, or in classes with chemistry majors. Variability was also seen in the time allotted for biochemistry--39 to 280 hours (total lecture and required laboratory hours); laboratory requirements--only 71%; and departmental affiliation of the instructor--17 different departments, primarily of chemistry (80%), biology (8%), and home economics (4%). Topics given greatest emphasis were descriptive ones, such as definitions, simple structures, and reactions of intermediary metabolism in general terms. Topics given least emphasis were those involving mechanistic and quantitative biochemistry, such as respiratory quotient (RQ), enzyme kinetics, calculations of energy from fat and carbohydrates, and specific structures of vitamins, ketones, and metabolic intermediates. The lack of communication between biochemistry and nutrition instructors and the great differences in the preparation of dietetic majors in biochemistry are sources of concern.

  11. Using Pamphlets to Teach Biochemistry: A Service-Learning Project

    Science.gov (United States)

    Harrison, Melinda A.; Dunbar, David; Lopatto, David

    2013-01-01

    A service-learning project appropriate for a biochemistry or advanced biochemistry course was designed and implemented. The project involved students partnering with a homeless shelter to design informational pamphlets to be displayed at the shelter for the clients' use. The pamphlet topics were based on diseases studied within the course.…

  12. Commentary: Biochemistry and Molecular Biology Educators Launch National Network

    Science.gov (United States)

    Bailey, Cheryl; Bell, Ellis; Johnson, Margaret; Mattos, Carla; Sears, Duane; White, Harold B.

    2010-01-01

    The American Society of Biochemistry and Molecular Biology (ASBMB) has launched an National Science Foundation (NSF)-funded 5 year project to support biochemistry and molecular biology educators learning what and how students learn. As a part of this initiative, hundreds of life scientists will plan and develop a rich central resource for…

  13. Blended Learning in Biochemistry Education: Analysis of Medical Students' Perceptions

    Science.gov (United States)

    Wardenski, Rosilaine de Fatima; de Espindola, Marina Bazzo; Struchiner, Miriam; Giannella, Tais Rabetti

    2012-01-01

    The objective of this study was to analyze first-year UFRJ medical students' perceptions about the implementation of a blended learning (BL) experience in their Biochemistry I course. During the first semester of 2009, three Biochemistry professors used the Constructore course management system to develop virtual learning environments (VLEs) for…

  14. Enhanced Podcasts for Teaching Biochemistry to Veterinary Students

    Science.gov (United States)

    Gough, Kevin C.

    2011-01-01

    The teaching of biochemistry within medical disciplines presents certain challenges; firstly to relay a large body of complex facts and abstract concepts, and secondly to motivate students that this relatively difficult topic is worth their time to study. Here, nutrient biochemistry was taught within a multidisciplinary module as part of an…

  15. A National Comparison of Biochemistry and Molecular Biology Capstone Experiences

    Science.gov (United States)

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the "American Society for Biochemistry and Molecular Biology" (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end,…

  16. Dyslipidemias as generating issue in Biochemistry classes

    Directory of Open Access Journals (Sweden)

    R. M. Lima

    2015-08-01

    Full Text Available The traditional didactic model is based on the transmission of the teacher's encyclopedic knowledge. In this model, the teaching of Science aims at the transmission of dominant values, regarded as absolute truths. The teacher is seen is an expert on scientific contents who transmits them to students without motivating them, and without taking into consideration their previous ideas and life experience. This model contributes to the formation of professionals who accept those values uncritically. An effective approach to break up this traditional teaching model in Biochemistry is the use of a generating issue. A Generating Issue is the starting point to the knowledge construction process which, in turn, replaces traditional models. Thus, this study aimed at developing a lesson for a 12th grade class at IF Fluminense on the following content: alcohol, carboxylic acid, ester, and esterification reaction, using dyslipidemias as the Generating Issue. To verify the value of such methodology in Biochemistry classroom, data was collected by applying a questionnaire and images with texts produced by students. In addition, they had a class based on the methodology known as Three Pedagogical Moments, proposed by Delizoicov et al. (2007. Several didactic resources designed by the authors were used, such as slide presentation, tridimensional molecular models, and a roulette game named “Bioquimicados”, based on the Facebook game “Perguntados” ("Trivia Crack". After this, students developed more grounded scientific concepts, making use of terms common in scientific language. This suggests that the use of the Generating Issue in a lesson based on problematization, and supported by a ludic activity, provided a meaningful contribution to improve the students' understanding of the scientific content. This type of non-traditional class promotes greater student motivation, resulting in meaningful learning.

  17. Production of macroaggregates from dissolved exopolymeric substances (EPS) of bacterial and diatom origin

    Digital Repository Service at National Institute of Oceanography (India)

    Bhaskar, P.V.; Grossart, H.P.; Bhosle, N.B.; Simon, M.

    .J. (1985) Bacterial cell walls and surfaces. In Bacterial Adhesion. (Savage D.C. and Fletcher M, Eds) Plenum press, New York, pp: 45-70. 53. Coombs, J. and Volcani, B. E. (1968) Studies on the biochemistry and fine structure of silica-shell formation...

  18. Online Communication Tools in Biochemistry Teaching

    Directory of Open Access Journals (Sweden)

    A. O. Ferreira

    2012-05-01

    Full Text Available The  online  communication  tools  enable  new  ways  of  learning, especially  the  forums  in the context of online courses, and the understanding of interactions and collaborations in the  forums  can  improve  them.  The  study  aimed  to  analyze  the  online relationships,  as well  as  obtaining  evidence  of  the  use of  other  learning  tools in  a  biochemistry  subject, focusing on how students use the tool forum and its contribution to learning. The study was  carried  out  from  data  pre  and  post  course  questionnaires  as  well  as  log  of environment  access  and  discussion  forum.  The  forums  have  been  restructured  and systematized  for  analysis  and  creating  discursive  flows  between  statements.  The questionnaires showed the central role of forum and wiki for learning,  the importance of interactions, which was highlighted by the forum analysis. The results indicate that one of the ways to improve online biochemistry teaching is to stimulate interactive activities, participatory  moderation  and  pedagogical  support  by  tutors  and  mentors,  also encouraging  and  creating  strategies  to  collaboration  of  students  to  solve problems  and to collaborative knowledge construction.

  19. Crystallization and preliminary X-ray diffraction studies of the putative haloalkane dehalogenase DppA from Plesiocystis pacifica SIR-I

    International Nuclear Information System (INIS)

    Bogdanović, Xenia; Hesseler, Martin; Palm, Gottfried J.; Bornscheuer, Uwe T.; Hinrichs, Winfried

    2010-01-01

    The crystallization and preliminary X-ray diffraction studies of DppA from P. pacifica SIR-I are reported. DppA from Plesiocystis pacifica SIR-I is a putative haloalkane dehalogenase (EC 3.8.1.5) and probably catalyzes the conversion of halogenated alkanes to the corresponding alcohols. The enzyme was expressed in Escherichia coli BL21 and purified to homogeneity by ammonium sulfate precipitation and reversed-phase and ion-exchange chromatography. The DppA protein was crystallized by the vapour-diffusion method and protein crystals suitable for data collection were obtained in the orthorhombic space group P2 1 2 1 2. The DppA crystal diffracted X-rays to 1.9 Å resolution using an in-house X-ray generator

  20. Optimal Learning for Efficient Experimentation in Nanotechnology and Biochemistry

    Science.gov (United States)

    2015-12-22

    AFRL-AFOSR-VA-TR-2016-0018 Optimal Learning for Efficient Experimentation in Nanotechnology, Biochemistry Warren Powell TRUSTEES OF PRINCETON... Biochemistry 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-12-1-0200 5c.  PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S) Warren Powell 5d.  PROJECT NUMBER 5e...scientists. 15. SUBJECT TERMS Biochemistry 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF 19a.  NAME OF RESPONSIBLE PERSON Warren

  1. Computational Biochemistry-Enzyme Mechanisms Explored.

    Science.gov (United States)

    Culka, Martin; Gisdon, Florian J; Ullmann, G Matthias

    2017-01-01

    Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Computational biochemistry aims at creation of a computational model of an enzyme in order to explain microscopic details of the catalytic process and reproduce or predict macroscopic experimental findings. Results of such computations are in part complementary to experimental data and provide an explanation of a biochemical process at the microscopic level. In order to evaluate the mechanism of an enzyme, a structural model is constructed which can be analyzed by several theoretical approaches. Several simulation methods can and should be combined to get a reliable picture of the process of interest. Furthermore, abstract models of biological systems can be constructed combining computational and experimental data. In this review, we discuss structural computational models of enzymatic systems. We first discuss various models to simulate enzyme catalysis. Furthermore, we review various approaches how to characterize the enzyme mechanism both qualitatively and quantitatively using different modeling approaches. © 2017 Elsevier Inc. All rights reserved.

  2. Hobby with Biochemistry: Use of active learning methodology in Biochemistry at the Medical School

    Directory of Open Access Journals (Sweden)

    S. R.T. Prado

    2015-08-01

    Full Text Available Introduction and objectives: The learning of Biochemistry is generally considered difficult by the graduates, because studies the molecular level the metabolism of living and it demands a great capacity for abstraction by students. Thus, researchers have tried alternative methods to provid an alternative study method. Materials and methods: 178 students of the School of Medicine, PUC-PR, that course the disciplines of Medical Biochemistry I and II, were divided into 50 groups, each with 3-4 students, and were have to draw up a hobby activity with a specific theme of the Biochemistry. The selected topics were, amino acids and proteins, enzymes, cellular respiration, glycogen metabolism, gluconeogenesis, lipid metabolism, metabolic integration, dyslipidemia and atherogenesis, pathophysiology of diabetes mellitus and metabolic syndrome, mechanisms of diabetes mellitus complications. The hobby activities chosen were direct, duplex, self-defined, cryptogram, bugs game. Both issues such as the type of hobby was drawn between groups. The groups had to: elaborate hobby; presents it to class orally, applying the questions prepared; printing and expose the hobby at the wall in the University; answer an evaluation regarding the preparation of work; and all groups should get together and organize one titled magazine "Hobby with Biochemistry" and deliver it printed. Results and conclusions: According the groups, the greatest difficulty was the adequacy of the questions posed in the required format, once they had only one issue and restricted space for the responses. Furthermore, the formatting was also identified as a point very difficult in activity elaboration. On the topic of learning through the development of work, and/or a new skill groups assigned grades ranging between 7.0 and 10.0 and about 90% of the groups attributed note 10 on satisfaction of seeing the work done and its ability to produce it. According to the results, the activity proved to be

  3. Biochemistry graduate student selected to meet with Nobel Laureates

    OpenAIRE

    Trulove, Susan

    2006-01-01

    January Haile of Athens, Tenn., a Ph.D. student in biochemistry at Virginia Tech has been selected by Oak Ridge Associated Universities (ORAU) to attend a meeting of Nobel Laureates in Lindau, Germany, in June.

  4. Egyptian Journal of Biochemistry and Molecular Biology - Vol 32, No ...

    African Journals Online (AJOL)

    The Egyptian Journal of Biochemistry and Molecular Biology. ... Therapeutic Impacts of Almond Oil and Olive Oil on Cholesterol Dynamics and ... Multidrug Resistance Proteins in Pancreatic Carcinoma · EMAIL FULL TEXT EMAIL FULL TEXT

  5. Can biochemistry drive drug discovery beyond simple potency measurements?

    Science.gov (United States)

    Chène, Patrick

    2012-04-01

    Among the fields of expertise required to develop drugs successfully, biochemistry holds a key position in drug discovery at the interface between chemistry, structural biology and cell biology. However, taking the example of protein kinases, it appears that biochemical assays are mostly used in the pharmaceutical industry to measure compound potency and/or selectivity. This limited use of biochemistry is surprising, given that detailed biochemical analyses are commonly used in academia to unravel molecular recognition processes. In this article, I show that biochemistry can provide invaluable information on the dynamics and energetics of compound-target interactions that cannot be obtained on the basis of potency measurements and structural data. Therefore, an extensive use of biochemistry in drug discovery could facilitate the identification and/or development of new drugs. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Lactation performance and serum biochemistry of dairy cows fed ...

    African Journals Online (AJOL)

    Serum biochemistry concentrations (serum glucose, cholesterol, triglyceride, total protein, and cortisol and insulin concentration) and blood hematology (red blood cell, hematocrit, hemoglobin concentration and percentage neutrophils, lymphocytes, monocytes, basophiles, eosinophils and ratio of neutrophils to ...

  7. Personalized System of Instruction (Keller Method) for Medical School Biochemistry

    Science.gov (United States)

    Weisman, Robert A.; Shapiro, David M.

    1973-01-01

    The Keller Method requires abolishing lectures as a vehicle of information transfer in favor of a study guide and breaking the biochemistry course into a number of units each to be mastered at the student's own pace. (Editor)

  8. Bacterial prostatitis.

    Science.gov (United States)

    Gill, Bradley C; Shoskes, Daniel A

    2016-02-01

    The review provides the infectious disease community with a urologic perspective on bacterial prostatitis. Specifically, the article briefly reviews the categorization of prostatitis by type and provides a distillation of new findings published on bacterial prostatitis over the past year. It also highlights key points from the established literature. Cross-sectional prostate imaging is becoming more common and may lead to more incidental diagnoses of acute bacterial prostatitis. As drug resistance remains problematic in this condition, the reemergence of older antibiotics such as fosfomycin, has proven beneficial. With regard to chronic bacterial prostatitis, no clear clinical risk factors emerged in a large epidemiological study. However, bacterial biofilm formation has been associated with more severe cases. Surgery has a limited role in bacterial prostatitis and should be reserved for draining of a prostatic abscess or the removal of infected prostatic stones. Prostatitis remains a common and bothersome clinical condition. Antibiotic therapy remains the basis of treatment for both acute and chronic bacterial prostatitis. Further research into improving prostatitis treatment is indicated.

  9. Medical Biochemistry as Subdiscipline of Laboratory Medicine in Serbia.

    Science.gov (United States)

    Jovičić, Snežana; Majkić-Singh, Nada

    2017-04-01

    Medical biochemistry is the usual name for clinical biochemistry or clinical chemistry in Serbia, and medical biochemist is the official name for the clinical chemist (or clinical biochemist). This is the largest sub-discipline of the laboratory medicine in Serbia. It includes all aspects of clinical chemistry, and also laboratory hematology with coagulation, immunology, etc. Medical biochemistry laboratories in Serbia and medical biochemists as a profession are part of Health Care System and their activities are regulated through: the Health Care Law and rules issued by the Chamber of Medical Biochemists of Serbia. The first continuous and organized education for Medical Biochemists (Clinical Chemists) in Serbia dates from 1945, when the Department of Medical Biochemistry was established at the Pharmaceutical Faculty in Belgrade. In 1987 at the same Faculty a five years undergraduate study program was established, educating Medical Biochemists under a special program. Since the academic year 2006/2007 the new five year undergraduate (according to Bologna Declaration) and four-year postgraduate program according to EC4 European Syllabus for Postgraduate Training in Clinical Chemistry and Laboratory Medicine has been established. The Ministry of Education and Ministry of Public Health accredited these programs. There are four requirements for practicing medical biochemistry in the Health Care System: University Diploma of the Faculty of Pharmacy (Study of Medical Biochemistry), successful completion of the professional exam at the Ministry of Health after completion of one additional year of obligatory practical training in the medical biochemistry laboratories, membership in the Serbian Chamber of Medical Biochemists and licence for skilled work issued by the Serbian Chamber of Medical Biochemists. In order to present laboratory medical biochemistry practice in Serbia this paper will be focused on the following: Serbian national legislation, healthcare services

  10. Assessment of learning gains in a flipped biochemistry classroom.

    Science.gov (United States)

    Ojennus, Deanna Dahlke

    2016-01-01

    The flipped classroom has become an increasingly popular pedagogical approach to teaching and learning. In this study, learning gains were assessed in a flipped biochemistry course and compared to gains in a traditional lecture. Although measured learning gains were not significantly different between the two courses, student perception of learning gains did differ and indicates a higher level of satisfaction with the flipped lecture format. © 2015 The International Union of Biochemistry and Molecular Biology.

  11. THE USE OF MULTIPLE TOOLS FOR TEACHING MEDICAL BIOCHEMISTRY

    OpenAIRE

    Sé, A.B.; Oxyradical Research Group, CEL, UnB; FM-UnB, Brasília, Brazil.; Passos, R.M.; Oxyradical Research Group, CEL, UnB; 2FM-UnB, Brasília, Brazil.; Rochadel, A.D; FM-UnB, Brasília, Brazil; Ono, A.H.; FM-UnB, Brasília, Brazil; Hermes-Lima, M.; Oxyradical Research Group, CEL, UnB

    2007-01-01

    The pros and cons of Problem Based Learning (PBL) have been extensivelydiscussed in the literature. We describe PBL-like strategies used at UnB (some ofthem since 1999) that may be useful elsewhere to improve undergraduatebiochemistry teaching with clinical applications. The main activities are: (i) aseminar/poster system, (ii) a true-or-false applied biochemistry exam (prepared bypeer tutors), (iii) a 9-hour-exam on metabolism (based in actual papers), (iv) anAdvanced Biochemistry course (di...

  12. A biochemistry discipline designed for the nutrition course

    Directory of Open Access Journals (Sweden)

    A.A.G. Bianco

    2004-05-01

    Full Text Available Biochemistry is widely considered an essential background in a Nutrition Course framework. At theFaculdade de Saude Publica, USP, it is a direct requirement to eight disciplines of the syllabus and anindirect requirement to another nine disciplines. Nevertheless, a previous interview study involvingNutrition students and Nutritionists revealed a contradictory image of Biochemistry. Although stu-dents and Nutritionists admitted the important role played by Biochemistry, most of the respondentsdeclared that they could not foresee any application of Biochemical contents in their professional life.Aiming to change this situation, a deep intervention in the Biochemistry discipline was carried on.The discipline was planned in such a way that all the contents to be taught was directly derived fromsubjects or situations matching the interests of nutrition students. Instead of a classical lecture basedcourse, collaborative learning was the methodological choice, taking advantage of practical activitiesinvolving educational software and laboratory work as well. The course was carried on in 180 hoursand a variety of strategies were employed, especially small group discussion and problem solving. Thestudents were given a booklet containing all the exercises and problems, which acted as course guide.At the end of the course, an evaluation survey was carried out. It is noticeable that, according tostudents answers: 100% agreed that Biochemistry was intimately linked to Nutrition; 83% appreciatedthe didactical methodologies employed; 89% would like to continue studying Biochemistry in a furtherdiscipline; 96% declared that the discipline has raised their interest in Biochemistry. In respect tothe assessment of the students, these results are in accordance with the opinion of teachers and TAsengaged in restructuring Biochemistry courses.

  13. Can Polyphosphate Biochemistry Affect Biological Apatite Saturation?

    Science.gov (United States)

    Omelon, S. J.; Matsuura, N.; Gorelikov, I.; Wynnyckyj, C.; Grynpas, M. D.

    2010-12-01

    Phosphorus (P) is an important and limiting element for life. One strategy for storing ortho phosphates (Pi) is polymerization. Polymerized Pi's (polyphosphates: (PO3-)n: polyPs) serve as a Pi bank, as well as a catiion chelator, energy source, & regulator of responses to stresses in the stationary phase of culture growth and development1. PolyP biochemistry has been investigated in yeasts, bacteria & plants2. Bigeochemical cycling of P includes the condensation of Pi into pyro (P2O7-4), & polyPs, & the release of Pi from these compounds by the hydrolytic degradation of Pi from phosphomonoester bonds. Alkaline phosphatase (ALP) is one of the predominate enzymes for regenerating Pi in aquatic systems3, & it cleaves Pi from polyPs. ALP is also the enzyme associated with apatite biomineralization in vertebrates4. PolyP was proposed to be the ALP substrate in bone mineralization5. Where calcium ions are plentiful in many aquatic environments, there is no requirement for aquatic life to generate Ca-stores. However, terrestrial vertebrates benefit from a bioavailable Ca-store such as apatite. The Pi storage strategy of polymerizing PO4-3 into polyPs dovetails well with Ca-banking, as polyPs sequester Ca, forming a neutral calcium polyphosphate (Ca-polyP: (Ca(PO3)2)n) complex. This neutral complex represents a high total [Ca+2] & [PO4-3], without the threat of inadvertent apatite precipitation, as the free [Ca+2] & [PO4-3], and therefore apatite saturation, are zero. Recent identification of polyP in regions of bone resorption & calcifying cartilage5 suggests that vertebrates may use polyP chemistry to bank Ca+2 and PO4-3. In vitro experiments with nanoparticulate Ca-polyP & ALP were undertaken to determine if carbonated apatite could precipitate from 1M Ca-polyP in Pi-free “physiological fluid” (0.1 M NaCl, 2 mM Ca+2, 0.8 mM Mg+2, pH ~8.0 ±0.5, 37 °C), as this is estimated to generate the [Ca+2] & [PO4-3] required to form the apatite content of bone tissue

  14. Using 3DClass To Flip Biochemistry Classroom

    Directory of Open Access Journals (Sweden)

    T. Silva

    2014-08-01

    Full Text Available The flipped classroom inverts traditional teaching methods, in order to have studentsprepared for topics and techniques covered in the following meeting. This approach wasadopted in a biochemistry course taught to biology freshmen students at the University ofCampinas, using a Virtual Learning Environment called 3DClass. Before each classroomsession, a quiz was delivered covering the following topic and students were allowed totake quizzes as many times as they wanted. This approach was utilized in order to betterprepare students in classes and to perform lab experiments. Every student attempt wasrecorded in a database. Before each classroom session, the instructors were provided witha summary of the class answers, highlighting questions where students had more difficultyand the ones that scored higher. This kind of information was helpful to design activities tocover the topics where students had more difficulties. Based on the 3DClass records thestudents behaviors were mapped, such as students taking the quizzes seriously, studentsguessing, students answering a quiz until scoring 100%, students that continue answeringafter scoring 100% in order to increase their grades, students that never score 100%.However, the most relevant information 3DClass brought us was the possibility to identifystudent’s confidence in their answers, which could be observed by the analysis of theirattempts for each question. If they had made different choices each try, it would haveindicated a low confidence level, while always providing the same answer indicated ahigher confidence level, even whilst picking incorrect answers. This experiment haverevealed that students coming to the classroom better prepared reflected positively on thedeveloped activities, but the number of students taking the quizzes seriously were not asgreat as we had expected, indicating that more actions should be taken to improvestudents engagement with these activities.

  15. Collective Construction of Knowledge in Clinical Biochemistry

    Directory of Open Access Journals (Sweden)

    S.B. Barreto

    2010-05-01

    Full Text Available The collective construction of knowledge occurs by the convergence of ideas and semantic. This paper was made for a graduation discipline, in 2009-2, with 240students who were separated into 4 groups: morning period (M1,M2 and night period (N1,N2. This study aims the collective construction of a abstract-manual of clinical biochemistry tests, due the difficulty in comprehension of certain concepts by the students; it intends to help them in the process of knowledge acquirement. The constructivist approach was adopted and the matters of the discipline were available in a “Student Group e-mail account”, a functional communication tool. The instructions were reachable on the web. M1,M2 and N1 made one part of the study at the first period. N2 did not conclude the study at the same time period of the other groups; therefore they received a new responsibility: they were supposed to conclude and correct the manual and its application which included 90 different kinds of labor exams. A textbook has been defined containing illustrative pictures of blood collection and biosecurity. Three banners were exposed inside the hall of the institution. Collective work is important for the effective arrangement in health area. In the process of teaching/learning, the teacher must proceed on practices and methodologies aiming the development of the student competences and skills which represent its professional identity.

  16. Effective Laboratory Work in Biochemistry Subject: Students' and Lecturers' Perspective in Indonesia

    Science.gov (United States)

    Anwar, Yunita Arian Sani; Senam; Laksono F. X., Endang Widjajanti

    2017-01-01

    Biochemistry subject had problem in learning and teaching, especially in laboratory work. We explored laboratory learning implementation in Biochemistry subject. Participants of this research were 195 students who took biochemistry subject and 4 lecturers of biochemistry in three universities in Indonesia. We obtained data using questionnaires and…

  17. Bacterial Vaginosis

    Science.gov (United States)

    ... Archive STDs Home Page Bacterial Vaginosis (BV) Chlamydia Gonorrhea Genital Herpes Hepatitis HIV/AIDS & STDs Human Papillomavirus ( ... of getting other STDs, such as chlamydia and gonorrhea . These bacteria can sometimes cause pelvic inflammatory disease ( ...

  18. The Biochemistry Over 20 Years In The High School Textbooks

    Directory of Open Access Journals (Sweden)

    C. E.S. Rocha

    2014-08-01

    Full Text Available   The Biochemistry Over 20 Years In The High School Textbooks   Rocha, C. E. S.1; Büttenbender, M. D.1; Denardin, E.L.G.2, Roehrs, R.1,2 1Grupo Interdisciplinar de Pesquisa em Práticas de Ensino, UNIPAMPA, RS. 2Laboratório de Estudos Físico Químicos e Produtos Naturais, UNIPAMPA, RS.   INTRODUCTION: Many teachers make use of textbook to lead content in the classroom. The chemistry books introduce concepts that should relate biochemistry to students in schools. It is important that this first contact turns out into an encouraging experience for the students, because once it worked as expected it arouses interest and makes the students see themselves curious to delve into the subject. The research aims to evaluate the presence of related concepts in biochemistry textbooks in chemistry in high school, over 20 years. MATERIAL AND METHODS: In order to perform this study, we analyzed the following content related to biochemistry: proteins, carbohydrates, lipids and nucleic acids in the books "Chemistry - Structure of Matter and Organic Chemistry" of the year 1993 and the book "Chemistry in approach to daily life" of the year 2012 with the purpose of verifying the changes in the content of biochemistry in the last 20 years. RESULTS AND DISCUSSION: In the 90s, as used in the book, concepts and explanations are introduced in a very objective approach, making a total of 22 pages. The current largest is 23 pages with experiments and curiosities. Through analysis we found that current textbooks present the same issues related to biochemistry, however, a greater amount of data, bringing students to more examples and applications in everyday life. Today we see that the contents and processes are most exploited and that there is a concern on the importance of the study of issues that relate to biochemistry. CONCLUSIONS: The study of the biochemistry textbooks has been more attractive in recent years, contextualizing content with the daily life of

  19. The Biochemistry Show: a new and fun tool for learning

    Directory of Open Access Journals (Sweden)

    A.H Ono

    2006-07-01

    Full Text Available The traditional methods to teach biochemistry in most universities are based on the memorization of chemical structures,  biochemical  pathways  and  reagent  names,  which  is  many  times  dismotivating  for  the  students.  We presently describe an innovative, interactive and alternative method for teaching biochemistry to medical and nutrition undergraduate students, called the Biochemistry Show (BioBio Show.The Biobio show is based on active participation of the students. They are divided in groups and the groups face each other. One group faces another one group at a time, in a game based on true or false questions that involve subjects of applied biochemistry (exercise, obesity, diabetes, cholesterol, free radicals, among others. The questions of the Show are previously elaborated by senior students. The Biobio Show has four phases, the first one is a selection exam, and from the second to the fourth phase, eliminatory confrontations happen. On a confrontation, the first group must select a certain quantity of questions for the opponent to answer.  The group who choses the questions must know how to answer and justify the selected questions. This procedure is repeated on all phases of the show. On the last phase, the questions used are taken from an exam previously performed by the students: either the 9-hour biochemistry exam (Sé et al. A 9-hour biochemistry exam. An iron man competition or a good way of evaluating undergraduate students? SBBq 2005, abstract K-6 or the True-or-False exam (TFE (Sé et al. Are tutor-students capable of writing good biochemistry exams? SBBq 2004, abstract K-18. The winner group receives an extra 0,5 point on the final grade. Over 70% of the students informed on a questionnaire that the Biobio Show is a valuable tool for learning biochemistry.    That is a new way to enrich the discussion of biochemistry in the classroom without the students getting bored. Moreover, learning

  20. An Integrated Biochemistry Laboratory, Including Molecular Modeling

    Science.gov (United States)

    Hall, Adele J. Wolfson Mona L.; Branham, Thomas R.

    1996-11-01

    The dilemma of designing an advanced undergraduate laboratory lies in the desire to teach and reinforce basic principles and techniques while at the same time exposing students to the excitement of research. We report here on a one-semester, project-based biochemistry laboratory that combines the best features of a cookbook approach (high success rate, achievement of defined goals) with those of an investigative, discovery-based approach (student involvement in the experimental design, excitement of real research). Individual modules may be selected and combined to meet the needs of different courses and different institutions. The central theme of this lab is protein purification and design. This laboratory accompanies the first semester of biochemistry (Structure and Function of Macromolecules, a course taken mainly by junior and senior chemistry and biological chemistry majors). The protein chosen as the object of study is the enzyme lysozyme, which is utilized in all projects. It is suitable for a student lab because it is easily and inexpensively obtained from egg white and is extremely stable, and its high isoelectric point (pI = 11) allows for efficient separation from other proteins by ion-exchange chromatography. Furthermore, a literature search conducted by the resourceful student reveals a wealth of information, since lysozyme has been the subject of numerous studies. It was the first enzyme whose structure was determined by crystallography (1). Hendrickson et al. (2) have previously described an intensive one-month laboratory course centered around lysozyme, although their emphasis is on protein stability rather than purification and engineering. Lysozyme continues to be the focus of much exciting new work on protein folding and dynamics, structure and activity (3 - 5). This lab course includes the following features: (i) reinforcement of basic techniques, such as preparation of buffers, simple enzyme kinetics, and absorption spectroscopy; (ii

  1. Raising environmental awareness through applied biochemistry laboratory experiments.

    Science.gov (United States)

    Salman Ashraf, S

    2013-01-01

    Our environment is under constant pressure and threat from various sources of pollution. Science students, in particular chemistry students, must not only be made aware of these issues, but also be taught that chemistry (and science) can provide solutions to such real-life issues. To this end, a newly developed biochemistry laboratory experiment is described that guides students to learn about the applicability of peroxidase enzymes to degrade organic dyes (as model pollutants) in simulated waste water. In addition to showing how enzymes can potentially be used for waste water remediation, various factors than can affect enzyme-based reactions such as pH, temperature, concentration of substrates/enzymes, and denaturants can also be tested. This "applied biotechnology" experiment was successfully implemented in an undergraduate biochemistry laboratory course to enhance students' learning of environmental issues as well important biochemistry concepts. Student survey confirmed that this laboratory experiment was successful in achieving the objectives of raising environmental awareness in students and illustrating the usefulness of chemistry in solving real-life problems. This experiment can be easily adopted in an introductory biochemistry laboratory course and taught as an inquiry-guided exercise. © 2013 by The International Union of Biochemistry and Molecular Biology.

  2. FACEBOOK AS A MEDIATION TOOL IN BIOCHEMISTRY DISCIPLINE

    Directory of Open Access Journals (Sweden)

    P. X. Gomes

    2015-08-01

    Full Text Available Introduction: The current students generation are daily connected to the Internet, wich encourages the use of mobile tools in education. Many of the students of Biochemistry feel apprehensive about the discipline and the use of facebook may contribute, among other factors, motivating them. Objectives: It was analyzed the use of facebook as a mediator and motivator in the discipline of Biochemistry, basing on socioconstrutivist interventions. Material and methods: This work was developed in the action-research perspective, using the quali-quantitative method. An investigative questionnaire was used, using Likert scale and open questions, to investigate the facebook use, as well as the preferences of students, focusing on Biochemistry group in the Biomedicine course.  The posts were analyzed identifying: frequency of the interaction`s types (post, comment, likes;  interaction's categories (question, answer, motivational; and the content itself of the post. Results: It was highlighted students' interest to search materials, answering questions, and especially seeking information about the discipline. It was emphasized that the group was motivating for learning Biochemistry, encouragement the group to study, with quick and easy access to the professor by chat. Conclusions: The results indicate a preference for students at facebook, with a great motivational potential, is at easy access to colleagues, professor and monitor, or even the ease of obtaining the materials and ask questions in real time, indicating that this tool as a possible way, still little explored, to enhance the teaching of Biochemistry.

  3. Identifying Opportunities for Vertical Integration of Biochemistry and Clinical Medicine.

    Science.gov (United States)

    Wendelberger, Karen J.; Burke, Rebecca; Haas, Arthur L.; Harenwattananon, Marisa; Simpson, Deborah

    1998-01-01

    Objectives: Retention of basic science knowledge, as judged by National Board of Medical Examiners' (NBME) data, suffers due to lack of apparent relevance and isolation of instruction from clinical application, especially in biochemistry. However, the literature reveals no systematic process for identifying key biochemical concepts and associated clinical conditions. This study systematically identified difficult biochemical concepts and their common clinical conditions as a critical step towards enhancing relevance and retention of biochemistry.Methods: A multi-step/ multiple stakeholder process was used to: (1) identify important biochemistry concepts; (2) determine students' perceptions of concept difficulty; (3) assess biochemistry faculty, student, and clinical teaching scholars' perceived relevance of identified concepts; and (4) identify associated common clinical conditions for relevant and difficult concepts. Surveys and a modified Delphi process were used to gather data, subsequently analyzed using SPSS for Windows.Results: Sixteen key biochemical concepts were identified. Second year medical students rated 14/16 concepts as extremely difficult while fourth year students rated nine concepts as moderately to extremely difficult. On average, each teaching scholar generated common clinical conditions for 6.2 of the 16 concepts, yielding a set of seven critical concepts and associated clinical conditions.Conclusions: Key stakeholders in the instructional process struggle to identify biochemistry concepts that are critical, difficult to learn and associated with common clinical conditions. However, through a systematic process beginning with identification of concepts and associated clinical conditions, relevance of basic science instruction can be enhanced.

  4. BACTERIAL CONSORTIUM

    Directory of Open Access Journals (Sweden)

    Payel Sarkar

    2013-01-01

    Full Text Available Petroleum aromatic hydrocarbons like benzen e, toluene, ethyl benzene and xylene, together known as BTEX, has almost the same chemical structure. These aromatic hydrocarbons are released as pollutants in th e environment. This work was taken up to develop a solvent tolerant bacterial cons ortium that could degrade BTEX compounds as they all share a common chemical structure. We have isolated almost 60 different types of bacterial strains from different petroleum contaminated sites. Of these 60 bacterial strains almost 20 microorganisms were screene d on the basis of capability to tolerate high concentration of BTEX. Ten differe nt consortia were prepared and the compatibility of the bacterial strains within the consortia was checked by gram staining and BTEX tolerance level. Four successful mi crobial consortia were selected in which all the bacterial strains concomitantly grew in presence of high concentration of BTEX (10% of toluene, 10% of benzene 5% ethyl benzene and 1% xylene. Consortium #2 showed the highest growth rate in pr esence of BTEX. Degradation of BTEX by consortium #2 was monitored for 5 days by gradual decrease in the volume of the solvents. The maximum reduction observed wa s 85% in 5 days. Gas chromatography results also reveal that could completely degrade benzene and ethyl benzene within 48 hours. Almost 90% degradation of toluene and xylene in 48 hours was exhibited by consortium #2. It could also tolerate and degrade many industrial solvents such as chloroform, DMSO, acetonitrile having a wide range of log P values (0.03–3.1. Degradation of aromatic hydrocarbon like BTEX by a solvent tolerant bacterial consortium is greatly significant as it could degrade high concentration of pollutants compared to a bacterium and also reduces the time span of degradation.

  5. Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature.

    Science.gov (United States)

    Chaloupkova, Radka; Prokop, Zbynek; Sato, Yukari; Nagata, Yuji; Damborsky, Jiri

    2011-08-01

    The effect of pH and temperature on structure, stability, activity and enantioselectivity of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110 was investigated in this study. Conformational changes have been assessed by circular dichroism spectroscopy, functional changes by kinetic analysis, while quaternary structure was studied by gel filtration chromatography. Our study shows that the DbjA enzyme is highly tolerant to pH changes. Its secondary and tertiary structure was not affected by pH in the ranges 5.3-10.3 and 6.2-10.1, respectively. Oligomerization of DbjA was strongly pH-dependent: monomer, dimer, tetramer and a high molecular weight cluster of the enzyme were distinguished in solution at different pH conditions. Moreover, different oligomeric states of DbjA possessed different thermal stabilities. The highest melting temperature (T(m) = 49.1 ± 0.2 °C) was observed at pH 6.5, at which the enzyme occurs in dimeric form. Maximal activity was detected at 50 °C and in the pH interval 7.7-10.4. While pH did not have any effect on enantiodiscriminination of DbjA, temperature significantly altered DbjA enantioselectivity. A decrease in temperature results in significantly enhanced enantioselectivity. The temperature dependence of DbjA enantioselectivity was analysed with 2-bromobutane, 2-bromopentane, methyl 2-bromopropionate and ethyl 2-bromobutyrate, and differential activation parameters Δ(R-S)ΔH and Δ(R-S)ΔS were determined. The thermodynamic analysis revealed that the resolution of β-bromoalkanes was driven by both enthalpic and entropic terms, while the resolution of α-bromoesters was driven mainly by an enthalpic term. Unique catalytic activity and structural stability of DbjA in a broad pH range, combined with high enantioselectivity with particular substrates, make this enzyme a very versatile biocatalyst. Enzyme EC3.8.1.5 haloalkane dehalogenase. © 2011 The Authors Journal compilation © 2011 FEBS.

  6. My Lifelong Passion for Biochemistry and Anaerobic Microorganisms.

    Science.gov (United States)

    Thauer, Rudolf Kurt

    2015-01-01

    Early parental influence led me first to medical school, but after developing a passion for biochemistry and sensing the need for a deeper foundation, I changed to chemistry. During breaks between semesters, I worked in various biochemistry labs to acquire a feeling for the different areas of investigation. The scientific puzzle that fascinated me most was the metabolism of the anaerobic bacterium Clostridium kluyveri, which I took on in 1965 in Karl Decker's lab in Freiburg, Germany. I quickly realized that little was known about the biochemistry of strict anaerobes such as clostridia, methanogens, acetogens, and sulfate-reducing bacteria and that these were ideal model organisms to study fundamental questions of energy conservation, CO2 fixation, and the evolution of metabolic pathways. My passion for anaerobes was born then and is unabated even after 50 years of study.

  7. Blended learning in biochemistry education: analysis of medical students' perceptions.

    Science.gov (United States)

    de Fátima Wardenski, Rosilaine; de Espíndola, Marina Bazzo; Struchiner, Miriam; Giannella, Taís Rabetti

    2012-07-01

    The objective of this study was to analyze first-year UFRJ medical students' perceptions about the implementation of a blended learning (BL) experience in their Biochemistry I course. During the first semester of 2009, three Biochemistry professors used the Constructore course management system to develop virtual learning environments (VLEs) for complementing course Modules I, II, and IV, using different resources and activities. Forty-nine students (46%) took part in the study. Results show that, in general, students gave positive evaluations to their experiences with BL, indicating that the VLEs have not only motivated but also facilitated learning. Most of the students reported that access to resources in the three modules provided a more in-depth approach to Biochemistry education and greater study autonomy. Students suggested that the VLEs could be better used for promoting greater communication among participants. Copyright © 2012 Wiley Periodicals, Inc.

  8. Using augmented reality to teach and learn biochemistry.

    Science.gov (United States)

    Vega Garzón, Juan Carlos; Magrini, Marcio Luiz; Galembeck, Eduardo

    2017-09-01

    Understanding metabolism and metabolic pathways constitutes one of the central aims for students of biological sciences. Learning metabolic pathways should be focused on the understanding of general concepts and core principles. New technologies such Augmented Reality (AR) have shown potential to improve assimilation of biochemistry abstract concepts because students can manipulate 3D molecules in real time. Here we describe an application named Augmented Reality Metabolic Pathways (ARMET), which allowed students to visualize the 3D molecular structure of substrates and products, thus perceiving changes in each molecule. The structural modification of molecules shows students the flow and exchange of compounds and energy through metabolism. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):417-420, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  9. The use of multiple tools for teaching medical biochemistry.

    Science.gov (United States)

    Sé, Alexandre B; Passos, Renato M; Ono, André H; Hermes-Lima, Marcelo

    2008-03-01

    In this work, we describe the use of several strategies employing the philosophies of active learning and problem-based learning (PBL) that may be used to improve the teaching of metabolic biochemistry to medical and nutritional undergraduate students. The main activities are as follows: 1) a seminar/poster system in a mini-congress format (using topics of applied biochemistry); 2) a true/false applied biochemistry exam (written by peer tutors); 3) a 9-h exam on metabolism (based in real publications); 4) the Advanced Biochemistry course (directed to peer tutors, where students learn how to read and criticize real medical papers); 5) experiments about nutrition and metabolism, using students as volunteers, and about free radicals (real science for students); 6) the BioBio blog (taking advantage of the "web age," this enhances out of class exchanges of information between the professor, students, and peer tutors); 7) student lectures on public health issues and metabolic disorders directed to the community and lay people; and 8) the BioBio quiz show. The main objective of these activities is to provide students with a more practical and interesting approach to biochemistry, such as the application of theoretical knowledge to real situations (diseases, experiments, media information, and scientific discoveries). In addition, we emphasize the importance of peer tutor activities for optimized learning of both students and peer tutors, the importance of a closer interaction between students and teaching staff, and the necessity to initiate students precociously in two broad fields of medical activity: "real" basic science and contact with the public (also helping students--future doctors and nutritionists--to be able to communicate with lay people). Most activities were evaluated by the students through written questionnaires and informal conversations, along various semesters, indicating good acceptance and approval of these methods. Good student scores in the

  10. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    , which influence the transition from a planktonic lifestyle to a sessile lifestyle, have been studied. Protein conditioning film formation was found to influence bacterial adhesion and subsequent biofilm formation considerable, and an aqueous extract of fish muscle tissue was shown to significantly...... tract to the microbial flocs in waste water treatment facilities. Microbial biofilms may however also cause a wide range of industrial and medical problems, and have been implicated in a wide range of persistent infectious diseases, including implantassociated microbial infections. Bacterial adhesion...... is the first committing step in biofilm formation, and has therefore been intensely scrutinized. Much however, still remains elusive. Bacterial adhesion is a highly complex process, which is influenced by a variety of factors. In this thesis, a range of physico-chemical, molecular and environmental parameters...

  11. Bacterial meningitis

    NARCIS (Netherlands)

    Heckenberg, Sebastiaan G. B.; Brouwer, Matthijs C.; van de Beek, Diederik

    2014-01-01

    Bacterial meningitis is a neurologic emergency. Vaccination against common pathogens has decreased the burden of disease. Early diagnosis and rapid initiation of empiric antimicrobial and adjunctive therapy are vital. Therapy should be initiated as soon as blood cultures have been obtained,

  12. Bacterial lipases

    NARCIS (Netherlands)

    Jaeger, Karl-Erich; Ransac, Stéphane; Dijkstra, Bauke W.; Colson, Charles; Heuvel, Margreet van; Misset, Onno

    Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation,

  13. Bacterial stress

    Indian Academy of Sciences (India)

    First page Back Continue Last page Graphics. Bacterial stress. Physicochemical and chemical parameters: temperature, pressure, pH, salt concentration, oxygen, irradiation. Nutritional depravation: nutrient starvation, water shortage. Toxic compounds: Antibiotics, heavy metals, toxins, mutagens. Interactions with other cells: ...

  14. Institute of Biochemistry and Biophysics. Research Report 1996-1997

    International Nuclear Information System (INIS)

    1998-01-01

    Scientific interests of the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences have evolved from classical biochemistry, biophysics and physiological chemistry to up-to-date molecular biology. Research interests are focussed on replication, mutagenesis and repair of DNA; regulation of gene expression at various levels; biosynthesis and post-translational modifications of proteins; gene sequencing and functional analysis of open reading frames; structure, function and regulation of enzymes; conformation of proteins and peptides; modelling of structures and prediction of functions of proteins; mechanisms of electron transfer in polypeptides

  15. Institute of Biochemistry and Biophysics. Research Report 1996-1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-07-01

    Scientific interests of the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences have evolved from classical biochemistry, biophysics and physiological chemistry to up-to-date molecular biology. Research interests are focussed on replication, mutagenesis and repair of DNA; regulation of gene expression at various levels; biosynthesis and post-translational modifications of proteins; gene sequencing and functional analysis of open reading frames; structure, function and regulation of enzymes; conformation of proteins and peptides; modelling of structures and prediction of functions of proteins; mechanisms of electron transfer in polypeptides.

  16. Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites.

    Science.gov (United States)

    Jiménez, Diego Javier; Dini-Andreote, Francisco; Ottoni, Júlia Ronzella; de Oliveira, Valéria Maia; van Elsas, Jan Dirk; Andreote, Fernando Dini

    2015-05-01

    The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes. © 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  17. Compositional profile of α/β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites

    Science.gov (United States)

    Jiménez, Diego Javier; Dini-Andreote, Francisco; Ottoni, Júlia Ronzella; de Oliveira, Valéria Maia; van Elsas, Jan Dirk; Andreote, Fernando Dini

    2015-01-01

    The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes. PMID:25171437

  18. Adaptation of Xanthobacter autotrophicus GJ10 to bromoacetate due to activation and mobilization of the haloacetate dehalogenase gene by insertion element IS1247

    DEFF Research Database (Denmark)

    van der Ploeg, J; Willemsen, M; Van Hall, Gerrit

    1995-01-01

    B gene. In mutant GJ10M50, a DNA fragment (designated IS1247) had copied itself from a position on the chromosome that was not linked to the dhlB region to a site immediately upstream of dhlB, resulting in a 1,672-bp insertion. IS1247 was found to encode an open reading frame corresponding to 464 amino...... acids which showed similarity to putative transposases from two other insertion elements. In most of the other MBA-resistant mutants of GJ10, IS1247 was also present in one more copy than in the wild type, which had two copies located within 20 kb. After insertion to a site proximal to dhlB, IS1247...... was able to transpose itself together with the dhlB gene to a plasmid, without the requirement of a second insertion element being present downstream of dhlB. The results show that IS1247 causes bromoacetate resistance by overexpression and mobilization of the haloacid dehalogenase gene, which mimics steps...

  19. Teaching of biochemistry: analyze of works presented in Congress the Society Brazilian Biochemistry and Molecular Biology - SBBq

    Directory of Open Access Journals (Sweden)

    D.F. Escoto

    2013-05-01

    Full Text Available Introduction: In recent decades the strategies to improve science education has grown exponentially. Thus, the scientific production in the area is also growing, with the purpose of identifying parameters and methodologies that contribute to their qualification. The teaching of biochemistry is intimately linked to that context. However, it is still little explored in basic education and with character technicist in higher education. The aim of this study was identify areas that received most attention in the scientific literature about teaching and education in biochemistry that were presented at the Congress of the Brazilian Society of Biochemistry and Molecular Biology from 2004 to 2012. Material and Methods: To conduct the survey were analyzed summaries available on the website of the Brazilian Journal of Education for Biochemistry and Molecular Biology published in the proceedings of the event, where they were encontrados176 summaries. For expression of results was used categorization from the content analysis. Results and Discussion: The results observed to establish nine categories based on the analysis of the titles and content of the work, which, in descending order, were: information and communication technologies, alternative methods teaching and learning, biochemistry in Elementary Education and / or Medium, experiential activities, teacher training, dissemination of science, proposition and evaluation of content and / or science curricular and History and Philosophy. It is noticed that the three most important categories were consolidated along editions. In education, however, there was a significant decrease in the number of abstracts submitted abstracts for the past five years. Conclusions: We conclude that all categories listed seeking alternatives to improve teaching practices and promote education of biochemistry in different contexts.

  20. Utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorous lyase

    DEFF Research Database (Denmark)

    Hove-Jensen, Bjarne; Zechel, David L; Jochimsen, Bjarne

    2014-01-01

    After several decades of use of glyphosate, the active ingredient in weed killers such as Roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. Glyphosate is a member of a l...

  1. Haematology, serum biochemistry and organ weight changes of ...

    African Journals Online (AJOL)

    A total of fifty Wistar albino rats weighing 50-60g were randomly allocated to five dietary treatments in a completely randomized design to investigate the haematology, serum biochemistry and organ weight changes on diets containing processed dehulled jack bean. Four diets containing 10% crude protein were formulated ...

  2. Haematology and serum biochemistry of laying hens fed red pepper ...

    African Journals Online (AJOL)

    The hematology and serum biochemistry of ISA brown laying hens fed red pepper (Capsicum annum. L.) as feed additive in their diet was studied. Sixty (60) laying birds (in their 32nd week) were randomly allotted to four different dietary treatments with graded levels of red pepper (Capsicum annum. L.) as additive.

  3. Imaging spectroscopy of foliar biochemistry in forestry environments ...

    African Journals Online (AJOL)

    Remote sensing estimates of leaf biochemicals provide valuable information on ecosystem functioning, vitality and state at local to global spatial scales. This paper aims to give an overview of the state of the art of foliar biochemistry assessment in general and, where possible, attention is given to: (1) Eucalyptus forest ...

  4. Blood and serum biochemistry of omentopexed West African Dwarf ...

    African Journals Online (AJOL)

    This study investigated the blood and serum biochemistry following peritoneum sutured and not sutured techniques of laparotomy sutures in omentopexed WAD goats. Twentyfive male WAD goats were randomly divided into 5 groups (A – E). In group A, peritoneum was not sutured, while in group B, the peritoneum was ...

  5. Aspects of the serum biochemistry, carcass quality and organoleptic ...

    African Journals Online (AJOL)

    The effects of feeding alkaline treated date pits (TDP) on serum biochemistry, carcass quality and organoleptic characteristics were investigated in 396 commercial broiler chicks of the Hybro strain. The values of glucose, albumin, protein, calcium, pH and GPT and GOT showed no significance difference when compared ...

  6. Semen quality, biochemistry and mineral content of five strains of ...

    African Journals Online (AJOL)

    The study was conducted to evaluate the genetic effect on semen quality, biochemistry and mineral content of three strains of Nigerian indigenous and two exotic cocks. One hundred (100) adult local breeding cocks comprising 20 normal, 20 frizzle and 20 naked necks, 20 dominant black and 20 dominant blue feather were ...

  7. Phosphinic acid compounds in biochemistry, biology and medicine

    Czech Academy of Sciences Publication Activity Database

    Collinsová, Michaela; Jiráček, Jiří

    2000-01-01

    Roč. 7, - (2000), s. 629-647 ISSN 0929-8673 R&D Projects: GA ČR GA203/97/0039; GA AV ČR KSK2055603 Institutional research plan: CEZ:AV0Z4055905 Subject RIV: CE - Biochemistry Impact factor: 4.909, year: 2000

  8. Assessment of Learning Gains in a Flipped Biochemistry Classroom

    Science.gov (United States)

    Ojennus, Deanna Dahlke

    2016-01-01

    The flipped classroom has become an increasingly popular pedagogical approach to teaching and learning. In this study, learning gains were assessed in a flipped biochemistry course and compared to gains in a traditional lecture. Although measured learning gains were not significantly different between the two courses, student perception of…

  9. Raising Environmental Awareness through Applied Biochemistry Laboratory Experiments

    Science.gov (United States)

    Salman Ashraf, S.

    2013-01-01

    Our environment is under constant pressure and threat from various sources of pollution. Science students, in particular chemistry students, must not only be made aware of these issues, but also be taught that chemistry (and science) can provide solutions to such real-life issues. To this end, a newly developed biochemistry laboratory experiment…

  10. Using Augmented Reality to Teach and Learn Biochemistry

    Science.gov (United States)

    Vega Garzón, Juan Carlos; Magrini, Marcio Luiz; Galembeck, Eduardo

    2017-01-01

    Understanding metabolism and metabolic pathways constitutes one of the central aims for students of biological sciences. Learning metabolic pathways should be focused on the understanding of general concepts and core principles. New technologies such Augmented Reality (AR) have shown potential to improve assimilation of biochemistry abstract…

  11. Biochemistry Instructors' Perceptions of Analogies and Their Classroom Use

    Science.gov (United States)

    Orgill, MaryKay; Bussey, Thomas J.; Bodner, George M.

    2015-01-01

    Biochemistry education relies heavily on students' abilities to conceptualize abstract cellular and molecular processes, mechanisms, and components. From a constructivist standpoint, students build their understandings of these abstract processes by connecting, expanding, or revising their prior conceptions and experiences. As such, biochemistry…

  12. Estimating foliar biochemistry from hyperspectral data in mixed forest canopy

    DEFF Research Database (Denmark)

    Huber Gharib, Silvia; Kneubühler, Mathias; Psomas, Achilleas

    2008-01-01

    data to estimate the foliar concentration of nitrogen, carbon and water in three mixed forest canopies in Switzerland. With multiple linear regression models, continuum-removed and normalized HyMap spectra were related to foliar biochemistry on an individual tree level. The six spectral wavebands used...

  13. Differentiating Biochemistry Course Laboratories Based on Student Experience

    Science.gov (United States)

    Jakubowski, Henry V.

    2011-01-01

    Content and emphases in undergraduate biochemistry courses can be readily tailored to accommodate the standards of the department in which they are housed, as well as the backgrounds of the students in the courses. A more challenging issue is how to construct laboratory experiences for a class with both chemistry majors, who usually have little or…

  14. Undergraduate Performance in Solving Ill-Defined Biochemistry Problems

    Science.gov (United States)

    Sensibaugh, Cheryl A.; Madrid, Nathaniel J.; Choi, Hye-Jeong; Anderson, William L.; Osgood, Marcy P.

    2017-01-01

    With growing interest in promoting skills related to the scientific process, we studied performance in solving ill-defined problems demonstrated by graduating biochemistry majors at a public, minority-serving university. As adoption of techniques for facilitating the attainment of higher-order learning objectives broadens, so too does the need to…

  15. The Use of Multiple Tools for Teaching Medical Biochemistry

    Science.gov (United States)

    Se, Alexandre B.; Passos, Renato M.; Ono, Andre H.; Hermes-Lima, Marcelo

    2008-01-01

    In this work, we describe the use of several strategies employing the philosophies of active learning and problem-based learning (PBL) that may be used to improve the teaching of metabolic biochemistry to medical and nutritional undergraduate students. The main activities are as follows: 1) a seminar/poster system in a mini-congress format (using…

  16. Using Assessment to Improve Learning in the Biochemistry Classroom

    Science.gov (United States)

    Loertscher, Jennifer

    2010-01-01

    In recent years, major drivers of undergraduate science education reform including the National Science Foundation (NSF) and the Howard Hughes Medical Institute (HHMI) have called on college and university instructors to take a more scientific approach to their teaching. Although many biochemistry instructors are gaining confidence in using…

  17. The New Biochemistry: Blending the Traditional with the Other.

    Science.gov (United States)

    Boyer, Rodney

    2000-01-01

    Points out the difficulties in designing and presenting a modern chemistry course with an overabundance of topics to cover in a limited amount of class time. Presents a model syllabi for biochemistry majors and the shorter survey course for non-majors, usually consisting of health professionals and biological science majors. (Contains 24…

  18. Blog Construction as an Effective Tool in Biochemistry Active Learning

    Science.gov (United States)

    Cubas Rolim, Estêvão; Martins de Oliveira, Julia; Dalvi, Luana T.; Moreira, Daniel C.; Garcia Caldas, Natasha; Fernandes Lobo, Felipe; André Polli, Démerson; Campos, Élida G.; Hermes-Lima, Marcelo

    2017-01-01

    To boost active learning in undergraduate students, they were given the task of preparing blogs on topics of clinical biochemistry. This "experiment" lasted for 12 teaching-semesters (from 2008 to 2013), and included a survey on the blogs' usefulness at the end of each semester. The survey (applied in the 2008-2010 period) used a…

  19. A Laboratory Course in Clinical Biochemistry Emphasizing Interest and Relevance

    Science.gov (United States)

    Schwartz, Peter L.

    1975-01-01

    Ten laboratory experiments are described which are used in a successful clinical biochemistry laboratory course (e.g. blood alcohol, glucose tolerance, plasma triglycerides, coronary risk index, gastric analysis, vitamin C and E). Most of the experiments are performed on the students themselves using simple equipment with emphasis on useful…

  20. An "in Silico" DNA Cloning Experiment for the Biochemistry Laboratory

    Science.gov (United States)

    Elkins, Kelly M.

    2011-01-01

    This laboratory exercise introduces students to concepts in recombinant DNA technology while accommodating a major semester project in protein purification, structure, and function in a biochemistry laboratory for junior- and senior-level undergraduate students. It is also suitable for forensic science courses focused in DNA biology and advanced…

  1. Retraction 2 | Shafik | Egyptian Journal of Biochemistry and ...

    African Journals Online (AJOL)

    Value of co-peptin/ plasminogen activator inhibitor-1 axis in early diagnosis of preterm labor risk among pre-eclamptic Egyptian women. Noha M. Shafik1, Soha S. Zakaria1, Ahmed M. Hagras2 and Ghada M. Abou-Fard3 Departments of Medical Biochemistry1, Gynecology2 and Physiology3, Faculty of Medicine, Tanta ...

  2. An Integrated Approach to Teaching Biochemistry for Pharmacy Students.

    Science.gov (United States)

    Poirier, Therese I.; Borke, Mitchell L.

    1982-01-01

    A Duquesne course integrating biochemistry lectures, clinical applications lectures, and laboratory sessions has the objectives of (1) making the course more relevant to students' perceived needs; (2) enhancing the learning process; (3) introducing clinical applications early in the students' program; and (4) demonstrating additional…

  3. [Bacterial vaginosis].

    Science.gov (United States)

    Romero Herrero, Daniel; Andreu Domingo, Antonia

    2016-07-01

    Bacterial vaginosis (BV) is the main cause of vaginal dysbacteriosis in the women during the reproductive age. It is an entity in which many studies have focused for years and which is still open for discussion topics. This is due to the diversity of microorganisms that cause it and therefore, its difficult treatment. Bacterial vaginosis is probably the result of vaginal colonization by complex bacterial communities, many of them non-cultivable and with interdependent metabolism where anaerobic populations most likely play an important role in its pathogenesis. The main symptoms are an increase of vaginal discharge and the unpleasant smell of it. It can lead to serious consequences for women, such as an increased risk of contracting sexually transmitted infections including human immunodeficiency virus and upper genital tract and pregnancy complications. Gram stain is the gold standard for microbiological diagnosis of BV, but can also be diagnosed using the Amsel clinical criteria. It should not be considered a sexually transmitted disease but it is highly related to sex. Recurrence is the main problem of medical treatment. Apart from BV, there are other dysbacteriosis less characterized like aerobic vaginitis of which further studies are coming slowly but are achieving more attention and consensus among specialists. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

  4. Differences in serum biochemistry between breast-fed and formula-fed infants

    Directory of Open Access Journals (Sweden)

    Tzee-Chung Wu

    2011-11-01

    Conclusion: Different sources of nutrition may result in different metabolic responses; these differences are reflected by different serum biochemistries. The reference values for serum biochemistry levels also differ according to the infant’s postnatal age.

  5. Glycogen with short average chain length enhances bacterial durability

    Science.gov (United States)

    Wang, Liang; Wise, Michael J.

    2011-09-01

    Glycogen is conventionally viewed as an energy reserve that can be rapidly mobilized for ATP production in higher organisms. However, several studies have noted that glycogen with short average chain length in some bacteria is degraded very slowly. In addition, slow utilization of glycogen is correlated with bacterial viability, that is, the slower the glycogen breakdown rate, the longer the bacterial survival time in the external environment under starvation conditions. We call that a durable energy storage mechanism (DESM). In this review, evidence from microbiology, biochemistry, and molecular biology will be assembled to support the hypothesis of glycogen as a durable energy storage compound. One method for testing the DESM hypothesis is proposed.

  6. Biochemistry Students' Ideas about Shape and Charge in Enzyme-Substrate Interactions

    Science.gov (United States)

    Linenberger, Kimberly J.; Bretz, Stacey Lowery

    2014-01-01

    Biochemistry is a visual discipline that requires students to develop an understanding of numerous representations. However, there is very little known about what students actually understand about the representations that are used to communicate ideas in biochemistry. This study investigated biochemistry students' understanding of multiple…

  7. Biochemistry - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available tests. Data file File name: open_tggates_biochemistry.zip File URL: ftp://ftp.biosciencedbc.jp/archive/open-...tggates/LATEST/open_tggates_biochemistry.zip File size: 666 KB Simple search URL ...http://togodb.biosciencedbc.jp/togodb/view/open_tggates_biochemistry#en Data acquisition method - Data analy

  8. Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands

    Czech Academy of Sciences Publication Activity Database

    Stsiapanava, A.; Chaloupková, R.; Fořtová, A.; Brynda, Jiří; Weiss, M.S.; Damborský, J.; Kutá-Smatanová, Ivana

    2011-01-01

    Roč. 67, - (2011), s. 253-257 ISSN 1744-3091 R&D Projects: GA MŠk(CZ) LC06010 Grant - others:GA ČR(CZ) GA310/09/1407 Program:GA Institutional research plan: CEZ:AV0Z50520514; CEZ:AV0Z60870520 Keywords : haloalkane dehalogenases * DhaA * Rhodococcus rhodochrous * microseeding * atomic resolution Subject RIV: EB - Genetics ; Molecular Biology; CD - Macromolecular Chemistry (UEK-B) Impact factor: 0.506, year: 2011

  9. Bacterial mitosis

    DEFF Research Database (Denmark)

    Møller-Jensen, Jakob; Borch, Jonas; Dam, Mette

    2003-01-01

    Bacterial DNA segregation takes place in an active and ordered fashion. In the case of Escherichia coli plasmid R1, the partitioning system (par) separates paired plasmid copies and moves them to opposite cell poles. Here we address the mechanism by which the three components of the R1 par system...... act together to generate the force required for plasmid movement during segregation. ParR protein binds cooperatively to the centromeric parC DNA region, thereby forming a complex that interacts with the filament-forming actin-like ParM protein in an ATP-dependent manner, suggesting that plasmid...

  10. Site-Specific, Covalent Immobilization of Dehalogenase ST2570 Catalyzed by Formylglycine-Generating Enzymes and Its Application in Batch and Semi-Continuous Flow Reactors

    Directory of Open Access Journals (Sweden)

    Hui Jian

    2016-07-01

    Full Text Available Formylglycine-generating enzymes can selectively recognize and oxidize cysteine residues within the sulfatase sub motif at the terminus of proteins to form aldehyde-bearing formylglycine (FGly residues, and are normally used in protein labeling. In this study, an aldehyde tag was introduced to proteins using formylglycine-generating enzymes encoded by a reconstructed set of the pET28a plasmid system for enzyme immobilization. The haloacid dehalogenase ST2570 from Sulfolobus tokodaii was used as a model enzyme. The C-terminal aldehyde-tagged ST2570 (ST2570CQ exhibited significant enzymological properties, such as new free aldehyde groups, a high level of protein expression and improved enzyme activity. SBA-15 has widely been used as an immobilization support for its large surface and excellent thermal and chemical stability. It was functionalized with amino groups by aminopropyltriethoxysilane. The C-terminal aldehyde-tagged ST2570 was immobilized to SBA-15 by covalent binding. The site-specific immobilization of ST2570 avoided the chemical denaturation that occurs in general covalent immobilization and resulted in better fastening compared to physical adsorption. The site-specific immobilized ST2570 showed 3-fold higher thermal stability, 1.2-fold higher catalytic ability and improved operational stability than free ST2570. The site-specific immobilized ST2570 retained 60% of its original activity after seven cycles of batch operation, and it was superior to the ST2570 immobilized to SBA-15 by physical adsorption, which loses 40% of its original activity when used for the second time. It is remarkable that the site-specific immobilized ST2570 still retained 100% of its original activity after 10 cycles of reuse in the semi-continuous flow reactor. Overall, these results provide support for the industrial-scale production and application of site-specific, covalently immobilized ST2570.

  11. Myoglobin structure and function: A multiweek biochemistry laboratory project.

    Science.gov (United States)

    Silverstein, Todd P; Kirk, Sarah R; Meyer, Scott C; Holman, Karen L McFarlane

    2015-01-01

    We have developed a multiweek laboratory project in which students isolate myoglobin and characterize its structure, function, and redox state. The important laboratory techniques covered in this project include size-exclusion chromatography, electrophoresis, spectrophotometric titration, and FTIR spectroscopy. Regarding protein structure, students work with computer modeling and visualization of myoglobin and its homologues, after which they spectroscopically characterize its thermal denaturation. Students also study protein function (ligand binding equilibrium) and are instructed on topics in data analysis (calibration curves, nonlinear vs. linear regression). This upper division biochemistry laboratory project is a challenging and rewarding one that not only exposes students to a wide variety of important biochemical laboratory techniques but also ties those techniques together to work with a single readily available and easily characterized protein, myoglobin. © 2015 International Union of Biochemistry and Molecular Biology.

  12. How to Search for Life by the Detection of Biochemistry

    Science.gov (United States)

    McKay, C. P.; Davila, A.; Sun, H. J.

    2013-12-01

    We consider how to search for life by the detection of biochemistry in three relevance case: 1) in samples returned to Earth, 2) In situ in the organic rich plume of Enceladus, and 3) On Mars, following the discovery of organics. A search for organic biomarkers can address several questions including: 1) Evidence for present or past life, 2) Evidence for a second genesis of life, 3) Hazard assessment for human explorers and sample return and 4) Detection of bioload from Earth. Some useful analogs for the search for organic biomarkers on other worlds include 1) Ancient Earth sediment record, an example of a poorly preserved ancient biochemistry, 2) Modern environments including anoxic Antarctic sediments 3)Extreme cold desert surfaces in the High Antarctic Dry Valleys 4) Extremely dry soils such as the Atacama Desert 5) Evaporites. Sample preparation is a key issue, often unappreciated in past. Illustrated by the interference of perchlorate with organic detection on Viking and SAM.

  13. Current research in Radiation Biology and Biochemistry Division

    International Nuclear Information System (INIS)

    Tarachand, U.; Singh, B.B.

    1995-01-01

    The Radiation Biology and Biochemistry Division, Bhabha Atomic Research Centre, Bombay has been engaged in research in the frontier areas of (i) radiation biology related to tumour therapy and injury caused by free radicals; (ii) molecular basis of diseases of physiological origin; (iii) molecular aspects of chemical carcinogenesis and (iv) structure of genome and genome related functions. The gist of research and development activities carried out in the Division during the last two years are documented

  14. A biochemistry laboratory course designed to enhance students autonomy

    Directory of Open Access Journals (Sweden)

    T. Silva

    2015-08-01

    Full Text Available INTRODUCTION: Laboratory sessions are responsible for promoting instrumentation skills desirable in biochemistry and biochemistry related careers. They are traditionally based on experimental protocols that lead to the expected results, and students usually have not autonomy to plan and execute their experiments. GOALS: This work aimed to enhance a traditional biochemistry lab course, applying pre-lab quizzes on protein biochemistry and lab techniques in order to have students better prepared to plan, execute and interpret experiments. This approach also aims to bring the laboratory sessions into an inquiry-based environment capable to improve students’ independent capabilities in 2 autonomy domains: learning and communication. MATERIAL AND METHODS: Online quizzes are delivered one week before each laboratory session, containing questions regarding the experimental techniques and theoretical basis related to them. Laboratory activities are presented in an inquiry-based approach where the first class of each activity is dedicated to plan experiments in order to answer the research questions presented by instructors. Activities are also organized in order to enhance students’ autonomy. The first activity is the simplest and more instructor-controlled and the last one is the most complex and less driven, transferring gradually to students the responsibility for their decisions in laboratory, supporting students’ autonomy. RESULTS: Online quizzes allowed instructors to identify students’ difficulties and to timely intervene. Scientific reports presented by students at the end of each activity showed that they performed better on less driven activities in which autonomy support were more complex than in the instructor controlled activities. CONCLUSIONS: Scientific reports analysis reveals students capabilities related to different scopes of autonomy, such as: discuss different strategies; find multiple solutions to solve problems; make their

  15. Current research in Radiation Biology and Biochemistry Division

    Energy Technology Data Exchange (ETDEWEB)

    Tarachand, U; Singh, B B [eds.; Bhabha Atomic Research Centre, Bombay (India). Radiation Biology and Biochemistry Div.

    1996-12-31

    The Radiation Biology and Biochemistry Division, Bhabha Atomic Research Centre, Bombay has been engaged in research in the frontier areas of (i) radiation biology related to tumour therapy and injury caused by free radicals; (ii) molecular basis of diseases of physiological origin; (iii) molecular aspects of chemical carcinogenesis and (iv) structure of genome and genome related functions. The gist of research and development activities carried out in the Division during the last two years are documented.

  16. Game Development as Didactic Strategy for Biochemistry Teaching

    Directory of Open Access Journals (Sweden)

    G.G. Hornink

    2010-05-01

    Full Text Available It is well known that students and teachers have difficulties in learning and teaching Biochemistry due to its abstract and interconnected contents. This work proposes a didactic strategy in order to facilitate teaching and learning process in Biochemistry. The strategy was implemented with biological science undergraduate students. At first, the students were divided into groups with a specific topic to develop a game. During the semester, problem based learning cases, online activities like crossword puzzle, essay questions and educational softwares were used to present the content of each topic. The groups were oriented in classroom and online, to choose and organize contents and create ways to approach them in games. At the end of the course the groups played each other games, which were evaluated by teacher and students following some criteria like: creativity, content organization, interdisciplinarity, proposal coherence, instructions clarity, specific content. The game elaboration contributed to the development of social and cognitive functions, such as teamwork and troubleshooting, providing an interesting perspective to the student about knowledge construction process. The strategy showed up students' creativity and ability to reorganize their knowledge to a different education level. In an overview, the results indicate that the proposed didactic strategy is an effective way to enhance learning and to motivate students into Biochemistry topics.

  17. THE USE OF MULTIPLE TOOLS FOR TEACHING MEDICAL BIOCHEMISTRY

    Directory of Open Access Journals (Sweden)

    A.B. Sé

    2007-05-01

    Full Text Available The pros and cons of Problem Based Learning (PBL have been extensivelydiscussed in the literature. We describe PBL-like strategies used at UnB (some ofthem since 1999 that may be useful elsewhere to improve undergraduatebiochemistry teaching with clinical applications. The main activities are: (i aseminar/poster system, (ii a true-or-false applied biochemistry exam (prepared bypeer tutors, (iii a 9-hour-exam on metabolism (based in actual papers, (iv anAdvanced Biochemistry course (directed to peer tutors, (v pizza-and-pasta (formetabolism teaching and free radicals (real science for students experiments,(vi the BioBio blog (http://www.biobio-unb.blogspot.com, (vii student lectures onhealth issues directed to the community, and (viii the BioBio Show. The mainobjective of these activities is providing students with a more practical andentertaining approach to biochemistry using philosophic PBL principles such asthe application of basic knowledge to real situations (diseases, experiments andscientific discoveries. We also emphasize (a the importance of peer-tutor activityfor optimized learning of students and peer tutors, (b the relevance of a closerinteraction between students and professors, and (c the necessity to initiatestudents precociously in actual basic/medical science and contact with the public.Most activities have been evaluated by the students through written questionnairesand informal conversations, for several semesters, indicating good acceptanceand approval of these methods.

  18. Lecture-free biochemistry: A Process Oriented Guided Inquiry Approach.

    Science.gov (United States)

    Minderhout, Vicky; Loertscher, Jennifer

    2007-05-01

    Biochemistry courses at Seattle University have been taught exclusively using process oriented guided inquiry learning (POGIL) without any traditional lecture component since 1997. In these courses, students participate in a structured learning environment, which includes a preparatory assignment, an in-class activity, and a follow-up skill exercise. Instructor-designed learning activities provide the content of the course while the cooperative learning structure provides the content-free procedures that promote development of critical process skills needed for learning. This format enables students to initially explore a topic independently, work together in groups to construct and refine knowledge, and eventually develop deep understanding of the essential concepts. These stages of exploration and concept development form the foundation for application to high level biochemical problems. At the end of this course, most students report feeling confident in their knowledge of biochemistry and report substantial gains in independence, critical thinking, and respect for others. Copyright © 2007 International Union of Biochemistry and Molecular Biology, Inc.

  19. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    compounds these must first be undergo extracellular hydrolysis. Bacteria have a great diversity with respect to types of metabolism that far exceeds the metabolic repertoire of eukaryotic organisms. Bacteria play a fundamental role in the biosphere and certain key processes such as, for example......, the production and oxidation of methane, nitrate reduction and fixation of atmospheric nitrogen are exclusively carried out by different groups of bacteria. Some bacterial species – ‘extremophiles’ – thrive in extreme environments in which no eukaryotic organisms can survive with respect to temperature, salinity...... biogeochemical processes are carried exclusively by bacteria. * Bacteria play an important role in all types of habitats including some that cannot support eukaryotic life....

  20. Bacterial Actins.

    Science.gov (United States)

    Izoré, Thierry; van den Ent, Fusinita

    2017-01-01

    A diverse set of protein polymers, structurally related to actin filaments contributes to the organization of bacterial cells as cytomotive or cytoskeletal filaments. This chapter describes actin homologs encoded by bacterial chromosomes. MamK filaments, unique to magnetotactic bacteria, help establishing magnetic biological compasses by interacting with magnetosomes. Magnetosomes are intracellular membrane invaginations containing biomineralized crystals of iron oxide that are positioned by MamK along the long-axis of the cell. FtsA is widespread across bacteria and it is one of the earliest components of the divisome to arrive at midcell, where it anchors the cell division machinery to the membrane. FtsA binds directly to FtsZ filaments and to the membrane through its C-terminus. FtsA shows altered domain architecture when compared to the canonical actin fold. FtsA's subdomain 1C replaces subdomain 1B of other members of the actin family and is located on the opposite side of the molecule. Nevertheless, when FtsA assembles into protofilaments, the protofilament structure is preserved, as subdomain 1C replaces subdomain IB of the following subunit in a canonical actin filament. MreB has an essential role in shape-maintenance of most rod-shaped bacteria. Unusually, MreB filaments assemble from two protofilaments in a flat and antiparallel arrangement. This non-polar architecture implies that both MreB filament ends are structurally identical. MreB filaments bind directly to membranes where they interact with both cytosolic and membrane proteins, thereby forming a key component of the elongasome. MreB filaments in cells are short and dynamic, moving around the long axis of rod-shaped cells, sensing curvature of the membrane and being implicated in peptidoglycan synthesis.

  1. Are tutor-students capable of writing good biochemistry exams?

    Directory of Open Access Journals (Sweden)

    Sé Alexandre B.

    2004-05-01

    Full Text Available In a previous article we described the relevance of student seminars for the learning process of appliedbiochemistry for medical and nutrition students (Hermes-Lima et al., Biochem. Mol.Biol.Educ. 30:30-34,2002. First semester students of a basic biochemistry course (BioBio are divided in 10 groupsof 5 members, and each group is assigned to a specic topic (diabetes, cholesterol, etc under thesupervision of a tutor-student. The tutors have already coursed BioBio and are currently undertakingan advanced biochemistry course. In order to evaluate the learning of applied biochemistry for BioBiostudents a true or false exam (TFE is performed. This exam is made of 50 questions (5 on eachtopic elaborated by the tutors under the supervision of the teacher. The TFE corresponds to 10percent of the grade of BioBio and focus on clinical and/or applied biochemistry situations. At theend of the exam, BioBio students were asked to share their opinions about TFEs (n = 401, from2001/1 to 2003/2. When asked to give a 0-to-4 score regarding (a the diculty level of the test,(b the technical quality and (c if the exam makes an appropriate evaluation of applied biochemistryknowledge, the scores were 2.9, 3.4 and 2.9, respectively. BioBio students were also asked if they ndvalid to be evaluated by a tutor-made exam and if they would like to participate in the making ofTFEs; 96 and 58 percent answered yes, respectively.In another survey, we interviewed former BioBio students from the 2nd to the 7th semesters (n=95about TFEs (since 1999-1 regarding technical aspects, which included (1 clarity of questions, (2 levelof diculty, (3 clinical application and (4 thinking (as opposed to memorizing abilities demanded;the 0-to-4 scores were 3.1, 2.9, 2.6, and 2.5, respectively. Other four questions were on the validityof tutors writing TFEs and their capacity to perform such a task; the average score was 3.2. Oursurveys show the students good acceptance of the seminar system

  2. Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology (edited by Gerhard Michal)

    Science.gov (United States)

    Voige, Reviewed By William H.

    2000-02-01

    feature to the hyperlinks in an electronic document.) The book's index is comprehensive and useful. Entries for "phenylketonuria" and "sickle cell anemia", for example, lead to commendably concise summaries of these hereditary diseases (and the relevant metabolic pathway, in the former case). Looking up a specific molecule, however, is less helpful. The listing for fumarate hydratase, a citric acid cycle enzyme, directs the reader to the chapter on special bacterial metabolism but not to the section on the citric acid cycle itself. Literature references are included at the end of each section and are mainly from the 1990s, but they could be more useful. A long section on heme proteins, for example, concludes with eight citations, but their titles are not included, so it is impossible to determine what topic each one addresses. This book will be most useful to those with a good understanding of the fundamentals of biochemistry. Some of the information it presents could easily confuse less experienced readers. For example, it classifies selenocysteine as a standard amino acid in a figure but not in the accompanying text. In the diagram of anaerobic glycolysis, a double-headed arrow for the hexokinase reaction reinforces the frustratingly common student misperception that the phosphoryl group of glucose-6-phosphate can be used to phosphorylate ADP. Biochemical Pathways compiles a large amount of information in a single source. Its good index and clear, concise text and diagrams should make it a reliable way of gaining insight into many biochemical topics. With a price similar to that of most textbooks, it merits a place in the libraries of individuals and academic departments that teach biochemistry.

  3. TEACHING BIOCHEMISTRY USING EDUCATIONAL GAMES AND GAMIFICATION STRATEGIES

    Directory of Open Access Journals (Sweden)

    Yuri Rafael de Oliveira Silva

    2016-11-01

    Full Text Available INTRODUCTION: Biotechnology is a new bachelor degree in UFPA, and has been stablished with excellency in the state of Pará. However, there is the need to promote comprehension and learning in Biochemistry, as well as interdisciplinarity, that is an essential part of biotechnology. OBJECTIVES:  To increase learning and interdisciplinarity, educational games were used as tools. The students were instigated to develop educational games in different topics of energy metabolism. MATERIALS AND METHODS: The games were developed to be used in any teaching environment, since they were made with low-cost and accessible materials. This strategy was applied in three semesters in different Biochemistry classes, between 2012 and 2014. The best games in each class were used in following semesters. DISCUSSION AND RESULTS: Since the first semester, the failing rates dropped 15% compared to the previous semester, in which educational games were not used. An increase in learning (by observation could be noticed, including comprehension of metabolic pathways and their conections. Twenty games were developed in three semesters, and four of them are still being improved and used in other classes. The participant students answered a questionnaire, in which 47% defined the games as “Relaxing and Instigating”, 33% said the games “Accomplished their didactic and educational role” and 54% said they would recommend the use of these games as a reviewing activity. At the moment, another approach is being used to teach Biochemistry – Gamification, which uses elements found in games, as conflict, cooperation, rules and fun, to improve students’ motivation and engagement. CONCLUSION: As a partial result, there was greater in-class interest and engagement, better comprehension of the course content and the activities gave the students the opportunity to work in groups, to think critically about the themes and to develop opinions based on interdisciplinar and formal

  4. A national comparison of biochemistry and molecular biology capstone experiences.

    Science.gov (United States)

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices. © 2015 The International Union of Biochemistry and Molecular Biology.

  5. Comparative analysis of the biochemistry undergraduate courses in Brazil

    Directory of Open Access Journals (Sweden)

    P. A. Granjeiro

    2014-08-01

    Full Text Available INTRODUCTION: The economic and social development of Brazil during the recent decades has contributed to the installation of several new undergraduate and graduate study programs, as is the case of the undergraduate biochemistry programs at UFV, UFSJ and UEM. The new biochemical professionals are being prepared to work mainly in Industries, research Institutes, government agencies and Universities in all fields that involve Biochemistry and Molecular Biology. The aim of this study was to conduct a comparative analysis of the courses in Biochemistry in Brazil. MATERIAL AND METHODS: Comparative analysis of the course units of the UFV, UFSJ and UEM programs, centered on the curricula contents and organization and on the profiles of the students in terms of parameters such as the number of admissions and the graduation completion rates. RESULTS AND DISCUSSION: The UFV and UEM programs present a very similar distribution of workload over the biological, exact sciences, humanities, biochemical specialties and technological applications. The UFSJ program presents higher workloads in the areas of biological sciences and technological applications. No significant differences in the distribution of the workloads of mandatory and optional disciplines, complementary activities and supervised activities were detected. Over the past five years there was a decrease in the number of students that abandoned the programs, despite the increased retention time in the three courses. Most graduated students at both UFV and UFSJ continue their academic career toward the Master or Doctor degrees. CONCLUSION: Little difference between the study programs analyzed. This is somewhat surprising if one considers the fact that individual conception of each program was based on different local conditions and needs, which indeed justify small differences. The similarity of the programs, on the other hand, reflects the universality of the biochemical sciences and their broad

  6. The applied biochemistry of PEDF and implications for tissue homeostasis

    Science.gov (United States)

    BROADHEAD, MATTHEW L.; BECERRA, S. PATRICIA; CHOONG, PETER F. M.; DASS, CRISPIN R.

    2012-01-01

    Pigment epithelium-derived factor (PEDF) is an endogenously produced glycoprotein with a spectrum of biological roles across diverse pathologies. Recent research has focused on the biochemical properties of PEDF and its associated receptors. This review discusses the recent developments in PEDF biochemistry and how this new knowledge will help progress our understanding of PEDF as a molecular mediator for anti-angiogenesis and -tumorigenesis. Additionally, pathophysiological roles for PEDF in healing and tissue homeostasis are being revealed and our enhanced understanding of the interactions between PEDF and its receptors may yet prove useful in propelling PEDF towards clinical application. PMID:20166889

  7. Effect of irradiation on biochemistry properties of shrimp allergen

    International Nuclear Information System (INIS)

    Gu Kefei; Gao Meixu; Li Chunhong; Li Shurong; Pan Jiarong

    2007-01-01

    Study on the effects of 60 Co γ-rays irradiation at the dose of 0,3,5,7,10 kGy on shrimp allergen biochemistry properties was conducted. The results indicated that the allergen protein molecule can be broken down to smaller molecules or coagulated to larger molecules by irradiation. The hydrophobicity and turbidity of irradiated allergen increased with the increase of absorbed dose. The results also show that allergen solution is more sensitive to irradiation than allergen in solid state or in the whole shrimp. (authors)

  8. Cell complexes of transition metals in biochemistry and medicine

    International Nuclear Information System (INIS)

    Voloshin, Ya.Z.; Varzatskij, O.A.; Bubnov, Yu.N.

    2007-01-01

    Basic directions and prospects of use of cell complexes of transition metals in medicine and biochemistry are considered: incapsulation of radioactive metal ions for radiotherapy and diagnostics; preparation of contrast compounds for magnetic resonance tomography, antidotes and pharmaceutical preparation of prolonged effect, preparations for boron-neutron-capture therapy of neoplasms, antioxidants; membrane transport of metal ions; study of interaction of cell metal complexes with nucleic acids; possibility of use of self-assembly of cell complexes for imitation of ligases and use of clathrochelates as linkers; design of inhibitors of viruses for AIDS therapy [ru

  9. Hartmut Lichtenthaler: an authority on chloroplast structure and isoprenoid biochemistry.

    Science.gov (United States)

    Sharkey, Thomas D; Govindjee

    2016-05-01

    We pay tribute to Hartmut Lichtenthaler for making important contributions to the field of photosynthesis research. He was recently recognized for ground-breaking discoveries in chloroplast structure and isoprenoid biochemistry by the Rebeiz Foundation for Basic Research (RFBR; http://vlpbp.org/ ), receiving a 2014 Lifetime Achievement Award for Photosynthesis. The ceremony, held in Champaign, Illinois, was attended by many prominent researchers in the photosynthesis field. We provide below a brief note on his education, and then describe some of the areas in which Hartmut Lichtenthaler has been a pioneer.

  10. Construction of concept maps as tool for Biochemistry learning

    Directory of Open Access Journals (Sweden)

    Silvia Lopes de Menezes

    2006-07-01

    Full Text Available The use of concept maps on the teaching of sciences has been object of worldwide research with different purposes: to detect the previous knowledge of the students on certain topics or to evaluate learning, among others. Based on Ausubel´s cognitive psychology, concept maps assume that the learning is accomplished by assimilation of new concepts and propositions to the students´ cognitive structure, contributing to establish links between the previous and new knowledge. It is especially interesting on the approach of interdisciplinary issues, as many studied in Biochemistry.The relevance of the use of concept maps on biochemistry learning was evaluated on a thirty-hour undergraduation optional course, with interdisciplinary topics, which are not usually included on introductory Biochemistry courses. The course Biochemistry of Animal Venoms was structured in seven module where the biochemical action mechanisms of the venoms of Crotalus sp (south american rattlesnake, Bothrops sp (jararaca, Loxosceles sp (brown spider, Tityus sp (yellow scorpion, Phoneutria sp (armed spider, Apis mellifera (honey bee and Latrodectus sp (black widowwere discussed. The students worked in small groups and, at each module, there were (1 an oriented study, guided by questions, texts and schemes, supervised by the teachers, (2 the construction of individual concept maps, where the local and systemic effects of the venoms should be predicted by their biochemical composition and (3 the construction of a new map by the group, incorporating the information of the individual maps. The difficulty level of these tasks was gradually increased throughout the course, with lesser time to carry out the tasks, lesser assistance during the oriented study and even lesser information on the venom effects.The course assessment was given by the number, quality and correction of the concepts relationship present in the concept maps, through a questionnaire and by the

  11. Construction of Hypertexts in a Biochemistry Pos- Graduation Discipline

    OpenAIRE

    W.B. Maia; B.S. dos Santos; J.M. Martins; B.C. Araujo; A.A. Pimenta Filho; T.G. Araújo; M.C. Martins; C.R.F.C. Mota; A.L. Castro- Neto; V.L.M. Lima,

    2009-01-01

    Virtual reality is an innovating manner of comprehending and acting on how the world is and, also, considered a new way of intellectual exercise.  This work took place in a  biochemistry masters discipline (Advanced Formation in ScientificEducation) and had as its observation context the forum (on-line tool) viability, intending the construction of hypertexts (active  collaborative writing ) by the 15 registered students in the  discipline in 2008. The discipline was available on the web, in ...

  12. Are tutor-students capable of writing good biochemistry exams?

    OpenAIRE

    Alexandre B., Sé; Depto. Biologia Celular, UnB, Brasília, DF, 70910-900; Passos, Renato M.; Depto. Biologia Celular, UnB, Brasília, DF, 70910-900; Hermes-Lima, Marcelo; Depto. Biologia Celular, UnB, Brasília, DF, 70910-900

    2004-01-01

    In a previous article we described the relevance of student seminars for the learning process of appliedbiochemistry for medical and nutrition students (Hermes-Lima et al., Biochem. Mol.Biol.Educ. 30:30-34,2002). First semester students of a basic biochemistry course (BioBio) are divided in 10 groupsof 5 members, and each group is assigned to a specic topic (diabetes, cholesterol, etc) under thesupervision of a tutor-student. The tutors have already coursed BioBio and are currently undertakin...

  13. A guide on instrument of biochemistry and molecular biology

    International Nuclear Information System (INIS)

    1995-10-01

    This book is about instrument on biochemistry and molecular biology, which consists of six chapters. It deals with introduction of advanced bio-instrument, common utilization and maintain, explanation of each instrument like capillary electrophoresis, interactive laser cytometer, personal computer and software, an electron microscope and DNA/RNS synthesis instrument, large equipment and special system like information system and network, analysis system for genome and large spectro graph, outside donation, examples for common utilization and appendix on data like application form for use.

  14. CUREs in biochemistry-where we are and where we should go.

    Science.gov (United States)

    Bell, Jessica K; Eckdahl, Todd T; Hecht, David A; Killion, Patrick J; Latzer, Joachim; Mans, Tamara L; Provost, Joseph J; Rakus, John F; Siebrasse, Erica A; Ellis Bell, J

    2017-01-02

    Integration of research experience into classroom is an important and vital experience for all undergraduates. These course-based undergraduate research experiences (CUREs) have grown from independent instructor lead projects to large consortium driven experiences. The impact and importance of CUREs on students at all levels in biochemistry was the focus of a National Science Foundation funded think tank. The state of biochemistry CUREs and suggestions for moving biochemistry forward as well as a practical guide (supplementary material) are reported here. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):7-12, 2017. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

  15. Accumulation of Peptidoglycan O-Acetylation Leads to Altered Cell Wall Biochemistry and Negatively Impacts Pathogenesis Factors of Campylobacter jejuni.

    Science.gov (United States)

    Ha, Reuben; Frirdich, Emilisa; Sychantha, David; Biboy, Jacob; Taveirne, Michael E; Johnson, Jeremiah G; DiRita, Victor J; Vollmer, Waldemar; Clarke, Anthony J; Gaynor, Erin C

    2016-10-21

    Campylobacter jejuni is a leading cause of bacterial gastroenteritis in the developed world. Despite its prevalence, its mechanisms of pathogenesis are poorly understood. Peptidoglycan (PG) is important for helical shape, colonization, and host-pathogen interactions in C. jejuni Therefore, changes in PG greatly impact the physiology of this organism. O-acetylation of peptidoglycan (OAP) is a bacterial phenomenon proposed to be important for proper cell growth, characterized by acetylation of the C6 hydroxyl group of N-acetylmuramic acid in the PG glycan backbone. The OAP gene cluster consists of a PG O-acetyltransferase A (patA) for translocation of acetate into the periplasm, a PG O-acetyltransferase B (patB) for O-acetylation, and an O-acetylpeptidoglycan esterase (ape1) for de-O-acetylation. In this study, reduced OAP in ΔpatA and ΔpatB had minimal impact on C. jejuni growth and fitness under the conditions tested. However, accumulation of OAP in Δape1 resulted in marked differences in PG biochemistry, including O-acetylation, anhydromuropeptide levels, and changes not expected to result directly from Ape1 activity. This suggests that OAP may be a form of substrate level regulation in PG biosynthesis. Ape1 acetylesterase activity was confirmed in vitro using p-nitrophenyl acetate and O-acetylated PG as substrates. In addition, Δape1 exhibited defects in pathogenesis-associated phenotypes, including cell shape, motility, biofilm formation, cell surface hydrophobicity, and sodium deoxycholate sensitivity. Δape1 was also impaired for chick colonization and adhesion, invasion, intracellular survival, and induction of IL-8 production in INT407 cells in vitro The importance of Ape1 in C. jejuni biology makes it a good candidate as an antimicrobial target. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. CUREs in biochemistry?where we are and where we should go

    OpenAIRE

    Bell, Jessica K.; Eckdahl, Todd T.; Hecht, David A.; Killion, Patrick J.; Latzer, Joachim; Mans, Tamara L.; Provost, Joseph J.; Rakus, John F.; Siebrasse, Erica A.; Ellis Bell, J.

    2016-01-01

    Abstract Integration of research experience into classroom is an important and vital experience for all undergraduates. These course?based undergraduate research experiences (CUREs) have grown from independent instructor lead projects to large consortium driven experiences. The impact and importance of CUREs on students at all levels in biochemistry was the focus of a National Science Foundation funded think tank. The state of biochemistry CUREs and suggestions for moving biochemistry forward...

  17. Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands

    International Nuclear Information System (INIS)

    Stsiapanava, Alena; Chaloupkova, Radka; Fortova, Andrea; Brynda, Jiri; Weiss, Manfred S.; Damborsky, Jiri; Kuta Smatanova, Ivana

    2011-01-01

    Crystals of the wild-type haloalkane dehalogenase DhaA derived from R. rhodochrous NCIMB 13064 and of its catalytically inactive variant DhaA13 were grown in the presence of various ligands and diffraction data were collected to high and atomic resolution. Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon–halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P2 1 2 1 2 1 as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively

  18. Biochemistry of Microbial Degradation of Hexachlorocyclohexane and Prospects for Bioremediation

    Science.gov (United States)

    Lal, Rup; Pandey, Gunjan; Sharma, Pooja; Kumari, Kirti; Malhotra, Shweta; Pandey, Rinku; Raina, Vishakha; Kohler, Hans-Peter E.; Holliger, Christof; Jackson, Colin; Oakeshott, John G.

    2010-01-01

    Summary: Lindane, the γ-isomer of hexachlorocyclohexane (HCH), is a potent insecticide. Purified lindane or unpurified mixtures of this and α-, β-, and δ-isomers of HCH were widely used as commercial insecticides in the last half of the 20th century. Large dumps of unused HCH isomers now constitute a major hazard because of their long residence times in soil and high nontarget toxicities. The major pathway for the aerobic degradation of HCH isomers in soil is the Lin pathway, and variants of this pathway will degrade all four of the HCH isomers although only slowly. Sequence differences in the primary LinA and LinB enzymes in the pathway play a key role in determining their ability to degrade the different isomers. LinA is a dehydrochlorinase, but little is known of its biochemistry. LinB is a hydrolytic dechlorinase that has been heterologously expressed and crystallized, and there is some understanding of the sequence-structure-function relationships underlying its substrate specificity and kinetics, although there are also some significant anomalies. The kinetics of some LinB variants are reported to be slow even for their preferred isomers. It is important to develop a better understanding of the biochemistries of the LinA and LinB variants and to use that knowledge to build better variants, because field trials of some bioremediation strategies based on the Lin pathway have yielded promising results but would not yet achieve economic levels of remediation. PMID:20197499

  19. The potential of fluorinated surfactants in membrane biochemistry.

    Science.gov (United States)

    Shepherd, F H; Holzenburg, A

    1995-01-01

    Detergents are important reagents in membrane biochemistry. Since each membrane system studied places different demands on the detergent in terms of desirous physicochemical properties, detergents new to biochemistry must continuously be sought. Ammonium perfluorooctanoate (APFO) was investigated, as representative of fluorinated surfactants, in terms of its suitability as a "biological detergent." It did not interfere with the Markwell modification of the Lowry procedure at detergent concentrations of up to 2% (w/v). Critical micellization concentration (cmc) values (0.013-0.0275 M) for this detergent were determined in a number of buffers of biological interest. It was demonstrated that the detergent can be removed by dialysis, albeit slowly. This slow removal may be particularly useful for reconstitution/crystallization studies. Solubilization studies on several membrane systems containing the proteins listed (the major protein of the membrane sector of the vacuolar H(+)-ATPase (16 kDa protein); photosystem II; equine herpes virus (EHV) envelope proteins) indicate that it is a potent solubilizing agent, likely to enhance the yield in cases where solubilization has already been demonstrated, and, in other cases, to solubilize proteins formerly recalcitrant to solubilization. The removal of APFO from solubilized 16-kDa protein by means of Extracti-Gel D resin as a means of exchanging detergents quickly and with a minimum requirement for second detergent was investigated.

  20. Medical biochemistry: Is it time to change the teaching style?

    Science.gov (United States)

    Palocaren, Jeeji; Pillai, Lekha S; Celine, T M

    2016-01-01

    The Medical Council of India (MCI) recommendations on medical education suggest a shift from didactic lectures to more interactive lectures. This study assessed the effectiveness of different pedagogical methods in biochemistry and the perceptions of students and teachers about the shift from didactic to interactive lectures. An interventional crossover study was done with the topic divided into three biochemical modules and one clinical module. The students were divided into two batches, one of which was given didactic and the other, interactive lectures. They were assessed immediately after the lecture and four months later. Anonymous feedback was obtained to gauge the students' perceptions regarding the mode of teaching. The teachers' feedback on the use of both pedagogical styles was also obtained. There was no significant difference between the performance of the two groups in either examination in three of the modules. However, there was a statistically significant difference between the two groups' performance in the module that had clinical applications, with students from the interactive lecture group performing better. All students preferred interactive classes, irrespective of the topic taught. The teachers indicated that, although at the outset the interactive lectures were difficult to manage, both in terms of content and time, these drawbacks could be overcome with time and practice. Interactive lectures are an effective teaching method in biochemistry, especially in topics involving clinical application.

  1. Learning needs in clinical biochemistry for doctors in foundation years.

    Science.gov (United States)

    Khromova, Victoria; Gray, Trevor A

    2008-01-01

    Most medical school curricula have reduced the amount of time available for teaching in pathology despite the fact that junior staff in the early stages of their training were responsible for requesting the majority of pathology tests on acutely ill hospital patients. So, the lack of specific training in this area means that test requesting may be poorly performed and the results ill understood by these staff. This paper describes a questionnaire, which was designed to assist laboratory staff providing targeted teaching in this area. Doctors in Foundation year 1 (F1) and Foundation year 2 (F2) in Sheffield teaching hospitals were given a questionnaire to ascertain how confident they were in requesting and interpreting the results of clinical biochemistry tests. The doctors were also asked about which areas of laboratory medicine they would like to be taught. Responses were received from 82 doctors, about half those in F1 and F2. The survey revealed areas where juniors are less confident in requesting tests and interpreting results. Despite lack of confidence in interpreting the result, 18% were confident about requesting tests. Doctors were also unsure of the effects of common problems like haemolysis on the interpretation of results. More than 70% of the doctors requested specific teaching in these areas. Foundation doctors have learning needs in clinical biochemistry, addressing which would assist them in patient care. While better training in medical school may help in future, there are specific needs for those on the wards now that require targeted teaching.

  2. Abstracts of the 27. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

    International Nuclear Information System (INIS)

    1998-01-01

    This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology

  3. Abstracts of the 26. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

    International Nuclear Information System (INIS)

    1997-01-01

    This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology

  4. Poster Display as an Alternative Evaluation Method to Biochemistry Teaching

    Directory of Open Access Journals (Sweden)

    Silas P. Rodrigues

    2004-05-01

    Full Text Available Biochemistry is present in dierent professional under gradation courses in which it seeks to attendseveral objectives. The discipline oered to the students of Biology Science Course at UFES is tra-ditionally organized in a series of lectures to the basic information, a laboratory class related to eachtopic and a three written tests. Our students, as many from other courses, study biochemistry justbecause they have to. The teacher can alter the student behavior by changing the way in which theyexamine them. This work describes and analyses the experience of using poster display as an assess-ment and includes feedback from the students and teachers. At the beginning of the term the activityis explained to the class and groups are formed. They are oriented to search a full research paper, with\\metabolism as a key word. During the students presentation, teachers and graduation studentsevaluate the production of a self-explanatory poster, assurance in the chosen work and involvementof all components of the group. A multiple-choice questionnaire was applied to 15-30 students fromthe ve classes that had already done the activity. The teachers and the graduation students also hadtheir opinions heard. 62.3 % of the students agreed that the activity accomplishes its objective tostimulate the integration of general knowledge and comprehension of a specic scientic work, while itpromotes the practice of presentation at seminars. 62.2 % believed that it allows the learner to showits knowledge in a better way and 51 % of the students were very much motivated within the activity.For 91.2 % of the students, they should choose the article, as it allows a better correlation betweenbiochemistry and personal anities (42.7 %. Also, 98 % believed that the activity should be carriedout in groups, because it allows a deeper discussion (53.6 %, stimulate group activities (20 % orpermits the materials costs division (22 %. Only 1.8 % of the learners thought that the

  5. Complementing theoretical biochemistry with the uso of computer aids (Symposium

    Directory of Open Access Journals (Sweden)

    R Herrera

    2012-05-01

    Full Text Available Teaching  biochemistry  in  the  current  state  of  science  and  society  requires  a  special motivation for learning, especially for students where Biochemistry is one of the courses on  their  careers.  The  traditional  way  of  teaching,  based  on  the  teacher-student relationship,  mostly  unidirectional,  does  not  fulfil  the  needs  imposed  in  this  era. Considering  the  current  situation,  University  students  require  new  abilities  in  their training  and  the  use  of  computers  can  be  a  facility  for  discovering  and  research, enabling the experience of new and  diverse situations. The design of teaching material for undergraduate students who take biochemistry as complementary course should be seen  as  an  opportunity  to  complement  theoretical  aspect  on  the  current  courses.  We have used three different approaches: (I Modelling proteins indicating key motifs at the three-dimensional structure and residues where inhibitors can be attach. (II Generation of  activities  by  the  use  of  sensors.  And  (III  elaborating  active  quizzes  where  students can  be  drive  on  their  learning.  Building  knowledge  based  on  practical  experience  can improve  student’s  competence  on  basic  science  and  the  learning  process  can  be complemented in the use of dynamics models.

  6. Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands.

    Science.gov (United States)

    Stsiapanava, Alena; Chaloupkova, Radka; Fortova, Andrea; Brynda, Jiri; Weiss, Manfred S; Damborsky, Jiri; Smatanova, Ivana Kuta

    2011-02-01

    Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon-halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P2(1)2(1)2(1) as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively.

  7. The disruptive effect of lysozyme on the bacterial cell wall explored by an in-silico structural outlook.

    Science.gov (United States)

    Primo, Emiliano D; Otero, Lisandro H; Ruiz, Francisco; Klinke, Sebastián; Giordano, Walter

    2018-01-01

    The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall and disrupt the bacterial life cycle by cleaving the linkage between the NAG and NAM carbohydrates. Lab exercises focused on the effects of lysozyme on the bacterial cell wall are frequently incorporated in biochemistry classes designed for undergraduate students in diverse fields as biology, microbiology, chemistry, agronomy, medicine, and veterinary medicine. Such exercises typically do not include structural data. We describe here a sequence of computer tasks designed to illustrate and reinforce both physiological and structural concepts involved in lysozyme effects on the bacterial cell-wall structure. This lab class usually lasts 3.5 hours. First, the instructor presents introductory concepts of the bacterial cell wall and the effect of lysozyme on its structure. Then, students are taught to use computer modeling to visualize the three-dimensional structure of a lysozyme in complex with bacterial cell-wall fragments. Finally, the lysozyme inhibitory effect on a bacterial culture is optionally proposed as a simple microbiological assay. The computer lab exercises described here give students a realistic understanding of the disruptive effect of lysozymes on the bacterial cell wall, a crucial component in bacterial survival. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):83-90, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

  8. $^{31}$Mg $\\beta$-NMR applied in chemistry and biochemistry

    CERN Multimedia

    Magnesium ions, Mg$^{2+}$, are essential in biological systems, taking part in practically all phosphate chemistry, in photosynthesis as an integral component of chlorophyll, and they are regulated via transport through selective membrane proteins. Nonetheless, the function of magnesium ions in biochemistry is difficult to characterize, as it is practically invisible to current experimental techniques. With this proposal we aim to advance the use of $^{31}$Mg $\\beta$-NMR to liquid samples, building on the experience from the successful Letter of Intent INTC-I-088 “$\\beta$-NMR as a novel technique for biological applications”. Initially a series of experiments will be conducted aiming to characterize the coordination chemistry of Mg$^{2+}$ in ionic liquids (ILs), demonstrating that it is possible within the lifetime of the radioisotope to achieve binding of Mg$^{2+}$ to a molecule dissolved in the IL. ILs are chosen as they display a very low vapor pressure, and are thus straightforwardly compatible with t...

  9. The construction and application of didactic models in Biochemistry teaching

    Directory of Open Access Journals (Sweden)

    Maximiliano de Souza Zierer

    2017-10-01

    Full Text Available This work describes how to build and use didactic models as a teaching resource to a more creative teaching in Biochemistry. Students are organized into groups to discuss the creation, planning and execution of models. Previously, the teacher guides the use of various materials for preparation and encourages the use of low cost materials. The day of the activity, held in the classroom, students build their models and are evaluated orally by the teacher about the functions or processes represented. At the end of class, we propose the presentation by each group, plus a general discussion about them. We find that that this methodology makes the classroom an environment highly conducive to creative expression, allowing students to develop their potential and making them effective learning, meaningful and longer lasting when compared to traditional teaching methods.

  10. Development of a virtual classroom to teach biochemistry

    Directory of Open Access Journals (Sweden)

    R.S. Rodrigues

    2005-07-01

    Full Text Available Knowing  the  difficulties to  teach  some biochemistry concepts  because  of their  dynamic  and  spatial characteristics, computers  have been adopted  to help in these  visualizations.  Pictures, three  dimen- sional structures and animations were built and used to display in classes and distributed to students. Behind  these  specific illustrations, an  informatics  environment has  been  developed  to  support bio- chemistry  teaching.    Based  in  free software,  it fits  in  a single CD  that works  independent of any software installed  on the computer, even the operating  system, and is compatible  with most hardware configurations.This technique is called live-CD. It is based on Linux architecture, which is not only free software but also more flexible to be configured.  After some tests with Linux distributions, Slackware has been chosen because of its easy manipulation and  because it makes the  best use of the hardware  allowing to be installed  in old or limited  equipments. It has been configured to make the best optimization of the computer  and have all software needed for most biochemistry classrooms.It  was installed:   an  Internet browser  compatible  with  a 3D molecule visualization plug-in,  text editor,  presentation editor,  picture  editor  and  some didactic  material  specific for biochemistry.  The interface was configured for people with no experience in the Linux environment.The  system  can  also work in an  intranet, where  a computer  would  be operated  by the  teacher and it would have some special control configurations  as: web site access control, power control of the others  machines  and  even an option  that would bring  the  desktop  of other  machine  to the  teacher´s what  allows him to make a straight orientation for a student from his screen.This new system,  which is a common platform  for other

  11. Comparative biochemistry of renins and angiotensins in the vertebrates.

    Science.gov (United States)

    Nakajima, T; Khosla, M C; Sakakibara, S

    1978-09-01

    Comparative biochemistry of renins and angiotensins was discussed. Renin extracted from hog kidney was different from that from mouse submaxillary glands in immunoreactivity and carbohydrate content. Rat kidney renin was also different from hog kidney renin in the amino acid composition. The presence of big and big-big renins was pointed out immunochemically. These big renins were considered to be precursors of kidney renin. Angiotensins in mammalian and nonmammalian species produced by renal or extrarenal renin have been differentiated by some biochemical and pharmacological criteria. Some of these angiotensins were analyzed sequentially. The replacements of amino acid residues at positions 1, 5, and/or 9 of angiotensin I have been demonstrated in nonmammalian species. Specific pressor activities have been determined using synthetic angiotensins by a 4 point assay in rat. Specific pressor activities of various angiotensins were obtained from the dose-blood pressure-response curves using a single angiotensin sample per assay rat.

  12. Glycobiology, How to Sugar-Coat an Undergraduate Advanced Biochemistry Laboratory

    Science.gov (United States)

    McReynolds, Katherine D.

    2006-01-01

    A second semester biochemistry laboratory has been implemented as an independent projects course at California State University, Sacramento since 1999. To incorporate aspects of carbohydrate biochemistry, or glycobiology, into our curriculum, projects in lectin isolation and purification were undertaken over the course of two semesters. Through…

  13. Reactivity II: A Second Foundation-Level Course in Integrated Organic, Inorganic, and Biochemistry

    Science.gov (United States)

    Schaller, Chris P.; Graham, Kate J.; McIntee, Edward J.; Jones, T. Nicholas; Johnson, Brian J.

    2016-01-01

    A foundation-level course is described that integrates material related to reactivity in organic, inorganic, and biochemistry. Designed for second-year students, the course serves majors in chemistry, biochemistry, and biology, as well as prehealth-professions students. Building on an earlier course that developed concepts of nucleophiles and…

  14. Lignin biochemistry and soil N determine crop residue decomposition and soil priming

    Science.gov (United States)

    Cropping history can affect soil properties, including available N, but little is known about the interactive effects of residue biochemistry, temperature and cropping history on residue decomposition. A laboratory incubation examined the role of residue biochemistry and temperature on the decomposi...

  15. Teaching Arrangements of Carbohydrate Metabolism in Biochemistry Curriculum in Peking University Health Science Center

    Science.gov (United States)

    Chen, Hao; Ni, Ju-Hua

    2013-01-01

    Biochemistry occupies a unique place in the medical school curricula, but the teaching of biochemistry presents certain challenges. One of these challenges is facilitating students' interest in and mastery of metabolism. The many pathways and modes of regulation can be overwhelming for students to learn and difficult for professors to teach in an…

  16. Developing and Supporting Students' Autonomy to Plan, Perform, and Interpret Inquiry-Based Biochemistry Experiments

    Science.gov (United States)

    Silva, Thanuci; Galembeck, Eduardo

    2017-01-01

    Laboratory sessions are designed to develop the experimental skills and the acquaintance with instruments that may contribute to a successful career in Biochemistry and associated fields. This study is a report on improving a traditional Biochemistry course by devising the laboratory sessions as an inquiry-based environment to develop the…

  17. Combining Content and Elements of Communication into an Upper-Level Biochemistry Course

    Science.gov (United States)

    Whittington, Carli P.; Pellock, Samuel J.; Cunningham, Rebecca L.; Cox, James R.

    2014-01-01

    This report describes how a science communication module was incorporated into an advanced biochemistry course. Elements of communication were taught synergistically with biochemistry content in this course in an effort to expose students to a variety of effective oral communication strategies. Students were trained to use these established…

  18. Vertical Integration of Biochemistry and Clinical Medicine Using a Near-Peer Learning Model

    Science.gov (United States)

    Gallan, Alexander J.; Offner, Gwynneth D.; Symes, Karen

    2016-01-01

    Vertical integration has been extensively implemented across medical school curricula but has not been widely attempted in the field of biochemistry. We describe a novel curricular innovation in which a near-peer learning model was used to implement vertical integration in our medical school biochemistry course. Senior medical students developed…

  19. Biochemistry Instructors' Views toward Developing and Assessing Visual Literacy in Their Courses

    Science.gov (United States)

    Linenberger, Kimberly J.; Holme, Thomas A.

    2015-01-01

    Biochemistry instructors are inundated with various representations from which to choose to depict biochemical phenomena. Because of the immense amount of visual know-how needed to be an expert biochemist in the 21st century, there have been calls for instructors to develop biochemistry students' visual literacy. However, visual literacy has…

  20. Biochemistry Students' Ideas about How an Enzyme Interacts with a Substrate

    Science.gov (United States)

    Linenberger, Kimberly J.; Bretz, Stacey Lowery

    2015-01-01

    Enzyme-substrate interactions are a fundamental concept of biochemistry that is built upon throughout multiple biochemistry courses. Central to understanding enzyme-substrate interactions is specific knowledge of exactly how an enzyme and substrate interact. Within this narrower topic, students must understand the various binding sites on an…

  1. Learning Effectiveness and Satisfaction of International Medical Students: Introducing a Hybrid-PBL Curriculum in Biochemistry

    Science.gov (United States)

    Yan, Qiu; Ma, Li; Zhu, Lina; Zhang, Wenli

    2017-01-01

    A biochemistry course is a fundamental but important subject in medical education in China. In recent years, the number of international medical students has increased. Curriculum reform in biochemistry teaching is needed because of the knowledge limitations of students, a close linkage of biochemical content with clinics, the shortcomings of…

  2. Case Study of How Turkish University Students Improve Their Biochemistry Achievement

    Science.gov (United States)

    Sadi, Özlem

    2013-01-01

    Biochemistry courses have an important place as a common subject in faculties of medicine, food engineering, biology and chemistry. MSLQ, Metacognitive Awareness Inventory and Learning Approach Questionnaire were used. The study also involves repeated observations of the same instructor in a biochemistry class over eight weeks to describe…

  3. Experiences from introduction of peer-to-peer teaching methods in Advanced Biochemistry E2010

    DEFF Research Database (Denmark)

    Brodersen, Ditlev; Etzerodt, Michael; Rasmussen, Jan Trige

    2012-01-01

    During the autumn semester 2010, we experimented with a range of active teaching methods on the course, Advanced Biochemistry, at the Department of Molecular Biology and Genetics.......During the autumn semester 2010, we experimented with a range of active teaching methods on the course, Advanced Biochemistry, at the Department of Molecular Biology and Genetics....

  4. 75 FR 8147 - Notice of Consideration of Amendment Request for Decommissioning of Analytical Bio-Chemistry...

    Science.gov (United States)

    2010-02-23

    ... NUCLEAR REGULATORY COMMISSION [Docket No. 030-05154; NRC-2010-0056] Notice of Consideration of Amendment Request for Decommissioning of Analytical Bio-Chemistry Laboratories, Inc. Sanitary Lagoon... license amendment to Byproduct Material License No. 24- 13365-01 issued to Analytical Bio-Chemistry...

  5. Discovery of novel bacterial toxins by genomics and computational biology.

    Science.gov (United States)

    Doxey, Andrew C; Mansfield, Michael J; Montecucco, Cesare

    2018-06-01

    Hundreds and hundreds of bacterial protein toxins are presently known. Traditionally, toxin identification begins with pathological studies of bacterial infectious disease. Following identification and cultivation of a bacterial pathogen, the protein toxin is purified from the culture medium and its pathogenic activity is studied using the methods of biochemistry and structural biology, cell biology, tissue and organ biology, and appropriate animal models, supplemented by bioimaging techniques. The ongoing and explosive development of high-throughput DNA sequencing and bioinformatic approaches have set in motion a revolution in many fields of biology, including microbiology. One consequence is that genes encoding novel bacterial toxins can be identified by bioinformatic and computational methods based on previous knowledge accumulated from studies of the biology and pathology of thousands of known bacterial protein toxins. Starting from the paradigmatic cases of diphtheria toxin, tetanus and botulinum neurotoxins, this review discusses traditional experimental approaches as well as bioinformatics and genomics-driven approaches that facilitate the discovery of novel bacterial toxins. We discuss recent work on the identification of novel botulinum-like toxins from genera such as Weissella, Chryseobacterium, and Enteroccocus, and the implications of these computationally identified toxins in the field. Finally, we discuss the promise of metagenomics in the discovery of novel toxins and their ecological niches, and present data suggesting the existence of uncharacterized, botulinum-like toxin genes in insect gut metagenomes. Copyright © 2018. Published by Elsevier Ltd.

  6. DIABETES MELLITUS: GENERATING ISSUES FOR THE TEACHING OF BIOCHEMISTRY

    Directory of Open Access Journals (Sweden)

    Rodrigo Maciel Lima

    2016-11-01

    Full Text Available INTRODUCTION: Current education has been grounded on traditional teaching practices; in other words, learning is regarded as an accumulation of knowledge given by the teachers. Use of resources such as videos and games can raise the interest of teachers since they are an attractive and less traditional alternative. Nevertheless, the use of generating issues stands out as it may help teachers to develop contextualized lessons. According to Freire (1987, this is the starting point in the process of constructing knowledge, replacing traditional practices and questioning the student’s previous knowledge of Biochemistry. OBJECTIVES: Thus, the aim of this study was to prepare and present a lesson to a 12th grade class at IF Fluminense on carbohydrates, diabetes mellitus, and isomerism based on the theme “Diabetes Mellitus”. MATERIALS AND METHODS: In order to collect data and check the validity of the use of such methodology in classes of Biochemistry, we used procedures such as: presentation of a video made by the authors about diabetes, a styrofoam model of a hepatic cell and biscuit models to show its metabolic functioning regarding metabolism of carbohydrates, styrofoam and toothpick molecular models aimed at explaining isomerism among main hexoses and, to finish the process, a roulette game named “Spinning with Biochemistry”, adapted from the television show Roda a Roda Jequiti, presented by SBT network. In addition, students had a class based on the “Three Pedagogical Moments” methodology proposed by Delizoicov et al. (2007. DISCUSSION AND RESULTS: After this, students developed more grounded scientific concepts, making use of terms common in scientific language. This suggests that the use of a Generating Issues, in a class based on problem-solving methods supported by playful strategies, was a meaningful contribution to improve the understanding of scientific knowledge. CONCLUSION: This type of class grounded on less traditional

  7. Neglected issues concerning teaching human adrenal steroidogenesis in popular biochemistry textbooks.

    Science.gov (United States)

    Han, Zhiyong; Elliott, Mark S

    2017-11-01

    In the human body, the adrenal steroids collectively regulate a plethora of fundamental functions, including electrolyte and water balance, blood pressure, stress response, intermediary metabolism, inflammation, and immunity. Therefore, adrenal steroidogenesis is an important biochemistry topic for students to learn in order for them to understand health consequences caused by deficiencies of enzymes in the adrenal steroidogenic pathways. However, popular biochemistry textbooks contain insufficient information and may sometimes give students a misimpression about certain aspects of human adrenal steroidogenesis. This article highlights two neglected issues in teaching human adrenal steroidogenesis in popular biochemistry textbooks. The purpose of this article is to draw attention to these issues. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):469-474, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  8. The return of metabolism: biochemistry and physiology of the pentose phosphate pathway

    Science.gov (United States)

    Stincone, Anna; Prigione, Alessandro; Cramer, Thorsten; Wamelink, Mirjam M. C.; Campbell, Kate; Cheung, Eric; Olin-Sandoval, Viridiana; Grüning, Nana-Maria; Krüger, Antje; Alam, Mohammad Tauqeer; Keller, Markus A.; Breitenbach, Michael; Brindle, Kevin M.; Rabinowitz, Joshua D.; Ralser, Markus

    2015-01-01

    The pentose phosphate pathway (PPP) is a fundamental component of cellular metabolism. The PPP is important to maintain carbon homoeostasis, to provide precursors for nucleotide and amino acid biosynthesis, to provide reducing molecules for anabolism, and to defeat oxidative stress. The PPP shares reactions with the Entner–Doudoroff pathway and Calvin cycle and divides into an oxidative and non-oxidative branch. The oxidative branch is highly active in most eukaryotes and converts glucose 6-phosphate into carbon dioxide, ribulose 5-phosphate and NADPH. The latter function is critical to maintain redox balance under stress situations, when cells proliferate rapidly, in ageing, and for the ‘Warburg effect’ of cancer cells. The non-oxidative branch instead is virtually ubiquitous, and metabolizes the glycolytic intermediates fructose 6-phosphate and glyceraldehyde 3-phosphate as well as sedoheptulose sugars, yielding ribose 5-phosphate for the synthesis of nucleic acids and sugar phosphate precursors for the synthesis of amino acids. Whereas the oxidative PPP is considered unidirectional, the non-oxidative branch can supply glycolysis with intermediates derived from ribose 5-phosphate and vice versa, depending on the biochemical demand. These functions require dynamic regulation of the PPP pathway that is achieved through hierarchical interactions between transcriptome, proteome and metabolome. Consequently, the biochemistry and regulation of this pathway, while still unresolved in many cases, are archetypal for the dynamics of the metabolic network of the cell. In this comprehensive article we review seminal work that led to the discovery and description of the pathway that date back now for 80 years, and address recent results about genetic and metabolic mechanisms that regulate its activity. These biochemical principles are discussed in the context of PPP deficiencies causing metabolic disease and the role of this pathway in biotechnology, bacterial and

  9. THE CYBERSPACE IN THE CONTINUED CLINICAL BIOCHEMISTRY EDUCATION

    Directory of Open Access Journals (Sweden)

    J.M. Martins

    2008-05-01

    Full Text Available The cybernetic spaces simulate the real world with interactive multimedia. This work  has been applied since January, 2007 on the curricular student’s apprenticeship at high school and graduation, in the site “bioq.educacao.biz/ULAB-HC-UFPE”. It has been developed to provide continuity to the technical-scientific learning of students and professionals, and also to improve their human social relations on the  labour  environment.  It’s comprises a virtual space, destined to communication and collective building of knowledge on the clinical biochemistry.   It’s about an interactive environment which allows the users registered as coordinator professor (professional  or the scientist student (trainee,  unlimited access to  posting contents (classes, texts, presentations, animations, consultations, non-synchronic discussions (on orkut, forums, e-mail and synchronic discussions (on chats, videoconferences. After a few live tutorials  about new  input in this environment, and the use of the new learning tool,  the collective building of knowledge on cyberspace begins. As a trainee’s program task, the scientist student would have to build a space of his own, under guidance and supervision of the coordinator teachers.  The cyberspace efficiency was evaluated from reports collected in February, 2008: the adherence to this  work was satisfactory, regarding this period, with 68 registered users, 870 accesses and 52 contents available on the several sections of the virtual laboratory. Our work is still being applied, and new adhesions are  happening everyday. We intend to amplify this cyber environment in order to make it a  permanent  continued education site on the health area.  From interest contracts and common knowledge,  the technological interfaces constitute an interaction, in which everyone is a potential author.  Keywords: Cyberspace, online biochemistry education, continued education.

  10. The use of software in Biochemistry teaching classes

    Directory of Open Access Journals (Sweden)

    M.B. Büttenbender

    2013-05-01

    Full Text Available INTRODUCTION: The rising of new technologies meant  to improve education could be considered a high advance to pedagogic methodologies. Software is defined as computer programs and may be considered educative when they present a methodology which assists and contextualizes the teaching-learning process. Specifically regarding Biochemistry, a knowledge area which explains physiological and pathological phenomena that occur in human beings, applying the use of software would turn out an easy way to observe suchphenomena. MATERIAL AND METHODS: In order to carry out this work, two free software designed to be used in Biochemistry area and developed at Universidade Estadual de Campinas (“Síntese Proteica” (Protein Synthesisand “A cinética da reação enzimática” (Kinetics of enzymatic reaction, were compared. Interface, how to work contents, advantages and disadvantages in the use of such kind of technology inside classroom were some of the evaluated parameters. DISCUSSION AND RESULTS: Both programs present a fine graphic design, allowing easy command comprehension. At the beginning the objectives of the programs and the contents they hold are presented, showing also a brief introduction to the topic. The programs also  present instruction manuals that explain how the experiments work. They are small basic and simple programs that run easily where they are placed, not needing internet access after their download. “Kinetics of enzymatic reaction” presented more interactive options than the other, and its operation could be considered more intuitive. CONCLUSION: We considered “Kinetics of enzymatic reaction” a better software,cause it allows the student to observe the experiment and perform the calculationsproposed, improving the learning process in a significantly way. The use ofnew technologies inside classrooms should be encouraged as a way to attractthe attention and interest of students, since they are

  11. Predictors of performance of students in biochemistry in a doctor of chiropractic curriculum.

    Science.gov (United States)

    Shaw, Kathy; Rabatsky, Ali; Dishman, Veronica; Meseke, Christopher

    2014-01-01

    Objective : This study investigated the effect of completion of course prerequisites, undergraduate grade point average (GPA), undergraduate degree, and study habits on the performance of students in the biochemistry course at Palmer College of Chiropractic Florida. Methods : Students self-reported information regarding academic preparation at the beginning of the semester using a questionnaire. Final exam grade and final course grade were noted and used as measures of performance. Multivariate analysis of variance was used to determine if number of prerequisites completed, undergraduate GPA, undergraduate degree, hours spent studying in undergraduate study, and hours spent studying in the first quarter of the chiropractic program were associated significantly with the biochemistry final exam grade or the final grade for the biochemistry course. Results : The number of prerequisites completed, undergraduate degree, hours spent studying in undergraduate study, and hours spent studying in the first quarter of the chiropractic program did not significantly affect the biochemistry final exam grade or the final grade for the biochemistry course, but undergraduate GPA did. Subsequent univariate analysis and Tukey's post hoc comparisons revealed that students with an undergraduate GPA in the 3.5 to 3.99 range earned significantly higher final course grades than students with an undergraduate GPA in the 2.5 to 2.99 range. Conclusion : No single variable was determined to be a factor that determines student success in biochemistry. The interrelationship between the factors examined warrants further investigation to understand fully how to predict the success of a student in the biochemistry course.

  12. Biochemistry and physiology of anabolic androgenic steroids doping.

    Science.gov (United States)

    Lippi, G; Franchini, M; Banfi, G

    2011-05-01

    Anabolic Androgenic Steroids (AASs) are chemical and pharmacological derivatives of the male hormone testosterone which are widely used for increasing burst and sprinting activities in sports. Although AASs are thought to be transversal to the plurality of sports disciplines, they are principally misused by bodybuilders, weightlifters, shot, hammer, discus or javelin throwers, rugby and American football players as well as by swimmers and runners. AAS exert a kaleidoscope of effects on human biology, principally through the 5-α-reductase-mediated conversion into dihydrotestosterone, the aromatase-mediated conversion into female sex hormones, a competitive antagonism to the glucocorticoid receptors, the potential stimulation of erythropoietin secretion as well as psychoactive effects on the brain. The influence of AASs on physical performance is still undefined, since the large number of studies published so far have described discordant and often contradictory outcomes. Nevertheless, animal and human investigations support the hypothesis that the administration of AASs might increase lean body mass, muscle mass, and maximal voluntary strength especially in men, so that they would represent an appealing form of doping for increasing power capacity, sustaining intensive training periods and, last but not least, as a cosmetic muscle makeover. The aim of this article is to review the biochemistry, physiology and the ergogenic effects of AASs.

  13. Virtual Biochemistry – pH effect on enzyme activity

    Directory of Open Access Journals (Sweden)

    D.N. Heidrich

    2011-04-01

    Full Text Available Protocols of laboratory experiments, followed by teacher's explanation, not always clearly translate to the student the dynamics to beadopted for the implementation of the proposed practice. One of these cases is related to the study of the effect of pH on enzyme activity. For better help the understanding of the technical procedure, a hypermedia was built based on a protocol adopted at the Department of Biochemistry, UFSC. The hypermedia shows how theeffect of variations in pH can be observed  in vitro. Taking as example salivary amylase and the consumption of starch (substrate by means of iodine staining, a set of pH buffers was tested to identify the best pH for this enzyme  activity. This hypermedia as introductory tool for such practice was tested on aNutrition course classroom. Students agree that the hypermedia provided a better understanding of the proposed activities. Teachers also notice a smallerreagents consumption and reduction of the time spent by the students in the achievement of the experiment.

  14. Exercise redox biochemistry: Conceptual, methodological and technical recommendations

    Directory of Open Access Journals (Sweden)

    James N. Cobley

    2017-08-01

    Full Text Available Exercise redox biochemistry is of considerable interest owing to its translational value in health and disease. However, unaddressed conceptual, methodological and technical issues complicate attempts to unravel how exercise alters redox homeostasis in health and disease. Conceptual issues relate to misunderstandings that arise when the chemical heterogeneity of redox biology is disregarded: which often complicates attempts to use redox-active compounds and assess redox signalling. Further, that oxidised macromolecule adduct levels reflect formation and repair is seldom considered. Methodological and technical issues relate to the use of out-dated assays and/or inappropriate sample preparation techniques that confound biochemical redox analysis. After considering each of the aforementioned issues, we outline how each issue can be resolved and provide a unifying set of recommendations. We specifically recommend that investigators: consider chemical heterogeneity, use redox-active compounds judiciously, abandon flawed assays, carefully prepare samples and assay buffers, consider repair/metabolism, use multiple biomarkers to assess oxidative damage and redox signalling. Keywords: Exercise, Oxidative stress, Free radical, Antioxidants, Redox signalling

  15. Contributions of nuclear magnetic resonance to renal biochemistry

    International Nuclear Information System (INIS)

    Ross, B.; Freeman, D.; Chan, L.

    1986-01-01

    31 P NMR as a descriptive technique is of interest to nephrologists. Particular contributions of 31 P NMR to our understanding of renal function may be enumerated.: Free metabolite levels are different from those classically accepted; in particular, ADP and Pi are low with implications for the control of renal metabolism and Pi transport, and, via the phosphorylation potential, for Na+ transport. Renal pH is heterogeneous; between cortex, outer medulla, and papilla, and between cell and lumen, a large pH gradient exists. Also, quantitation between cytosol and mitochondrion of the pH gradient is now feasible. In acute renal failure of either ischemic or nonischemic origin, both ATP depletion and acidification of the renal cell result in damage, with increasing evidence for the importance of the latter. Measurements of renal metabolic rate in vivo suggest the existence of a prodromal phase of acute renal failure, which could lead to its detection at an earlier and possibly reversible stage. Human renal cancers show a unique 31 P NMR spectrum and a very acidic environment. Cancer chemotherapy may alter this and detection of such changes with NMR offers a method of therapeutic monitoring with significance beyond nephrology. Renal cortex and medulla have a different T1 relaxation time, possibly due to differences in lipid composition. It seems that NMR spectroscopy has much to offer to the future understanding of the relationship between renal biochemistry and function. 56 references

  16. The Next Frontier: Quantitative Biochemistry in Living Cells.

    Science.gov (United States)

    Honigmann, Alf; Nadler, André

    2018-01-09

    Researchers striving to convert biology into an exact science foremost rely on structural biology and biochemical reconstitution approaches to obtain quantitative data. However, cell biological research is moving at an ever-accelerating speed into areas where these approaches lose much of their edge. Intrinsically unstructured proteins and biochemical interaction networks composed of interchangeable, multivalent, and unspecific interactions pose unique challenges to quantitative biology, as do processes that occur in discrete cellular microenvironments. Here we argue that a conceptual change in our way of conducting biochemical experiments is required to take on these new challenges. We propose that reconstitution of cellular processes in vitro should be much more focused on mimicking the cellular environment in vivo, an approach that requires detailed knowledge of the material properties of cellular compartments, essentially requiring a material science of the cell. In a similar vein, we suggest that quantitative biochemical experiments in vitro should be accompanied by corresponding experiments in vivo, as many newly relevant cellular processes are highly context-dependent. In essence, this constitutes a call for chemical biologists to convert their discipline from a proof-of-principle science to an area that could rightfully be called quantitative biochemistry in living cells. In this essay, we discuss novel techniques and experimental strategies with regard to their potential to fulfill such ambitious aims.

  17. Collaborating with Undergraduates To Contribute to Biochemistry Community Resources.

    Science.gov (United States)

    Haas, Kathryn L; Heemstra, Jennifer M; Medema, Marnix H; Charkoudian, Louise K

    2018-01-30

    Course-based undergraduate research experiences (CUREs) have gained traction as effective ways to expand the impact of undergraduate research while fulfilling pedagogical goals. In this Perspective, we present innovative ways to incorporate fundamental benefits and principles of CUREs into a classroom environment through information/technology-based research projects that lead to student-generated contributions to digital community resources (CoRes). These projects represent an attractive class of CUREs because they are less resource-intensive than laboratory-based CUREs, and the projects align with the expectations of today's students to create rapid and publicly accessible contributions to society. We provide a detailed discussion of two example types of CoRe projects that can be implemented in courses to impact research and education at the chemistry-biology interface: bioinformatics annotations and development of educational tools. Finally, we present current resources available for faculty interested in incorporating CUREs or CoRe projects into their pedagogical practices. In sharing these stories and resources, we hope to lower the barrier for widespread adoption of CURE and CoRe approaches and generate discussions about how to utilize the classroom experience to make a positive impact on our students and the future of the field of biochemistry.

  18. Tryptophan Biochemistry: Structural, Nutritional, Metabolic, and Medical Aspects in Humans.

    Science.gov (United States)

    Palego, Lionella; Betti, Laura; Rossi, Alessandra; Giannaccini, Gino

    2016-01-01

    L-Tryptophan is the unique protein amino acid (AA) bearing an indole ring: its biotransformation in living organisms contributes either to keeping this chemical group in cells and tissues or to breaking it, by generating in both cases a variety of bioactive molecules. Investigations on the biology of Trp highlight the pleiotropic effects of its small derivatives on homeostasis processes. In addition to protein turn-over, in humans the pathways of Trp indole derivatives cover the synthesis of the neurotransmitter/hormone serotonin (5-HT), the pineal gland melatonin (MLT), and the trace amine tryptamine. The breakdown of the Trp indole ring defines instead the "kynurenine shunt" which produces cell-response adapters as L-kynurenine, kynurenic and quinolinic acids, or the coenzyme nicotinamide adenine dinucleotide (NAD(+)). This review aims therefore at tracing a "map" of the main molecular effectors in human tryptophan (Trp) research, starting from the chemistry of this AA, dealing then with its biosphere distribution and nutritional value for humans, also focusing on some proteins responsible for its tissue-dependent uptake and biotransformation. We will thus underscore the role of Trp biochemistry in the pathogenesis of human complex diseases/syndromes primarily involving the gut, neuroimmunoendocrine/stress responses, and the CNS, supporting the use of -Omics approaches in this field.

  19. Visual Literacy and Biochemistry Learning: The role of external representations

    Directory of Open Access Journals (Sweden)

    V.J.S.V. Santos

    2011-04-01

    Full Text Available Visual Literacy can bedefined as people’s ability to understand, use, think, learn and express themselves through external representations (ER in a given subject. This research aims to investigate the development of abilities of ERs reading and interpretation by students from a Biochemistry graduate course of theFederal University of São João Del-Rei. In this way, Visual Literacy level was  assessed using a questionnaire validatedin a previous educational research. This diagnosis questionnaire was elaborated according to six visual abilitiesidentified as essential for the study of the metabolic pathways. The initial statistical analysis of data collectedin this study was carried out using ANOVA method. Results obtained showed that the questionnaire used is adequate for the research and indicated that the level of Visual Literacy related to the metabolic processes increased significantly with the progress of the students in the graduation course. There was also an indication of a possible interference in the student’s performancedetermined by the cutoff punctuation in the university selection process.

  20. Some applications of radiation chemistry to biochemistry and radiobiology

    International Nuclear Information System (INIS)

    Wardman, P.

    1987-01-01

    In this chapter illustrate the use of radiation chemistry as a tool in investigating biologically important radical reactions, and also outline some studies of models for radiobiological damage. Because aqueous solutions usually offer the most important matrix, an appreciation of the main features of water radiolysis will be essential. Most of the illustrations involve pulse radiolysis, and some familiarity with chemical kinetics is assumed. In addition to these and other chapters in this book, readers find the proceedings of a recent NATO Advanced Study Institute most useful. The authors shall not try to review here all the applications of radiation chemistry to biochemistry and biology, but they will illustrate, using selected examples, the main principles and practical advantages and problems. Another recent volume covers the main contributions of flash photolysis and pulse radiolysis to the chemistry of biology and medicine, complementing earlier reviews. Papers from symposia on radical processes in radiobiology and carcinogenesis, and on super-oxide dismutases, and proceedings of recent international congresses of radiation research, together with the other publications referred to above will enable the reader to gain a comprehensive overview of the role of radicals in biological processes and the contributions of radiation chemistry

  1. The physical basis of biochemistry the foundations of molecular biophysics

    CERN Document Server

    Bergethon, Peter R

    1998-01-01

    The objective of this book is to provide a unifying approach to the study of biophysical chemistry for the advanced undergraduate who has had a year of physics, organic chem­ istry, calculus, and biology. This book began as a revised edition of Biophysical Chemistry: Molecules to Membranes, which Elizabeth Simons and I coauthored. That short volume was written in an attempt to provide a concise text for a one-semester course in biophysical chemistry at the graduate level. The experience of teaching biophysical chemistry to bi­ ologically oriented students over the last decade has made it clear that the subject requires a more fundamental text that unifies the many threads of modem science: physics, chem­ istry, biology, mathematics, and statistics. This book represents that effort. This volume is not a treatment of modem biophysical chemistry with its rich history and many contro­ versies, although a book on that topic is also needed. The Physical Basis of Biochemistry is an introduction to the philosophy...

  2. Current status of verification practices in clinical biochemistry in Spain.

    Science.gov (United States)

    Gómez-Rioja, Rubén; Alvarez, Virtudes; Ventura, Montserrat; Alsina, M Jesús; Barba, Núria; Cortés, Mariano; Llopis, María Antonia; Martínez, Cecilia; Ibarz, Mercè

    2013-09-01

    Verification uses logical algorithms to detect potential errors before laboratory results are released to the clinician. Even though verification is one of the main processes in all laboratories, there is a lack of standardization mainly in the algorithms used and the criteria and verification limits applied. A survey in clinical laboratories in Spain was conducted in order to assess the verification process, particularly the use of autoverification. Questionnaires were sent to the laboratories involved in the External Quality Assurance Program organized by the Spanish Society of Clinical Biochemistry and Molecular Pathology. Seven common biochemical parameters were included (glucose, cholesterol, triglycerides, creatinine, potassium, calcium, and alanine aminotransferase). Completed questionnaires were received from 85 laboratories. Nearly all the laboratories reported using the following seven verification criteria: internal quality control, instrument warnings, sample deterioration, reference limits, clinical data, concordance between parameters, and verification of results. The use of all verification criteria varied according to the type of verification (automatic, technical, or medical). Verification limits for these parameters are similar to biological reference ranges. Delta Check was used in 24% of laboratories. Most laboratories (64%) reported using autoverification systems. Autoverification use was related to laboratory size, ownership, and type of laboratory information system, but amount of use (percentage of test autoverified) was not related to laboratory size. A total of 36% of Spanish laboratories do not use autoverification, despite the general implementation of laboratory information systems, most of them, with autoverification ability. Criteria and rules for seven routine biochemical tests were obtained.

  3. Exercise redox biochemistry: Conceptual, methodological and technical recommendations.

    Science.gov (United States)

    Cobley, James N; Close, Graeme L; Bailey, Damian M; Davison, Gareth W

    2017-08-01

    Exercise redox biochemistry is of considerable interest owing to its translational value in health and disease. However, unaddressed conceptual, methodological and technical issues complicate attempts to unravel how exercise alters redox homeostasis in health and disease. Conceptual issues relate to misunderstandings that arise when the chemical heterogeneity of redox biology is disregarded: which often complicates attempts to use redox-active compounds and assess redox signalling. Further, that oxidised macromolecule adduct levels reflect formation and repair is seldom considered. Methodological and technical issues relate to the use of out-dated assays and/or inappropriate sample preparation techniques that confound biochemical redox analysis. After considering each of the aforementioned issues, we outline how each issue can be resolved and provide a unifying set of recommendations. We specifically recommend that investigators: consider chemical heterogeneity, use redox-active compounds judiciously, abandon flawed assays, carefully prepare samples and assay buffers, consider repair/metabolism, use multiple biomarkers to assess oxidative damage and redox signalling. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  4. An Experiment Using Sucrose Density Gradients in the Undergraduate Biochemistry Laboratory.

    Science.gov (United States)

    Turchi, Sandra L.; Weiss, Monica

    1988-01-01

    Describes an experiment to be performed in an undergraduate biochemistry laboratory that is based on a gradient centrifugation system employing a simple bench top centrifuge, a freezer, and frozen surcose gradient solution to separate macromolecules and subcellular components. (CW)

  5. Biochemistry students' ideas about shape and charge in enzyme-substrate interactions.

    Science.gov (United States)

    Linenberger, Kimberly J; Bretz, Stacey Lowery

    2014-01-01

    Biochemistry is a visual discipline that requires students to develop an understanding of numerous representations. However, there is very little known about what students actually understand about the representations that are used to communicate ideas in biochemistry. This study investigated biochemistry students' understanding of multiple representations of enzyme-substrate interactions through both student interviews (N = 25) and responses by a national sample (N = 707) to the Enzyme-Substrate Interactions Concept Inventory. This manuscript reports the findings regarding one category of misconceptions measured by the concept inventory, namely, students' understandings of shape and charge in the context of enzyme-substrate interactions. Students interpret molecular representations depicting such interactions by determining the complementarity between enzyme and substrate by focusing upon charge and hydrogen bonding, but with a disregard for stereochemistry. Copyright © 2014 by The International Union of Biochemistry and Molecular Biology.

  6. Approaches to enhance the teaching quality of experimental biochemistry for MBBS students in TSMU, China.

    Science.gov (United States)

    Yu, Lijuan; Yi, Shuying; Zhai, Jing; Wang, Zhaojin

    2017-07-08

    With the internationalization of medical education in China, the importance of international students' education in medical schools is also increasing. Except foreign students majoring in Chinese language, English Bachelor of Medicine, Bachelor of Surgery (MBSS) students are the largest group of international students. Based on problems in the teaching process for experimental biochemistry, we designed teaching models adapted to the background of international students and strengthened teachers' teaching ability at Taishan Medical University. Several approaches were used in combination to promote teaching effects and increase the benefit of teaching to teachers. The primary data showed an increased passion for basic medical biochemistry and an improved theoretical background for MBSS students, which will be helpful for their later clinical medicine studies. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):360-364, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  7. Biochemistry for Medical Students: A Flexible Student-Oriented Approach. AMEE Case Study No. 3

    Science.gov (United States)

    Macqueen, D.; And Others

    1976-01-01

    A personalized account of some experiences in the Department of Biochemistry at the University of Dundee during a radical revision of the course for medical students is offered. Innovations of the course are described in detail. (LBH)

  8. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995.

  9. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    International Nuclear Information System (INIS)

    1996-01-01

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995

  10. Biochemistry of cellulose degradation and cellulose utilization for feeds and for protein

    Energy Technology Data Exchange (ETDEWEB)

    Sadara, J C; Lachke, A H; Shewale, J G

    1979-01-01

    A review discussing production of single-cell protein, fuel, and glucose from cellulose decomposition; surface or solid fermentations of single-cell protein; production of cellulases; and the biochemistry of cellulose degradation was presented.

  11. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-31

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995.

  12. Titration of Alanine Monitored by NMR Spectroscopy: A Biochemistry Laboratory Experiment

    Science.gov (United States)

    Waller, Francis J.; And Others

    1977-01-01

    The experiment described here involves simultaneous monitoring of pH and NMR chemical shifts during an aqueous titration of alpha- and beta-alanine. This experiment is designed for use in an undergraduate biochemistry course. (MR)

  13. Learning Biochemistry through Manga--Helping Students Learn and Remember, and Making Lectures More Exciting.

    Science.gov (United States)

    Nagata, Ryoichi

    1999-01-01

    Uses panels taken from manga, Japanese comics and cartoons, to supplement explanations of biochemical terms and topics in biochemistry classes. Results indicate that the use of manga helped students remember what they had learned. (Author/CCM)

  14. Bacterial lung abscess

    International Nuclear Information System (INIS)

    Groskin, S.A.; Panicek, D.M.; Ewing, D.K.; Rivera, F.; Math, K.; Teixeira, J.; Heitzman, E.R.

    1987-01-01

    A retrospective review of patients with bacterial lung abscess was carried out. Demographic, clinical, and radiographical features of this patient group are compared with similar data from patients with empyema and/or cavitated lung carcinoma; differential diagnostic points are stressed. The entity of radiographically occult lung abscess is discussed. Complications associated with bacterial lung abscess are discussed. Current therapeutic options and treatment philosophy for patients with bacterial lung abscess are noted

  15. Peritonitis - spontaneous bacterial

    Science.gov (United States)

    Spontaneous bacterial peritonitis (SBP); Ascites - peritonitis; Cirrhosis - peritonitis ... who are on peritoneal dialysis for kidney failure. Peritonitis may have other causes . These include infection from ...

  16. Hematologic and biochemistry values for black-faced spoonbills (Platalea minor) with and recovering from botulism.

    Science.gov (United States)

    Chou, Shih-Jen; Shieh, Yao-Ching; Yu, Chang-You

    2008-07-01

    Type C1 botulism outbreaks in Black-faced Spoonbills (Platalea minor) occurred in Taiwan from 2002 to 2003, and hematologic and biochemistry parameters from botulism-paralyzed birds and recovered birds were compared. Values for creatinine and uric acid were higher (Pbirds with botulism than in recovered birds. Lower white blood cell counts (Pbirds. Based on these observations, we suggest that hematologic and biochemistry analyses should be performed to assess the health condition of birds recovering from botulism.

  17. [Modeling and implementation method for the automatic biochemistry analyzer control system].

    Science.gov (United States)

    Wang, Dong; Ge, Wan-cheng; Song, Chun-lin; Wang, Yun-guang

    2009-03-01

    In this paper the system structure The automatic biochemistry analyzer is a necessary instrument for clinical diagnostics. First of is analyzed. The system problems description and the fundamental principles for dispatch are brought forward. Then this text puts emphasis on the modeling for the automatic biochemistry analyzer control system. The objects model and the communications model are put forward. Finally, the implementation method is designed. It indicates that the system based on the model has good performance.

  18. Historic production evaluation in Biochemistry Education area during the SBBq annual meetings between 1993 and 2016

    Directory of Open Access Journals (Sweden)

    A. V.; N. N.; G. G. Pereira; Gonçalves; Hornink

    2017-07-01

    Full Text Available The annual meetings of the Brazilian Society Biochemistry and Molecular Biology (SBBq, with the inclusion of the area of education in Biochemistry in 1993, present themselves as important spaces for the presentation and discussion of the work in the area of Biochemistry and Molecular Biology teaching. OBJECTIVES: Systematize and evaluate the historical development of abstracts in the Education in Biochemistry area, in the SBBq annual meeting, indicating quantitative and qualitative data. MATERIAL AND METHODS: A total of 408 abstracts were evaluated, from the panels presented in the area of Education in Biochemistry, from 1993 to 2016. The quantitative evaluation was done by surveying the thematic content, institutions, regions, methods and qualitative analysis based on content analysis (Bardin of the works of the two most frequently approached themes. RESULTS AND DISCUSSION: The works of the southeast region (65,4% of papers presented were highlighted, with 32% of the works with qualitative methodology, 10% quantitative and 33% quali-quantitative. The most studied topics were Biochemistry teaching (107 papers and metabolism (94 papers. In the contents analysis of the two most frequently addressed themes, the constructivist and socio-interacionist foundations as the most used teaching-learning processes, as well as the use of software as the most used didactic strategy in both themes. The most used didactic resources were texts / informative in the subject of Teaching of Biochemistry (33% and games (21% in the subject of Metabolism. CONCLUSIONS: The results evidenced the major focus of the work addressing undergraduate courses, with a qualitative or quantitative method, focusing mainly on Biochemistry teaching, as well as on metabolism, with an expressive amount of activities using educational software, followed by practical classes. There has been a change in the prevailing fundamentals of the teaching-learning process with the emergence in the

  19. Known structure, unknown function: An inquiry?based undergraduate biochemistry laboratory course

    OpenAIRE

    Gray, Cynthia; Price, Carol W.; Lee, Christopher T.; Dewald, Alison H.; Cline, Matthew A.; McAnany, Charles E.; Columbus, Linda; Mura, Cameron

    2015-01-01

    Abstract Undergraduate biochemistry laboratory courses often do not provide students with an authentic research experience, particularly when the express purpose of the laboratory is purely instructional. However, an instructional laboratory course that is inquiry? and research?based could simultaneously impart scientific knowledge and foster a student's research expertise and confidence. We have developed a year?long undergraduate biochemistry laboratory curriculum wherein students determine...

  20. Reflections on the Value of Mapping the Final Theory Examination in a Molecular Biochemistry Unit †

    OpenAIRE

    Eri, Rajaraman; Cook, Anthony; Brown, Natalie

    2014-01-01

    This article assesses the impact of examination mapping as a tool to enhancing assessment and teaching quality in a second-year biochemistry unit for undergraduates. Examination mapping is a process where all questions in a written examination paper are assessed for links to the unit’s intended learning outcomes. We describe how mapping a final written examination helped visualise the impact of the assessment task on intended learning outcomes and skills for that biochemistry unit. The method...

  1. Construction of Hypertexts in a Biochemistry Pos- Graduation Discipline

    Directory of Open Access Journals (Sweden)

    W.B. Maia

    2009-05-01

    Full Text Available Virtual reality is an innovating manner of comprehending and acting on how the world is and, also, considered a new way of intellectual exercise.  This work took place in a  biochemistry masters discipline (Advanced Formation in ScientificEducation and had as its observation context the forum (on-line tool viability, intending the construction of hypertexts (active  collaborative writing by the 15 registered students in the  discipline in 2008. The discipline was available on the web, in  bioq.educacao.biz , where the students, teachers and monitors couldsubscribe. The virtual space was set with several environments (agenda,classroom, dictionary, email and forum; all of which were used during thediscipline. The forum, called orkuteducation, was destined to the hypertextelaboration, which was focused in three themes: 1º How to work with technology at school;   2º Teaching/learning methods and new information and communication technology; 3º Constructivism. The virtual learning environment had 2,275accesses to its content; being the forum the most visited one, with 1,026.   The built hypertext presented clear ideas about the approached themes, and realized the important role which a qualified teacher plays in the educational process. The new ways of create, organize and interact with information changes the relationship between the subject and the information itself. The hype rtext constitutes "high level computer tools", through which is possible to explore knowledge in a non -linear and interactive way. Hypertext remains a revolutionary concept oforganization and access to information and its generalization impact in society  is not known yet.

  2. THE POTENTIAL OF BIOCHEMISTRY EDUCATION APPS IN THE FORMATIVE ASSESSMENT

    Directory of Open Access Journals (Sweden)

    M. L. Oliveira

    2015-08-01

    Full Text Available Introduction and objectives: Apps can be designed to provide usage data, and most of them do. These data are usually used to map users interests and to deliver more effective ads that are more likely to result in clicks, and sales. We have applied some of these metrics to understand how can it be used to map students’ behavior and to promote a formative assessment using educational software. The purpose of a formative assessment is to monitor student learning to provide ongoing feedback that can be used by instructors and students to improve the teaching and learning process. Thus, this modality aims to help both students and instructors to identify strengths and weaknesses that need to be developed. This study aimed to describe the potential of educational apps in the formative assessment process. Material and Methods: We have implemented assessment tools embedded in three apps (ARMET, The Cell and 3D Class used to teach: 1 Metabolic Pathways; 2 Scale of the cellular structures, and 3 Concepts from techniques used in a Biochemistry Lab course. The implemented tools allow to verify on what issues there were recurring mistakes, the total number of mistakes presented, which questions they most achieved, how long they took to perform the activity and other relevant information. Results and conclusion: Educational apps can provide transparent and coherent evaluation metrics to enable instructors to systematize more consistent criteria and indicators, reducing the subjectivity of the formative assessment process and the time spent for preparation, tabulation and analysis of assessment data. This approach allows instructors to understand better where students struggle, giving to them a more effective feedback. It also helps instructor to plan interventions to help students to perform better and to achieve the learning objectives.

  3. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    . As such, adhesion represents the Achilles heel of crucial pathogenic functions. It follows that interference with adhesion can reduce bacterial virulence. Here, we illustrate this important topic with examples of techniques being developed that can inhibit bacterial adhesion. Some of these will become...

  4. Fundamentals on the biochemistry of peroxynitrite and protein tyrosine nitration

    Directory of Open Access Journals (Sweden)

    Silvina Bartesaghi

    2018-04-01

    Full Text Available In this review we provide an analysis of the biochemistry of peroxynitrite and tyrosine nitration. Peroxynitrite is the product of the diffusion-controlled reaction between superoxide (O2•- and nitric oxide (•NO. This process is in competition with the enzymatic dismutation of O2•- and the diffusion of •NO across cells and tissues and its reaction with molecular targets (e.g. guanylate cyclase. Understanding the kinetics and compartmentalization of the O2•- / •NO interplay is critical to rationalize the shift of •NO from a physiological mediator to a cytotoxic intermediate. Once formed, peroxynitrite (ONOO- and ONOOH; pKa = 6,8 behaves as a strong one and two-electron oxidant towards a series of biomolecules including transition metal centers and thiols. In addition, peroxynitrite anion can secondarily evolve to secondary radicals either via its fast reaction with CO2 or through proton-catalyzed homolysis. Thus, peroxynitrite can participate in direct (bimolecular and indirect (through secondary radical intermediates oxidation reactions; through these processes peroxynitrite can participate as cytotoxic effector molecule against invading pathogens and/or as an endogenous pathogenic mediator. Peroxynitrite can cause protein tyrosine nitration in vitro and in vivo. Indeed, tyrosine nitration is a hallmark of the reactions of •NO-derived oxidants in cells and tissues and serves as a biomarker of oxidative damage. Protein tyrosine nitration can mediate changes in protein structure and function that affect cell homeostasis. Tyrosine nitration in biological systems is a free radical process that can be promoted either by peroxynitrite-derived radicals or by other related •NO-dependent oxidative processes. Recently, mechanisms responsible of tyrosine nitration in hydrophobic biostructures such as membranes and lipoproteins have been assessed and involve the parallel occurrence and connection with lipid

  5. Quantitative application of sigma metrics in medical biochemistry.

    Science.gov (United States)

    Nanda, Sunil Kumar; Ray, Lopamudra

    2013-12-01

    Laboratory errors are result of a poorly designed quality system in the laboratory. Six Sigma is an error reduction methodology that has been successfully applied at Motorola and General Electric. Sigma (σ) is the mathematical symbol for standard deviation (SD). Sigma methodology can be applied wherever an outcome of a process has to be measured. A poor outcome is counted as an error or defect. This is quantified as defects per million (DPM). A six sigma process is one in which 99.999666% of the products manufactured are statistically expected to be free of defects. Six sigma concentrates, on regulating a process to 6 SDs, represents 3.4 DPM (defects per million) opportunities. It can be inferred that as sigma increases, the consistency and steadiness of the test improves, thereby reducing the operating costs. We aimed to gauge performance of our laboratory parameters by sigma metrics. Evaluation of sigma metrics in interpretation of parameter performance in clinical biochemistry. The six month internal QC (October 2012 to march 2013) and EQAS (external quality assurance scheme) were extracted for the parameters-Glucose, Urea, Creatinine, Total Bilirubin, Total Protein, Albumin, Uric acid, Total Cholesterol, Triglycerides, Chloride, SGOT, SGPT and ALP. Coefficient of variance (CV) were calculated from internal QC for these parameters. Percentage bias for these parameters was calculated from the EQAS. Total allowable errors were followed as per Clinical Laboratory Improvement Amendments (CLIA) guidelines. Sigma metrics were calculated from CV, percentage bias and total allowable error for the above mentioned parameters. For parameters - Total bilirubin, uric acid, SGOT, SGPT and ALP, the sigma values were found to be more than 6. For parameters - glucose, Creatinine, triglycerides, urea, the sigma values were found to be between 3 to 6. For parameters - total protein, albumin, cholesterol and chloride, the sigma values were found to be less than 3. ALP was the best

  6. Impact of e-resources on learning in biochemistry: first-year medical students’ perceptions

    Science.gov (United States)

    2012-01-01

    Background E-learning resources (e-resources) have been widely used to facilitate self-directed learning among medical students. The Department of Biochemistry at Christian Medical College (CMC), Vellore, India, has made available e-resources to first-year medical students to supplement conventional lecture-based teaching in the subject. This study was designed to assess students’ perceptions of the impact of these e-resources on various aspects of their learning in biochemistry. Methods Sixty first-year medical students were the subjects of this study. At the end of the one-year course in biochemistry, the students were administered a questionnaire that asked them to assess the impact of the e-resources on various aspects of their learning in biochemistry. Results Ninety-eight percent of students had used the e-resources provided to varying extents. Most of them found the e-resources provided useful and of a high quality. The majority of them used these resources to prepare for periodic formative and final summative assessments in the course. The use of these resources increased steadily as the academic year progressed. Students said that the extent to which they understood the subject (83%) and their ability to answer questions in assessments (86%) had improved as a result of using these resources. They also said that they found biochemistry interesting (73%) and felt motivated to study the subject (59%). Conclusions We found that first-year medical students extensively used the e-resources in biochemistry that were provided. They perceived that these resources had made a positive impact on various aspects of their learning in biochemistry. We conclude that e-resources are a useful supplement to conventional lecture-based teaching in the medical curriculum. PMID:22510159

  7. Impact of e-resources on learning in biochemistry: first-year medical students' perceptions.

    Science.gov (United States)

    Varghese, Joe; Faith, Minnie; Jacob, Molly

    2012-05-16

    E-learning resources (e-resources) have been widely used to facilitate self-directed learning among medical students. The Department of Biochemistry at Christian Medical College (CMC), Vellore, India, has made available e-resources to first-year medical students to supplement conventional lecture-based teaching in the subject. This study was designed to assess students' perceptions of the impact of these e-resources on various aspects of their learning in biochemistry. Sixty first-year medical students were the subjects of this study. At the end of the one-year course in biochemistry, the students were administered a questionnaire that asked them to assess the impact of the e-resources on various aspects of their learning in biochemistry. Ninety-eight percent of students had used the e-resources provided to varying extents. Most of them found the e-resources provided useful and of a high quality. The majority of them used these resources to prepare for periodic formative and final summative assessments in the course. The use of these resources increased steadily as the academic year progressed. Students said that the extent to which they understood the subject (83%) and their ability to answer questions in assessments (86%) had improved as a result of using these resources. They also said that they found biochemistry interesting (73%) and felt motivated to study the subject (59%). We found that first-year medical students extensively used the e-resources in biochemistry that were provided. They perceived that these resources had made a positive impact on various aspects of their learning in biochemistry. We conclude that e-resources are a useful supplement to conventional lecture-based teaching in the medical curriculum.

  8. Teaching biochemistry to medical students in Singapore--from organic chemistry to problem-based learning.

    Science.gov (United States)

    Khoo, H E

    2005-07-01

    The medical faculty in the National University of Singapore started in 1905 but the Chair in Biochemistry was only established in 1927. For many years the biochemistry course consisted of the teaching of the organic chemistry of substances of physiological importance, nutrition, metabolism and hormones. In 1961, clinical biochemistry was introduced and in the 1980s, genetics and molecular biology were included. By then, most of the organic chemistry content had been removed as greater emphasis was placed on clinical correlation. Laboratory classes consisted of mock glucose tolerance tests and the measurement of various enzymes. By the 1990s, students were no longer interested in such practical classes, so a bold decision was made around 1995 to remove laboratory classes from the curriculum. Unfortunately, this meant that the medical students who might have been interested in laboratory work could no longer do such work. However, the new curriculum in 1999 gave the department an opportunity to offer a laboratory course as an elective for interested students. This new curriculum adopted an integrated approach with Genetics being taught as part of Paediatrics, and a new module (Structural and Cell Biology) comprising aspects of cell biology and biochemistry was introduced. This module is currently taught by staff from Anatomy, Physiology and Biochemistry. Some biochemistry content is now incorporated into the clinical problem scenarios of problem-based learning such as jaundice, diabetes mellitus, anorexia nervosa, etc. So the evolution of teaching biochemistry to medical students in Singapore has paralleled worldwide trends and moved from the didactic teaching of organic chemistry of biomolecules to problem-based learning using clinical cases.

  9. Medical biochemistry in Macedonia: a profession for physicians and natural scientists.

    Science.gov (United States)

    Traikovska, S; Dzhekova-Stojkova, S

    2001-06-01

    Medical biochemistry or clinical chemistry in its roots is an interdisciplinary science between natural sciences and medicine. The largest part of medical biochemistry is natural science (chemistry, biochemistry, biology, physics, mathematics), which is very well integrated in deduction of medical problems. Medical biochemistry throughout the world, including Macedonia, should be a professional field open to both physicians and natural scientists, according to its historical development, theoretical characteristics and applied practice. Physicians and natural scientists follow the same route in clinical chemistry during the postgraduate training of specialization in medical biochemistry/clinical chemistry. However, in Macedonia the specialization in medical biochemistry/clinical chemistry is today regulated by law only for physicians and pharmacists. The study of clinical chemistry in Europe has shown its interdisciplinary character. In most European countries different professions, such as physicians, chemists/biochemists, pharmacists, biologists and others could specialize in clinical chemistry. The question for the next generation of specialists in Macedonia is whether to accept the present conditions or to attempt to change the law to include chemists/biochemists and biologists as well. The latter used to be a practice in Macedonia 20 years ago, and still is in many European countries. Such change in law would also result in changes in the postgraduate educational program in medical biochemistry in Macedonia. The new postgraduate program has to follow the European Syllabus, recommended by EC4. To obtain sufficient knowledge in clinical chemistry, the duration of vocational training (undergraduate and postgraduate) for all trainees (physicians, pharmaceutics, chemists/biochemists and biologists) should be 8 years.

  10. Essential concepts and underlying theories from physics, chemistry, and mathematics for "biochemistry and molecular biology" majors.

    Science.gov (United States)

    Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry, and Mathematics that all Biochemistry or Molecular Biology majors must understand to complete their major coursework. The allied fields working group created a survey to validate foundational concepts from Physics, Chemistry, and Mathematics identified from participant feedback at various workshops. One-hundred twenty participants responded to the survey and 68% of the respondents answered yes to the question: "We have identified the following as the core concepts and underlying theories from Physics, Chemistry, and Mathematics that Biochemistry majors or Molecular Biology majors need to understand after they complete their major courses: 1) mechanical concepts from Physics, 2) energy and thermodynamic concepts from Physics, 3) critical concepts of structure from chemistry, 4) critical concepts of reactions from Chemistry, and 5) essential Mathematics. In your opinion, is the above list complete?" Respondents also delineated subcategories they felt should be included in these broad categories. From the results of the survey and this analysis the allied fields working group constructed a consensus list of allied fields concepts, which will help inform Biochemistry and Molecular Biology educators when considering the ASBMB recommended curriculum for Biochemistry or Molecular Biology majors and in the development of appropriate assessment tools to gauge student understanding of how these concepts relate to biochemistry and molecular biology. © 2013 by The International Union of Biochemistry and Molecular Biology.

  11. In Vivo Biochemistry: Single-Cell Dynamics of Cyclic Di-GMP in Escherichia coli in Response to Zinc Overload.

    Science.gov (United States)

    Yeo, Jongchan; Dippel, Andrew B; Wang, Xin C; Hammond, Ming C

    2018-01-09

    Intracellular signaling enzymes drive critical changes in cellular physiology and gene expression, but their endogenous activities in vivo remain highly challenging to study in real time and for individual cells. Here we show that flow cytometry can be performed in complex media to monitor single-cell population distributions and dynamics of cyclic di-GMP signaling, which controls the bacterial colonization program. These in vivo biochemistry experiments are enabled by our second-generation RNA-based fluorescent (RBF) biosensors, which exhibit high fluorescence turn-on in response to cyclic di-GMP. Specifically, we demonstrate that intracellular levels of cyclic di-GMP in Escherichia coli are repressed with excess zinc, but not with other divalent metals. Furthermore, in both flow cytometry and fluorescence microscopy setups, we monitor the dynamic increase in cellular cyclic di-GMP levels upon zinc depletion and show that this response is due to de-repression of the endogenous diguanylate cyclase DgcZ. In the presence of zinc, cells exhibit enhanced cell motility and increased sensitivity to antibiotics due to inhibited biofilm formation. Taken together, these results showcase the application of RBF biosensors in visualizing single-cell dynamic changes in cyclic di-GMP signaling in direct response to environmental cues such as zinc and highlight our ability to assess whether observed phenotypes are related to specific signaling enzymes and pathways.

  12. Postviral Complications: Bacterial Pneumonia.

    Science.gov (United States)

    Prasso, Jason E; Deng, Jane C

    2017-03-01

    Secondary bacterial pneumonia after viral respiratory infection remains a significant source of morbidity and mortality. Susceptibility is mediated by a variety of viral and bacterial factors, and complex interactions with the host immune system. Prevention and treatment strategies are limited to influenza vaccination and antibiotics/antivirals respectively. Novel approaches to identifying the individuals with influenza who are at increased risk for secondary bacterial pneumonias are urgently needed. Given the threat of further pandemics and the heightened prevalence of these viruses, more research into the immunologic mechanisms of this disease is warranted with the hope of discovering new potential therapies. Published by Elsevier Inc.

  13. Order of draw practices in venous blood sampling at clinical biochemistry departments in the Danish health care system

    DEFF Research Database (Denmark)

    Jacobsen, Katja Kemp; Brandt, Ida; Christensen, Anne Vindahl

    2018-01-01

    the procedures in venous blood sampling among clinical biochemistry departments to assess the uniformity of order of blood draw and adherence to international guidelines in the Danish health care system. METHODS: We collected venous order of draw procedures from 49 clinical biochemistry departments at 22 public...... 15189:2012 accreditation (p = .57). CONCLUSIONS: Venous order of draw procedures is diverse at Danish clinical biochemistry departments and show moderate adherence to international guidelines....

  14. Known structure, unknown function: An inquiry‐based undergraduate biochemistry laboratory course

    Science.gov (United States)

    Gray, Cynthia; Price, Carol W.; Lee, Christopher T.; Dewald, Alison H.; Cline, Matthew A.; McAnany, Charles E.

    2015-01-01

    Abstract Undergraduate biochemistry laboratory courses often do not provide students with an authentic research experience, particularly when the express purpose of the laboratory is purely instructional. However, an instructional laboratory course that is inquiry‐ and research‐based could simultaneously impart scientific knowledge and foster a student's research expertise and confidence. We have developed a year‐long undergraduate biochemistry laboratory curriculum wherein students determine, via experiment and computation, the function of a protein of known three‐dimensional structure. The first half of the course is inquiry‐based and modular in design; students learn general biochemical techniques while gaining preparation for research experiments in the second semester. Having learned standard biochemical methods in the first semester, students independently pursue their own (original) research projects in the second semester. This new curriculum has yielded an improvement in student performance and confidence as assessed by various metrics. To disseminate teaching resources to students and instructors alike, a freely accessible Biochemistry Laboratory Education resource is available at http://biochemlab.org. © 2015 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 43(4):245–262, 2015. PMID:26148241

  15. Known structure, unknown function: An inquiry-based undergraduate biochemistry laboratory course.

    Science.gov (United States)

    Gray, Cynthia; Price, Carol W; Lee, Christopher T; Dewald, Alison H; Cline, Matthew A; McAnany, Charles E; Columbus, Linda; Mura, Cameron

    2015-01-01

    Undergraduate biochemistry laboratory courses often do not provide students with an authentic research experience, particularly when the express purpose of the laboratory is purely instructional. However, an instructional laboratory course that is inquiry- and research-based could simultaneously impart scientific knowledge and foster a student's research expertise and confidence. We have developed a year-long undergraduate biochemistry laboratory curriculum wherein students determine, via experiment and computation, the function of a protein of known three-dimensional structure. The first half of the course is inquiry-based and modular in design; students learn general biochemical techniques while gaining preparation for research experiments in the second semester. Having learned standard biochemical methods in the first semester, students independently pursue their own (original) research projects in the second semester. This new curriculum has yielded an improvement in student performance and confidence as assessed by various metrics. To disseminate teaching resources to students and instructors alike, a freely accessible Biochemistry Laboratory Education resource is available at http://biochemlab.org. © 2015 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

  16. Guidelines for Educational Research in Biochemistry on Internet Sites

    Directory of Open Access Journals (Sweden)

    R.M. Lima

    2012-05-01

    Full Text Available The Internet has been used to support research in different areas, such as practical and educational  research  in  medical  and  biomedical  research.  There  are  several recommended  sites  for  carrying  biomedical  and  medical  research  (BERGER,  2003. Nevertheless,  few  studies  report  on  the  use  of  the  Internet  in  the  teaching  of Biochemistry. Considering the fact that there is no specific legislation for the use of the Internet  in  Brazil,  it  is  necessary  to  stimulate  self-regulation  of  the  sector  in  order  to establish  minimum  quality  standards,  safety,  and  reliability  of  sites  containing information  in  the  educational  area.  This  study  establishes  some  parameters  to  help guiding research for educational purposes on the internet. The following aspects should be  checked:  if  the  site  has  an  editorial  board  responsible  for  content  selection,  and whether  it  is  made  up  of  experts  in  the  area  of  expertise;  if  the  site  releases  updated scientific materials, and provides pedagogical content that fosters teaching and learning such  as  images  that  contribute  to  the  understanding  of  the  content,  educational software,  and  animation;  if  the  site  is  recommended  by  universities,  public  and  private qualified  institutions.  In  addition,  educational  sites  should  present  other  aspects, including transparency (regarding their educational purpose, quality (scientifically based information,  privacy  (related  to  the  user’s  personal  data,  responsibility  and  reliable sources.  Such  procedures  are  necessary  to  guarantee  that  searching  for  educational objectives will provide access to theoretical and pedagogical information quality.

  17. Correlation of preadmission organic chemistry courses and academic performance in biochemistry at a midwest chiropractic doctoral program.

    Science.gov (United States)

    McRae, Marc P

    2010-01-01

    Organic chemistry has been shown to correlate with academic success in the preclinical years of medicine, dentistry, and graduate physiology. The purpose of this study is to examine the relationship between undergraduate organic chemistry grades and first-semester biochemistry grades at a Midwest chiropractic doctoral program. Students enrolled in a first-semester biochemistry course who had completed the prerequisite courses in organic chemistry offered at this same institution were entered into the study. The total grade for each of the three courses was calculated using the midterm and final exam raw scores with a weighting of 50% each. Analysis consisted of obtaining correlation coefficients between the total grades of organic 1 with biochemistry and organic 2 with biochemistry. Using the biochemistry total grade, the students were divided into quartiles and course grades for both organic chemistry 1 and 2 were calculated. For the 109 students in the study, the correlation coefficient between the biochemistry and organic chemistry 1 and biochemistry and organic chemistry 2 courses was r = 0.744 and r = 0.725, respectively. The difference in organic chemistry grades between those in the first and fourth quartiles was 63.2% and 86.9% for organic chemistry 1 (p organic chemistry 2 (p organic chemistry can be used as an indicator of future academic success in a chiropractic biochemistry course. Knowledge of such a relationship could prove useful to identify students who may potentially run into academic difficulty with first-year biochemistry.

  18. Bacterial vaginosis - aftercare

    Science.gov (United States)

    Bacterial vaginosis (BV) is a type of vaginal infection. The vagina normally contains both healthy bacteria and unhealthy bacteria. BV occurs when more unhealthy bacteria grow than healthy bacteria. No one knows ...

  19. Bacterial surface adaptation

    Science.gov (United States)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  20. Bacterial intermediate filaments

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Cabeen, M.; Jacobs-Wagner, C.

    2009-01-01

    Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...

  1. Diagnosis of bacterial infection

    African Journals Online (AJOL)

    direct or indirect evidence of a compatible bacterial pathogen. Inflammation may be .... cardinal features (fever, confusion, headache and neck stiffness). .... specificity, inappropriate indications or poor sampling technique may diminish this ...

  2. A semester-long project-oriented biochemistry laboratory based on Helicobacter pylori urease.

    Science.gov (United States)

    Farnham, Kate R; Dube, Danielle H

    2015-01-01

    Here we present the development of a 13 week project-oriented biochemistry laboratory designed to introduce students to foundational biochemical techniques and then enable students to perform original research projects once they have mastered these techniques. In particular, we describe a semester-long laboratory that focuses on a biomedically relevant enzyme--Helicobacter pylori (Hp) urease--the activity of which is absolutely required for the gastric pathogen Hp to colonize the human stomach. Over the course of the semester, students undertake a biochemical purification of Hp urease, assess the success of their purification, and investigate the activity of their purified enzyme. In the final weeks of the semester, students design and implement their own experiments to study Hp urease. This laboratory provides students with an understanding of the importance of biochemistry in human health while empowering them to engage in an active area of research. © 2015 The International Union of Biochemistry and Molecular Biology.

  3. Promoting active learning of graduate student by deep reading in biochemistry and microbiology pharmacy curriculum.

    Science.gov (United States)

    Peng, Ren

    2017-07-08

    To promote graduate students' active learning, deep reading of high quality papers was done by graduate students enrolled in biochemistry and microbiology pharmacy curriculum offered by college of life science, Jiangxi Normal University from 2013 to 2015. The number of graduate students, who participated in the course in 2013, 2014, and 2015 were eleven, thirteen and fifteen, respectively. Through deep reading of papers, presentation, and group discussion in the lecture, these graduate students have improved their academic performances effectively, such as literature search, PPT document production, presentation management, specialty document reading, academic inquiry, and analytical and comprehensive ability. The graduate students also have increased their understanding level of frontier research, scientific research methods, and experimental methods. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):305-312, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  4. Uncovering protein–protein interactions through a team-based undergraduate biochemistry course

    Science.gov (United States)

    Cookmeyer, David L.; Winesett, Emily S.; Kokona, Bashkim; Huff, Adam R.; Aliev, Sabina; Bloch, Noah B.; Bulos, Joshua A.; Evans, Irene L.; Fagre, Christian R.; Godbe, Kerilyn N.; Khromava, Maryna; Konstantinovsky, Daniel M.; Lafrance, Alexander E.; Lamacki, Alexandra J.; Parry, Robert C.; Quinn, Jeanne M.; Thurston, Alana M.; Tsai, Kathleen J. S.; Mollo, Aurelio; Cryle, Max J.; Fairman, Robert

    2017-01-01

    How can we provide fertile ground for students to simultaneously explore a breadth of foundational knowledge, develop cross-disciplinary problem-solving skills, gain resiliency, and learn to work as a member of a team? One way is to integrate original research in the context of an undergraduate biochemistry course. In this Community Page, we discuss the development and execution of an interdisciplinary and cross-departmental undergraduate biochemistry laboratory course. We present a template for how a similar course can be replicated at other institutions and provide pedagogical and research results from a sample module in which we challenged our students to study the binding interface between 2 important biosynthetic proteins. Finally, we address the community and invite others to join us in making a larger impact on undergraduate education and the field of biochemistry by coordinating efforts to integrate research and teaching across campuses. PMID:29091712

  5. Comprehensive experiment-clinical biochemistry: determination of blood glucose and triglycerides in normal and diabetic rats.

    Science.gov (United States)

    Jiao, Li; Xiujuan, Shi; Juan, Wang; Song, Jia; Lei, Xu; Guotong, Xu; Lixia, Lu

    2015-01-01

    For second year medical students, we redesigned an original laboratory experiment and developed a combined research-teaching clinical biochemistry experiment. Using an established diabetic rat model to detect blood glucose and triglycerides, the students participate in the entire experimental process, which is not normally experienced during a standard clinical biochemistry exercise. The students are not only exposed to techniques and equipment but are also inspired to think more about the biochemical mechanisms of diseases. When linked with lecture topics about the metabolism of carbohydrates and lipids, the students obtain a better understanding of the relevance of abnormal metabolism in relation to diseases. Such understanding provides a solid foundation for the medical students' future research and for other clinical applications. © 2014 Biochemistry and Molecular Biology Education.

  6. Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry.

    Science.gov (United States)

    Higgins, Sean A; Savage, David F

    2018-01-09

    A fundamental goal of protein biochemistry is to determine the sequence-function relationship, but the vastness of sequence space makes comprehensive evaluation of this landscape difficult. However, advances in DNA synthesis and sequencing now allow researchers to assess the functional impact of every single mutation in many proteins, but challenges remain in library construction and the development of general assays applicable to a diverse range of protein functions. This Perspective briefly outlines the technical innovations in DNA manipulation that allow massively parallel protein biochemistry and then summarizes the methods currently available for library construction and the functional assays of protein variants. Areas in need of future innovation are highlighted with a particular focus on assay development and the use of computational analysis with machine learning to effectively traverse the sequence-function landscape. Finally, applications in the fundamentals of protein biochemistry, disease prediction, and protein engineering are presented.

  7. Uncovering protein-protein interactions through a team-based undergraduate biochemistry course.

    Science.gov (United States)

    Cookmeyer, David L; Winesett, Emily S; Kokona, Bashkim; Huff, Adam R; Aliev, Sabina; Bloch, Noah B; Bulos, Joshua A; Evans, Irene L; Fagre, Christian R; Godbe, Kerilyn N; Khromava, Maryna; Konstantinovsky, Daniel M; Lafrance, Alexander E; Lamacki, Alexandra J; Parry, Robert C; Quinn, Jeanne M; Thurston, Alana M; Tsai, Kathleen J S; Mollo, Aurelio; Cryle, Max J; Fairman, Robert; Charkoudian, Louise K

    2017-11-01

    How can we provide fertile ground for students to simultaneously explore a breadth of foundational knowledge, develop cross-disciplinary problem-solving skills, gain resiliency, and learn to work as a member of a team? One way is to integrate original research in the context of an undergraduate biochemistry course. In this Community Page, we discuss the development and execution of an interdisciplinary and cross-departmental undergraduate biochemistry laboratory course. We present a template for how a similar course can be replicated at other institutions and provide pedagogical and research results from a sample module in which we challenged our students to study the binding interface between 2 important biosynthetic proteins. Finally, we address the community and invite others to join us in making a larger impact on undergraduate education and the field of biochemistry by coordinating efforts to integrate research and teaching across campuses.

  8. Combining content and elements of communication into an upper-level biochemistry course.

    Science.gov (United States)

    Whittington, Carli P; Pellock, Samuel J; Cunningham, Rebecca L; Cox, James R

    2014-01-01

    This report describes how a science communication module was incorporated into an advanced biochemistry course. Elements of communication were taught synergistically with biochemistry content in this course in an effort to expose students to a variety of effective oral communication strategies. Students were trained to use these established techniques and incorporated them into various presentations throughout the course. Three students describe their use of specific resources and how the skills learned relate to their future career. The importance and relevance of science communication are receiving unprecedented national attention. The academic scientific community must respond by incorporating more communication-centered instruction and opportunities in the classroom and laboratory. © 2013 by The International Union of Biochemistry and Molecular Biology.

  9. Uncovering protein-protein interactions through a team-based undergraduate biochemistry course.

    Directory of Open Access Journals (Sweden)

    David L Cookmeyer

    2017-11-01

    Full Text Available How can we provide fertile ground for students to simultaneously explore a breadth of foundational knowledge, develop cross-disciplinary problem-solving skills, gain resiliency, and learn to work as a member of a team? One way is to integrate original research in the context of an undergraduate biochemistry course. In this Community Page, we discuss the development and execution of an interdisciplinary and cross-departmental undergraduate biochemistry laboratory course. We present a template for how a similar course can be replicated at other institutions and provide pedagogical and research results from a sample module in which we challenged our students to study the binding interface between 2 important biosynthetic proteins. Finally, we address the community and invite others to join us in making a larger impact on undergraduate education and the field of biochemistry by coordinating efforts to integrate research and teaching across campuses.

  10. Genomics and Biochemistry of Saccharomyces cerevisiae Wine Yeast Strains.

    Science.gov (United States)

    Eldarov, M A; Kishkovskaia, S A; Tanaschuk, T N; Mardanov, A V

    2016-12-01

    Saccharomyces yeasts have been used for millennia for the production of beer, wine, bread, and other fermented products. Long-term "unconscious" selection and domestication led to the selection of hundreds of strains with desired production traits having significant phenotypic and genetic differences from their wild ancestors. This review summarizes the results of recent research in deciphering the genomes of wine Saccharomyces strains, the use of comparative genomics methods to study the mechanisms of yeast genome evolution under conditions of artificial selection, and the use of genomic and postgenomic approaches to identify the molecular nature of the important characteristics of commercial wine strains of Saccharomyces. Succinctly, data concerning metagenomics of microbial communities of grapes and wine and the dynamics of yeast and bacterial flora in the course of winemaking is provided. A separate section is devoted to an overview of the physiological, genetic, and biochemical features of sherry yeast strains used to produce biologically aged wines. The goal of the review is to convince the reader of the efficacy of new genomic and postgenomic technologies as tools for developing strategies for targeted selection and creation of new strains using "classical" and modern techniques for improving winemaking technology.

  11. The biochemistry and medical significance of the flavonoids.

    Science.gov (United States)

    Havsteen, Bent H

    2002-01-01

    Flavonoids are plant pigments that are synthesised from phenylalanine, generally display marvelous colors known from flower petals, mostly emit brilliant fluorescence when they are excited by UV light, and are ubiquitous to green plant cells. The flavonoids are used by botanists for taxonomical classification. They regulate plant growth by inhibition of the exocytosis of the auxin indolyl acetic acid, as well as by induction of gene expression, and they influence other biological cells in numerous ways. Flavonoids inhibit or kill many bacterial strains, inhibit important viral enzymes, such as reverse transcriptase and protease, and destroy some pathogenic protozoans. Yet, their toxicity to animal cells is low. Flavonoids are major functional components of many herbal and insect preparations for medical use, e.g., propolis (bee's glue) and honey, which have been used since ancient times. The daily intake of flavonoids with normal food, especially fruit and vegetables, is 1-2 g. Modern authorised physicians are increasing their use of pure flavonoids to treat many important common diseases, due to their proven ability to inhibit specific enzymes, to simulate some hormones and neurotransmitters, and to scavenge free radicals.

  12. Learning-oriented assessment increases performance and written skills in a second year metabolic biochemistry course.

    Science.gov (United States)

    Vanderlelie, Jessica J; Alexander, Heather G

    2016-07-08

    Assessment plays a critical role in learning and teaching and its power to enhance engagement and student outcomes is still underestimated in tertiary education. The current project considers the impact of a staged redesign of an assessment strategy that emphasized relevance of learning, formative assessment, student engagement, and feedback on student performance, failure rates and overall engagement in the course. Significant improvements in final grades (p Biochemistry and Molecular Biology, 44(4):412-420, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

  13. Bacterial Cell Mechanics.

    Science.gov (United States)

    Auer, George K; Weibel, Douglas B

    2017-07-25

    Cellular mechanical properties play an integral role in bacterial survival and adaptation. Historically, the bacterial cell wall and, in particular, the layer of polymeric material called the peptidoglycan were the elements to which cell mechanics could be primarily attributed. Disrupting the biochemical machinery that assembles the peptidoglycan (e.g., using the β-lactam family of antibiotics) alters the structure of this material, leads to mechanical defects, and results in cell lysis. Decades after the discovery of peptidoglycan-synthesizing enzymes, the mechanisms that underlie their positioning and regulation are still not entirely understood. In addition, recent evidence suggests a diverse group of other biochemical elements influence bacterial cell mechanics, may be regulated by new cellular mechanisms, and may be triggered in different environmental contexts to enable cell adaptation and survival. This review summarizes the contributions that different biomolecular components of the cell wall (e.g., lipopolysaccharides, wall and lipoteichoic acids, lipid bilayers, peptidoglycan, and proteins) make to Gram-negative and Gram-positive bacterial cell mechanics. We discuss the contribution of individual proteins and macromolecular complexes in cell mechanics and the tools that make it possible to quantitatively decipher the biochemical machinery that contributes to bacterial cell mechanics. Advances in this area may provide insight into new biology and influence the development of antibacterial chemotherapies.

  14. Biodegradability of bacterial surfactants.

    Science.gov (United States)

    Lima, Tânia M S; Procópio, Lorena C; Brandão, Felipe D; Carvalho, André M X; Tótola, Marcos R; Borges, Arnaldo C

    2011-06-01

    This work aimed at evaluating the biodegradability of different bacterial surfactants in liquid medium and in soil microcosms. The biodegradability of biosurfactants by pure and mixed bacterial cultures was evaluated through CO(2) evolution. Three bacterial strains, Acinetobacter baumanni LBBMA ES11, Acinetobacter haemolyticus LBBMA 53 and Pseudomonas sp. LBBMA 101B, used the biosurfactants produced by Bacillus sp. LBBMA 111A (mixed lipopeptide), Bacillus subtilis LBBMA 155 (lipopeptide), Flavobacterium sp. LBBMA 168 (mixture of flavolipids), Dietzia Maris LBBMA 191(glycolipid) and Arthrobacter oxydans LBBMA 201(lipopeptide) as carbon sources in minimal medium. The synthetic surfactant sodium dodecyl sulfate (SDS) was also mineralized by these microorganisms, but at a lower rate. CO(2) emitted by a mixed bacterial culture in soil microcosms with biosurfactants was higher than in the microcosm containing SDS. Biosurfactant mineralization in soil was confirmed by the increase in surface tension of the soil aqueous extracts after incubation with the mixed bacterial culture. It can be concluded that, in terms of biodegradability and environmental security, these compounds are more suitable for applications in remediation technologies in comparison to synthetic surfactants. However, more information is needed on structure of biosurfactants, their interaction with soil and contaminants and scale up and cost for biosurfactant production.

  15. A Survey on Faculty Perspectives on the Transition to a Biochemistry Course-Based Undergraduate Research Experience Laboratory

    Science.gov (United States)

    Craig, Paul A.

    2017-01-01

    It will always remain a goal of an undergraduate biochemistry laboratory course to engage students hands-on in a wide range of biochemistry laboratory experiences. In 2006, our research group initiated a project for "in silico" prediction of enzyme function based only on the 3D coordinates of the more than 3800 proteins "of unknown…

  16. Drug Synthesis and Analysis on a Dime: A Capstone Medicinal Chemistry Experience for the Undergraduate Biochemistry Laboratory

    Science.gov (United States)

    Streu, Craig N.; Reif, Randall D.; Neiles, Kelly Y.; Schech, Amanda J.; Mertz, Pamela S.

    2016-01-01

    Integrative, research-based experiences have shown tremendous potential as effective pedagogical approaches. Pharmaceutical development is an exciting field that draws heavily on organic chemistry and biochemistry techniques. A capstone drug synthesis/analysis laboratory is described where biochemistry students synthesize azo-stilbenoid compounds…

  17. Diverse Assessment and Active Student Engagement Sustain Deep Learning: A Comparative Study of Outcomes in Two Parallel Introductory Biochemistry Courses

    Science.gov (United States)

    Bevan, Samantha J.; Chan, Cecilia W. L.; Tanner, Julian A.

    2014-01-01

    Although there is increasing evidence for a relationship between courses that emphasize student engagement and achievement of student deep learning, there is a paucity of quantitative comparative studies in a biochemistry and molecular biology context. Here, we present a pedagogical study in two contrasting parallel biochemistry introductory…

  18. Reactivity I: A Foundation-Level Course for Both Majors and Nonmajors in Integrated Organic, Inorganic, and Biochemistry

    Science.gov (United States)

    Schaller, Chris P.; Graham, Kate J.; Johnson, Brian J.; Jones, T. Nicholas; McIntee, Edward J.

    2015-01-01

    A foundation level course is presented that integrates aspects of organic, inorganic and biochemistry in the context of reactivity. The course was designed to serve majors in chemistry and other sciences (biochemistry, biology, nutrition), as well as nursing and pre-health professions students. Themes of the course were designed to highlight a…

  19. History of Biochemistry at the University of Geneva From the Boulevard des Philosophes to Quai Ernest-Ansermet.

    Science.gov (United States)

    Deshusses, Jacques; Riezman, Howard

    2009-12-01

    A brief account of the developments in biochemistry at the Faculty of Science of the University of Geneva is given from its emergence from organic chemistry at the Ancienne Ecole de chimie to today's Department of Biochemistry at the Section de chimie et biochimie.

  20. Protein Biochemistry and Expression Regulation of Cadmium/Zinc Pumping ATPases in the Hyperaccumulator Plants Arabidopsis halleri and Noccaea caerulescens

    Czech Academy of Sciences Publication Activity Database

    Mishra, S.; Mishra, Archana; Küpper, Hendrik

    2017-01-01

    Roč. 8, May 22 (2017), č. článku 835. ISSN 1664-462X R&D Projects: GA MŠk EF15_003/0000336 Institutional support: RVO:60077344 Keywords : cellular compartmentation * zinc homeostasis * cadmium * metal hyperaccumulator plants Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 4.298, year: 2016

  1. Bacterial meningitis in children

    International Nuclear Information System (INIS)

    Marji, S.

    2007-01-01

    To demonstrate the epidemiology, clinical manifestations and bacteriological profile of bacterial meningitis in children beyond the neonatal period in our hospital. This was a retrospective descriptive study conducted at Prince Rashid Hospital in Irbid, Jordan. The medical records of 50 children with the diagnosis of bacterial meningitis during 4 years period, were reviewed. The main cause of infection was streptococcus pneumoniae, followed by Haemophilus influenza and Niesseria meningitides. Mortality was higher in infants and meningococcal infection, while complications were more encountered in cases of streptococcus pneumoniae. Cerebrospinal fluid culture was positive in 11 cases and Latex agglutination test in 39. There is a significant reduction of the numbers of bacterial meningitis caused by Haemophilus influenza type B species. (author)

  2. Biochemistry, physiology and biotechnology of sulfate-reducing bacteria.

    Science.gov (United States)

    Barton, Larry L; Fauque, Guy D

    2009-01-01

    Chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to ATP synthesis. These bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. This chapter deals with the distribution in the environment and the major physiological and metabolic characteristics of sulfate-reducing bacteria (SRB). This chapter presents our current knowledge of soluble electron transfer proteins and transmembrane redox complexes that are playing an essential role in the dissimilatory sulfate reduction pathway of SRB of the genus Desulfovibrio. Environmentally important activities displayed by SRB are a consequence of the unique electron transport components or the production of high levels of H(2)S. The capability of SRB to utilize hydrocarbons in pure cultures and consortia has resulted in using these bacteria for bioremediation of BTEX (benzene, toluene, ethylbenzene and xylene) compounds in contaminated soils. Specific strains of SRB are capable of reducing 3-chlorobenzoate, chloroethenes, or nitroaromatic compounds and this has resulted in proposals to use SRB for bioremediation of environments containing trinitrotoluene and polychloroethenes. Since SRB have displayed dissimilatory reduction of U(VI) and Cr(VI), several biotechnology procedures have been proposed for using SRB in bioremediation of toxic metals. Additional non-specific metal reductase activity has resulted in using SRB for recovery of precious metals (e.g. platinum, palladium and gold) from waste streams. Since bacterially produced sulfide contributes to the souring of oil fields, corrosion of concrete, and discoloration of stonework is a serious problem, there is considerable interest in controlling the sulfidogenic activity of the SRB. The

  3. Promoting Active Learning of Graduate Student by Deep Reading in Biochemistry and Microbiology Pharmacy Curriculum

    Science.gov (United States)

    Peng, Ren

    2017-01-01

    To promote graduate students' active learning, deep reading of high quality papers was done by graduate students enrolled in biochemistry and microbiology pharmacy curriculum offered by college of life science, Jiangxi Normal University from 2013 to 2015. The number of graduate students, who participated in the course in 2013, 2014, and 2015 were…

  4. Purification and Characterization of Taq Polymerase: A 9-Week Biochemistry Laboratory Project for Undergraduate Students

    Science.gov (United States)

    Bellin, Robert M.; Bruno, Mary K.; Farrow, Melissa A.

    2010-01-01

    We have developed a 9-week undergraduate laboratory series focused on the purification and characterization of "Thermus aquaticus" DNA polymerase (Taq). Our aim was to provide undergraduate biochemistry students with a full-semester continuing project simulating a research-like experience, while having each week's procedure focus on a single…

  5. A Learner-Centered Molecular Modeling Exercise for Allied Health Majors in a Biochemistry Class

    Science.gov (United States)

    Fletcher, Terace M.; Ershler, Jeff

    2014-01-01

    Learner-centered molecular modeling exercises in college science courses can be especially challenging for nonchemistry majors as students typically have a higher degree of anxiety and may not appreciate the relevance of the work. This article describes a learner-centered project given to allied health majors in a Biochemistry course. The project…

  6. Exploring Protein Structure and Dynamics through a Project-Oriented Biochemistry Laboratory Module

    Science.gov (United States)

    Lipchock, James M.; Ginther, Patrick S.; Douglas, Bonnie B.; Bird, Kelly E.; Loria, J. Patrick

    2017-01-01

    Here, we present a 10-week project-oriented laboratory module designed to provide a course-based undergraduate research experience in biochemistry that emphasizes the importance of biomolecular structure and dynamics in enzyme function. This module explores the impact of mutagenesis on an important active site loop for a biomedically-relevant…

  7. Teaching Protein Purification and Characterization Techniques: A Student-Initiated, Project-Oriented Biochemistry Laboratory Course

    Science.gov (United States)

    MacDonald, Gina

    2008-01-01

    This report describes a biochemistry laboratory that is completely project-oriented. Upper-level biology and chemistry majors work in teams to purify a protein of their choice. After the student groups have completed literature searches, ordered reagents, and made buffers they continue to learn basic protein purification and biochemical techniques…

  8. A Semester-Long Project-Oriented Biochemistry Laboratory Based on "Helicobacter pylori" Urease

    Science.gov (United States)

    Farnham, Kate R.; Dube, Danielle H.

    2015-01-01

    Here we present the development of a 13 week project-oriented biochemistry laboratory designed to introduce students to foundational biochemical techniques and then enable students to perform original research projects once they have mastered these techniques. In particular, we describe a semester-long laboratory that focuses on a biomedically…

  9. Green Fluorescent Protein-Focused Bioinformatics Laboratory Experiment Suitable for Undergraduates in Biochemistry Courses

    Science.gov (United States)

    Rowe, Laura

    2017-01-01

    An introductory bioinformatics laboratory experiment focused on protein analysis has been developed that is suitable for undergraduate students in introductory biochemistry courses. The laboratory experiment is designed to be potentially used as a "stand-alone" activity in which students are introduced to basic bioinformatics tools and…

  10. Biochemistry and biology: heart-to-heart to investigate cardiac progenitor cells.

    Science.gov (United States)

    Chimenti, Isotta; Forte, Elvira; Angelini, Francesco; Messina, Elisa; Giacomello, Alessandro

    2013-02-01

    Cardiac regenerative medicine is a rapidly evolving field, with promising future developments for effective personalized treatments. Several stem/progenitor cells are candidates for cardiac cell therapy, and emerging evidence suggests how multiple metabolic and biochemical pathways strictly regulate their fate and renewal. In this review, we will explore a selection of areas of common interest for biology and biochemistry concerning stem/progenitor cells, and in particular cardiac progenitor cells. Numerous regulatory mechanisms have been identified that link stem cell signaling and functions to the modulation of metabolic pathways, and vice versa. Pharmacological treatments and culture requirements may be exploited to modulate stem cell pluripotency and self-renewal, possibly boosting their regenerative potential for cell therapy. Mitochondria and their many related metabolites and messengers, such as oxygen, ROS, calcium and glucose, have a crucial role in regulating stem cell fate and the balance of their functions, together with many metabolic enzymes. Furthermore, protein biochemistry and proteomics can provide precious clues on the definition of different progenitor cell populations, their physiology and their autocrine/paracrine regulatory/signaling networks. Interdisciplinary approaches between biology and biochemistry can provide productive insights on stem/progenitor cells, allowing the development of novel strategies and protocols for effective cardiac cell therapy clinical translation. This article is part of a Special Issue entitled Biochemistry of Stem Cells. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Application of radioisotopes in biochemistry of proteins, hydrocarbons and lipids of viruses

    International Nuclear Information System (INIS)

    Budarkov, V.A.; Bakulov, I.A.; Makarov, V.V.; Chumak, R.M.

    1990-01-01

    The article desribes the methods of radioisotope application in biochemistry of proteins, hydrocarbons and lipids of viruses: - radionuclide analysis of immunocompetent cell surface components; - technique of radionuclide introduction into viruse and cell proteins; - method of investigating of viruse glycoproteins; - method of measuring viruse ferment activity. 383 refs.; 2 figs.; 4 tabs

  12. Creating a Cell Map as an Active-Learning Tool in a Biochemistry Course

    Science.gov (United States)

    Del Bianco, Cristina

    2010-01-01

    Teaching metabolism to a biochemistry class with diverse academic backgrounds is a challenging task. Often students lack the global perspective that is needed to understand how different metabolic pathways are reciprocally regulated. The classroom activity presented in this article is designed to facilitate the learning of metabolism by having the…

  13. Comprehensive Experiment--Clinical Biochemistry: Determination of Blood Glucose and Triglycerides in Normal and Diabetic Rats

    Science.gov (United States)

    Jiao, Li; Xiujuan, Shi; Juan, Wang; Song, Jia; Lei, Xu; Guotong, Xu; Lixia, Lu

    2015-01-01

    For second year medical students, we redesigned an original laboratory experiment and developed a combined research-teaching clinical biochemistry experiment. Using an established diabetic rat model to detect blood glucose and triglycerides, the students participate in the entire experimental process, which is not normally experienced during a…

  14. Use of Mushroom Tyrosinase to Introduce Michaelis-Menten Enzyme Kinetics to Biochemistry Students

    Science.gov (United States)

    Flurkey, William H.; Inlow, Jennifer K.

    2017-01-01

    An inexpensive enzyme kinetics laboratory exercise for undergraduate biochemistry students is described utilizing tyrosinase from white button mushrooms. The exercise can be completed in one or two three-hour lab sessions. The optimal amounts of enzyme, substrate (catechol), and inhibitor (kojic acid) are first determined, and then kinetic data is…

  15. A Two-Week Guided Inquiry Protein Separation and Detection Experiment for Undergraduate Biochemistry

    Science.gov (United States)

    Carolan, James P.; Nolta, Kathleen V.

    2016-01-01

    A laboratory experiment for teaching protein separation and detection in an undergraduate biochemistry laboratory course is described. This experiment, performed in two, 4 h laboratory periods, incorporates guided inquiry principles to introduce students to the concepts behind and difficulties of protein purification. After using size-exclusion…

  16. The Concept Lens Diagram: A New Mechanism for Presenting Biochemistry Content in Terms of "Big Ideas"

    Science.gov (United States)

    Rowland, Susan L.; Smith, Christopher A.; Gillam, Elizabeth M. A.; Wright, Tony

    2011-01-01

    A strong, recent movement in tertiary education is the development of conceptual, or "big idea" teaching. The emphasis in course design is now on promoting key understandings, core competencies, and an understanding of connections between different fields. In biochemistry teaching, this radical shift from the content-based tradition is…

  17. A Statistical Analysis of College Biochemistry Textbooks in China: The Statuses on the Publishing and Usage

    Science.gov (United States)

    Zhou, Ping; Wang, Qinwen; Yang, Jie; Li, Jingqiu; Guo, Junming; Gong, Zhaohui

    2015-01-01

    This study aimed to investigate the statuses on the publishing and usage of college biochemistry textbooks in China. A textbook database was constructed and the statistical analysis was adopted to evaluate the textbooks. The results showed that there were 945 (~57%) books for theory teaching, 379 (~23%) books for experiment teaching and 331 (~20%)…

  18. Implementing an Active Learning Environment to Influence Students' Motivation in Biochemistry

    Science.gov (United States)

    Cicuto, Camila Aparecida Tolentino; Torres, Bayardo Baptista

    2016-01-01

    The Biochemistry: Biomolecules Structure and Metabolism course's goal is to promote meaningful learning through an active learning environment. Thus, study periods (SP) and discussion groups (DG) are used as a substitute for lecture classes. The goal of this study was to evaluate how this learning environment influences students' motivation (n =…

  19. A Guide to Using Case-Based Learning in Biochemistry Education

    Science.gov (United States)

    Kulak, Verena; Newton, Genevieve

    2014-01-01

    Studies indicate that the majority of students in undergraduate biochemistry take a surface approach to learning, associated with rote memorization of material, rather than a deep approach, which implies higher cognitive processing. This behavior relates to poorer outcomes, including impaired course performance and reduced knowledge retention. The…

  20. Essential Concepts and Underlying Theories from Physics, Chemistry, and Mathematics for "Biochemistry and Molecular Biology" Majors

    Science.gov (United States)

    Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A.; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry,…

  1. The Views of Undergraduates about Problem-Based Learning Applications in a Biochemistry Course

    Science.gov (United States)

    Tarhan, Leman; Ayyildiz, Yildizay

    2015-01-01

    The effect of problem-based learning (PBL) applications in an undergraduate biochemistry course on students' interest in this course was investigated through four modules during one semester. Students' views about active learning and improvement in social skills were also collected and evaluated. We conducted the study with 36 senior students from…

  2. Foundational Concepts and Underlying Theories for Majors in "Biochemistry and Molecular Biology"

    Science.gov (United States)

    Tansey, John T.; Baird, Teaster, Jr.; Cox, Michael M.; Fox, Kristin M.; Knight, Jennifer; Sears, Duane; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members and science educators from around the country that focused on identifying: 1) core principles of biochemistry and molecular biology, 2) essential concepts and underlying theories from physics, chemistry, and mathematics, and 3)…

  3. Known Structure, Unknown Function: An Inquiry-Based Undergraduate Biochemistry Laboratory Course

    Science.gov (United States)

    Gray, Cynthia; Price, Carol W.; Lee, Christopher T.; Dewald, Alison H.; Cline, Matthew A.; McAnany, Charles E.; Columbus, Linda; Mura, Cameron

    2015-01-01

    Undergraduate biochemistry laboratory courses often do not provide students with an authentic research experience, particularly when the express purpose of the laboratory is purely instructional. However, an instructional laboratory course that is inquiry- and research-based could simultaneously impart scientific knowledge and foster a student's…

  4. Need Assessment of Enhancing the Weightage of Applied Biochemistry in the Undergraduate Curriculum at MGIMS, Sevagram

    Science.gov (United States)

    Kumar, Satish; Jena, Lingaraja; Vagha, Jayant

    2016-01-01

    In order to review the need assessment of enhancing the weightage of Applied Biochemistry in the undergraduate curriculum at Mahatma Gandhi Institute of Medical Sciences (MGIMS), Sevagram, a validated questionnaire was sent to 453 participants which include 387 undergraduate students, 11 interns, 23 postgraduate students, and 32 faculty members. A…

  5. Reactivity III: An Advanced Course in Integrated Organic, Inorganic, and Biochemistry

    Science.gov (United States)

    Schaller, Chris P.; Graham, Kate J.; Jakubowski, Henry V.

    2017-01-01

    Reactivity III is a new course that presents chemical reactions from the domains of organic, inorganic, and biochemistry that are not readily categorized by electrophile-nucleophile interactions. Many of these reactions involve the transfer of a single electron, in either an intermolecular fashion in the case of oxidation/reduction reactions or an…

  6. Motivating Active Learning of Biochemistry through Artistic Representation of Scientific Concepts

    Science.gov (United States)

    Bruna, Carola

    2013-01-01

    First-year students often feel discouraged, especially with courses that require complex thinking and involve establishing relations between different subjects such as biochemistry. It has been proposed that student-centred pedagogy can achieve motivation and improve learning. In this context, this case study reports the use of art as a strategy…

  7. Neglected Issues Concerning Teaching Human Adrenal Steroidogenesis in Popular Biochemistry Textbooks

    Science.gov (United States)

    Han, Zhiyong; Elliott, Mark S.

    2017-01-01

    In the human body, the adrenal steroids collectively regulate a plethora of fundamental functions, including electrolyte and water balance, blood pressure, stress response, intermediary metabolism, inflammation, and immunity. Therefore, adrenal steroidogenesis is an important biochemistry topic for students to learn in order for them to understand…

  8. Student Conceptions about Energy Transformations: Progression from General Chemistry to Biochemistry

    Science.gov (United States)

    Wolfson, Adele J.; Rowland, Susan L.; Lawrie, Gwendolyn A.; Wright, Anthony H.

    2014-01-01

    Students commencing studies in biochemistry must transfer and build on concepts they learned in chemistry and biology classes. It is well established, however, that students have difficulties in transferring critical concepts from general chemistry courses; one key concept is "energy." Most previous work on students' conception of energy…

  9. Learning Medical School Biochemistry Through Self-Directed Case-Oriented Study.

    Science.gov (United States)

    Morley, Colin G. D.; Blumberg, Phyllis

    1987-01-01

    Describes an alternative medical school curriculum for the first two years of preclinical basic science studies. Discusses student and faculty selection for the program. Details the format for teaching biochemistry in the Alternative Curriculum, including program structure, content organization and exams. Evaluates the success of the program. (CW)

  10. Teaching Biochemistry at a Medical Faculty with a Problem-Based Learning System.

    Science.gov (United States)

    Rosing, Jan

    1997-01-01

    Highlights the differences between classical teaching methods and problem-based learning. Describes the curriculum and problem-based approach of the Faculty of Medicine at the Maastricht University and gives an overview of the implementation of biochemistry in the medical curriculum. Discusses the procedure for student assessment and presents…

  11. The Importance of Undergraduate General and Organic Chemistry to the Study of Biochemistry in Medical School.

    Science.gov (United States)

    Scimone, Anthony; Scimone, Angelina A.

    1996-01-01

    Investigates chemistry topics necessary to facilitate the study of biochemistry in U.S. medical schools. Lists topics considered especially important and topics considered especially unimportant in general chemistry and organic chemistry. Suggests that in teaching undergraduate general or organic chemistry, the topics categorized as exceptionally…

  12. Teaching of Biochemistry in Medical School: A Well-Trodden Pathway?

    Science.gov (United States)

    Mathews, Michael B.; Stagnaro-Green, Alex

    2008-01-01

    Biochemistry and molecular biology occupy a unique place in the medical school curriculum. They are frequently studied prior to medical school and are fundamental to the teaching of biomedical sciences in undergraduate medical education. These two circumstances, and the trend toward increased integration among the disciplines, have led to…

  13. The pattern of clinical advice sought by general practitioners from a medical consultant in clinical biochemistry.

    Science.gov (United States)

    Bhatnagar, D

    1997-01-01

    Clinical biochemistry departments can be a valuable source of clinical advice for further investigations and the need for referral to specialist clinics. This paper outlines the pattern of clinical advice sought by general practitioners in a district hospital setting, and addresses some of the issues regarding seeking such advice and the implications for continuing medical education and training. PMID:9196966

  14. Biochemistry students' ideas about how an enzyme interacts with a substrate.

    Science.gov (United States)

    Linenberger, Kimberly J; Bretz, Stacey Lowery

    2015-01-01

    Enzyme-substrate interactions are a fundamental concept of biochemistry that is built upon throughout multiple biochemistry courses. Central to understanding enzyme-substrate interactions is specific knowledge of exactly how an enzyme and substrate interact. Within this narrower topic, students must understand the various binding sites on an enzyme and be able to reason from simplistic lock and key or induced fit models to the more complex energetics model of transition state theory. Learning to understand these many facets of enzyme-substrate interactions and reasoning from multiple models present challenges where students incorrectly make connections between concepts or make no connection at all. This study investigated biochemistry students' understanding of enzyme-substrate interactions through the use of clinical interviews and a national administration (N = 707) of the Enzyme-Substrate Interactions Concept Inventory. Findings include misconceptions regarding the nature of enzyme-substrate interactions, naïve ideas about the active site, a lack of energetically driven interactions, and an incomplete understanding of the specificity pocket. © 2015 by the International Union of Biochemistry and Molecular Biology.

  15. Impact of Virtual Patients as Optional Learning Material in Veterinary Biochemistry Education.

    Science.gov (United States)

    Kleinsorgen, Christin; von Köckritz-Blickwede, Maren; Naim, Hassan Y; Branitzki-Heinemann, Katja; Kankofer, Marta; Mándoki, Míra; Adler, Martin; Tipold, Andrea; Ehlers, Jan P

    2018-01-01

    Biochemistry and physiology teachers from veterinary faculties in Hannover, Budapest, and Lublin prepared innovative, computer-based, integrative clinical case scenarios as optional learning materials for teaching and learning in basic sciences. These learning materials were designed to enhance attention and increase interest and intrinsic motivation for learning, thus strengthening autonomous, active, and self-directed learning. We investigated learning progress and success by administering a pre-test before exposure to the virtual patients (vetVIP) cases, offered vetVIP cases alongside regular biochemistry courses, and then administered a complementary post-test. We analyzed improvement in cohort performance and level of confidence in rating questions. Results of the performance in biochemistry examinations in 2014, 2015, and 2016 were correlated with the use of and performance in vetVIP cases throughout biochemistry courses in Hannover. Surveys of students reflected that interactive cases helped them understand the relevance of basic sciences in veterinary education. Differences between identical pre- and post-tests revealed knowledge improvement (correct answers: +28% in Hannover, +9% in Lublin) and enhanced confidence in decision making ("I don't know" answers: -20% in Hannover, -7.5% in Lublin). High case usage and voluntary participation (use of vetVIP cases in Hannover and Lublin >70%, Budapest learning could be extended and generated cases should be shared across veterinary faculties.

  16. Improving Student Understanding of Lipids Concepts in a Biochemistry Course Using Test-Enhanced Learning

    Science.gov (United States)

    Horn, Savannah; Hernick, Marcy

    2015-01-01

    Test-enhanced learning has successfully been used as a means to enhance learning and promote knowledge retention in students. We have examined whether this approach could be used in a biochemistry course to enhance student learning about lipids-related concepts. Students were provided access to two optional learning modules with questions related…

  17. Thermodynamic Exploration of Eosin-Lysozyme Binding: A Physical Chemistry and Biochemistry Laboratory Experiment

    Science.gov (United States)

    Huisman, Andrew J.; Hartsell, Lydia R.; Krueger, Brent P.; Pikaart, Michael J.

    2010-01-01

    We developed a modular pair of experiments for use in the undergraduate physical chemistry and biochemistry laboratories. Both experiments examine the thermodynamics of the binding of a small molecule, eosin Y, to the protein lysozyme. The assay for binding is the quenching of lysozyme fluorescence by eosin through resonant energy transfer. In…

  18. The Metabolic Effects of Low-Carbohydrate Diets and Incorporation into a Biochemistry Course

    Science.gov (United States)

    Pogozelski, Wendy; Arpaia, Nicholas; Priore, Salvatore

    2005-01-01

    One of the challenges in teaching biochemistry is facilitating students' interest in and mastery of metabolism. The many pathways and modes of regulation can be overwhelming for students to learn and difficult for professors to teach in an engaging manner. We have found it useful to take advantage of prevailing interest in popular yet…

  19. Using Adobe Flash Animations of Electron Transport Chain to Teach and Learn Biochemistry

    Science.gov (United States)

    Teplá, Milada; Klímová, Helena

    2015-01-01

    Teaching the subject of the electron transport chain is one of the most challenging aspects of the chemistry curriculum at the high school level. This article presents an educational program called "Electron Transport Chain" which consists of 14 visual animations including a biochemistry quiz. The program was created in the Adobe Flash…

  20. Technical and didactic problems of virtual lab exercises in biochemistry and biotechnology education

    DEFF Research Database (Denmark)

    May, Michael; Skriver, Karen; Dandanell, Gert

    from a lack of conceptual analysis of what actually constitutes virtual labs. A clarification of these conceptual issues is suggested as part of a Danish research and development project on virtual lab exercises in biochemistry, molecular biology and biotechnology education. The main outcome...

  1. What Skills Should Students of Undergraduate Biochemistry and Molecular Biology Programs Have upon Graduation?

    Science.gov (United States)

    White, Harold B.; Benore, Marilee A.; Sumter, Takita F.; Caldwell, Benjamin D.; Bell, Ellis

    2013-01-01

    Biochemistry and molecular biology (BMB) students should demonstrate proficiency in the foundational concepts of the discipline and possess the skills needed to practice as professionals. To ascertain the skills that should be required, groups of BMB educators met in several focused workshops to discuss the expectations with the ultimate goal of…

  2. Abstracts of the 30. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

    International Nuclear Information System (INIS)

    2001-01-01

    Several aspects concerning biochemistry and molecular biology of either animals, plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioreceptor assay) and nuclear magnetic resonance are the most applied techniques

  3. Abstracts of the 29. annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

    International Nuclear Information System (INIS)

    2000-01-01

    Several aspects concerning biochemistry and molecular biology of either animals (including man), plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioenzymatic assay, radioreceptor assay and nuclear magnetic resonance are the most applied techniques

  4. Integrative Metabolism: An Interactive Learning Tool for Nutrition, Biochemistry, and Physiology

    Science.gov (United States)

    Carey, Gale

    2010-01-01

    Metabolism is a dynamic, simultaneous, and integrative science that cuts across nutrition, biochemistry, and physiology. Teaching this science can be a challenge. The use of a scenario-based, visually appealing, interactive, computer-animated CD may overcome the limitations of learning "one pathway at a time" and engage two- and…

  5. Effects of age and sex on haematological and serum biochemistry in ...

    African Journals Online (AJOL)

    haematology and serum biochemistry) at different ages (in weeks) in male and female Japanese quails. A total of hundred (100) unsexed day-old quail chicks were purchased and sorted based on sex at the third week. Blood samples were collected ...

  6. Students' Preferred Teaching Techniques for Biochemistry in Biomedicine and Medicine Courses

    Science.gov (United States)

    Novelli, Ethel L.B.; Fernandes, Ana Angelica H.

    2007-01-01

    The aim of this study was to investigate the students' preferred teaching techniques, such as traditional blackboard, power-point, or slide-projection, for biochemistry discipline in biomedicine and medicine courses from Sao Paulo State University, UNESP, Botucatu, Sao Paulo, Brazil. Preferences for specific topic and teaching techniques were…

  7. A course director's perspectives on problem-based learning curricula in biochemistry.

    Science.gov (United States)

    Smith, Harold C

    2002-12-01

    Knowledge of the applications of biochemistry, molecular biology, and genetics in the practice of medicine has been and continues to be a vital part of medical students' and continuing education. The technical background and the rapid expansion of information and new applications have made it an arduous task to learn and teach this material within the already crowded medical school curriculum. Problem-based learning (PBL) formats are rapidly being adopted at all levels of education as not only a major paradigm shift in education but also a solution for the instruction of biochemistry in medical school. Designing an effective biochemistry curriculum with PBL-based or lecture-based formats requires an appreciation for their strengths and weakness. The author's experiences in the Double Helix Curriculum at the University of Rochester School of Medicine and Dentistry (which employs PBL cases and complementing lectures) has shown that students are excited about learning in the PBL environment and explore in depth ways of integrating biochemistry, cell biology, genetics, and molecular biology into the practice of medicine. At the same time, complementary lectures greatly enhance uniformity in the quality and, importantly, the accuracy of the students' learning.

  8. Integrating Bio-Inorganic and Analytical Chemistry into an Undergraduate Biochemistry Laboratory

    Science.gov (United States)

    Erasmus, Daniel J.; Brewer, Sharon E.; Cinel, Bruno

    2015-01-01

    Undergraduate laboratories expose students to a wide variety of topics and techniques in a limited amount of time. This can be a challenge and lead to less exposure to concepts and activities in bio-inorganic chemistry and analytical chemistry that are closely-related to biochemistry. To address this, we incorporated a new iron determination by…

  9. Abstracts of the 28. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

    International Nuclear Information System (INIS)

    1999-01-01

    Biochemistry, genetic and molecular biology aspects of either animals (including man), plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioenzymatic assay, radioreceptor assay) and nuclear magnetic resonance are the most applied techniques

  10. Adult bacterial meningitis

    DEFF Research Database (Denmark)

    Meyer, C N; Samuelsson, I S; Galle, M

    2004-01-01

    Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin susceptibi......Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin...

  11. The Use of PDB database as a Tool for Biochemistry Active Learning of Undergraduate Students

    Directory of Open Access Journals (Sweden)

    T.M.F. Günther et al.

    2017-07-01

    Full Text Available Traditional Biochemistry teaching-learning is still an ongoing practice at UFSC. There are few published reports about innovative pedagogical practices of this discipline at this University. To ensure motivation through active learning of Basic Biochemistry we started to apply new methodologies back to 2005. This approach intended to stimulate undergraduate students in learning Biochemistry proactively. Objectives: Use PDB as a tool to improve skills related to Biochemistry education, while using specific information available; provide virtual data in order to stimulate student autonomy in active teaching-learning processes through methodologies based on the use of safe and suitable scientific information. Material and Methods: At the beginning, students were exposed to Biochemistry of Proteins content through traditional lectures. On the following stage, an introduction to PDB was made at the digital environment (http://www.rcsb.org/pdb/home/home.do depicting scientific information. Students received a model-instruction describing myoglobin characteristics at PDB (https://pdb101.rcsb.org/motm/1. This Powerpoint™ presentation gave clues on how the work was to be done. A lottery was made and each pair of students was allowed to select a protein and then developed Powerpoint™ presentations. Proteins were chosen from the PDB categories and obtained from the academic educational plan for Basic Biochemistry related to the Nutrition-Course. The Moodle plataform provided virtual materials, allowing full interactivity to all student presentations. Results and Discussion: There was total adherence to the pedagogical proposal. The student presentations in Powerpoint™ were adequate and made available to the attendees in the Moodle platform. Items surveyed in the presented script with the highest hit rates (grade ten were: biological importance (100%, amino acid composition (92.30%, structural information (89.75%, occurrence (89.74%, URL cited (79

  12. Creation and implementation of a flipped jigsaw activity to stimulate interest in biochemistry among medical students.

    Science.gov (United States)

    Williams, Charlene; Perlis, Susan; Gaughan, John; Phadtare, Sangita

    2018-05-06

    Learner-centered pedagogical methods that are based on clinical application of basic science concepts through active learning and problem solving are shown to be effective for improving knowledge retention. As the clinical relevance of biochemistry is not always apparent to health-profession students, effective teaching of medical biochemistry should highlight the implications of biochemical concepts in pathology, minimize memorization, and make the concepts memorable for long-term retention. Here, we report the creation and successful implementation of a flipped jigsaw activity that was developed to stimulate interest in learning biochemistry among medical students. The activity combined the elements of a flipped classroom for learning concepts followed by a jigsaw activity to retrieve these concepts by solving clinical cases, answering case-based questions, and creating concept maps. The students' reception of the activity was very positive. They commented that the activity provided them an opportunity to review and synthesize information, helped to gage their learning by applying this information and work with peers. Students' improved performance especially for answering the comprehension-based questions correctly in the postquiz as well as the depth of information included in the postquiz concept maps suggested that the activity helped them to understand how different clinical scenarios develop owing to deviations in basic biochemical pathways. Although this activity was created for medical students, the format of this activity can also be useful for other health-professional students as well as undergraduate and graduate students. © 2018 by The International Union of Biochemistry and Molecular Biology, 2018. © 2018 The International Union of Biochemistry and Molecular Biology.

  13. Reference intervals for selected serum biochemistry analytes in cheetahs Acinonyx jubatus.

    Science.gov (United States)

    Hudson-Lamb, Gavin C; Schoeman, Johan P; Hooijberg, Emma H; Heinrich, Sonja K; Tordiffe, Adrian S W

    2016-02-26

    Published haematologic and serum biochemistry reference intervals are very scarce for captive cheetahs and even more for free-ranging cheetahs. The current study was performed to establish reference intervals for selected serum biochemistry analytes in cheetahs. Baseline serum biochemistry analytes were analysed from 66 healthy Namibian cheetahs. Samples were collected from 30 captive cheetahs at the AfriCat Foundation and 36 free-ranging cheetahs from central Namibia. The effects of captivity-status, age, sex and haemolysis score on the tested serum analytes were investigated. The biochemistry analytes that were measured were sodium, potassium, magnesium, chloride, urea and creatinine. The 90% confidence interval of the reference limits was obtained using the non-parametric bootstrap method. Reference intervals were preferentially determined by the non-parametric method and were as follows: sodium (128 mmol/L - 166 mmol/L), potassium (3.9 mmol/L - 5.2 mmol/L), magnesium (0.8 mmol/L - 1.2 mmol/L), chloride (97 mmol/L - 130 mmol/L), urea (8.2 mmol/L - 25.1 mmol/L) and creatinine (88 µmol/L - 288 µmol/L). Reference intervals from the current study were compared with International Species Information System values for cheetahs and found to be narrower. Moreover, age, sex and haemolysis score had no significant effect on the serum analytes in this study. Separate reference intervals for captive and free-ranging cheetahs were also determined. Captive cheetahs had higher urea values, most likely due to dietary factors. This study is the first to establish reference intervals for serum biochemistry analytes in cheetahs according to international guidelines. These results can be used for future health and disease assessments in both captive and free-ranging cheetahs.

  14. Baseline hematology and serum biochemistry results for Indian leopards (Panthera pardus fusca)

    Science.gov (United States)

    Shanmugam, Arun Attur; Muliya, Sanath Krishna; Deshmukh, Ajay; Suresh, Sujay; Nath, Anukul; Kalaignan, Pa; Venkataravanappa, Manjunath; Jose, Lyju

    2017-01-01

    Aim: The aim of the study was to establish the baseline hematology and serum biochemistry values for Indian leopards (Panthera pardus fusca), and to assess the possible variations in these parameters based on age and gender. Materials and Methods: Hemato-biochemical test reports from a total of 83 healthy leopards, carried out as part of routine health evaluation in Bannerghatta Biological Park and Manikdoh Leopard Rescue Center, were used to establish baseline hematology and serum biochemistry parameters for the subspecies. The hematological parameters considered for the analysis included hemoglobin (Hb), packed cell volume, total erythrocyte count (TEC), total leukocyte count (TLC), mean corpuscular volume (MCV), mean corpuscular Hb (MCH), and MCH concentration. The serum biochemistry parameters considered included total protein (TP), albumin, globulin, aspartate aminotransferase, alanine aminotransferase (ALT), blood urea nitrogen, creatinine, triglycerides, calcium, and phosphorus. Results: Even though few differences were observed in hematologic and biochemistry values between male and female Indian leopards, the differences were statistically not significant. Effects of age, however, were evident in relation to many hematologic and biochemical parameters. Sub-adults had significantly greater values for Hb, TEC, and TLC compared to adults and geriatric group, whereas they had significantly lower MCV and MCH compared to adults and geriatric group. Among, serum biochemistry parameters the sub-adult age group was observed to have significantly lower values for TP and ALT than adult and geriatric leopards. Conclusion: The study provides a comprehensive analysis of hematologic and biochemical parameters for Indian leopards. Baselines established here will permit better captive management of the subspecies, serve as a guide to assess the health and physiological status of the free ranging leopards, and may contribute valuable information for making effective

  15. Baseline hematology and serum biochemistry results for Indian leopards (Panthera pardus fusca

    Directory of Open Access Journals (Sweden)

    Arun Attur Shanmugam

    2017-07-01

    Full Text Available Aim: The aim of the study was to establish the baseline hematology and serum biochemistry values for Indian leopards (Panthera pardus fusca, and to assess the possible variations in these parameters based on age and gender. Materials and Methods: Hemato-biochemical test reports from a total of 83 healthy leopards, carried out as part of routine health evaluation in Bannerghatta Biological Park and Manikdoh Leopard Rescue Center, were used to establish baseline hematology and serum biochemistry parameters for the subspecies. The hematological parameters considered for the analysis included hemoglobin (Hb, packed cell volume, total erythrocyte count (TEC, total leukocyte count (TLC, mean corpuscular volume (MCV, mean corpuscular Hb (MCH, and MCH concentration. The serum biochemistry parameters considered included total protein (TP, albumin, globulin, aspartate aminotransferase, alanine aminotransferase (ALT, blood urea nitrogen, creatinine, triglycerides, calcium, and phosphorus. Results: Even though few differences were observed in hematologic and biochemistry values between male and female Indian leopards, the differences were statistically not significant. Effects of age, however, were evident in relation to many hematologic and biochemical parameters. Sub-adults had significantly greater values for Hb, TEC, and TLC compared to adults and geriatric group, whereas they had significantly lower MCV and MCH compared to adults and geriatric group. Among, serum biochemistry parameters the sub-adult age group was observed to have significantly lower values for TP and ALT than adult and geriatric leopards. Conclusion: The study provides a comprehensive analysis of hematologic and biochemical parameters for Indian leopards. Baselines established here will permit better captive management of the subspecies, serve as a guide to assess the health and physiological status of the free ranging leopards, and may contribute valuable information for making

  16. Reference intervals for selected serum biochemistry analytes in cheetahs (Acinonyx jubatus

    Directory of Open Access Journals (Sweden)

    Gavin C. Hudson-Lamb

    2016-02-01

    Full Text Available Published haematologic and serum biochemistry reference intervals are very scarce for captive cheetahs and even more for free-ranging cheetahs. The current study was performed to establish reference intervals for selected serum biochemistry analytes in cheetahs. Baseline serum biochemistry analytes were analysed from 66 healthy Namibian cheetahs. Samples were collected from 30 captive cheetahs at the AfriCat Foundation and 36 free-ranging cheetahs from central Namibia. The effects of captivity-status, age, sex and haemolysis score on the tested serum analytes were investigated. The biochemistry analytes that were measured were sodium, potassium, magnesium, chloride, urea and creatinine. The 90% confidence interval of the reference limits was obtained using the non-parametric bootstrap method. Reference intervals were preferentially determined by the non-parametric method and were as follows: sodium (128 mmol/L – 166 mmol/L, potassium (3.9 mmol/L – 5.2 mmol/L, magnesium (0.8 mmol/L – 1.2 mmol/L, chloride (97 mmol/L – 130 mmol/L, urea (8.2 mmol/L – 25.1 mmol/L and creatinine (88 µmol/L – 288 µmol/L. Reference intervals from the current study were compared with International Species Information System values for cheetahs and found to be narrower. Moreover, age, sex and haemolysis score had no significant effect on the serum analytes in this study. Separate reference intervals for captive and free-ranging cheetahs were also determined. Captive cheetahs had higher urea values, most likely due to dietary factors. This study is the first to establish reference intervals for serum biochemistry analytes in cheetahs according to international guidelines. These results can be used for future health and disease assessments in both captive and free-ranging cheetahs.

  17. Evaluation of Student-made Blogs in Basicand Advanced Biochemistry Classes

    Directory of Open Access Journals (Sweden)

    E. Cubas

    2011-04-01

    Full Text Available Preliminary results of the experience of student-made clinical biochemistry blogs were reported at SBBq-2010 (abstract K-5. Herein, five teaching-semesters and the opinion of former students were evaluated. Since the teaching-semester of 2008-1, Basic Biochemistry (BioBio students should prepare blog-assignments on clinical issues. Students' acceptance was evaluated through 6-point Likert-type questionnaires. Positive responses were those marking 4 to 6. A total of 348 BioBio students from five teaching-semesters answered the questionnaire; 77% of them agreed that preparing blogs was enjoyable, having a positive effect on their formation. Moreover, 81% of students agreed that BioBio blogs are relevant learning tools and 78% believedthat BioBio blogs boosted interest for biochemistry. Moreover, students' acceptance 1 year after taking BioBio was evaluated. Students (n=50 were dividedin (i those who had attended BioBio only, and (ii those who had also taken Advanced Biochemistry, together with blog tutoring. In the first group, 72% agreed that the information acquired during blog elaboration was useful atthe time of interview; 76% judged that blog elaboration boosted interest for the discipline. For thosein the second group evaluations were 100% and 82%, respectively. Results show maintenance of acceptance over 1 year and effective interest for blog-assignment for thosein basic and advanced biochemistry classes.

  18. Enhancing Predictive Accuracy of Cardiac Autonomic Neuropathy Using Blood Biochemistry Features and Iterative Multitier Ensembles.

    Science.gov (United States)

    Abawajy, Jemal; Kelarev, Andrei; Chowdhury, Morshed U; Jelinek, Herbert F

    2016-01-01

    Blood biochemistry attributes form an important class of tests, routinely collected several times per year for many patients with diabetes. The objective of this study is to investigate the role of blood biochemistry for improving the predictive accuracy of the diagnosis of cardiac autonomic neuropathy (CAN) progression. Blood biochemistry contributes to CAN, and so it is a causative factor that can provide additional power for the diagnosis of CAN especially in the absence of a complete set of Ewing tests. We introduce automated iterative multitier ensembles (AIME) and investigate their performance in comparison to base classifiers and standard ensemble classifiers for blood biochemistry attributes. AIME incorporate diverse ensembles into several tiers simultaneously and combine them into one automatically generated integrated system so that one ensemble acts as an integral part of another ensemble. We carried out extensive experimental analysis using large datasets from the diabetes screening research initiative (DiScRi) project. The results of our experiments show that several blood biochemistry attributes can be used to supplement the Ewing battery for the detection of CAN in situations where one or more of the Ewing tests cannot be completed because of the individual difficulties faced by each patient in performing the tests. The results show that AIME provide higher accuracy as a multitier CAN classification paradigm. The best predictive accuracy of 99.57% has been obtained by the AIME combining decorate on top tier with bagging on middle tier based on random forest. Practitioners can use these findings to increase the accuracy of CAN diagnosis.

  19. [Bacterial biofilms and infection].

    Science.gov (United States)

    Lasa, I; Del Pozo, J L; Penadés, J R; Leiva, J

    2005-01-01

    In developed countries we tend to think of heart disease and the numerous forms of cancer as the main causes of mortality, but on a global scale infectious diseases come close, or may even be ahead: 14.9 million deaths in 2002 compared to cardiovascular diseases (16.9 million deaths) and cancer (7.1 million deaths) (WHO report 2004). The infectious agents responsible for human mortality have evolved as medical techniques and hygienic measures have changed. Modern-day acute infectious diseases caused by specialized bacterial pathogens such as diphtheria, tetanus, cholera, plague, which represented the main causes of death at the beginning of XX century, have been effectively controlled with antibiotics and vaccines. In their place, more than half of the infectious diseases that affect mildly immunocompromised patients involve bacterial species that are commensal with the human body; these can produce chronic infections, are resistant to antimicrobial agents and there is no effective vaccine against them. Examples of these infections are the otitis media, native valve endocarditis, chronic urinary infections, bacterial prostatitis, osteomyelitis and all the infections related to medical devices. Direct analysis of the surface of medical devices or of tissues that have been foci of chronic infections shows the presence of large numbers of bacteria surrounded by an exopolysaccharide matrix, which has been named the "biofilm". Inside the biofilm, bacteria grow protected from the action of the antibodies, phagocytic cells and antimicrobial treatments. In this article, we describe the role of bacterial biofilms in human persistent infections.

  20. Interfering with bacterial gossip

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

    2011-01-01

    that appropriately target bacteria in their relevant habitat with the aim of mitigating their destructive impact on patients. In this review we describe molecular mechanisms involved in “bacterial gossip” (more scientifically referred to as quorum sensing (QS) and c-di-GMP signaling), virulence, biofilm formation...

  1. Bacterial fingerprints across Europe

    NARCIS (Netherlands)

    Glasner, Corinna

    2014-01-01

    Bacterial pathogens, such as Staphylococcus aureus and carbapenemase-producing Enterobacteriaceae (CPE), impose major threats to human health worldwide. Both have a ‘Jekyll & Hyde’ character, since they can be present as human commensals, but can also become harmful invasive pathogens especially

  2. Bacterial membrane proteomics.

    Science.gov (United States)

    Poetsch, Ansgar; Wolters, Dirk

    2008-10-01

    About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

  3. [Spontaneous bacterial peritonitis].

    Science.gov (United States)

    Velkey, Bálint; Vitális, Eszter; Vitális, Zsuzsanna

    2017-01-01

    Spontaneous bacterial peritonitis occurs most commonly in cirrhotic patients with ascites. Pathogens get into the circulation by intestinal translocation and colonize in peritoneal fluid. Diagnosis of spontaneous bacterial peritonitis is based on elevated polymorphonuclear leukocyte count in the ascites (>0,25 G/L). Ascites culture is often negative but aids to get information about antibiotic sensitivity in positive cases. Treatment in stable patient can be intravenous then orally administrated ciprofloxacin or amoxicillin/clavulanic acid, while in severe cases intravenous III. generation cephalosporin. Nosocomial spontaneous bacterial peritonitis often caused by Gram-positive bacteria and multi-resistant pathogens can also be expected thus carbapenem should be the choice of the empiric treatment. Antibiotic prophylaxis should be considered. Norfloxacin is used most commonly, but changes are expected due to increase in quinolone resistance. As a primary prophylaxis, a short-term antibiotic treatment is recommended after gastrointestinal bleeding for 5 days, while long-term prophylaxis is for patients with low ascites protein, and advanced disease (400 mg/day). Secondary prophylaxis is recommended for all patients recovered from spontaneous bacterial peritonitis. Due to increasing antibiotic use of antibiotics prophylaxis is debated to some degree. Orv. Hetil., 2017, 158(2), 50-57.

  4. Corticosteroids for Bacterial Keratitis

    Science.gov (United States)

    Srinivasan, Muthiah; Mascarenhas, Jeena; Rajaraman, Revathi; Ravindran, Meenakshi; Lalitha, Prajna; Glidden, David V.; Ray, Kathryn J.; Hong, Kevin C.; Oldenburg, Catherine E.; Lee, Salena M.; Zegans, Michael E.; McLeod, Stephen D.; Lietman, Thomas M.; Acharya, Nisha R.

    2013-01-01

    Objective To determine whether there is a benefit in clinical outcomes with the use of topical corticosteroids as adjunctive therapy in the treatment of bacterial corneal ulcers. Methods Randomized, placebo-controlled, double-masked, multicenter clinical trial comparing prednisolone sodium phosphate, 1.0%, to placebo as adjunctive therapy for the treatment of bacterial corneal ulcers. Eligible patients had a culture-positive bacterial corneal ulcer and received topical moxifloxacin for at least 48 hours before randomization. Main Outcome Measures The primary outcome was best spectacle-corrected visual acuity (BSCVA) at 3 months from enrollment. Secondary outcomes included infiltrate/scar size, reepithelialization, and corneal perforation. Results Between September 1, 2006, and February 22, 2010, 1769 patients were screened for the trial and 500 patients were enrolled. No significant difference was observed in the 3-month BSCVA (−0.009 logarithm of the minimum angle of resolution [logMAR]; 95% CI, −0.085 to 0.068; P = .82), infiltrate/scar size (P = .40), time to reepithelialization (P = .44), or corneal perforation (P > .99). A significant effect of corticosteroids was observed in subgroups of baseline BSCVA (P = .03) and ulcer location (P = .04). At 3 months, patients with vision of counting fingers or worse at baseline had 0.17 logMAR better visual acuity with corticosteroids (95% CI, −0.31 to −0.02; P = .03) compared with placebo, and patients with ulcers that were completely central at baseline had 0.20 logMAR better visual acuity with corticosteroids (−0.37 to −0.04; P = .02). Conclusions We found no overall difference in 3-month BSCVA and no safety concerns with adjunctive corticosteroid therapy for bacterial corneal ulcers. Application to Clinical Practice Adjunctive topical corticosteroid use does not improve 3-month vision in patients with bacterial corneal ulcers. PMID:21987582

  5. Bacterial infec tions in travellers

    African Journals Online (AJOL)

    namely bacterial causes of travellers' diarrhoea and skin infections, as well as .... Vaccination: protective efficacy against typhoid may be overcome by ingesting a high bacterial load. Vaccine ..... preparation such as cream sauce. Only after ...

  6. METABOLIC WAR: A VARIATION FOR METABOLIC BIOCHEMISTRY LEARNING OF A WORLDLY KNOWN BOARD GAME

    Directory of Open Access Journals (Sweden)

    C. M. Anjos

    2008-05-01

    Full Text Available Biomedical careers are highly wished by young students in Brazil. Although future jobs,  academic knowledge and higher earnings  are tempting reasons for this life choice, few of them are aware  of  the difficult path through the  basic classes. Advanced and specific disciplines  are easier to associate with the professional career itself, but few students can identify the importance  of the basic knowledge for their future work. Biochemistry is one of the most difficult  disciplines  for Brazilian students, probably due to the level of abstraction needed to fully learn and understand the topics. Some recent experimental tools, such as bioinformatics, are now helping students with the learning process, providing visual data for understanding biomolecule structure.  In addition to this, biochemical reactions  could be even tougher because of the many variables involved.  To facilitate the learning process for metabolic biochemistry, we created a game based on the board game WAR®,  using Photoshop software. Named Metabolic War, it keeps the same basic rules of WAR®, but with some minor changes. The continents are metabolic pathways (citric acid cycle, glycolysis, beta-oxidation, etc and the countries are metabolic intermediates. Similarly to the original game, players must conquer an objective (one or more metabolic pathways by dominating intermediates. But the desired intermediate must be a possible product from an intermediate the player already owns. This  and other  games were produced by Biomedicine  undergraduate  students  in Metabolic Biochemistry classes. It was presented to other students, who tested and acknowledged it as a great help in understanding metabolic biochemistry,  giving a great understanding of integrative metabolism. Keywords: game; Biochemistry; Metabolic Biochemistry learning; science learning; playful learning.

  7. Correlation of Preadmission Organic Chemistry Courses and Academic Performance in Biochemistry at a Midwest Chiropractic Doctoral Program*

    Science.gov (United States)

    McRae, Marc P.

    2010-01-01

    Purpose: Organic chemistry has been shown to correlate with academic success in the preclinical years of medicine, dentistry, and graduate physiology. The purpose of this study is to examine the relationship between undergraduate organic chemistry grades and first-semester biochemistry grades at a Midwest chiropractic doctoral program. Methods: Students enrolled in a first-semester biochemistry course who had completed the prerequisite courses in organic chemistry offered at this same institution were entered into the study. The total grade for each of the three courses was calculated using the midterm and final exam raw scores with a weighting of 50% each. Analysis consisted of obtaining correlation coefficients between the total grades of organic 1 with biochemistry and organic 2 with biochemistry. Using the biochemistry total grade, the students were divided into quartiles and course grades for both organic chemistry 1 and 2 were calculated. Results: For the 109 students in the study, the correlation coefficient between the biochemistry and organic chemistry 1 and biochemistry and organic chemistry 2 courses was r = 0.744 and r = 0.725, respectively. The difference in organic chemistry grades between those in the first and fourth quartiles was 63.2% and 86.9% for organic chemistry 1 (p organic chemistry 2 (p organic chemistry can be used as an indicator of future academic success in a chiropractic biochemistry course. Knowledge of such a relationship could prove useful to identify students who may potentially run into academic difficulty with first-year biochemistry PMID:20480012

  8. Structure of bacterial lipopolysaccharides.

    Science.gov (United States)

    Caroff, Martine; Karibian, Doris

    2003-11-14

    Bacterial lipopolysaccharides are the major components of the outer surface of Gram-negative bacteria They are often of interest in medicine for their immunomodulatory properties. In small amounts they can be beneficial, but in larger amounts they may cause endotoxic shock. Although they share a common architecture, their structural details exert a strong influence on their activity. These molecules comprise: a lipid moiety, called lipid A, which is considered to be the endotoxic component, a glycosidic part consisting of a core of approximately 10 monosaccharides and, in "smooth-type" lipopolysaccharides, a third region, named O-chain, consisting of repetitive subunits of one to eight monosaccharides responsible for much of the immunospecificity of the bacterial cell.

  9. Cooperative Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2009-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a novel optimization algorithm based on the social foraging behavior of E. coli bacteria. This paper presents a variation on the original BFO algorithm, namely, the Cooperative Bacterial Foraging Optimization (CBFO, which significantly improve the original BFO in solving complex optimization problems. This significant improvement is achieved by applying two cooperative approaches to the original BFO, namely, the serial heterogeneous cooperation on the implicit space decomposition level and the serial heterogeneous cooperation on the hybrid space decomposition level. The experiments compare the performance of two CBFO variants with the original BFO, the standard PSO and a real-coded GA on four widely used benchmark functions. The new method shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  10. Bacterial control of cyanobacteria

    CSIR Research Space (South Africa)

    Ndlela, Luyanda L

    2017-08-01

    Full Text Available of biological control appears to be direct contact. • Ndlela, L. L. et al. (2016) ‘An overview of cyanobacterial bloom occurrences and research in Africa over the last decade’, Harmful Algae, 60 • Gumbo, J.R. et al. (2010) The Isolation and identification... of Predatory Bacteria from a Microcystis algal Bloom.. African Journal of Biotechnology, 9. *Special acknowledgement goes to the National Research foundation for funding this presentation Bacterial control of cyanobacteria Luyanda...

  11. Bacterial growth kinetics

    International Nuclear Information System (INIS)

    Boonkitticharoen, V.; Ehrhardt, J.C.; Kirchner, P.T.

    1989-01-01

    Quantitative measurement of bacterial growth may be made using a radioassay technique. This method measures, by scintillation counting, the 14 CO 2 derived from the bacterial metabolism of a 14 C-labeled substrate. Mathematical growth models may serve as reliable tools for estimation of the generation rate constant (or slope of the growth curve) and provide a basis for evaluating assay performance. Two models, i.e., exponential and logistic, are proposed. Both models yielded an accurate fit to the data from radioactive measurement of bacterial growth. The exponential model yielded high precision values of the generation rate constant, with an average relative standard deviation of 1.2%. Under most conditions the assay demonstrated no changes in the slopes of growth curves when the number of bacteria per inoculation was changed. However, the radiometric assay by scintillation method had a growth-inhibiting effect on a few strains of bacteria. The source of this problem was thought to be hypersensitivity to trace amounts of toluene remaining on the detector

  12. Adaptive Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2011-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a recently developed nature-inspired optimization algorithm, which is based on the foraging behavior of E. coli bacteria. Up to now, BFO has been applied successfully to some engineering problems due to its simplicity and ease of implementation. However, BFO possesses a poor convergence behavior over complex optimization problems as compared to other nature-inspired optimization techniques. This paper first analyzes how the run-length unit parameter of BFO controls the exploration of the whole search space and the exploitation of the promising areas. Then it presents a variation on the original BFO, called the adaptive bacterial foraging optimization (ABFO, employing the adaptive foraging strategies to improve the performance of the original BFO. This improvement is achieved by enabling the bacterial foraging algorithm to adjust the run-length unit parameter dynamically during algorithm execution in order to balance the exploration/exploitation tradeoff. The experiments compare the performance of two versions of ABFO with the original BFO, the standard particle swarm optimization (PSO and a real-coded genetic algorithm (GA on four widely-used benchmark functions. The proposed ABFO shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  13. Adjusting a biochemistry course for physical education majors: A case study.

    Science.gov (United States)

    da Costa, Caetano; Torres, Bayardo B

    2004-03-01

    The purpose of this study was to investigate and analyze the events responsible for curricular characteristics that lead to positive outcomes in university teaching using a biochemistry course taught to physical education students as a model. The research was carried out as a case study, supported by questionnaires, classroom observation, document analysis, and interviews. The overall analyses of obtained data were validated by means of triangulation protocols, which proved the following reasons for the course achievements: 1) teaching staff deeply committed to the course; 2) contents adaptation to students' careers; 3) gradual adjustment of the teaching strategies and evaluation tools; 4) valorization of formative evaluation; and 5) providing a suitable affective milieu. Copyright © 2004 International Union of Biochemistry and Molecular Biology, Inc.

  14. Haematology and Plasma Biochemistry of Wild Black Flying-Foxes, (Pteropus alecto in Queensland, Australia.

    Directory of Open Access Journals (Sweden)

    Lee McMichael

    Full Text Available This paper establishes reference ranges for hematologic and plasma biochemistry values in wild Black flying-foxes (Pteropus alecto captured in South East Queensland, Australia. Values were found to be consistent with those of other Pteropus species. Four hundred and forty-seven animals were sampled over 12 months and significant differences were found between age, sex, reproductive and body condition cohorts in the sample population. Mean values for each cohort fell within the determined normal adult reference range, with the exception of elevated levels of alkaline phosphatase in juvenile animals. Hematologic and biochemistry parameters of injured animals showed little or no deviation from the normal reference values for minor injuries, while two animals with more severe injury or abscessation showed leucocytosis, anaemia, thrombocytosis, hyperglobulinemia and hypoalbuminemia.

  15. 50 years of comparative biochemistry: The legacy of Peter Hochachka.

    Science.gov (United States)

    Buck, L T; Burness, G; Campbell, K L; Darveau, C-A; Driedzic, W; Guderley, H; McClelland, G B; Moon, T W; Moyes, C D; Schulte, P M

    2018-02-28

    Peter Hochachka was an early pioneer in the field of comparative biochemistry. He passed away in 2002 after 4 decades of research in the discipline. To celebrate his contributions and to coincide with what would have been his 80th birthday, a group of his former students organized a symposium that ran as a satellite to the 2017 Canadian Society of Zoologists annual meeting in Winnipeg, Manitoba (Canada). This Special Issue of CBP brings together manuscripts from symposium attendees and other authors who recognize the role Peter played in the evolution of the discipline. In this article, the symposium organizers and guest editors look back on his career, celebrating his many contributions to research, acknowledging his role in training of generations of graduate students and post-doctoral fellows in comparative biochemistry and physiology. Copyright © 2018. Published by Elsevier Inc.

  16. Comprehensive Experiment—Clinical Biochemistry: Determination of Blood Glucose and Triglycerides in Normal and Diabetic Rats

    Science.gov (United States)

    Jiao, Li; Xiujuan, Shi; Juan, Wang; Song, Jia; Lei, Xu; Guotong, Xu; Lixia, Lu

    2015-01-01

    For second year medical students, we redesigned an original laboratory experiment and developed a combined research-teaching clinical biochemistry experiment. Using an established diabetic rat model to detect blood glucose and triglycerides, the students participate in the entire experimental process, which is not normally experienced during a standard clinical biochemistry exercise. The students are not only exposed to techniques and equipment but are also inspired to think more about the biochemical mechanisms of diseases. When linked with lecture topics about the metabolism of carbohydrates and lipids, the students obtain a better understanding of the relevance of abnormal metabolism in relation to diseases. Such understanding provides a solid foundation for the medical students' future research and for other clinical applications. PMID:25521692

  17. Integrating bio-inorganic and analytical chemistry into an undergraduate biochemistry laboratory.

    Science.gov (United States)

    Erasmus, Daniel J; Brewer, Sharon E; Cinel, Bruno

    2015-01-01

    Undergraduate laboratories expose students to a wide variety of topics and techniques in a limited amount of time. This can be a challenge and lead to less exposure to concepts and activities in bio-inorganic chemistry and analytical chemistry that are closely-related to biochemistry. To address this, we incorporated a new iron determination by atomic absorption spectroscopy exercise as part of a five-week long laboratory-based project on the purification of myoglobin from beef. Students were required to prepare samples for chemical analysis, operate an atomic absorption spectrophotometer, critically evaluate their iron data, and integrate these data into a study of myoglobin. © 2015 The International Union of Biochemistry and Molecular Biology.

  18. Clinical biochemistry and MRI follow up study in postpartum pituitary enlargement

    International Nuclear Information System (INIS)

    Chen Weipeng; Huang Shaoqiang; Lu Xiaofan; Cai Baimang; Liu Xuguang

    2004-01-01

    Objective: To investigate the relationship between enlargement of pituitary in postpartum females and the clinical biochemistry. Methods: In total 6 postpartum women were studied by MRI of pituitary and clinical biochemistry assessment, the data was collected especially in puerperium period. Results: Enlargement of pituitary gland was most remarkable in the first week of puerperium period, while endocrine changes including HCG, Progesterone, E 2 also reached considerable high peak in the same time especially the first and second day after labor. Prolactin also increased. βHCG, Progesterone, and E 2 rapidly decreased after the first week of puerperium period and the size of pituitary gland recovered to normal size. Conclusion: Postpartum enlargement of pituitary gland is physiological and related with internal environment change in gravitation, which is not to be misdiagnosed as a lesion

  19. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism

    DEFF Research Database (Denmark)

    Nikel, Pablo I.; de Lorenzo, Víctor

    2018-01-01

    are presented for substantiating the worth of P. putida as one of the favorite workhorses for sustainable manufacturing of fine and bulk chemicals in the current times of the 4th Industrial Revolution. The potential of P. putida to extend its rich native biochemistry beyond existing boundaries is discussed...... biochemistry is naturally geared to generate reductive currency [i.e., NAD(P)H] that makes this bacterium a phenomenal host for redox-intensive reactions. In some cases, genetic editing of the indigenous biochemical network of P. putida (cis-metabolism) has sufficed to obtain target compounds of industrial...... stresses. Over the years, these properties have been capitalized biotechnologically owing to the expanding wealth of genetic tools designed for deep-editing the P. putida genome. A suite of dedicated vectors inspired in the core tenets of synthetic biology have enabled to suppress many of the naturally...

  20. BIOCHEMISTRYGUIDE: A GUIDE TO STUDY BIOCHEMISTRY IN THE PALM OF YOUR HAND

    Directory of Open Access Journals (Sweden)

    M. L.C. Zago

    2015-08-01

    Full Text Available The new generation has grown driven by the digital technologies. Nowadays, the access to information has extended to the mobile technologies, like cell phones and tablets, increasing the technological resources for use in education. Educational institutions are opening more and more space to technologies, which have a new teaching, and learning methodology. The internet is an inexhaustible source of knowledge. With so much available material, the student finds difficulties in choosing the best source to study. Develop a cell phone app that works as a biochemistry study guide, providing materials from safe source and easy access. The app was developed at the website "Factory of apps", for free, and available for all the operational systems (Android, IOS, windows, enabling the download in any device. Were inserted in it materials like: summaries of the main subjects dealt in the discipline with clear and objective language, scientific articles to complementary reading, video-classes and exercises. Offering fast and practical access to the material, facilitating the process of studying and learning. The student does not have to let his mobile phone in preference of studying and does not find difficulties to filter available information in the internet. After the app's use, was applied a questionnaire to the participating students for this tool's assessment, such as layout, quality of the available material, access facilities. All the participants have approved the listed aspects and have said that the use of the tool can help at the biochemistry study, by the reliable material and by being available in a mobile device providing quick and immediate access, at any time in the palm of the hand. The use of this tool can be applied in the classroom to help the professor in getting materials and to help the students by its practicality.Acknowledgements: CnpQ, Unipampa. Keywords: App, BiochemistryGuide, Biochemistry

  1. NEW MATERIALS FOR PEDAGOGICAL TEACHING-LEARNING IN BIOCHEMISTRY: MONITORING PARTICIPATION

    OpenAIRE

    Campos, R. S.; Fernandes, I. L.; Andrade, G. P.V.; Matta, L. D.M.; Filgueira, L. G.A.

    2015-01-01

    This summary consists of an experience report about actions taken by biochemical monitors with pharmacy students. The reason of our work was the intention to both improve the process of teaching and also learning and invalidate the labels owned by biochemistry of hard and high-level-failure subject. The three actors: teachers, students and monitor could act on an integrated basis for the construction of an articulated  pedagogical process between theory/practice and learning signification. Ou...

  2. LLUSTRATION OF AMINO ACIDS REACTIONS AND PROTEINS CHARACTERIZATION FOR EXPERIMENTAL BIOCHEMISTRY CLASSES

    Directory of Open Access Journals (Sweden)

    I. Parreira

    2008-05-01

    Full Text Available New teaching methodologies have been developed to facilitate the learning of biochemistry concepts. A new  approach to Biochemistry  teaching  has become more frequent,  one that does not  require reagents but use photos, videos, softwares etc. Experimental Biochemistry classes, i.e. covering characterization of amino acids and proteins,  might be more productive with the use of complementary didactic material.  Furthermore,  if experiments cannot be implemented, classes may  be well illustrated with complementary didactic material covering from the simplest to the most  complex experiments.  In order to  aid Biochemistry classes without practical experiments, some tests and reactions were documented in our laboratory through digital photos, for  instance: (1 the biuret reaction wherein the blue reagent turns violet in the presence of proteins and changes to pink when combined with short-chain polypeptides; (2 the ninhydrin test used in amino acid analysis of proteins: most of the amino acids are hydrolyzed and react with ninhydrin; when reacting with these free amines, a deep blue or purple color appears; (3 methods for detecting proteins wherein spectrophotometry is used, that deals with the relationship between absorbance, concentration and path length, which constitute the Beer-Lambert Law. A didactic material constituted by texts, schemes and illustrated by photos has been created for each class topic. This material can be used either as a teacher script or in a presentation form to illustrate classes without experimental activities. Financial Support: Pro-Reitoria Graduação-USP, CNPq.

  3. The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry

    DEFF Research Database (Denmark)

    Byrne, Stephen L.; Erthmann, Pernille Østerbye; Agerbirk, Niels

    2017-01-01

    The genus Barbarea has emerged as a model for evolution and ecology of plant defense compounds, due to its unusual glucosinolate profile and production of saponins, unique to the Brassicaceae. One species, B. vulgaris, includes two ‘types’, G-type and P-type that differ in trichome density, and t...... deter larvae to the extent that they die. The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding....

  4. Polish Academy of Sciences. Institute of Biochemistry and Biophysics. Research Report 1998-1999

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-07-01

    The report presented research activities of the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, in 1998-1999. Research interests focus on: replication, mutagenesis and repair of DNA, regulation of gene expression, biosynthesis and post-translational modifications of proteins, gene sequencing and functional gene analysis, structure and function of enzymes, conformation of proteins and peptides, modeling of structures and prediction of function of proteins.

  5. Notable Expressions: Transcriptional Regulation from Biochemistry to Immunology | Center for Cancer Research

    Science.gov (United States)

    Dinah Singer, Ph.D., came to NCI in 1975 as a Postdoctoral Fellow in the Laboratory of Biochemistry, but soon created a career for herself in the Experimental Immunology Branch. Her interest in how genes are regulated to control biological function led her to focus on major histocompatibility complex class I genes (MHC Class I)—molecules critical to immune system function—as a

  6. Attitudes toward plagiarism among pharmacy and medical biochemistry students – cross-sectional survey study

    OpenAIRE

    Pupovac, Vanja; Bilic-Zulle, Lidija; Mavrinac, Martina; Petrovecki, Mladen

    2010-01-01

    Introduction: Plagiarism is one of the most frequent and serious forms of misconduct in academic environment. The cross-sectional survey study was done with aim to explore the attitudes toward plagiarism. Materials and methods: First year students of Faculty of Pharmacy and Medical Biochemistry, University of Zagreb, Croatia (N = 146) were anonymously tested using Attitude toward Plagiarism (ATP) questionnaire. The questionnaire is composed of 29 statements on a 5 point Likert scale, (1 - ...

  7. STUDENTS’ MISCONCEPTIONS ABOUT THE NATURE OF MATTER AND HOW IT IMPAIRS BIOCHEMISTRY LEARNING

    Directory of Open Access Journals (Sweden)

    E. Montagna

    2015-08-01

    Full Text Available Introduction: It is widely known that misconceptions impairs student’s learning. IUBMB proposed a concept inventory which defines biochemistry’s teaching scope. Even though it is known that many of them are subject of misconceptions by students, we collected informal data suggesting a deeper and most pervasive misconception related to the students’ perceptions about what is and is not a molecule through their classroom statements and tests. We hypothesize that students’ impairments on biochemistry learning possibly come from failure to assume that names are related to well defined molecules indicating lack of matter’s representative levels of integration. Objectives The present work aims to detect in freshmen students’ misconceptions about the chemical nature of main small and macromolecules which potentialy impairs biochemistry learning. Materials and methods: A list of assertions about real life situations involving and citing main biomolecules – ATP, DNA, protein, lipid, carbohydrate, enzyme, hormon, vitamin – were mixed with other containing vague common terms – toxin, transgenic, healthy, unwanted elements, chemical compound – not suggesting hazardous situations in order to capture students’ impressions. More than 150 students from five courses in three different higher education institutions answered true or false on 35 assertions. Results and discussion: More than 70% of students had more than 80% error in this task designed to be not tricky, misleading or with unpreviously studied concepts. Results suggests students do not understand compounds as molecules but as entities unrelated to real life situations; on the other hand vague terms triggers a negative perception not necessarily related to harm or hazardous situations. We suggest that it is originated by poor scientific literacy from previous scholarity as well as lack of criteria on media vehicles about the topics here cited. Conclusion: We conclude that many

  8. Polish Academy of Sciences. Institute of Biochemistry and Biophysics. Research Report 1998-1999

    International Nuclear Information System (INIS)

    2000-01-01

    The report presented research activities of the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, in 1998-1999. Research interests focus on: replication, mutagenesis and repair of DNA, regulation of gene expression, biosynthesis and post-translational modifications of proteins, gene sequencing and functional gene analysis, structure and function of enzymes, conformation of proteins and peptides, modeling of structures and prediction of function of proteins

  9. Application of indices Cp and Cpk to improve quality control capability in clinical biochemistry laboratories.

    Science.gov (United States)

    Chen, Ming-Shu; Wu, Ming-Hsun; Lin, Chih-Ming

    2014-04-30

    The traditional criteria for acceptability of analytic quality may not be objective in clinical laboratories. To establish quality control procedures intended to enhance Westgard multi-rules for improving the quality of clinical biochemistry tests, we applied the Cp and Cpk quality-control indices to monitor tolerance fitting and systematic variation of clinical biochemistry test results. Daily quality-control data of a large Taiwanese hospital in 2009 were analyzed. The test items were selected based on an Olympus biochemistry machine and included serum albumin, aspartate aminotransferase, cholesterol, glucose and potassium levels. Cp and Cpk values were calculated for normal and abnormal levels, respectively. The tolerance range was estimated with data from 50 laboratories using the same instruments and reagents. The results showed a monthly trend of variation for the five items under investigation. The index values of glucose were lower than those of the other items, and their values were usually quality control, but also for revealing inter-laboratory qualitycontrol capability differences.

  10. HEMATOLOGY, SERUM BIOCHEMISTRY, AND URINALYSIS VALUES IN THE ADULT GIANT PANDA ( AILUROPODA MELANOLEUCA).

    Science.gov (United States)

    Burrell, Caitlin; Zhang, Hemin; Li, Desheng; Wang, Chengdong; Li, Caiwu; Aitken-Palmer, Copper

    2017-12-01

    The giant panda ( Ailuropoda melanoleuca) is a high-profile threatened species with individuals in captivity worldwide. As a result of advances in captive animal management and veterinary medicine, the ex situ giant panda population is aging, and improved understanding of age-related changes is necessary. Urine and blood samples were collected in April and July 2015 and analyzed for complete blood count, serum biochemistry, and biochemical and microscopic urine analysis for all individuals sampled ( n = 7, 7-16 yr of age) from giant panda housed at the China Research and Conservation Centre for the Giant Panda in Bifengxia, Sichuan Province, China. Hematology and serum biochemistry values were similar to those previously reported for giant panda aged 2-20 yr and to Species360 (formerly International Species Information System) values. Urine was overall dilute (urine specific gravity range: 1.001-1.021), acellular, and acidic (pH range: 6-7). This is the first report of hematologic and serum biochemistry, with associated urinalysis values, in the giant panda aged 7-16 yr.

  11. The Teaching of Biochemistry: An Innovative Course Sequence Based on the Logic of Chemistry

    Science.gov (United States)

    Jakubowski, Henry V.; Owen, Whyte G.

    1998-06-01

    An innovative course sequence for the teaching of biochemistry is offered, which more truly reflects the common philosophy found in biochemistry texts: that the foundation of biological phenomena can best be understood through the logic of chemistry. Topic order is chosen to develop an emerging understanding that is based on chemical principles. Preeminent biological questions serve as a framework for the course. Lipid and lipid-aggregate structures are introduced first, since it is more logical to discuss the intermolecular association of simple amphiphiles to form micelle and bilayer formations than to discuss the complexities of protein structure/folding. Protein, nucleic acid, and carbohydrate structures are studied next. Binding, a noncovalent process and the simplest expression of macromolecular function, follows. The physical (noncovalent) transport of solute molecules across a biological membrane is studied next, followed by the chemical transformation of substrates by enzymes. These are logical extensions of the expression of molecular function, first involving a simpler (physical transport) and second, a more complex (covalent transformation) process. The final sequence involves energy and signal transduction. This unique course sequence emerges naturally when chemical logic is used as an organizing paradigm for structuring a biochemistry course. Traditional order, which seems to reflect historic trends in research, or even an order derived from the central dogma of biology can not provide this logical framework.

  12. Introduction to the Minireview Series on Modern Technologies for In-cell Biochemistry.

    Science.gov (United States)

    Lutsenko, Svetlana

    2016-02-19

    The last decade has seen enormous progress in the exploration and understanding of the behavior of molecules in their natural cellular environments at increasingly high spatial and temporal resolution. Advances in microscopy and the development of new fluorescent reagents as well as genetic editing techniques have enabled quantitative analysis of protein interactions, intracellular trafficking, metabolic changes, and signaling. Modern biochemistry now faces new and exciting challenges. Can traditionally "in vitro" experiments, e.g. analysis of protein folding and conformational transitions, be done in cells? Can the structure and behavior of endogenous and/or non-tagged recombinant proteins be analyzed and altered within the cell or in cellular compartments? How can molecules and their actions be studied mechanistically in tissues and organs? Is personalized cellular biochemistry a reality? This thematic series summarizes recent studies that illustrate some first steps toward successfully answering these modern biochemical questions. The first minireview focuses on utilization of three-dimensional primary enteroids and organoids for mechanistic studies of intestinal biology with molecular resolution. The second minireview describes application of single chain antibodies (nanobodies) for monitoring and regulating protein dynamics in vitro and in cells. The third minireview highlights advances in using NMR spectroscopy for analysis of protein folding and assembly in cells. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Using Adobe Flash animations of electron transport chain to teach and learn biochemistry.

    Science.gov (United States)

    Teplá, Milada; Klímová, Helena

    2015-01-01

    Teaching the subject of the electron transport chain is one of the most challenging aspects of the chemistry curriculum at the high school level. This article presents an educational program called "Electron Transport Chain" which consists of 14 visual animations including a biochemistry quiz. The program was created in the Adobe Flash CS3 Professional animation program and is designed for high school chemistry students. Our goal is to develop educational materials that facilitate the comprehension of this complex subject through dynamic animations which show the course of the electron transport chain and simultaneously explain its nature. We record the process of the electron transport chain, including connections with oxidative phosphorylation, in such a way as to minimize the occurrence of discrepancies in interpretation. The educational program was evaluated in high schools through the administration of a questionnaire, which contained 12 opened-ended items and which required participants to evaluate the graphics of the animations, chemical content, student preferences, and its suitability for high school biochemistry teaching. © 2015 The International Union of Biochemistry and Molecular Biology.

  14. The development and implementation of an online applied biochemistry bridge course for a dental hygiene curriculum.

    Science.gov (United States)

    Gadbury-Amyot, Cynthia C; Overman, Pamela R; Crain, Geralyn

    2009-01-01

    This article describes a curricular change project designed to improve instruction in biochemistry. After years of unsatisfactory outcomes from a dental hygiene biochemistry course, a decision was made to change the traditional lecture-based course to an online format. Using online technology and principles of educational pedagogy, a course was developed that fosters application of biomaterials principles to dental hygiene practice and provides a bridge between prerequisite chemistry coursework and biochemistry in a health professions program. Members of the dental hygiene graduating Classes of 2007 and 2008 participated in the revised course. The outcome measures used to assess the effectiveness of the revised course were student end-of-semester course evaluations, graduating senior survey results, student course performance, and National Board examination performance. While the results are based on only two classes, the positive outcomes suggest that the revision was a worthwhile endeavor. The use of technology in teaching holds the potential for solving many of the curriculum and instruction issues currently under discussion: overcrowding of the curriculum, lack of active learning methods, and basic sciences taught in isolation from the rest of the curriculum. It is hoped that the results of this change will be helpful to other faculty members seeking curricular change and innovation.

  15. A survey validation and analysis of undergraduate medical biochemistry practical curriculum in maharashtra, India.

    Science.gov (United States)

    Dandekar, Sucheta P; Maksane, Shalini N; McKinley, Danette

    2012-01-01

    In order to review the strengths and weaknesses of medical biochemistry practical curriculum for undergraduates and to generate ideas to improve it, a questionnaire was sent to 50 biochemistry faculty members selected (through simple random sampling method) from 42 medical colleges of Maharashtra, India. 39 responded to the questionnaire, representing a 78% response rate. The internal consistency of the questionnaire sections was found to be satisfactory (>0.7). The respondents did not agree that the ongoing curriculum was in alignment with learning outcomes (8%), that it encouraged active learning (28%), helped to apply knowledge to clinical situations (18%) and promoted critical thinking and problem solving skills (28%). There were a number of qualitative experiments that were rated 'irrelevant'. Qualitative and quantitative experiments related to recent advances were suggested to be introduced by the respondents. Checklists for the practicals and new curriculum objectives provided in the questionnaire were also approved. The results of the curriculum evaluation suggest a need for re-structuring of practical biochemistry curriculum and introduction of a modified curriculum with more clinical relevance.

  16. Virtual Practice of Biochemistry: Ascendant Chromatography on Paper of Amino acids.

    Directory of Open Access Journals (Sweden)

    G. Zanatta

    2010-05-01

    Full Text Available Chromatography is a method used for analyses of mixture components based on different criteria: adsorbility, solubility, molecular mass, ionic charge and affinity. It is an important subject of Biochemistry. This work reports the development and the validation of a software that simulated a laboratory activity named Ascendant Chromatography on Paper of Aminoacids. The organization and the multimedia material collection were done during the 2008/2 semester. The most representative images were inserted into the learning object. The tool used for the software development was Adobe® Flash® CS3. The first application of this object was in Biochemistry I (Pharmacy-UFRGS in 2009/1. Using this experience, a new version was developed which was tested by the students of the same subject in 2009/2. After a 50-minute class (theoretical-practical, the students of both semesters were divided in two groups. Group I answered a questionnaire about chromatography basic concepts and after used the software. Group II was submitted to an inverse protocol. The groups also evaluated the technical aspects of the software animation/simulation and the activity carried out. Associating both applications results (2009/1 and 2009/2, the present learning object can be valid as a support for practical teaching of basic biochemistry.

  17. Haematology and Clinical Biochemistry Findings Associated with Equine Diseases - a Review

    Directory of Open Access Journals (Sweden)

    Onyinyechukwu A. AGINA

    2017-03-01

    Full Text Available The course and outcome of a disease process is dependent upon factors such as the disease-causing agent and its cell tropism, defense mechanisms of the host, genetic resistance of the species or breed affected, as well as the age, nutritional status and hormonal levels of the affected animal. When haematology, clinical biochemistry and cytology test results are combined with other laboratory procedures, complete physical examination and also with the history of the patient, a veterinarian is well armed to arrive at a definitive diagnosis, make a certain prognosis (good, poor or guarded and can also make a concluding statement on the efficacy of the instituted therapy. In clinical biochemistry, demonstration of specific enzyme activity and concentration of analytes in serum/plasma facilitates the disease diagnosis. Also, evaluation of haematology, clinical biochemistry and diagnostic cytology tests can help establish the presence or absence of diseases of internal organs, and by serial performance of these tests, may help to determine whether a disease process remains static, progressive or regressive. This review therefore provides the haematological, serum biochemical and cytological characteristics of diseases caused by the main bacteria, viruses, fungi, protozoa, helminths, arthropods, nutritional deficiencies, endocrine disturbances, neoplasm, allergy, toxins (phytoxins and zootoxins and inorganic poisons in horses.

  18. The Proteomics Stock Market Project. A Cross-Disciplinary Collaboration in Biochemistry and Business Education

    Science.gov (United States)

    Keller, Heath; Cox, James R.

    2004-04-01

    Students taking courses in different disciplines can work together to add unique elements to their educational experience. A model for this type of pedagogical approach has been established in the Proteomics Stock Market Project, a collaborative effort between instructors and students in the Department of Chemistry and Department of Management, Marketing, and Business Administration at Murray State University. Stage I involved biochemistry students investigating the topic of proteomics and choosing companies for potential investment based only on scientific investigation. Marketing and management students completed Stage II and provided an investment analysis on the companies selected in Stage I. In Stage III, the biochemistry students focused on a particular company and investigated a protein-based therapeutic product. Blackboard software was utilized in each stage of the project to facilitate the exchange of information and electronic documents. This project was designed to give biochemistry students an appreciation for the emerging field of proteomics and the marketing and management students a flavor for real-world applications of business principles. During the project, students were exposed to ideas and concepts not typically covered in their courses. With this involvement, the students had the opportunity to gain a broader perspective of course content compared to a more traditional curriculum.

  19. Trends in the use of stable isotopes in biochemistry and pharmacology

    International Nuclear Information System (INIS)

    Matwiyoff, N.A.; Walker, T.E.

    1977-01-01

    Recent trends in the use of the stable isotopes 13 C, 15 N and 18 O in biochemistry and pharmacology are reviewed with emphasis on the studies that have employed nuclear magnetic resonance (nmr) spectroscopy and mass spectrometry as analytical techniques. Pharmacological studies with drugs and other compounds labelled with stable isotopes have developed in parallel with the rapid progress in the enhancement of sensitivity and selectivity of gas chromatography - mass spectrometric analyses, and have been directed largely to an evaluation of pharmako-kinetics and drug metabolic pathways. In these studies, illustrated with selected samples, isotopically labelled compounds have been used to advantage as internal standards for the mass spectrometric analyses and as in vivo tracers for metabolites. In the broader discipline of biochemistry, stable isotopes and isotopically labelled compounds have been used increasingly in conjuction with both nmr spectroscopy and mass spectrometry in tracer and structural studies. The more recent trends in the use of stable isotopes in these biochemical studies are discussed in the context of the improvements in analytical techniques. Specific examples will be drawn from investigations of the biosynthesis of natural products by micro-organisms; the protein, fat and carbohydrate fluxes in humans; and the structure and function of enzymes, membranes and other macro-molecular assemblages. The potential for the future development of stable isotopes in biochemistry and pharmacology are considered briefly, together with some of the problems that must be solved if their considerable potential is to be realized. (author)

  20. Identification of the students' critical thinking skills through biochemistry laboratory work report

    Science.gov (United States)

    Anwar, Yunita Arian Sani; Senam, Laksono, Endang W.

    2017-08-01

    This work aims to (1) identify the critical thinking skills of student based on their ability to set up laboratory work reports, and (2) analyze the implementation of biochemistry laboratory work. The method of quantitative content analysis was employed. Quantitative data were in the form of critical thinking skills through the assessment of students' laboratory work reports and questionnaire data. Hoyo rubric was used to measure critical thinking skills with 10 indicators, namely clarity, accuracy, precision, consistency, relevance, evidence, reason, depth, breadth, and fairness. The research sample consisted of 105 students (35 male, 70 female) of Mataram University who took a Biochemistry course and 2 lecturers of Biochemistry course. The results showed students' critical thinking skills through laboratory work reports were still weak. Analysis of the questionnaire showed that three indicators become the biggest problems during the laboratory work implementation, namely, lecturers' involved in laboratory work implementation, the integration of laboratory work implementation of learning in the classroom has not been done optimally and laboratory work implementation as an effort to train critical thinking skills is not optimal yet.

  1. A Survey of Final-year Undergraduate Laboratory Projects in Biochemistry and Related Degrees in Great Britain.

    Science.gov (United States)

    Austin, Caroline A.

    1997-01-01

    Analyzes undergraduate research projects in biochemistry and related subjects at British universities. Discusses the trend toward students doing less research as part of their undergraduate study. Reasons cited for this trend include increased student numbers and costs. (DDR)

  2. Program and abstracts of the 25. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

    International Nuclear Information System (INIS)

    1996-01-01

    The meeting was about biochemistry and molecular biology.In this meeting it was also discussed the following subjects: biotechnology, metabolism, enzymes, proteins, immunology, drugs and others related topics

  3. Studies on the life span, reproduction, tissue biochemistry and diesel oil toxicity in the estuarine cladocera Diaphanosoma celebensis

    Digital Repository Service at National Institute of Oceanography (India)

    PrabhuKonkar, S.R.; Achuthankutty, C.T.

    , neonate production, tissue biochemistry and toxicity of diesel oil have been described in the paper. Variations were observed in the life span and rate of neonate production between individuals of the 1 st and 2 nd generations. Both were found...

  4. Symposium 19: Federal University of Rio Grande do Sul: its Role in the Biochemistry Teaching in the Southernmost Brazilian States

    Directory of Open Access Journals (Sweden)

    Clóvis M.D. Wannmacher

    2014-08-01

    Full Text Available K-Education(Portuguese Chair: V. Trindade Bayardo Torres; Clovis Wannmacher; Denise Macedo  Federal University of Rio Grande do Sul: its Role in the Biochemistry Teaching in the Southernmost Brazilian States. Wannmacher, C.M.D. Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.   At present, most Biochemistry teaching in Rio Grande do Sul and Santa Catarina has its origin in the Department of Biochemistry of the Federal University of Rio Grande do Sul. In the 70’s, all the teachers of the Department wrote a book together: “Fundamental Biochemistry”. This book was always used in the classes by groups of students of different careers supervised by the respective teacher. At the same time, this methodology was not used by pharmaceutical teachers, but they recommended the Department’s book to their students. Along the next years, Biochemistry teaching was adapted according to the professional course and to the teacher’s personal characteristics. Today, there are two extremes strategies again: one traditional for the most basic biochemistry student’s formation (including theoretical, laboratorial, seminars and informatics classes and the other, experimental-clinical, for physician’s formation (including seminars of molecular approach to the most prevalent diseases, mainly, those leading to failure of organs/systems and the interaction with patients from HCPA by the interpretation of their biochemical data. On the other hand, the Post Graduation Program, at first, emphasized biochemistry teaching in a traditional form, but gradually changed the emphasis to investigation, and most classes changed to scientific paper reports. To stimulate the teaching formation, two activities were offered to post-graduation students: Biochemistry Teaching Methodology and Teaching Practice in Biochemistry. These activities promote opportunity for the students to

  5. AN ALTERNATIVE STRATEGY TO ANALYZE THE CONTENTS OF BIOCHEMISTRY INTRODUCTORY COURSES

    Directory of Open Access Journals (Sweden)

    A.K. Miskalo

    2008-05-01

    Full Text Available A common problem  educators  from  different areas face  is  to  fit the increasing  amount  of information  with the maintenance  and/or,  not seldom,  a decrease in the class load of their courses. This actual situation  necessarily forces the educator  to severely select the topics to be worked out. In the cur rent scenario of most teaching institutions, this decision  is  taken by the teacher.  In order to do this, a  list of the topics considered to be essential  for an appropriate biochemistry course is necessary. Taking for granted that questions from biochemistry courses tests reflect  the topics  considered most relevant by teachers,  questions from different courses offered by Biochemistry Department of USP were analyzed. The objective of this analysis  was  to  answer two main questions, namely (1  Which is the exte nt and  depth  of the common topics  in  biochemistry  introductory courses? and (2  Are there (and ,  if  there are,  which are they?  specific topics  for  different careers?  The  method we adopted was to verify  the demanded topics  in  written tests and  to  classify  their  cognitive level according to Bloom’s Taxonomy.  The most recurring topics found are Protein Structure and Metabolism Regulation. The results indicate a strong predominance of  low-level categories  (Knowledge e Comprehension,  with little  occurrence  of high-level categories (from Application on.  It is expected, from further development of this study,  to outline  the topics considered  relevant  to  set the basis for  the discussion  on the establishment of a minimum curriculum for biochemistry courses. Key words: Bloom’s Taxonomy, minimum curriculum, written tests analysis.

  6. Radiology of bacterial pneumonia

    International Nuclear Information System (INIS)

    Vilar, Jose; Domingo, Maria Luisa; Soto, Cristina; Cogollos, Jonathan

    2004-01-01

    Bacterial pneumonia is commonly encountered in clinical practice. Radiology plays a prominent role in the evaluation of pneumonia. Chest radiography is the most commonly used imaging tool in pneumonias due to its availability and excellent cost benefit ratio. CT should be used in unresolved cases or when complications of pneumonia are suspected. The main applications of radiology in pneumonia are oriented to detection, characterisation and follow-up, especially regarding complications. The classical classification of pneumonias into lobar and bronchial pneumonia has been abandoned for a more clinical classification. Thus, bacterial pneumonias are typified into three main groups: Community acquired pneumonia (CAD), Aspiration pneumonia and Nosocomial pneumonia (NP).The usual pattern of CAD is that of the previously called lobar pneumonia; an air-space consolidation limited to one lobe or segment. Nevertheless, the radiographic patterns of CAD may be variable and are often related to the causative agent. Aspiration pneumonia generally involves the lower lobes with bilateral multicentric opacities. Nosocomial Pneumonia (NP) occurs in hospitalised patients. The importance of NP is related to its high mortality and, thus, the need to obtain a prompt diagnosis. The role of imaging in NP is limited but decisive. The most valuable information is when the chest radiographs are negative and rule out pneumonia. The radiographic patterns of NP are very variable, most commonly showing diffuse multifocal involvement and pleural effusion. Imaging plays also an important role in the detection and evaluation of complications of bacterial pneumonias. In many of these cases, especially in hospitalised patients, chest CT must be obtained in order to better depict these associate findings

  7. Radiology of bacterial pneumonia

    Energy Technology Data Exchange (ETDEWEB)

    Vilar, Jose E-mail: vilar_jlu@gva.es; Domingo, Maria Luisa; Soto, Cristina; Cogollos, Jonathan

    2004-08-01

    Bacterial pneumonia is commonly encountered in clinical practice. Radiology plays a prominent role in the evaluation of pneumonia. Chest radiography is the most commonly used imaging tool in pneumonias due to its availability and excellent cost benefit ratio. CT should be used in unresolved cases or when complications of pneumonia are suspected. The main applications of radiology in pneumonia are oriented to detection, characterisation and follow-up, especially regarding complications. The classical classification of pneumonias into lobar and bronchial pneumonia has been abandoned for a more clinical classification. Thus, bacterial pneumonias are typified into three main groups: Community acquired pneumonia (CAD), Aspiration pneumonia and Nosocomial pneumonia (NP).The usual pattern of CAD is that of the previously called lobar pneumonia; an air-space consolidation limited to one lobe or segment. Nevertheless, the radiographic patterns of CAD may be variable and are often related to the causative agent. Aspiration pneumonia generally involves the lower lobes with bilateral multicentric opacities. Nosocomial Pneumonia (NP) occurs in hospitalised patients. The importance of NP is related to its high mortality and, thus, the need to obtain a prompt diagnosis. The role of imaging in NP is limited but decisive. The most valuable information is when the chest radiographs are negative and rule out pneumonia. The radiographic patterns of NP are very variable, most commonly showing diffuse multifocal involvement and pleural effusion. Imaging plays also an important role in the detection and evaluation of complications of bacterial pneumonias. In many of these cases, especially in hospitalised patients, chest CT must be obtained in order to better depict these associate findings.

  8. Pulmonary biochemistry

    International Nuclear Information System (INIS)

    Mavis, R.D.

    1986-01-01

    Regeneration of vitamin E from its intermediate oxidation product, the chromanoxyl radical, was studied as a heat-labile, vitamin E-dependent antioxidant activity of glutathione in delaying peroxidation of a microsomal fraction of liver and lung in vitro. The characteristics of this system are consistent with an enzyme-catalyzed reaction between glutathione and the chromanoxyl radical. We have developed a method of labeling the vitamin E of microsomes with tracer amounts of tritiated α-tocopherol. The oxidation of tocopherol can thus be monitored coincidentally with the peroxidation of fatty acids. Fatty acid peroxidation is monitored by spectrophotometrically measuring malondialdehyde and oxidation of vitamin E is monitored by extracting and chromatographing the radiolabelled vitamin E in a system which separates -tocopherol from its oxidation products. We have found that the presence of glutathione in this system retards both peroxidation of membrane phospholipids and oxidation of membrane-associated α-tocopherol, with a time sequence that is consistent with regeneration of vitamin E by reduction of the chromanoxyl radical by glutathione

  9. Molecular biochemistry

    International Nuclear Information System (INIS)

    Anon.

    1985-01-01

    Structural studies were done on snake poison. The order of the amino acids of this protein was determined, as well as the effect of snake poison cardiotoxin on red blood cells; and the preparation of antibodies. Hydrogen 1 nmr spectra was used to determine the chemical structure of the proteins and toxins

  10. Ganglioside biochemistry.

    Science.gov (United States)

    Kolter, Thomas

    2012-01-01

    Gangliosides are sialic acid-containing glycosphingolipids. They occur especially on the cellular surfaces of neuronal cells, where they form a complex pattern, but are also found in many other cell types. The paper provides a general overview on their structures, occurrence, and metabolism. Key functional, biochemical, and pathobiochemical aspects are summarized.

  11. Clinical biochemistry

    Science.gov (United States)

    Alexander, W. C.; Leach, C. S.; Fischer, C. L.

    1975-01-01

    The objectives of the biochemical studies conducted for the Apollo program were (1) to provide routine laboratory data for assessment of preflight crew physical status and for postflight comparisons; (2) to detect clinical or pathological abnormalities which might have required remedial action preflight; (3) to discover as early as possible any infectious disease process during the postflight quarantine periods following certain missions; and (4) to obtain fundamental medical knowledge relative to man's adjustment to and return from the space flight environment. The accumulated data presented suggest that these requirements were met by the program described. All changes ascribed to the space flight environment were subtle, whereas clinically significant changes were consistent with infrequent illnesses unrelated to the space flight exposure.

  12. Actualization and perspectives of Bachelor degree in Biochemistry from Universidade Federal de Viçosa(UFV - (Symposium SBBq Brazil

    Directory of Open Access Journals (Sweden)

    J. L. R. Fietto

    2013-05-01

    Full Text Available The Bachelor Degree in Biochemistry of the UFV was  created in 2001 by the Biochemistry and Molecular Biology Department as a  groundbreaking initiative at Brazil. The program was an attempt to assume both academic and biotechnology sectors, preparing capable professionals for the development of new products and biochemical process. Our initial challenge came with the ingress of the first classes bringing doubts related to their formation and action profiles, sometimes confused with clinical analysts or pharmacists. Lecture series with professionals was used to demonstrate the present scenario with a growing market share, instigating discussions about the pedagogic project. The secondchallenge was the student’s pressure to recognition of under graduation programby the Brazilian Education Ministry (MEC and the biochemical professional recognition by one Regional Council. The bachelor degree was recognized by the MEC in 2004 and the Regional Council of Chemistry became our major partner. The  success of the initiative of the UFV has been giving good results such as the participation in the formation process of the Bachelor Degree in Biochemistry of the Federal University of São João Del Rei (UFSJ and stimulated the creation of another biochemistry course at State University of Maringá (UEM. The success of our students in Phd programs spread in Brazil evidences the quality of Biochemistry bachelors from UFV. Now the egresses have been recognized by biochemistry and biotechnology industry. However we still face problems with impaired recognition in many federal concourses that do not recognize the Biochemist as a chemistry and biotechnology professional. With high expectative, we wait that the biochemistry bachelordegree spreads widely in the country making possible the opening of new opportunities in all ways.

  13. EDUCACIONAL GAME OF LEARNING AS DIDATIC SUPPORT IN INTRODUCTION TO BIOCHEMISTRY DISCIPLINE

    Directory of Open Access Journals (Sweden)

    M. S. Vasconcelos

    2012-05-01

    Full Text Available The cellular respiration process is a crucial subject in biochemistry learning. The use of ludic tools appears to be a good strategy in education intensifying the teach and learning process. The aim of this work was to create and introduce a game as educational tool helping the students to construct the knowledge.  This work was accomplished in UFC involving three groups of 5 students of Introduction to Biochemistry discipline from Food Engineering course.  It was developed a board game  entitled:  The dynamics OXI-REDOXI in Respiratory Chain. The game consisted in a board with the scheme of the respiratory chain, chips to complete the gaps and 12 question cards. The students had previous classes about the subject and a survey right before  playing the game. The monitor explained the rules and the wrong answers of the students to question cards. During the game it was observed mistakes in the answers of the students to  question cards  and either  regarding placing the chips representing the reactions of the respiratory chain. The monitor stimulated the discussion among them and elucidated the doubts. The students demonstrated motivation and interest during the game.  The majority of the students found it easy to play and confirmed that it facilitate the learning process.  The application of the same survey after the game showed that they understood the  respiratory chain and the grades were at least 50% higher after the game.  This game reveals itself a dynamic and constructive tool for the learning  process in biochemistry.

  14. Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course.

    Science.gov (United States)

    Jaswal, Sheila S; O'Hara, Patricia B; Williamson, Patrick L; Springer, Amy L

    2013-01-01

    Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of structural representation tools into both laboratory and homework activities. First, early in the course we introduce the use of readily available open-source software for visualizing protein structure, coincident with modules on amino acid and peptide bond properties. Second, we use these same software tools in lectures and incorporate images and other structure representations in homework tasks. Third, we require a capstone project in which teams of students examine a protein-nucleic acid complex and then use the software tools to illustrate for their classmates the salient features of the structure, relating how the structure helps explain biological function. To ensure engagement with a range of software and database features, we generated a detailed template file that can be used to explore any structure, and that guides students through specific applications of many of the software tools. In presentations, students demonstrate that they are successfully interpreting structural information, and using representations to illustrate particular points relevant to function. Thus, over the semester students integrate information about structural features of biological macromolecules into the larger discussion of the chemical basis of function. Together these assignments provide an accessible introduction to structural representation tools, allowing students to add these methods to their biochemical toolboxes early in their scientific development. © 2013 by The International Union of Biochemistry and Molecular Biology.

  15. A proposal of collaborative education for biochemistry and cell biology teaching

    Directory of Open Access Journals (Sweden)

    A. A. Souza-Júnior

    2015-08-01

    Full Text Available INTRODUCTION: Currently students grow up in a world of digital tools that allow you to connect instantly with the world. At the same time, teachers face several challenges to increase student interest and learning efficiency. One such challenge is the pedagogical commitment of the density of biochemistry and cell biology contents, producing a conflict scenario, between meeting content and maintain the class quality. OBJECTIVES: From this perspective, this study aimed to evaluate the learning biochemistry and cell biology contents in high school classes of IFRN, using collaborative and digital tools in the Moodle. MATERIAL AND METHODS: The contents were offered using various tools such as video lectures, forums, questionnaires, portfolios, glossaries and electronic books. Then these tools were evaluated using an electronic form.  In addition to the tools, we evaluated the platform interaction, the performance of activities and the content gamification. RESULTS: The quantitative results revealed directly proportional relationship of the interaction of Moodle with the performance of activities. The content gamification was also assessed positively, with 61% of students considered good, very good or excellent. The best evaluated tools were video lectures, with 31% preference, and questionnaires, with 24%; followed by electronic book, with 10%, and portfolio, with 5.5%. The other tools totaled 30% of the preference. Qualitative results revealed an educational gain of content, because the student lived the experience of teaching and learning collaboratively. In addition, these tools decreased conflicts between content and schedule. CONCLUSION: Thus, the use of information and communication technology (ICT in a collaborative learning provides relevant results, bringing the reality of the world connected to the classroom. In addition, it assists in defining the content and creative development of a strategy for the construction of the concepts applied

  16. Clinical roles in clinical biochemistry: a national survey of practice in the UK.

    Science.gov (United States)

    Choudhury, Sirazum M; Williams, Emma L; Barnes, Sophie C; Alaghband-Zadeh, Jamshid; Tan, Tricia M; Cegla, Jaimini

    2017-05-01

    Background Using an online survey, we collected data to present a picture of how clinical authorization is performed in the UK. Methods A 21-question survey was uploaded to www.surveymonkey.com , and responses were invited via the mail base of the Association for Clinical Biochemistry and Laboratory Medicine. The questionnaire examined the intensity and function of the duty biochemist role and how different types of authorization are used to handle and release results. Results Of 70 responses received, 60 were suitable for analysis. Responses were received from every region of the UK. A typical duty biochemist shift started on average at 8:50, and finished at 17:25. The mean duration was 8 h 58 min. Clinical scientists are the most abundantly represented group on duty biochemist rotas. Higher banded clinical scientists and chemical pathologists covered out-of-hours shifts. Results were handled differently depending on the level of abnormality and the requesting area. Normal results tended to be released either directly from the analyser or after technical then autoauthorization (90%). A greater preference for clinical authorization was seen for abnormal and critical results originating from outpatients (49% and 69%, respectively) or general practice (51% and 71%) than for inpatients (33% and 53%) or A&E (25% and 37%). Conclusions The handling and authorization of biochemistry results varies greatly between laboratories. The role is clearly heterogeneous in the UK. Guidance from the Association for Clinical Biochemistry and Royal College of Pathologists may help to clarify the essential roles of the duty biochemist.

  17. The Use of Information and CommunicationTechnologies in Biochemistry Teaching

    Directory of Open Access Journals (Sweden)

    C. Munford

    2011-04-01

    Full Text Available The gap between traditional tools for teaching and the modern multimedia languages leads us to search for new methodologies of teaching. Using the Moodlesoftware as a Virtual Learning Environment (VLE, we give the students the opportunity to exchange experiences and research results, participate on debates and see animations. This work  was meant to createa VLE and investigate its impact  on the Biochemistry teaching-learning process. Besides observing students’ perception and attitude towards the VLE with questionnaires and Moodle’s statistical data, quantitative and qualitative studies were developed to understand the contribution of animations available in the VLE for the understanding of Biochemistry topics. The results showed that undergraduate students improved their academic results. Students mentioned that the biggest contribution of the VLE and animations was to make the study content more interesting and dynamic, motivating them tostudy harder. Moreover, students using only animations to study can achieve levels of knowledge similar to the ones obtained in traditional classes. Interestingly, our analysis also showed that watching animations and then attending to a traditional class makes students reach a level of knowledge that is impossible to reach only in classroom. This work demonstrates that the use of Information andCommunication Technologies (ICTs can be positive in the pedagogical processesinvolved in Biochemistry teaching, and they should be better spread amongst teaching institutions.

  18. Bacterial polyhydroxyalkanoates: Still fabulous?

    Science.gov (United States)

    Możejko-Ciesielska, Justyna; Kiewisz, Robert

    2016-11-01

    Bacterial polyhydroxyalkanoates (PHA) are polyesters accumulated as carbon and energy storage materials under limited growth conditions in the presence of excess carbon sources. They have been developed as biomaterials with unique properties for the past many years being considered as a potential substitute for conventional non-degradable plastics. Due to the increasing concern towards global climate change, depleting petroleum resource and problems with an utilization of a growing number of synthetic plastics, PHAs have gained much more attention from industry and research. These environmentally friendly microbial polymers have great potential in biomedical, agricultural, and industrial applications. However, their production on a large scale is still limited. This paper describes the backgrounds of PHAs and discussed the current state of knowledge on the polyhydroxyalkanoates. Ability of bacteria to convert different carbon sources to PHAs, the opportunities and challenges of their introduction to global market as valuable renewable products have been also discussed. Copyright © 2016 Elsevier GmbH. All rights reserved.

  19. Energetics of bacterial adhesion

    International Nuclear Information System (INIS)

    Loosdrecht, M.C.M. van; Zehnder, A.J.B.

    1990-01-01

    For the description of bacterial adhesion phenomena two different physico-chemical approaches are available. The first one, based on a surface Gibbs energy balance, assumes intimate contact between the interacting surfaces. The second approach, based on colloid chemical theories (DLVO theory), allows for two types of adhesion: 1) secondary minimum adhesion, which is often weak and reversible, and 2) irreversible primary minimum adhesion. In the secondary minimum adhesion a thin water film remains present between the interacting surface. The merits of both approaches are discussed in this paper. In addition, the methods available to measure the physico-chemical surface characteristics of bacteria and the influence of adsorbing (in)organic compounds, extracellular polymers and cell surface appendages on adhesion are summarized. (author) 2 figs., 1 tab., 50 refs

  20. Biosensors of bacterial cells.

    Science.gov (United States)

    Burlage, Robert S; Tillmann, Joshua

    2017-07-01

    Biosensors are devices which utilize both an electrical component (transducer) and a biological component to study an environment. They are typically used to examine biological structures, organisms and processes. The field of biosensors has now become so large and varied that the technology can often seem impenetrable. Yet the principles which underlie the technology are uncomplicated, even if the details of the mechanisms are elusive. In this review we confine our analysis to relatively current advancements in biosensors for the detection of whole bacterial cells. This includes biosensors which rely on an added labeled component and biosensors which do not have a labeled component and instead detect the binding event or bound structure on the transducer. Methods to concentrate the bacteria prior to biosensor analysis are also described. The variety of biosensor types and their actual and potential uses are described. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Bacterial mitotic machineries

    DEFF Research Database (Denmark)

    Gerdes, Kenn; Møller-Jensen, Jakob; Ebersbach, Gitte

    2004-01-01

    Here, we review recent progress that yields fundamental new insight into the molecular mechanisms behind plasmid and chromosome segregation in prokaryotic cells. In particular, we describe how prokaryotic actin homologs form mitotic machineries that segregate DNA before cell division. Thus, the P......M protein of plasmid R1 forms F actin-like filaments that separate and move plasmid DNA from mid-cell to the cell poles. Evidence from three different laboratories indicate that the morphogenetic MreB protein may be involved in segregation of the bacterial chromosome.......Here, we review recent progress that yields fundamental new insight into the molecular mechanisms behind plasmid and chromosome segregation in prokaryotic cells. In particular, we describe how prokaryotic actin homologs form mitotic machineries that segregate DNA before cell division. Thus, the Par...

  2. Exploring bacterial lignin degradation.

    Science.gov (United States)

    Brown, Margaret E; Chang, Michelle C Y

    2014-04-01

    Plant biomass represents a renewable carbon feedstock that could potentially be used to replace a significant level of petroleum-derived chemicals. One major challenge in its utilization is that the majority of this carbon is trapped in the recalcitrant structural polymers of the plant cell wall. Deconstruction of lignin is a key step in the processing of biomass to useful monomers but remains challenging. Microbial systems can provide molecular information on lignin depolymerization as they have evolved to break lignin down using metalloenzyme-dependent radical pathways. Both fungi and bacteria have been observed to metabolize lignin; however, their differential reactivity with this substrate indicates that they may utilize different chemical strategies for its breakdown. This review will discuss recent advances in studying bacterial lignin degradation as an approach to exploring greater diversity in the environment. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Studying bacterial multispecies biofilms

    DEFF Research Database (Denmark)

    Røder, Henriette Lyng; Sørensen, Søren Johannes; Burmølle, Mette

    2016-01-01

    The high prevalence and significance of multispecies biofilms have now been demonstrated in various bacterial habitats with medical, industrial, and ecological relevance. It is highly evident that several species of bacteria coexist and interact in biofilms, which highlights the need for evaluating...... the approaches used to study these complex communities. This review focuses on the establishment of multispecies biofilms in vitro, interspecies interactions in microhabitats, and how to select communities for evaluation. Studies have used different experimental approaches; here we evaluate the benefits...... and drawbacks of varying the degree of complexity. This review aims to facilitate multispecies biofilm research in order to expand the current limited knowledge on interspecies interactions. Recent technological advances have enabled total diversity analysis of highly complex and diverse microbial communities...

  4. Anaerobes in bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Aggarwal A

    2003-01-01

    Full Text Available Four hundred high vaginal swabs were taken from patients attending gynaecology and obstetrics department of Govt. medical college, Amritsar. The patients were divided into four groups i.e. women in pregnancy (Group I, in labour/post partum (Group II, with abnormal vaginal discharge or bacterial vaginosis (Group III and asymptomatic women as control (Group IV. Anaerobic culture of vaginal swabs revealed that out of 400 cases, 212(53% were culture positive. Maximum isolation of anaerobes was in group III (84% followed by group II (56%, group I (36% and control group (15%. Gram positive anaerobes (69.2% out numbered gram negatives (30.8%. Among various isolates Peptostreptococcus spp. and Bacteroides spp. were predominant.

  5. Identification of Forensic Samples via Mitochondrial DNA in the Undergraduate Biochemistry Laboratory

    Science.gov (United States)

    Millard, Julie T.; Pilon, André M.

    2003-04-01

    A recent forensic approach for identification of unknown biological samples is mitochondrial DNA (mtDNA) sequencing. We describe a laboratory exercise suitable for an undergraduate biochemistry course in which the polymerase chain reaction is used to amplify a 440 base pair hypervariable region of human mtDNA from a variety of "crime scene" samples (e.g., teeth, hair, nails, cigarettes, envelope flaps, toothbrushes, and chewing gum). Amplification is verified via agarose gel electrophoresis and then samples are subjected to cycle sequencing. Sequence alignments are made via the program CLUSTAL W, allowing students to compare samples and solve the "crime."

  6. Serum biochemistry and morbidity among runners presenting for medical care after an Australian mountain ultramarathon.

    Science.gov (United States)

    Reid, Stephen A; King, M Jonathan

    2007-07-01

    To determine if exercise-associated hyponatremia (EAH) was a cause of morbidity among runners requiring medical care at an Australian mountain ultramarathon. Case series. Six Foot Track mountain ultramarathon, New South Wales, Australia, March 2006. Runners presenting to the medical facility. Serum biochemistry. No cases of exercise-associated hyponatremia were identified among 9 athletes (from 775 starters) who were treated with intravenous fluid therapy. Unwell runners had a mean serum (Na) of 143 mmol/L (range 138-147 mmol/L). All runners tested had elevated serum urea and creatinine concentrations. In this setting, EAH was not a significant cause of morbidity.

  7. Secrets from the microbiome: molecular biology meets microbiology meets histopathology...meets clinical biochemistry.

    Science.gov (United States)

    Young, Caroline; Quirke, Philip

    2015-11-01

    The microbiome is the collective term used to describe the bacteria, viruses, fungi and archaea that reside on and in the human body. The majority of these organisms are found within the large bowel. Mounting evidence suggests that changes in the microbiome may be associated with the development of colorectal cancer, a disease which affects 1.3 million people a year worldwide. Using colorectal cancer as an example, this article presents the inter-specialty collaborative approach to microbiome research and discusses the key role that clinical biochemistry is likely to play. © The Author(s) 2015.

  8. Training in radioprotection in the School of Pharmacy and Biochemistry, University of Buenos Aires

    International Nuclear Information System (INIS)

    Rivera, Elena; Cremaschi, Graciela; Martin, Graciela; Zubillaga, Marcela; Davio, Carlos; Genaro, Ana; Cricco, Graciela; Mohamad, Nora; Bianchin, Ana; Goldman, Cinthia; Salgueiro, Jimena; Klecha, Alicia; Nunez, Mariel; Medina, Vanina; Cocca, Claudia; Leonardi, Natalia; Collia, Nicolas; Gutierrez, Alicia; Massari, Noelia; Bomben, Ana; Bergoc, Rosa

    2008-01-01

    The radioisotopes techniques have notably contributed to the advancement of knowledge in medicine and biomedicine during the last 60 years. The School of Pharmacy and Biochemistry of the University of Buenos Aires, Argentina, offers different Courses on methodology of radioisotopes in which the specialized knowledge on radioprotection is adapted to the following different groups: 1) A course for biochemistry students; 2) A course for physicians; 3) A course for graduates in biochemistry, biology, chemistry or other disciplines related to the health; 4) An up-dating course for licensed professionals; 5) A course for nuclear medicine technicians; and finally: 6) A course for Pharmacy students. The main objective of radiological protection teaching is specific and fitted to each level: the course (1) has been given (optional or mandatory) since 1960 for more than 7500 students. Part of the learning process in radioprotection is only informative, because in this case the students are not allowed to ask the Argentinean Nuclear Regulatory Authority authorization for radioactive material handling. Course (2) has been taken by more than 800 physicians since 1962. Here, the students receive a very intensive training in radioprotection which includes: justification, optimization and dose limits; dosimetric magnitudes and units; internal and external dosimetry of 99m Tc, 201 Tl, 60 Co and other isotopes used in medicine; safety in occupational exposure; national and international legislation. Since 1962, more than 1000 graduates have attended course (3). In this case the training in radioprotection is as intensive as in course (2) with special focusing in 125 I, 3 H, 14 C, 32 P and other isotopes used in biomedicine. Course (4) has been given from 1992 and the objective is to up-date knowledge and the intensity of training depends on the requirements of each professional. Course (5) has been given since 1997 and it is mainly directed to the operational aspects of

  9. Bacterial meningitis in immunocompromised patients

    NARCIS (Netherlands)

    van Veen, K.E.B.

    2018-01-01

    Bacterial meningitis is an acute infection of the meninges, in The Netherlands most commonly caused by Streptococcus pneumoniae and Neisseria meningitides. Risk factors for acquiring bacterial meningitis include a decreased function of the immune system. The aim of this thesis was to study

  10. Bacteriële meningitis

    NARCIS (Netherlands)

    Brouwer, M. C.; van de Beek, D.

    2012-01-01

    Bacterial meningitis is a severe disease which affects 35.000 Europeans each year and has a mortality rate of about 20%. During the past 25 years the epidemiology of bacterial meningitis has changed significantly due to the implementation of vaccination against Haemophilus influenzae, Neisseria

  11. Bacterial Protein-Tyrosine Kinases

    DEFF Research Database (Denmark)

    Shi, Lei; Kobir, Ahasanul; Jers, Carsten

    2010-01-01

    in exopolysaccharide production, virulence, DNA metabolism, stress response and other key functions of the bacterial cell. BY-kinases act through autophosphorylation (mainly in exopolysaccharide production) and phosphorylation of other proteins, which have in most cases been shown to be activated by tyrosine......Bacteria and Eukarya share essentially the same family of protein-serine/threonine kinases, also known as the Hanks-type kinases. However, when it comes to protein-tyrosine phosphorylation, bacteria seem to have gone their own way. Bacterial protein-tyrosine kinases (BY-kinases) are bacterial...... and highlighted their importance in bacterial physiology. Having no orthologues in Eukarya, BY-kinases are receiving a growing attention from the biomedical field, since they represent a particularly promising target for anti-bacterial drug design....

  12. Molecular approaches for bacterial azoreductases

    Directory of Open Access Journals (Sweden)

    Montira Leelakriangsak

    2013-12-01

    Full Text Available Azo dyes are the dominant types of synthetic dyes, widely used in textiles, foods, leather, printing, tattooing, cosmetics, and pharmaceutical industries. Many microorganisms are able to decolorize azo dyes, and there is increasing interest in biological waste treatment methods. Bacterial azoreductases can cleave azo linkages (-N=N- in azo dyes, forming aromatic amines. This review mainly focuses on employing molecular approaches, including gene manipulation and recombinant strains, to study bacterial azoreductases. The construction of the recombinant protein by cloning and the overexpression of azoreductase is described. The mechanisms and function of bacterial azoreductases can be studied by other molecular techniques discussed in this review, such as RT-PCR, southern blot analysis, western blot analysis, zymography, and muta-genesis in order to understand bacterial azoreductase properties, function and application. In addition, understanding the regulation of azoreductase gene expression will lead to the systematic use of gene manipulation in bacterial strains for new strategies in future waste remediation technologies.

  13. Symposium 20 - PABMB: Teaching biochemistry in a connected world: Hands-on inquiry-based biochemistry courses for improving scientific literacy of school teachers and students

    Directory of Open Access Journals (Sweden)

    Andrea T. da Poian

    2015-08-01

    Full Text Available Wednesday – August 26th, 2015 - 3:30 to 5:30 pm – Room: Iguaçu II – 5th floorSymposium 20 - PABMB: Teaching biochemistry in a connected world Chair: Miguel Castanho, Universidade de Lisboa, PortugalAbstract:In the last decades, Brazil has reached a prominent position in the world rank of scientific production. Despite this progress, the establishment of a scientific culture in Brazilian society is still challenging. Our group has been offering hands-on inquiry-based courses to primary and secondary students, which aim to introduce them to the scientific method and improve their interest in science. More recently, we started new initiatives focused on the improvement of the scientific literacy of school science teachers. Here we describe two intensive short-term courses designed in different formats. One consists in a discipline offered to a Master Program to school science teachers, in which the main objective was to work with core disciplinary concepts through an active teachers engagement in “doing science”. The discipline, named “Energy transformation in the living organisms”, intends to deal with the main Biochemistry subjects that take part of the high-school science curriculum, namely, fermentation, photosynthesis and cellular respiration processes. The other initiative was developed in Urucureá, a small community with about 600 residents, located on the banks of the River Arapiuns, in Amazonia region. We trained the local school teachers to act as tutors in the course offered to 40 students of the community, ages 10 to 17. The theme we chose to address was the properties and effects of snakes´ poisons, since poisoning events are a problem with which the local community frequently deal with. Another important point was that we adapted a number of experiments to make them feasible with very limited laboratory resources. Our results show that the activities that we have developed offer real opportunity of scientific training

  14. An interactive computer lab of the galvanic cell for students in biochemistry.

    Science.gov (United States)

    Ahlstrand, Emma; Buetti-Dinh, Antoine; Friedman, Ran

    2018-01-01

    We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δ r G, Δ r H, and Δ r S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material. Cloud computing platforms such as CoCalc facilitate the distribution of computer codes and allow students to access and apply interactive course tools beyond the course's scope. Despite some limitations imposed by cloud computing, the students appreciated the approach and the enhanced opportunities to discuss study questions with their classmates and instructor as facilitated by the interactive tools. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):58-65, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

  15. Cooperative learning combined with short periods of lecturing: A good alternative in teaching biochemistry.

    Science.gov (United States)

    Fernández-Santander, Ana

    2008-01-01

    The informal activities of cooperative learning and short periods of lecturing has been combined and used in the university teaching of biochemistry as part of the first year course of Optics and Optometry in the academic years 2004-2005 and 2005-2006. The lessons were previously elaborated by the teacher and included all that is necessary to understand the topic (text, figures, graphics, diagrams, pictures, etc.). Additionally, a questionnaire was prepared for every chapter. All lessons contained three parts: objectives, approach and development, and the assessment of the topic. Team work, responsibility, and communication skills were some of the abilities developed with this new methodology. Students worked collaboratively in small groups of two or three following the teacher's instructions with short periods of lecturing that clarified misunderstood concepts. Homework was minimized. On comparing this combined methodology with the traditional one (only lecture), students were found to exhibit a higher satisfaction with the new method. They were more involved in the learning process and had a better attitude toward the subject. The use of this new methodology showed a significant increase in the mean score of the students' academic results. The rate of students who failed the subject was significantly inferior in comparison with those who failed in the previous years when only lecturing was applied. This combined methodology helped the teacher to observe the apprenticeship process of students better and to act as a facilitator in the process of building students' knowledge. Copyright © 2008 International Union of Biochemistry and Molecular Biology, Inc.

  16. An integrated biochemistry and genetics outreach program designed for elementary school students.

    Science.gov (United States)

    Ross, Eric D; Lee, Sarah K; Radebaugh, Catherine A; Stargell, Laurie A

    2012-02-01

    Exposure to genetic and biochemical experiments typically occurs late in one's academic career. By the time students have the opportunity to select specialized courses in these areas, many have already developed negative attitudes toward the sciences. Given little or no direct experience with the fields of genetics and biochemistry, it is likely that many young people rule these out as potential areas of study or career path. To address this problem, we developed a 7-week (~1 hr/week) hands-on course to introduce fifth grade students to basic concepts in genetics and biochemistry. These young students performed a series of investigations (ranging from examining phenotypic variation, in vitro enzymatic assays, and yeast genetic experiments) to explore scientific reasoning through direct experimentation. Despite the challenging material, the vast majority of students successfully completed each experiment, and most students reported that the experience increased their interest in science. Additionally, the experiments within the 7-week program are easily performed by instructors with basic skills in biological sciences. As such, this program can be implemented by others motivated to achieve a broader impact by increasing the accessibility of their university and communicating to a young audience a positive impression of the sciences and the potential for science as a career.

  17. In search of mitochondrial mechanisms: interfield excursions between cell biology and biochemistry.

    Science.gov (United States)

    Bechtel, William; Abrahamsen, Adele

    2007-01-01

    Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to understanding the role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration.

  18. Are biochemistry interpretative comments helpful? Results of a general practitioner and nurse practitioner survey.

    Science.gov (United States)

    Barlow, Ian M

    2008-01-01

    Adding or incorporating clinical interpretative comments on biochemistry results is widespread in UK laboratories; although this consumes considerable human resource, there is still little evidence to suggest that it is either effective or appreciated by our clinical colleagues. I therefore decided to survey our local general practitioners (GPs) and nurse practitioners to analyse whether they found biochemistry comments on reports helpful. A simple questionnaire was designed and sent to 159 GPs and 81 nurse practitioners asking them whether they found this activity useful for the limited range of test groups that we routinely comment on and also whether they would like to see commenting on more groups of tests. Overall, 49.6% of questionnaires were returned. Of these, there was overwhelming support for commenting on reports and 77% would like to see comments on a greater range of tests. Although adding clinical interpretative comments is very time-consuming for senior laboratory staff, there is overwhelming support of this activity among our GPs and nurse practitioner users; therefore, our local policy of routinely adding clinical comments will remain for the foreseeable future.

  19. [Blood volume for biochemistry determinations--laboratory needs and everyday practice].

    Science.gov (United States)

    Sztefko, Krystyna; Mamica, Katarzyna; Bugajska, Jolanta; Maziarz, Barbara; Tomasik, Przemysław

    2014-01-01

    Blood loss due to diagnostic phlebotomy jest a very serious problem, especially for newborn, infants and critically ill patients on intensive care units. Although single blood loss can be easily tolerated in adults, in small babies and in patients who are frequently monitored based on laboratory tests iatrogenic anaemia can occur. To evaluate the blood volume drawn for routine biochemistry tests in relation to patient age and the number of parameters requested. Blood volume drawn for routine biochemistry measurements from patients hospitalized in University Children's Hospital (N = 2980, children age from one day to 18 years) and in University Hospital (N = 859, adults, aged > 1.8 years) in Cracow has been analyzed. Blood volume was calculated based on regular tube diameter and blood heights in the tube. In case of microvettes the blood volume was 0.2 ml. Statistical analysis has been performed by using PRISM 5.0. The statistical significance was set at p nurses and doctors should include the information about current laboratory automation and methods miniaturization; 2) The amount of blood volume needed by laboratory for the requested number of tests should always be taken into account when diagnostic phlebotomy is necessary.

  20. Anatomy and history of an external quality assessment program for interpretative comments in clinical biochemistry.

    Science.gov (United States)

    Vasikaran, Samuel D

    2015-05-01

    The provision of clinical interpretation of results, either verbally or in the printed report, may be considered an integral part of clinical biochemistry diagnostic service. Proficiency testing or external quality assessment (EQA) of such activity may be useful in education, training, continuing professional development and ensuring the quality of such service. Details of the Patient Report Comments Program (RPCProgram) developed by the Royal College of Pathologists of Australasia (RCPA) Chemical Pathology Quality Assurance Programs Pty Ltd (QAP) is described in this review. The program is aimed at pathologists, clinical scientists and trainees. Registered participants are provided a report with case details and a set of clinical biochemistry results at monthly intervals and submit an interpretative comment for the report. Comments received are broken up into components that are translated into common key phrases. An expert panel evaluates the key phrases, classifies them according to appropriateness and drafts a suggested comment, a case summary and a rationale, which are included in a summary report returned to participants. There is considerable diversity in the quality of interpretative comments received from participants of the PRCProgram. The primary purpose of EQA of interpretative commenting is educational self-assessment, and they are recognized as a continuing professional development activity. Whilst there is some evidence for the utility of interpretative comments in improving patient outcomes, evidence for the utility of EQA in improving quality of comments is awaited. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.