Escherichia coli strains that allow antibiotic-free plasmid selection and maintenance by repressor titration

We report the construction of two novel Escherichia coli strains (DH1lacdapD and DH1lacP2dapD) that facilitate the antibiotic-free selection and stable maintenance of recombinant plasmids in complex media. They contain the essential chromosomal gene, dapD, under the control of the lac operator/promoter. Unless supplemented with IPTG (which induces expression of dapD) or DAP, these cells lyse. However, when the strains are transformed with a multicopy plasmid containing the lac operator, the operator competitively titrates the LacI repressor and allows expression of dapD from the lac promoter. Thus transformants can be isolated and propagated simply by their ability to grow on any medium by repressor titration selection. No antibiotic resistance genes or other protein expressing sequences are required on the plasmid, and antibiotics are not necessary for plasmid selection, making these strains a valuable tool for therapeutic DNA and recombinant protein production. We describe the construction of these strains and demonstrate plasmid selection and maintenance by repressor titration, using the new pORT plasmid vectors designed to facilitate recombinant DNA exploitation.

Titration of chaos with added noise

Deterministic chaos has been implicated in numerous natural and man-made complex phenomena ranging from quantum to astronomical scales and in disciplines as diverse as meteorology, physiology, ecology, and economics. However, the lack of a definitive test of chaos vs. random noise in experimental time series has led to considerable controversy in many fields. Here we propose a numerical titration procedure as a simple “litmus test” for highly sensitive, specific, and robust detection of chaos in short noisy data without the need for intensive surrogate data testing. We show that the controlled addition of white or colored noise to a signal with a preexisting noise floor results in a titration index that: (i) faithfully tracks the onset of deterministic chaos in all standard bifurcation routes to chaos; and (ii) gives a relative measure of chaos intensity. Such reliable detection and quantification of chaos under severe conditions of relatively low signal-to-noise ratio is of great interest, as it may open potential practical ways of identifying, forecasting, and controlling complex behaviors in a wide variety of physical, biomedical, and socioeconomic systems.

The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme.

Beta-Lactamases are widespread in the bacterial world, where they are responsible for resistance to penicillins, cephalosporins, and related compounds, currently the most widely used antibacterial agents. Detailed structural and mechanistic understanding of these enzymes can be expected to guide the design of new antibacterial compounds resistant to their action. A number of high-resolution structures are available for class A beta-lactamases, whose catalytic mechanism involves the acylation of a serine residue at the active site. The identity of the general base which participates in the activation of this serine residue during catalysis has been the subject of controversy, both a lysine residue and a glutamic acid residue having been proposed as candidates for this role. We have used the pH dependence of chemical modification of epsilon-amino groups by 2,4,6,-trinitrobenzenesulfonate and the pH dependence of the epsilon-methylene 1H and 13C chemical shifts (in enzyme selectively labeled with [epsilon-13C]lysine) to estimate the pKa of the relevant lysine residue, lysine-73, of TEM-1 beta-lactamase. Both methods show that the pKa of this residue is > 10, making it very unlikely that this residue could act as a proton acceptor in catalysis. An alternative mechanism in which this role is performed by glutamate-166 through an intervening water molecule is described.

Formación tardía de etringita en fibrocemento.

La temperatura de curado, utilizada por la industria de fibrocemento como catalizador en la hidratación del cemento para lograr alta resistencia inicial en sus productos, genera la hipótesis de expansión causada por formación tardía de etringita. Para el planteamiento de dicha hipótesis, el siguiente estudio contempló dos grupos de muestras con el objetivo de estudiar aisladamente su comportamiento químico y físico: uno de los grupos conformado por pasta cementicia con 35% de sustitución de calcario, y el otro conformado por fibrocemento con incorporación de PVA y celulosa. Por calorimetría isotérmica se observó la cinética de reacción de dos pastas, una de ellas curada a 23 ºC y la otra a 85 ºC donde esta última experimentó un efecto catalizador en sus reacciones. Ensayos de DRX y DTG/TG mostraron la presencia de etringita a 23 °C durante todas las edades de hidratación exhibiendo una tendencia de aumento en la intensidad de los picos y en la cantidad, respectivamente, en función del tiempo; sin embargo, a 85 ºC la presencia de esta fase fue inconstante durante las primeras edades de hidratación, a partir de mes de hidratación mostró aumento en cada una de las siguientes medidas realizadas mensualmente; a 85 °C hubo una menor formación de portlandita en comparación con los resultados obtenidos a 23 °C. Utilizando el método Rietveld y análisis químico fueron determinadas las cantidades y las composiciones químicas, respectivamente, de las fases del cemento anhidro y del calcario para alimentar el programa GEMS y simular la hidratación de la pasta estudiada en laboratorio para un tiempo infinito bajo la influencia de la temperatura. Simulaciones de la hidratación de la pasta se aproximaron a los resultados reportados por la revisión bibliográfica permitiendo predecir la presencia de fases en función de la estabilidad termodinámica. Resultados de porosimetría por inyección de mercurio mostraron una mayor concentración de poros, asociados a defectos, en muestras curadas a 85°C con respecto a las de 23 °C. Finalmente, medidas de variación longitudinal para muestras de fibrocemento elaboradas en laboratorio y en fábrica presentaron dispersión en los resultados de expansión para cada uno de los escenarios sin poder correlacionar todos los datos con el aumento de masa exhibido por cada una de las muestras; no obstante, se resalta el riesgo de deterioro del fibrocemento por el aumento de defectos causado por la temperatura así como la creación de todas las condiciones necesarias que favorecen la formación tardía de etringita a partir del proceso de fabricación empleado para este producto.

Chemical Reactors. Problem 3: Isothermal plug flow reactor with multiple reactions (2011-2012 Course)

Wording of problem 3: Isothermal plug flow reactor with multiple reactions.

Isothermal (liquid + liquid) equilibrium data at T = 313.15 K and isobaric (vapor + liquid + liquid) equilibrium data at 101.3 kPa for the ternary system (water + 1-butanol + p-xylene)

The (vapor + liquid), (liquid + liquid) and (vapor + liquid + liquid) equilibria of the ternary system (water + 1-butanol + p-xylene) have been determined. (Water + 1-butanol + p-xylene) is a type 2 heterogeneous ternary system with partially miscible (water + 1-butanol) and (water + p-xylene) pairs. By contrast, (1-butanol + p-xylene) is totally miscible under atmospheric conditions. This paper examines the (vapor + liquid) equilibrium in both heterogeneous and homogeneous regions at 101.3 kPa of pressure. (Liquid + liquid) equilibrium data at T = 313.15 K have also been determined, and for comparison, the obtained experimental data have been calculated by means of several thermodynamic models: UNIQUAC, UNIFAC and NRTL. Some discrepancies were found between the (vapor + liquid + liquid) correlations; however, the models reproduced the (liquid + liquid) equilibrium data well. The obtained data reveal a ternary heterogeneous azeotrope with mole fraction composition: 0.686 water, 0.146 1-butanol and 0.168 p-xylene.

La tagatose-1,6-bisphosphate aldolase et la fructose-1,6-bisphosphate aldolase de classe I : mécanisme et stéréospécificité

La tagatose-1,6-biphosphate aldolase de Streptococcus pyogenes est une aldolase qui fait preuve d'un remarquable manque de spécificité vis à vis de ses substrats. En effet, elle catalyse le clivage réversible du tagatose-1,6-bisphosphate (TBP), mais également du fructose-1,6-bisphosphate (FBP), du sorbose-1,6-bisphosphate et du psicose-1,6-bisphosphate, quatre stéréoisomères, en dihydroxyacétone phosphate (DHAP) et en glycéraldéhyde-3-phosphate (G3P). Aldolase de classe I, qui donc catalyse sa réaction en formant un intermédiaire covalent obligatoire, ou base de Schiff, avec son susbtrat, la TBP aldolase de S. pyogenes partage 14 % d’identité avec l’enzyme modèle de cette famille, la FBP aldolase de muscle de mammifère. Bien que le mécanime catalytique de la FBP aldolase des mammifères ait été examiné en détails et qu’il soit approprié d’en tirer des renseignements quant à celui de la TBP aldolase, le manque singulier de stéréospécificité de cette dernière tant dans le sens du clivage que celui de la condensation n’est toujours pas éclairci. Afin de mettre à jour les caractéristiques du mécanisme enzymatique, une étude structurale de la TBP aldolase de S. pyogenes, un pathogène humain extrêmement versatile, a été entreprise. Elle a permis la résolution des structures de l’enzyme native et mutée, en complexe avec des subtrats et des inhibiteurs compétitifs, à des résolutions comprises entre 1.8 Å et 2.5 Å. Le trempage des cristaux de TBP aldolase native et mutante dans une solution saturante de FBP ou TBP a en outre permis de piéger un authentique intermédiaire covalent lié à la Lys205, la lysine catalytique. La determination des profils pH de la TBP aldolase native et mutée, entreprise afin d'évaluer l’influence du pH sur la réaction de clivage du FBP et TBP et ìdentifier le(s) résidu(s) impliqué(s), en conjonction avec les données structurales apportées par la cristallographie, ont permis d’identifier sans équivoque Glu163 comme résidu responsable du clivage. En effet, le mode de liaison sensiblement différent des ligands utilisés selon la stéréochimie en leur C3 et C4 permet à Glu163, équivalent à Glu187 dans la FBP aldolase de classe I, d’abstraire le proton sur l’hydroxyle du C4 et ainsi d’amorcer le clivage du lien C3-C4. L’étude du mécanimse inverse, celui de la condensation, grâce par exemple à la structure de l’enzyme native en complexe avec ses substrats à trois carbones le DHAP et le G3P, a en outre permis d’identifier un isomérisme du substrat G3P comme possible cause de la synthèse des isomères en C4 par cette enzyme. Ce résultat, ainsi que la decouverte d’un possible isomérisme cis-trans autour du lien C2-C3 de la base de Schiff formée avec le DHAP, identifié précedemment, permet de cerner presque complètement les particularités du mécanisme de cette enzyme et d’expliquer comment elle est capable de synthétiser les quatres stéréoisomères 3(S/R), 4(S/R). De plus, la résolution de ces structures a permis de mettre en évidence trois régions très mobiles de la protéine, ce qui pourrait être relié au rôle postulé de son isozyme chez S. pyogenes dans la régulation de l’expression génétique et de la virulence de la bactérie. Enfin, la résolution de la structure du mutant Lys229→Met de la FBP aldolase de muscle en complexe avec la forme cyclique du FBP, de même que des études cristallographiques sur le mutant équivalent Lys205→Met de la TBP aldolase de S. pyogenes et des expériences de calorimétrie ont permis d’identifier deux résidus particuliers, Ala31 et Asp33 chez la FBP aldolase, comme possible cause de la discrimination de cette enzyme contre les substrats 3(R) et 4(S), et ce par encombrement stérique des substrats cycliques. La cristallographie par rayons X et la cinétique enzymatique ont ainsi permis d'avancer dans l'élucidation du mécanisme et des propriétés structurales de cette enzyme aux caractéristiques particulières.

Calorimetry in medicine,

"References": p. 84-98.

Methods and standards in bomb calorimetry /

"August 29, 1910."

Uber die Volhardsche Methode der quantitativen Pepsin- und Trypsinbestimmung dur Titration /

Thesis (doctoral)--Grossherzogl. Hessische Landes- Universitat Giessen, 1905.

Reducing the time period of steady state does not affect the accuracy of energy expenditure measurements by indirect calorimetry

Achievement of steady state during indirect calorimetry measurements of resting energy expenditure (REE) is necessary to reduce error and ensure accuracy in the measurement. Steady state is often defined as 5 consecutive min (5-min SS) during which oxygen consumption and carbon dioxide production vary by +/-10%. These criteria, however, are stringent and often difficult to satisfy. This study aimed to assess whether reducing the time period for steady state (4-min SS or 3-min SS) produced measurements of REE that were significantly different from 5-min SS. REE was measured with the use of open-circuit indirect calorimetry in 39 subjects, of whom only 21 (54%) met the 5-min SS criteria. In these 21 subjects, median biases in REE between 5-min SS and 4-min SS and between 5-min SS and 3-min SS were 0.1 and 0.01%, respectively. For individuals, 4-min SS measured REE within a clinically acceptable range of +/-2% of 5-min SS, whereas 3-min SS measured REE within a range of -2-3% of 5-min SS. Harris-Benedict prediction equations estimated REE for individuals within +/-20-30% of 5-min SS. Reducing the time period of steady state to 4 min produced measurements of REE for individuals that were within clinically acceptable, predetermined limits. The limits of agreement for 3-min SS fell outside the predefined limits of +/-2%; however, both 4-min SS and 3-min SS criteria greatly increased the proportion of subjects who satisfied steady state within smaller limits than would be achieved if relying on prediction equations.

Gelatinisation of starch in mixtures of sugars. II. Application of differential scanning calorimetry

Differential scanning calorimetry was used to investigate the effect of mixtures of glucose and fructose, and five types of honeys on starch gelatinisation. At a 1:1 starch:water ratio, glucose generally increased the enthalpy (DeltaH(gel)) and temperatures (T-onset, T-peak and T-end) of gelatinisation more than fructose. Upon mixing, DeltaH(gel) of the low-temperature endotherm decreased in comparison to the sole sugars, but was fairly constant (7.7 +/- 0.33 J/g dry starch). DeltaH(gel) of the high-temperature endotherm increased with the fructose content. For both endotherms, the gelatinisation temperatures were unchanged (CV less than or equal to 3%) for the mixtures. With the honeys (moisture, 14.9-18.0%; fructose, 37.2-44.0%; glucose, 28.3-31.9%) added at 1.1-4.4 g per g dry starch, the enthalpy and temperatures of gelatinisation did not vary significantly (CV less than or equal to 6%). Typical thermograms are presented, and the results are interpreted in the light of the various proposed mechanisms for starch gelatinisation in sugar-water systems, total sugar content and possible sugar-sugar interactions. The thermograms were broader in the presence of the sugars and honeys, and a biphasic character was consistently exhibited. The application of an exponential equation to the gelatinisation temperatures of the starch-honey mixtures revealed an opposing influence of fructose and glucose during gelatinisation. The mechanism of starch gelatinisation may be better understood if techniques could be perfected to quantify breakage and formation of hydrogen bonds in the starch granules, and suggested techniques are discussed. (C) 2004 Elsevier Ltd. All rights reserved.

Investigation of the starch gelatinisation phenomena in water-glycerol systems: application of modulated temperature differential scanning calorimetry

The use of modulated temperature differential scanning calorimetry (MTDSC) has provided further insight into the gelatinisation process since it allows the detection of glass transition during gelatinisation process. It was found in this work that the glass transition overlapped with the gelatinisation peak temperature for all maize starch formulations studied. Systematic investigation on maize starch gelatinisation over a range of water-glycerol concentrations with MTDSC revealed that the addition of glycerol increased the gelatinisation onset temperature with an extent that depended on the water content in the system. Furthermore, the addition of glycerol promoted starch gelatinisation at low water content (0.4 g water/g dry starch) and the enthalpy of gelatinisation varied with glycerol concentration (0.73-19.61 J/g dry starch) depending on the water content and starch type. The validities of published gelatinisation models were explored. These models failed to explain the glass transition phenomena observed during the course of gelatinisation and failed to describe the gelatinisation behaviour observed over the water-glycerol concentrations range investigated. A hypothesis for the mechanisms involved during gelatinisation was proposed based on the side chain liquid crystalline polymer model for starch structure and the concept that the order-disorder transition in starch requires that the hydrogen bonds (the major structural element in the granule packing) to be broken before the collapse of order (helix-coil transition) can take place. (C) 2004 Elsevier Ltd. All rights reserved.