A competition smFRET assay to study ligand-induced conformational changes of the dengue virus protease

Ligand binding to proteins often is accompanied by conformational transitions. Here, we describe a competition assay based on single molecule Förster resonance energy transfer (smFRET) to investigate the ligand-induced conformational changes of the dengue virus (DENV) NS2B-NS3 protease, which can adopt at least two different conformations. First, a competitive ligand was used to stabilize the closed conformation of the protease. Subsequent addition of the allosteric inhibitor reduced the fraction of the closed conformation and simultaneously increased the fraction of the open conformation, demonstrating that the allosteric inhibitor stabilizes the open conformation. In addition, the proportions of open and closed conformations at different concentrations of the allosteric inhibitor were used to determine its binding affinity to the protease. The K_D value observed is in accordance with the IC₅₀ determined in the fluorometric assay. Our novel approach appears to be a valuable tool to study conformational transitions of other proteases and enzymes.     

Performance of a new family of modular,bed-supported,chromatography devices

Prepacked chromatography columns and cassette filtration units offer many advantages in bioprocessing. These include reduced labor costs and processing times, ease of storage, and enhanced process flexibility. Rectangular formats are particularly attractive as they can be easily stacked and multiplexed together for continuous processing. Cylindrical chromatography beds have dominated bioprocessing even though their bed support and pressure-flow performance vary with bed dimensions. This work presents the performance of novel, rhombohedral chromatography devices with internally supported beds. They are compatible with existing chromatography workstations and can be packed with any standard commercial resin. The devices offer pressure-flow characteristics independent of container-volume, simple multiplexing, and separation performance comparable to cylindrical columns. Their bi-planar, internal bed support allows mechanically less-rigid resins to be used at up to four times higher maximal linear velocities, and productivities approaching 200 g/L/h for affinity resins, compared to the 20 g/L/h typical of many column-based devices. Three 5 L devices should allow processing of up to 3 kg of monoclonal antibody per hour.     

Biosynthesis and function of membrane bound and secreted forms of recombinant CD11b/CD18 (Mac-1)

Full-length (membrane bound) and truncated (secreted) forms of the beta 2 integrin heterodimer, CD11b/CD18 (Mac-1), were expressed in a human kidney cell line (293) that normally does not express leukocyte adhesion molecules (Leu-CAMs). The biosynthesis of recombinant Mac-1 in 293 cells differed from that reported for leukocytes in that heterodimer formation was not required for CD11b to be exported to the cell surface. A stable cell line was constructed that constitutively secreted the recombinant, truncated Mac-1 heterodimer into growth conditioned cell culture medium. A novel monoclonal antibody that enabled an immunoaffinity method for the selective purification of recombinant Mac-1 heterodimers was identified. Sufficient protein was purified to allow the first measurement of the 50% inhibitory concentration (IC₅₀) for CD11b/CD18 and for the direct comparison of the inhibitory activity of recombinant soluble Mac-1 with that of various CD18 and CD11b specific monoclonal antibodies. Purified recombinant soluble Mac-1 inhibited the binding of neutrophils, activated by opsonized zymosan or fMet-Leu-Phe peptide, to human umbilical vein endothelial cells. Similarly, the recombinant integrin was effective in inhibiting the binding of unactivated neutrophils to tumor necrosis factor (TNF-alpha) activated endothelial cells. The availability of an abundant source of purified, biologically active Mac-1 will enable direct physical and chemical investigations into the relationship between the structure and function of this leukocyte adhesion molecule.     

The low temperature,rapid dissolution of gellan away from root cultures

Summary A buffer system consisting of 50 mM Tris-HCl-TRIZMA base plus 10 mM EDTA was used to rapidly dissolve gellan gels used for maintaining transformed carrot root cultures. The optimum conditions of pH 7.5 in the presence of 10 mM EDTA for dissolving gellan were first worked out on a model test system containing 0.4% gellan, 0.025% MgSO₄·7H₂O, and blue dye. The conditions were then tested on gellan gels (0.2% gellan plus nutrients) containing carrot roots. This gel dissolution system was rapid (18 to 20 min), did not require heating, and could also be efficiently performed at 4 °C. Furthermore, the buffer system used for gel dissolution is a standard one used for plant cell fractionation studies.     

INORGANIC CARBON LIMITATION OF PHOTOSYNTHESIS IN ULVA ROTUNDATA (CHLOROPHYTA)1

A computerized oxygen electrode Astern was used to make rapid and accurate measurements of photosynthetic light and dissolved inorganic carbon (DIC) response cures with a macroalga. Ulva rotundata Blid. was grown in an outdoor, continuous flow system in seawater under sunlight or 9% of sunlight at Beaufort, North Carolina. The light compensation points in the shade- and sun-grown plants, measured in seawater, were at photon flux densities (PFDs) of 16 and 27 μmol. Photons·m^?2·s^?1, respectively but the quantum yield of O₂ evolution was not significantly different. Rates of photosynthesis in seawater per unit area of thallus under saturating light and rates of dark respiration were about 1.5-fold higher in sun- than in shade-grown plants. The concentration of DIC in seawater (approximately 2 mM) limited photosynthesis at absorbed PFDs above 60–70 μmol photons·m^?2·s^?1 Addition of 20 mM inorganic carbon had no effect on quantum yield but caused about a 1.5-fold increase in the light-saturated photosynthetic rate in both shade- and sun-grown Ulva. The effect of DIC supplementation was greatest in plants grown in October and least in plants grown in June. The light- and DIC-saturated rate of photosynthesis in seawater was similar to the maximum rate obtained by exposing Ulva to 10% CO₂, in the gas phase. The carbon isotope values (δ¹³C, reflecting the ¹³C/¹²C ratio compared to a standard) of Ulva grown in the same seawater supply were dependent on light and agitation. Samples from Beaufort Inlet were more negative (δ¹³C value, ?20.03‰) than those grown in bright light with agitation (δ¹³C value, ?17.78‰ outdoors; ?17.23‰ indoors), which may indicate DIC supply limited carbon uptake in seawater.     

Holocene vegetation and water level history in two bogs of the Cordillera de Talamanca, Costa Rica

Pollen records of Holocene sediment cores from the Costa Rican Cordillera de Talamanca (La Chonta bog, 2310 m and La Trinidad bog, 2700 m) show the postglacial development of the montane oak forest zone from ca. 9500 to 1500 yr BP. During the early Holocene (ca. 9500–700 yr BP), alder vegetation covered the La Chonta and La Trinidad bogs and their adjacent hills. The upper forest line is inferred to be at 2800–3000 m elevation. A Podocarpus-Quercus forest characterised the middle Holocene (ca. 7000–4500 yr BP). The upper forest line is located at >3000 m reaching the present-day altitudinal distribution. A Quercus forest characterised the late Holocene (ca. 4500–1500 yr BP). Compared to modern conditions, the early Holocene has similar average temperatures, but the moisture level was probably higher. Pollen evidence for the late Holocene indicates drier environmental conditions than today. In order to improve the paleoecological interpretation, we described the local vegetation and used moss samples as pollen traps at both montane bogs along strong soil moisture gradients.The Netherlands Centre for Geo-ecological Research, ICG     

Body Position,Age and Mass Effect of Adiposity on Adipose Tissue Red Cell Flux in Morbid Obesity

Objective: To measure red cell flux of adipose tissue in morbidly obese patients' pannus in the upright and supine position to determine factors which would render the lower pannus susceptible to ischemic necrosis. Design: A cohort study of morbidly obese subjects without ischemic necrosis. Setting: University teaching hospital. Patients: Twenty-three consecutive morbidly obese patients referred for gastroplasty. Measurements: Red cell flux, measured as RMS voltage by a laser Doppler velocimeter. An optical fiber with a tip diameter of 250μ was inserted into the upper and lower pannus and output recorded in the upright and supine positions. Other variables recorded were age, BMI, blood pressure and serum lipids. Results: Adipose tissue red cell flux demonstrates considerable spatial and temporal heterogeneity from subject to subject and in various locations in the pannus. No differences in red cell flux were detected in response to change in position. However, regression analysis demonstrated that the gradient between the upper and lower abdomen in the supine position was increasingly positive with age and in the upright position it was increasingly positive with increasing weight or BMI. Conclusions: These data suggest that red cell flux is heterogeneously distributed in the abdominal pannus and is not greatly influenced by body position. However, with increasing age and adiposity there is a gradient for decreased red cell flux to the lower portion of the pannus. This may be a factor in rendering this part of the pannus prone to ischemic fat necrosis.     

A carbon monoxide irreducible form of cytochrome c oxidase and other unusual properties of the “monomeric” shark enzyme

Contrary to previous reports, the functional and spectral properties of “monomeric” shark cytochrome c oxidases are not entirely similar to those of the “dimeric” beef enzyme. Most significantly, unlike the behavior of beef oxidase, the fully oxidized shark enzyme is not reducible by carbon monoxide. Also, preparations of the shark enzyme, isolated at pH 7.8-8.0, lead to more than 60% of the sample always being obtained in a resting form, whereas similarly prepared beef oxidase is very often obtained, both by ourselves and others, exclusively in the pulsed form. Although the electronic absorption, magnetic circular dichroism and electron paramagnetic resonance (EPR) spectra of cytochrome c oxidase obtained from several shark species are similar to those of the beef enzyme, there are some significant differences. In particular, the Soret maximum is at 422 nm in the case of the fully oxidized resting shark oxidases at physiological pH and not 418 nm as commonly found for the beef enzyme. Moreover, the resting shark oxidases do not necessarily exhibit a “g = 12” signal in their EPR spectra. The turnover numbers of recent preparations of the shark enzyme are higher than previously reported and, interestingly, do not differ within experimental uncertainty from those documented for several beef isoenzymes assayed under comparable conditions.