Topologies and measurements of turbulent flow in vertical slot fishways

Several vertical slot fishways have been built in France over the last 20 years. This type of pool fish pass is generally very effective in ensuring passage of the target species, particularly diadromous species. However, visual observations have shown that certain small species may be trapped in the large recirculation zones and seem to have difficulty in rapidly passing through very large pools. An experimental study was undertaken to characterize the turbulent flow for various configurations of vertical slot fishways and to determine how they might be modified to facilitate the passage of small species. The characteristics of mean flow and turbulence were studied by particle image velocimetry (PIV) for three slopes (I = 5%, 10%, 15%), three flow discharges (Q = 576, 736, 864 L/s) and four pool widths (B = 1.7, 2, 2.3, 2.7 m). The results showed that the flow pattern always follows one of two topological models depending on the length/width ratio of the pool. A strong link was found between the calculated volumetric dissipated power and the mean kinetic energy of velocity fluctuations measured in the pools. In order to study the extent to which the dimensions of recirculation zones can be reduced, the effect of the insertion of vertical cylinders within the pools was displayed by laser tomography.

Candida rugosa lipase-catalysed kinetic resolution of 2-substituted-aryloxyacetic esters with dimethylsulfoxide and isopropanol as additives

Candida rugosa lipase-catalysed hydrolysis of three different 2-substituted-aryloxyacetic esters was performed in aqueous buffer containing dimethyl sulphoxide and isopropanol from 0 to 80% v/v as additives, in order to obtain an enhancement of the enantioselectivity. For 2-(p-chlorophenoxy)acetic acid and 2-n-butyl-2-(p-chlorophenoxy)acetic acid ethyl esters, DMSO enhanced enzyme enantioselectivity more than IPA with an opposite enzymatic enantiopreference. The cosolvents moderately improved Candida rugosa lipase enantioselectivity for 2-phenyl-2-(p-chlorophenoxy)acetic acid ethyl ester.     

Partial destabilization of native structure by a combination of heat and denaturant facilitates cold denaturation in a hyperthermophile protein

Cold denaturation is a phenomenon seen in many different proteins. However, there have been no reports so far of its occurrence in hyperthermophile proteins. Here, using a recombinant triosephosphate isomerase (PfuTIM) from the hyperthermophile archaeon, Pyrococcus furiosus, we show that the heating of this protein through the low temperature side of its thermal unfolding transition in the presence of guanidinium hydrochloride (GdmCl) results in the formation of partially-disordered conformational ensembles that retain considerable native-like secondary and tertiary structure. Unlike PfuTIM itself, these thermochemically obtained partially-disordered PfuTIM ensembles display cold denaturation as they are cooled to room temperature. The protein thus shows hysteresis, adopting different structural states in a manner dependent upon the nature of the heating and cooling treatment, rather than upon the initial and final conditions of temperature and GdmCl concentration, indicating that some sort of a kinetic effect influences structure adoption and retention. The structure lost through cooling of partially-disordered PfuTIM is found to be regained through heating. The ability of GdmCl to thus apparently destabilize the highly thermodynamically and kinetically stable structure of PfuTIM (sufficiently, to cause it to display observable cold-denaturation and heat-renaturation transitions, in real-time, with cooling and heating) offers support to current ideas concerning the how hyperthermophile proteins achieve their high kinetic stabilities, and suggests that desolvation-solvation barriers may be responsible for high kinetic stability.     

Unstructured intermediate states in single protein force experiments

Recent single-molecule force measurements on single-domain proteins have highlighted a three-state folding mechanism where a stabilized intermediate state (I) is observed on the folding trajectory between the stretched state and the native state. Here we investigate on-lattice protein-like heteropolymer models that lead to a three-state mechanism and show that force experiments can be useful to determine the structure of I. We have mostly found that I is composed of a core stabilized by a high number of native contacts, plus an unstructured extended chain. The lifetime of I is shown to be sensitive to modifications of the protein that spoil the core. We then propose three types of modifications--point mutations, cuts, and circular permutations--aiming at: (1) confirming the presence of the core and (2) determining its location, within one amino acid accuracy, along the polypeptide chain. We also propose force jump protocols aiming to probe the on/off-pathway nature of I.     

Chromium ions phytoaccumulation by three floating aquatic macrophytes from a nutrient medium

In the present work, the trivalent and hexavalent chromium phytoaccumulation by three living free floating aquatic macrophytes Salvinia auriculata, Pistia stratiotes, and Eicchornia crassipes was investigated in greenhouse. These plants were grown in hydroponic solutions supplied with non-toxic Cr³⁺ and Cr⁶⁺ chromium concentrations, performing six collections of nutrient media and plants in time from a batch system. The total chromium concentrations into Cr-doped hydroponic media and dry roots and aerial parts were assayed, by using the Synchrotron radiation X-ray fluorescence technique. The aquatic plant-based chromium removal data were described by using a nonstructural kinetic model, obtaining different bioaccumulation rate, ranging from 0.015 to 0.837 l mg⁻¹ d⁻¹. The Cr³⁺ removal efficiency was about 90%, 50%, and 90% for the E. crassipes, P. stratiotes, and S. auriculata, respectively; while it was rather different for Cr⁶⁺ one, with values about 50%, 70%, and 90% for the E. crassipes, P. stratiotes, and S. auriculata.     

Proline 54 trans-cis isomerization is responsible for the kinetic partitioning at the last-step photocycle of photoactive yellow protein

Photoactive yellow protein (PYP), a blue-light photoreceptor for Ectothiorhodospira halophila, has provided a unique system for studying protein folding that is coupled with a photocycle. Upon receptor activation by blue light, PYP proceeds through a photocycle that includes a partially folded signaling state. The last-step photocycle is a thermal recovery reaction from the signaling state to the native state. Bi-exponential kinetics had been observed for the last-step photocycle; however, the slow phase of the bi-exponential kinetics has not been extensively studied. Here we analyzed both fast and slow phases of the last-step photocycle in PYP. From the analysis of the denaturant dependence of the fast and slow phases, we found that the last-step photocycle proceeds through parallel channels of the folding pathway. The burial of the solvent-accessible area was responsible for the transition state of the fast phase, while structural rearrangement from the compact state to the native state was responsible for the transition state of the slow phase. The photocycle of PYP was linked to the thermodynamic cycle that includes both unfolding and refolding of the fast- and slow-phase intermediates. In order to test the hypothesis of proline-limited folding for the slow phase, we constructed two proline mutants: P54A and P68A. We found that only a single phase of the last-step photocycle was observed in P54A. This suggests that there is a low energy barrier between trans to cis conformation in P54 in the light-induced state of PYP, and the resulting cis conformation of P54 generates a slow-phase kinetic trap during the photocycle-coupled folding pathway of PYP.     

Mutations that Allow SIR2 Orthologs to Function in a NAD+-Depleted Environment

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Simulated microgravity impairs respiratory burst activity in human promyelocytic cells

Summary The concept of microgravity (free-fall) influencing cellular functions in nonadherent cells has not been a part of mainstream scientific thought. Utilizing rotating wall vessels (RWVs) to generate simulated microgravity conditions, we found that respiratory burst activity was significantly altered in nonadherent promyelocytic (HL-60) cells. Specifically, HL-60 cells in simulated microgravity for 6, 19, 42, 47, and 49 d had 3.8-fold fewer cells that were able to participate in respiratory burst activity than cells from 1×g cultures (P=0.0011, N=5). The quantity of respiratory burst products from the cells in simulated microgravity was also significantly reduced. The fold increase over controls in mean fluorescence intensities for oxidative products from cells in microgravity was 1.1±0.1 versus 1.8±0.3 for cells at 1 ×g (P=0.013, N=4). Furthermore, the kinetic response for phorbol ester-stimulated burst activity was affected by simulated microgravity. These results demonstrate that simulated microgravity alters an innate cellular function (burst activity). If respiratory burst activity is impaired by true microgravity, then recovery from infections during spaceflight could be delayed. Finally, RWVs provide an excellent model for investigating the mechanisms associated with microgravity-induced changes in nonadherent cells.     

The effect of ethanol on the kinetics of lipase-mediated enantioselective esterification of 4-methyloctanoic acid and the hydrolysis of its ethyl ester.

The Novozym 435(R) catalyzed esterification and hydrolysis reactions of 4-methyloctanoic acid (ethyl ester) were investigated. In both the hydrolysis and esterification reactions, the increase of ethanol concentration led to an increase in enantiomeric ratio (E). For hydrolysis of the ethyl ester, the E-value increased from 5.5 [0% (v/v) EtOH] up to 12 [20% (v/v) EtOH]. In case of esterification, the E-value was already 16 [14% (v/v) EtOH] and rose to 57 [73% (v/v) EtOH]. When combining these results of esterification and hydrolysis, an enantiomeric ratio of 350 can be estimated for the sequential kinetic resolution of 4-methyloctanoic acid. In this way, enantiopure 4-methyloctanoic acid could be obtained after two consecutive reaction steps.