A noncytotoxic DsRed variant for whole-cell labeling

A common application of fluorescent proteins is to label whole cells, but many RFPs are cytotoxic when used with standard high-level expression systems. We engineered a rapidly maturing tetrameric fluorescent protein called DsRed-Express2 that has minimal cytotoxicity. DsRed-Express2 exhibits strong and stable expression in bacterial and mammalian cells, and it outperforms other available RFPs with regard to photostability and phototoxicity.     

Expression of the red fluorescent protein DsRed-Express in filamentous ascomycete fungi

The recently reported red fluorescent protein DsRed from the reef coral Discosoma sp. represents a new marker that has been codon-optimized for high expression in mammalian cells. To facilitate expression of DsRed in ascomycete fungi, we used the clone pDsRed-Express (Clontech) for constructing a plasmid vector, pPgpd-DsRed, containing the constitutive Aspergillus nidulans glyceraldehyde 3-phosphate (gpd) promoter. This vector was used for co-transformation of Penicillium paxilli, Trichoderma harzianum and Trichoderma virens (syn. Gliocladium virens) together with either pAN7-1 or gGFP, both containing a gene for hygromycin resistance for transformant selection. In addition, gGFP contains a green fluorescent protein (GFP) gene for expression in Ascomycetes. Expression of DsRed-Express was obtained in all three fungi, indicating that DsRed can be used as a highly effective vital marker in Ascomycetes. Dual marked transformants expressed both DsRed-Express and GFP in the same mycelium and were used for non-quantitative comparison of the intensity of the fluorescence using confocal laser scanning microscopy.     

A green fluorescent protein-based whole-cell bioreporter for the detection of phenylacetic acid

Phenylacetic acid (PAA) is produced by many bacteria as an antifungal agent and also appears to be an environmentally toxic chemical. The object of this study was to detect PAA using Pseudomonas putida harboring a reporter plasmid that has a PAA-inducible promoter fused to a green fluorescent protein (GFP) gene. Pseudomonas putida KT2440 was used to construct a green fluorescent protein-based reporter fusion using the paaA promoter region to detect the presence of PAA. The reporter strain exhibited a high level of gfp expression in minimal medium containing PAA; however, the level of GFP expression diminished when glucose was added to the medium, whereas other carbon sources, such as succinate and pyruvate, showed no catabolic repression. Interestingly, overexpression of a paaF gene encoding PAACoA ligase minimized catabolic repression. The reporter strain could also successfully detect PAA produced by other PAA-producing bacteria. This GFP-based bioreporter provides a useful tool for detecting bacteria producing PAA.     

Light stress in green and red Planktothrix strains: The orange carotenoid protein and its related photoprotective mechanism

Photosynthetic organisms need to sense and respond to fluctuating environmental conditions, to perform efficient photosynthesis and avoid the formation of harmful reactive oxygen species. Cyanobacteria have developed a photoprotective mechanism that decreases the energy arriving at the reaction centers by increasing thermal energy dissipation at the level of the phycobilisome, the extramembranal light-harvesting antenna. This mechanism is triggered by the photoactive orange carotenoid protein (OCP). In this study, we characterized OCP and the related photoprotective mechanism in non-stressed and light-stressed cells of three different strains of Planktothrix that can form impressive blooms. In addition to changing lake ecosystemic functions and biodiversity, Planktothrix blooms can have adverse effects on human and animal health as they produce toxins (e.g., microcystins). Three Planktothrix strains were selected: two green strains, PCC 10110 (microcystin producer) and PCC 7805 (non-microcystin producer), and one red strain, PCC 7821. The green strains colonize shallow lakes with higher light intensities while red strains proliferate in deep lakes. Our study allowed us to conclude that there is a correlation between the ecological niche in which these strains proliferate and the rates of induction and recovery of OCP-related photoprotection. However, differences in the resistance to prolonged high-light stress were correlated to a better replacement of damaged D1 protein and not to differences in OCP photoprotection. Finally, microcystins do not seem to be involved in photoprotection as was previously suggested.     

Biotin derivatives of D-Phe-Pro-Arg-CH2Cl for active-site-specific labeling of thrombin and other serine proteinases

Biotin derivatives of peptide chloromethyl ketones have ideal properties for specific labeling of the catalytic sites of serine proteinases but have not been widely used as probes because of the difficulty of synthesis and their instability. To make the reagents more accessible, a simple, economical method was developed for preparation of three biotin derivatives of the thrombin-specific inhibitor D-Phe-Pro-Arg-CH2Cl containing increasing lengths of the spacer connecting biotin. Reaction of the peptide with biotin-succinimidyl esters and purification by conventional chromatography yielded the compounds in 91-96% purity. The biotin-labeled inhibitors bound avidin with stoichiometries of 0.88-1.02 mol biotin compound/mol avidin subunits and irreversibly inactivated human thrombin with stoichiometries of 0.89-1.10 mol inhibitor/mol thrombin. Comparison of the three inhibitors by Western blotting indicated that a > or = 7- to 14-atom spacer was needed for sensitive (approximately 10 ng) detection of thrombin, with the derivative lacking a spacer only weakly detected because of its greatly reduced affinity for avidin. Application of the compounds to identify catalytically active products of factor Xa-catalyzed human prethrombin 1 activation in the absence of the protein cofactor, factor Va, allowed the direct observation of transient, low levels of the active intermediate, meizothrombin des-fragment 1, in addition to thrombin. Formation of this intermediate is concluded to reflect an intrinsic property of factor Xa activation of prethrombin 1 that is modulated by factor Va. The methods developed for preparation and characterization of the biotin-labeled inhibitors may be applicable to other tripeptide chloromethyl ketones, and the reagents can be employed for labeling of serine proteinases of diverse substrate specificity.     

Fluorescent and photoaffinity labeling derivatives of rhizoxin

A fluorescent probe (D-RZX) and a photoreactive fluorescent probe (AD-RZX) for studying the rhizoxin binding site on tubulin were prepared by the derivatization of rhizoxin (RZX). D-RZX consists of a rhizoxin moiety and a dansyl moiety. AD-RZX has a 5-azidonaphthalene-1-sulfonyl moiety instead of the dansyl moiety of D-RZX. Both D-RZX and AD-RZX bound tubulin in a mutually competitive manner with rhizoxin, indicating their binding to the rhizoxin site on tubulin. AD-RZX bound the rhizoxin site covalently after UV-irradiation, thus showing its usefulness as a photo-affinity probe for labeling of the rhizoxin site.     

Dual labeling with green fluorescent proteins for confocal microscopy

We report a dual labeling technique involving two green fluorescent protein (GFP) variants that is compatible with confocal microscopy. Two lasers were used to obtain images of (i) mixed cultures of cells, where one species contained GFPuv and another species contained GFPmut2 or GFPmut3, and (ii) a single species containing both GFPuv and GFPmut2 in the same cell. This method shows promise for monitoring gene expression and as a nondestructive and in situ technique for confocal microscopy of multispecies biofilms.     

Conversion of Congo red and 2-azoxyfluorene to mutagens following in vitro reduction by whole-cell rat cecal bacteria

Congo red, an azo dye derived from benzidine, and 2-azoxyfluorene, a derivative of 2-aminofluorene, were reduced during overnight incubation with a suspension of rat intestinal bacteria. High performance liquid chromatography and ultraviolet spectral analysis verified the presence of benzidine in extracts of the Congo red incubations and 2-aminofluorene in extracts of the 2-azoxyfluorene incubations. Extracts of the Congo red incubations were mutagenic toward Salmonella typhimurium TA1538 in the presence of a post-mitochondrial activating system, but Congo red was not mutagenic without this reductive pretreatment. Thus, the utility of the Ames test in screening for potential mutagens may be expanded by a reductive pretreatment utilizing cecal bacteria.     

Monofunctional derivatives of coproporphyrins for phosphorescent labeling of proteins and binding assays

p-Isothiocyanatophenyl derivatives of Pt(II)- and Pd(II)-coproporphyrin I are described as stable monofunctional reagents which enable simple covalent labeling of proteins and other biomolecules under mild conditions in aqueous solutions. Labeling procedure was optimized for antibodies, avidin, and neutravidin. Photophysical properties of resulting conjugates important for their use in binding assays based on time-resolved phosphorescence detection were studied. The functional activity and long-term storage stability of antibody conjugates were assessed in comparison with unmodified proteins. The new labels and their conjugates were evaluated in the solid-phase immunoassays using commercial time-resolved phosphorescence readers Victor(2) and Arcus-1230 (Wallac). Potential applications of these reagents in in vitro diagnostics are discussed.     

Photolabile derivatives of bile salts. Synthesis and suitability for photoaffinity labeling

In an approach to the identification of bile salt-binding carriers, the photoactivable bile acid derivatives A) 3 beta-azido, 7 alpha,12 alpha-dihydroxy-5 beta-cholan-24-oic acid, B) 7,7-azo-3 alpha,12 alpha-dihydroxy-5 beta-cholan-24-oic acid, and C) 11 xi-azido-12-oxo-3 alpha,7 alpha-dihydroxy-5 beta-cholan-24-oic acid were synthesized in unconjugated and taurine-conjugated form. Photolysis of the 3 beta-azido derivatives was studied using a light source with a maximum emission at 300 nm and established a half-life time of 18.5 min. The photochemistry of the 7,7-azo derivatives was investigated using light with a maximum at 350 nm and had a half-life time of 2.2 min. The 11 xi-azido-12-oxo derivatives were photolyzed with light having a maximum at 300 nm resulting in a half-life time of 8.5 min. The suitability of the 7,7-azo derivatives for photoaffinity labeling was demonstrated by photolyses in 14C-labeled methanol and acetonitrile. The generated carbene reacted with the solvents under covalent bond formation of 6 to 12%. The efficiency of all synthesized photolabile derivatives for photoaffinity labeling of bile salt binding proteins was demonstrated.     

Free and esterified carotenoids in green and red fruits of Capsicum annuum

Fully green and mature red fruits of the Yolo Wonder A variety of Capsicum annuum were analysed for their carotenoid content. The disappearance of chlorophyll was followed by an increased synthesis of carotenoids. Lutein was not detected in the red fruit in which capsanthin was the main carotenoid. It appeared as diester, monoester and free forms, while capsorubin occured as a diester only. Cryptocapsin was not esterified.     

Deuterium labeling of norbornene derivatives by iridium catalyzed H/D exchange catalysis

The H/D exchange catalysis using the Ir(I) complex [Tp^Me₂Ir(η⁴-2,3-dimethylbutadiene)] (Tp^Me₂=hydridotris(3,5-dimethylpyrazolyl)borate) as the precatalyst was studied for selective deuteration of norbornene derivatives. In dependence of the norbornene substitution in 2,3 positions, selective deuteration of the norbornene double bond could be achieved. (±)-endo,exo-6-Deutero-bicyclo[2.2.1]hept-5-ene-2,3-dicarboxylic acid diethyl ester was isolated in 82% yield.     

Azido derivatives of dicarboxylic acids for photoaffinity labeling of mitochondrial carriers

New photoaffinity probes, N-(4-azidosalicylic)-aminosuccinic acid, 3-(4-azidophenylazo)-4-hydroxyphenylmalonic acid, (4-azido-2-nitroanilino)-N-succinic acid, 4-azidophenacylthiosuccinic acid and 4-azidophenylsuccinic acid, were synthesized and characterized chemically. They differ in the distance between dicarboxylic and azido groups, hydrophobicity and acidic moiety. These between dicarboxylic and azido groups, hydrophobicity and acidic moiety. These reagents can be applied for photoaffinity labeling of mitochondrial anion carriers and enzymes interacting with dicarboxylic acids. Inhibition and labeling of the dicarboxylate carrier is presented.     

Life cycle assessment evaluation of green product labeling systems for residential construction

Purpose

Life cycle assessment (LCA) is a tool that can be utilized to holistically evaluate novel trends in the construction industry and the associated environmental impacts. Green labels are awarded by several organizations based on single or multiple attributes. The use of multi-criteria labels is a good start to the labeling process as opposed to single criteria labels that ignore a majority of impacts from products. Life cycle thinking, in theory, has the potential to improve the environmental impacts of labeling systems. However, LCA databases currently are lacking in detailed information about products or sometimes provide conflicting information.

Method

This study compares generic and green-labeled carpets, paints, and linoleum flooring using the Building for Environmental and Economic Sustainability (BEES) LCA database. The results from these comparisons are not intuitive and are contradictory in several impact categories with respect to the greenness of the product. Other data sources such as environmental product declarations and ecoinvent are also compared with the BEES data to compare the results and display the disparity in the databases.

Results

This study shows that partial LCAs focused on the production and transportation phase help in identifying improvements in the product itself and improving the manufacturing process but the results are uncertain and dependent upon the source or database. Inconsistencies in the data and missing categories add to the ambiguity in LCA results.

Conclusions

While life cycle thinking in concept can improve the green labeling systems available, LCA data is lacking. Therefore, LCA data and tools need to improve to support and enable market trends.     

Improving the photostability of bright monomeric orange and red fluorescent proteins

All organic fluorophores undergo irreversible photobleaching during prolonged illumination. Although fluorescent proteins typically bleach at a substantially slower rate than many small-molecule dyes, in many cases the lack of sufficient photostability remains an important limiting factor for experiments requiring large numbers of images of single cells. Screening methods focusing solely on brightness or wavelength are highly effective in optimizing both properties, but the absence of selective pressure for photostability in such screens leads to unpredictable photobleaching behavior in the resulting fluorescent proteins. Here we describe an assay for screening libraries of fluorescent proteins for enhanced photostability. With this assay, we developed highly photostable variants of mOrange (a wavelength-shifted monomeric derivative of DsRed from Discosoma sp.) and TagRFP (a monomeric derivative of eqFP578 from Entacmaea quadricolor) that maintain most of the beneficial qualities of the original proteins and perform as reliably as Aequorea victoria GFP derivatives in fusion constructs.     

Cofactor self-sufficient whole-cell biocatalysts for the production of 2-phenylethanol

The efficiency of biocatalysis is often affected by an insufficient supply and regeneration of cofactors and redox equivalents. To alleviate this shortcoming, a cofactor self-sufficient system was developed for enhanced production of 2-phenylethanol (2-PE) in E. coli. A “bridge” between the amino acid and its corresponding alcohol was designed in the system using glutamate dehydrogenase. By coupling glutamate dehydrogenase with transaminase and alcohol dehydrogenase, the cosubstrate (2-oxoglutarate) and redox equivalents (NAD(P)H) were regenerated simultaneously, so that no external cofactor or redox source was required. Thus, a cofactor self-sufficient system was developed, which improved the biocatalyst efficiency 3.8-fold. The ammonium generated in this process was removed using zeolite, which further improved the biosynthetic efficiency and resulted in a cleaner system. To the best of our knowledge, this system yielded the highest titer of 2-PE ever obtained in E. coli. Additionally, the wider applicability of this self-sufficient strategy was demonstrated in the production of D-phenyllactic acid. This study thus offers a new method to resolve the cofactor/redox imbalance problem and demonstrates the feasibility of the cofactor self-sufficient strategy for enhanced production of diverse chemicals.     

Formation of yellow, orange, and red pigments in the reaction of alk-2-enals with 2-thiobarbituric acid

The reaction of four to eight carbon straight-chain alk-2-enals with 2-thiobarbituric acid (TBA) produced yellow 455-nm-, orange 495-nm-, and red 532-nm-absorbing pigments depending upon the reaction conditions. The 1:1 reaction of the aldehydes with TBA in 15% acetic acid at 100 degrees C produced the yellow pigment at 0.25 h and the red at 6 h. The reaction of the aldehydes with TBA in excess at 100 degrees C produced the yellow at 0.25 h, the orange at 2-6 h, and the red at 0.25-6 h. The formation of these pigments required molecular oxygen. These pigments could be separated from each other on HPLC. The red pigment formed from the aldehydes could not be distinguished from the red 1:2 malonaldehyde-TBA adduct by absorption spectrum and HPLC. The red color yield was the highest in the 1:1 reaction and retarded in the reaction with TBA in excess. The red color due to these aldehydes may contribute in part to the color formed in the general TBA test of lipid oxidation. The 1:1 reaction initially produced colorless 1:1 adducts X, which were subsequently converted into the yellow and red pigments under aerobic conditions. The reaction of the aldehydes with TBA in excess might initially produce X and then another colorless 1:2 adducts Y; the latter being converted into yellow, orange, and red pigments under aerobic conditions.     

Evaluation of colors in green mutants isolated from purple bacteria as a host for colorimetric whole-cell biosensors

The change in carotenoid-based bacterial color from yellow to red can be applied to whole-cell biosensors. We generated several green mutants to emphasize the color change in such biosensors. The blue-green crtI-deleted mutant, Rhodopseudomonas palustris no.711, accumulated the colorless carotenoid precursor, phytoene. Green Rhodovulum sulfidophilum M31 accumulated neurosporene, a downstream product of phytoene. Another green mutant, Rhodobacter sphaeroides Ga, accumulated neurosporene and chloroxanthin, which are both downstream products of phytoene. All green mutants accumulated bacteriochlorophyll a. Photosynthetic membrane obtained from the green mutants all exhibited decreased absorption of wavelength range at 510–570 nm. Therefore, these indicate that the greenish bacterial colors were mainly caused by the existence of bacteriochlorophyll a and the changes in carotenoid composition in photosynthetic membrane. The colors of the green mutants and their wild-type strains were plotted in the CIE-L*a*b* color space, and the color difference (ΔE*ab) values between a green mutant and its wild type were calculated. ΔE*ab values were higher in the green mutants than in Rdv. sulfidophilum CDM2, the yellowish host strain of reported biosensors. These data indicate that change in bacterial color from green to red is more distinguishable than that from yellow to red as a reporter signal of carotenoid-based whole-cell biosensors.