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Stability and quantum yield effects of small molecule additives on solutions of semiconductor nanoparticles.

The effect of additives on the photostability of semiconductor nanoparticles was studied using CdSe, CdSe/ZnSe and CdSe/ZnS particles of various sizes and composition. The additives included phosphine oxides, amines, and antioxidants. Strong initial enhancement of band edge emission by hexadecylamine was observed for the uncoated particles but stability over a week period in light and air was shown to be poor. Inorganic coatings rendered the nanoparticles initially insensitive to additive but provided little extra stability in terms of photoluminescence. Antioxidant was shown to be effective at reducing the rate of photooxidative degradation for all particles in chloroform but not in toluene.

Adsorption↗

Monitoring manufacturing process yields, purity and stability of structural variants of PEGylated staphylokinase mutant SY161 by quantitative reverse-phase chromatography.

Staphylokinase variant SY161 is a recombinant mutant of the Staphylococcus aureus polypeptide staphylokinase (Sak), and is currently in human clinical trials as a thrombolytic agent. The 15 kDa single chain SY161 protein is expressed as a soluble cytoplasmic product in E. coli with a single cysteine inserted near the N-terminus. The protein as extracted from E. coli is a mixture of both monomeric and intermolecularly disulfide crosslinked species. To improve protein purification yields SY161 is sulfitolyzed during the early stages of production, preventing disulfide formation. The protein is later modified during manufacturing to incorporate a single 5 kDa polyethylene glycol group on the single sulfhydryl sidechain. We have developed and qualified a reverse-phase chromatographic method to quantitate SY161 during product manufacturing. We discuss the use of the assay during manufacturing development to monitor fermentation yields, the SY161 PEGylation reaction, and as an in-process manufacturing control assay. The assay has been applied as a product purity and identity release assay and is suitable for use in assessing product structural integrity during stability testing. The assay has a linear range of quantitation for SY161 from at least 0.15 to 16 micro g, and is-in addition capable of detecting and quantitating protein de-PEGylation events and host cell-derived protein contaminants.

Amino Acid Sequence↗

Increasing PCR fragment stability and protein yields in a cell-free system with genetically modified Escherichia coli extracts.

Escherichia coli cell-free protein synthesis is a highly productive system that can be applied to high throughput expression from polymerase chain reaction (PCR) products in 96-well plates for proteomic studies as well as protein evolution. However, linear DNA instability appears to be a major limitation of the system. We modified the genome of the E. coli strain A19 by removing the endA gene encoding the endonuclease I and replacing the recCBD operon (in which recD encodes the exonuclease V) by the lambda phage recombination system. Using the cell extract from this new strain increased the stability of PCR products amplified from a plasmid containing the cat gene. This resulted in CAT (chloramphenicol acetyltransferase) production from PCR products comparable to that from plasmids (500-600 microg/ml) in a batch reaction. We show that cell-free protein synthesis reactions using PCR products amplified from genomic DNA and extended with the T7 promoter and the T7 terminator give the same high yields of proteins (550 microg/ml) in 96-well plates. With this system, it was possible to rapidly express a range of cytoplasmic and periplasmic proteins.

Bacterial Proteins↗

Breeding of retroviruses by DNA shuffling for improved stability and processing yields.

Manufacturing of retroviral vectors for gene therapy is complicated by the sensitivity of these viruses to stress forces during purification and concentration. To isolate viruses that are resistant to these manufacturing processes, we performed breeding of six ecotropic murine leukemia virus (MLV) strains by DNA shuffling. The envelope regions were shuffled to generate a recombinant library of 5 x 106 replication-competent retroviruses. This library was subjected to the concentration process three consecutive times, with amplification of the surviving viruses after each cycle. Several viral clones with greatly improved stabilities were isolated, with the best clone exhibiting no loss in titer under conditions that reduced the titers of the parental viruses by 30- to 100-fold. The envelopes of these resistant viruses differed in DNA and protein sequence, and all were complex chimeras derived from multiple parents. These studies demonstrate the utility of DNA shuffling in breeding viral strains with improved characteristics for gene therapy.

Animals↗

Mushroom cryopreservation and its effect on survival, yield and genetic stability.

Mycelial stock cultures of Agaricus bisporus, A. Bitorquis, Pleurotus flabellatus, P. Sajor-caju, P. Ostreatus, P. Sapidus, Auricularia polytricha, Lentinula edodes, Morchella esculenta and Volvariella volvacea were maintained by frequent subculturing at an interval of two months and separately as wheat grain spawn in liquid nitrogen with 15 percent glycerol. Preservation of mushroom stock cultures as wheat grain spawn under liquid nitrogen proved to be the better method of maintenance. The percent recoveries of stored samples were unchanged from the first recovery after six months to the last recovery after 42 months in nine out of 11 stock cultures preserved under liquid nitrogen. However, a marginal decline in survival of 10 % was recorded in Auricularia polytricha and Volvariella volvacea. Yields before preservation of mushroom stock cultures and after 30 months of preservation exhibited static biological efficiency and fruitbody weight. The comparison of Random Amplified Polymorphic DNA (RAPD) and Internal Transcribed Spacers (ITS) PCR amplified products did not exhibit DNA fragment variation in banding patterns at the intraspecific level during preservation of stock cultures by either method. The modified cryopreservation protocol and experimental demonstration of genetic stability of stock cultures reported here validate the use of mushroom cryopreservation techniques and supports studies on genetic stability of preserved biological materials.

Agaricales↗

proBA complementation of an auxotrophic E. coli strain improves plasmid stability and expression yield during fermenter production of a recombinant antibody fragment.

The proline-auxotrophic Escherichia coli K12 strain JM83 harbouring an expression vector providing the proBA gene in trans was utilized for the fermenter production of the partially humanized IN-1 antibody F(ab) fragment. Thus, plasmid-mediated complementation of the chromosomal proBA deletion was employed as a second selection mechanism, together with a chloramphenicol resistance, in order to (i) abolish plasmid loss and (ii) benefit from E. coli JM83 as an expression strain with approved periplasmic protein secretion characteristics in the presence of a minimal medium. Starting from the generic vector pASK75, which makes use of the tightly regulated and chemically inducible tet promoter for foreign gene expression, a set of new vectors carrying the entire or part of the proBA operon was constructed and compared concerning their capability of functional Delta proBA complementation as well as recombinant protein yield. As a result, the vector pMF1 was developed, where transcription of the proBA operon is controlled by its own constitutive promoter and terminator sequences, permitting the transformed JM83 strain to grow under glucose/ammonia minimal culture conditions. When pMF1 was used for the fermenter production of the IN-1 F(ab) fragment, no plasmid loss was observed during the growth and induction phases, and the yield of functionally purified recombinant protein was found to be considerably improved.

Aldehyde Oxidoreductases↗

Reduced oxygen supply increases process stability and product yield with recombinant Pichia pastoris.

A single-chain antibody fragment directed against fimbriae of enterotoxigenic Escherichia coli was produced by recombinant Pichia pastoris under control of the methanol-inducible AOX1 promoter. In high-cell-density cultivation on defined medium, methanol-limited and methanol-saturated conditions were compared. After batch and fed-batch phase on glycerol, the methanol concentration was controlled to 1% (v/v) or methanol was fed with an exponentially increasing rate. Whereas methanol limitation impaired cell integrity and product quality, finally yielding no active product as a result of degradation, oxygen limitation was acceptable. To postpone the onset of limitation, the inlet air was enriched by pure oxygen. Because of faster methanol consumption, however, the process became sensitive to fluctuations in the feeding rate, and complete arrest of metabolism encountered upon small perturbations shortened the active production period. Without additional oxygen supply, the process was robust. Loss of culture integrity was monitored by flow cytometry and was found to precede changes in metabolic rates; it can thus serve as a sensitive indicator of forthcoming problems. Single-step downstream processing from the culture supernatant by His-affinity chromatography was efficient when antifoam agent that coagulates upon pH titration was omitted and yielded 1 g of purified lyophilized product from 6 L initial culture volume.

Bioreactors↗

Biophysical properties of human antibody variable domains.

There are great demands on the stability, expression yield and resistance to aggregation of antibody fragments. To untangle intrinsic domain effects from domain interactions, we present first a systematic evaluation of the isolated human immunoglobulin variable heavy (V(H)) and light (V(L)) germline family consensus domains and then a systematic series of V(H)-V(L) combinations in the scFv format. The constructs were evaluated in terms of their expression behavior, oligomeric state in solution and denaturant-induced unfolding equilibria under non-reducing conditions. The seven V(H) and seven V(L) domains represent the consensus sequences of the major human germline subclasses, derived from the Human Combinatorial Antibody Library (HuCAL). The isolated V(H) and V(L) domains with the highest thermodynamic stability and yield of soluble protein were V(H)3 and V(kappa)3, respectively. Similar measurements on all domain combinations in scFv fragments allowed the scFv fragments to be classified according to thermodynamic stability and in vivo folding yield. The scFv fragments containing the variable domain combinations H3kappa3, H1bkappa3, H5kappa3 and H3kappa1 show superior properties concerning yield and stability. Domain interactions diminish the intrinsic differences of the domains. ScFv fragments containing V(lambda) domains show high levels of stability, even though V(lambda) domains are surprisingly unstable by themselves. This is due to a strong interaction with the V(H) domain and depends on the amino acid sequence of the CDR-L3. On the basis of these analyses and model structures, we suggest possibilities for further improvement of the biophysical properties of individual frameworks and give recommendations for library design.

Amino Acid Sequence↗

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗

Chiral mutagenesis of insulin. Foldability and function are inversely regulated by a stereospecific switch in the B chain.

How insulin binds to its receptor is unknown despite decades of investigation. Here, we employ chiral mutagenesis-comparison of corresponding d and l amino acid substitutions in the hormone-to define a structural switch between folding-competent and active conformations. Our strategy is motivated by the T --> R transition, an allosteric feature of zinc-hexamer assembly in which an invariant glycine in the B chain changes conformations. In the classical T state, Gly(B8) lies within a beta-turn and exhibits a positive phi angle (like a d amino acid); in the alternative R state, Gly(B8) is part of an alpha-helix and exhibits a negative phi angle (like an l amino acid). Respective B chain libraries containing mixtures of d or l substitutions at B8 exhibit a stereospecific perturbation of insulin chain combination: l amino acids impede native disulfide pairing, whereas diverse d substitutions are well-tolerated. Strikingly, d substitutions at B8 enhance both synthetic yield and thermodynamic stability but markedly impair biological activity. The NMR structure of such an inactive analogue (as an engineered T-like monomer) is essentially identical to that of native insulin. By contrast, l analogues exhibit impaired folding and stability. Although synthetic yields are very low, such analogues can be highly active. Despite the profound differences between the foldabilities of d and l analogues, crystallization trials suggest that on protein assembly substitutions of either class can be accommodated within classical T or R states. Comparison between such diastereomeric analogues thus implies that the T state represents an inactive but folding-competent conformation. We propose that within folding intermediates the sign of the B8 phi angle exerts kinetic control in a rugged landscape to distinguish between trajectories associated with productive disulfide pairing (positive T-like values) or off-pathway events (negative R-like values). We further propose that the crystallographic T -->R transition in part recapitulates how the conformation of an insulin monomer changes on receptor binding. At the very least the ostensibly unrelated processes of disulfide pairing, allosteric assembly, and receptor binding appear to utilize the same residue as a structural switch; an "ambidextrous" glycine unhindered by the chiral restrictions of the Ramachandran plane. We speculate that this switch operates to protect insulin-and the beta-cell-from protein misfolding.

Amino Acid Sequence↗

Silylation reaction of dextran: effect of experimental conditions on silylation yield, regioselectivity, and chemical stability of silylated dextrans.

The controlled synthesis of biodegradable copolymers of dextran grafted with aliphatic polyesters first requires the preparation of polysaccharide derivatives soluble in organic solvents. Silylation of dextran can thus lead to such organosoluble derivatives and allows the polymerization of cyclic esters initiated from the nonsilylated OH functions. Silylation of dextran was studied in DMSO by different reactants such as 1,1,1,3,3,3-hexamethyldisilazane (HMDS) in the presence of various catalysts and N,O-bis(trimethylsilyl)acetamide (BSA). According to the silylating agent and the used experimental conditions, it was possible to obtain highly or totally silylated dextrans. In parallel, an investigation of the chemical stability of the dextran chain during silylation was performed. Thus, it was found that, when used at 50 degrees C, HMDS with or without catalysts gives a relatively high silylation yield and does not alter the dextran chain length, whereas at 80 degrees C, dextran degradation was observed. BSA is a very good silylating agent, which allows reaching 100% silylation even at 50 degrees C but provokes the degradation of the polysaccharide chains. The work was completed by a study of the reactivity order of the glucosidic OH functions toward silylation reaction. This order was found to be (OH(2) > OH(4) > OH(3)) as already reported for other reactions. 2D-NMR of highly silylated dextrans demonstrated that they are constituted of both quantitatively silylated glucose units and two types of disilylated ones.

Dextrans↗

Chemical modification of deoxycytidine at different sites yields adducts of different stabilities: characterization of N3- and O2-deoxycytidine and N3-deoxyuridine adducts of butadiene monoxide.

Eight adducts were characterized from the reaction of deoxycytidine with the chemical carcinogen, butadiene monoxide (BM). They were identified as diastereomeric pairs of N3-(2-hydroxy-3-buten-1-yl)deoxycytidine, N3-(2-hydroxy-3-buten-1-yl)deoxyuridine, N3-(1-hydroxy-3-buten-2-yl)deoxyuridine, and O2-(2-hydroxy-3-buten-1-yl)deoxycytidine based on UV spectra, 1H NMR, FAB/MS, and stability studies. The N3-(2-hydroxy-3-buten-1-yl)deoxycytidine adducts were unstable at pH 7.4, 37 degrees C, and deaminated to the corresponding N3-deoxyuridine adducts with half-lives of 2.3 and 2.5 h. The N3-(1-hydroxy-3-buten-2-yl)deoxycytidine diastereomers were not detected, apparently because of faster rates of deamination compared to the N3-(2-hydroxy-3-buten-1-yl)deoxycytidine adducts. The corresponding four N3-deoxyuridine adducts were stable for up to 168 h. The O2-deoxycytidine adducts were unstable and decomposed with a half-life of 11 h. The N3-(2-hydroxy-3-buten-1-yl)deoxycytidine adducts were initially the major adducts formed upon reaction of deoxycytidine with BM at 37 degrees C in phosphate buffer (pH 7.4), but the corresponding N3-deoxyuridine adducts showed a lag in formation due to the time needed for deamination. The N3-(1-hydroxy-3-buten-2-yl)deoxyuridine and O2-deoxycytidine adducts had linear formation rates, but were formed to a lesser extent. Heating the reaction mixture at 80 degrees C for 1 h converted all N3-deoxycytidine adducts to the stable N3-deoxyuridine adducts. Incubation of deoxycytidine with an excess of BM at pH 7.4, 37 degrees C, followed by the extraction and heating steps allowed calculation of the pseudo-first-order kinetic rate constants for the four uridine adducts. If the heating step was eliminated, then the pseudo-first-order kinetic rate constants could be calculated for the N3-(2-hydroxy-3-buten-1-yl)deoxycytidine and O2-(2-hydroxy-3-buten-1-yl)deoxycytidine adducts. The rate constants for N3-(2-hydroxy-3-buten1-yl)deoxycytidine and the corresponding N3-(2-hydroxy-3-buten-1-yl)deoxyuridine were five- to sixfold the rate constants for the N3-(1-hydroxy-3-buten-2-yl)deoxyuridine and O2-(2-hydroxy-3-buten-1-yl)deoxycytidine adducts. Thus, the results show that the reaction of deoxycytidine with BM yields adducts at different sites with different rates of formation and stabilities. Understanding the chemical interactions of deoxycytidine with BM and the stability of the various adducts may contribute to a better understanding of the molecular mechanisms of mutagenesis and carcinogenesis of BM and the development of useful biomarkers of exposure.

Carcinogens↗

Evaluating extraction and storage of a recombinant protein produced in agroinfiltrated lettuce.

Extraction and storage of a recombinant protein produced by transient expression following agroinfiltration of lettuce were investigated. Lettuce leaves expressing beta-glucuronidase (GUS) were extracted by homogenization in several buffer combinations, and the yield and stability were assessed. The reducing agent dithiothreitol (DTT) was found to be the most important (significant) component in the extraction buffer. An extraction buffer consisting of 50 mM sodium phosphate at pH 7.0 with 10 mM DTT produced a good yield and stabilized GUS. Leaching of GUS through intact agroinfiltrated lettuce leaves was determined to be infeasible, with a maximum flux of 10 microg GUS/h/m2 and recovery of 1.7% of the GUS content in 24 h. Freeze-drying was evaluated as a method to extend the shelf life of the perishable leaf material containing GUS. First- and second-order kinetic models and the Weibull distribution were compared to describe inactivation of GUS in the freeze-dried leaves and leaf extracts. The first-order model best fit the inactivation data. An Arrhenius model fit the first-order inactivation data with respect to temperature with R2 = 1.00. Freeze-drying the lettuce leaves extended the estimated half-life of GUS to 69 days at 21 degrees C versus 11 days at 4 degrees C for fresh lettuce.

Dithiothreitol↗

Effect of slotted wing tips on yawing moment characteristics.

The aerodynamic yawing moment characteristics of bird wings with slotted tips are dealt with. Emphasis is placed on the effect of sweep which the separated feathers constituting the wing tips show and which can reach significant values. Reference is made to basic aerodynamic characteristics of wings with sweep which yields a stabilizing yawing moment significantly larger than that of unswept wings. Then, the yawing moment characteristics are determined for a wing, the features of which are considered as representative of bird wings with sweep in their slotted tips. A sophisticated aerodynamic procedure is used for obtaining results of high precision. It is shown that the sweep in the slotted wing tips yields a stabilizing yawing moment of significant magnitude, considerably increasing with the lift coefficient. To make the significance of wing tip sweep for the ability to generate yawing moments more perspicuous, a wing modification the slotted tips of which are unswept is considered for comparison. It turns out that this wing shows yawing moments which are substantially smaller. A physical insight into the effect of slotted wing tip sweep on the aerodynamic yawing moment characteristics is provided by showing the underlying mechanism. From the results presented in this paper it follows that the sweep in slotted wing tips provides a substantial contribution to the aerodynamic yawing moment and, thus, to yaw stability. It may be concluded that this is an essential reason why there is sweep in the slotted tips of bird wings.

Animals↗

Relationship between thermal stability, degradation rate and expression yield of barnase variants in the periplasm of Escherichia coli.

An advantage of exporting a recombinant protein to the periplasm of Escherichia coli is decreased proteolysis in the periplasm compared with that in the cytoplasm. However, protein degradation in the periplasm also occurs. It has been widely accepted that the thermodynamic stability of a protein is an important factor for protein degradation in the cytoplasm of E.coli. To investigate the effect of the thermodynamic stability of an exported protein on the extent of proteolysis in the periplasm, barnase (an extracellular ribonuclease from Bacillus amyloliquefaciens) fused to alkaline phosphatase leader peptide was used as a model protein. A set of singly or doubly mutated barnase variants were constructed for export to the E.coli periplasm. It was found that the half-life of the barnase variants in vivo increased with their thermodynamic stability in vitro. A dominant factor for the final yield of exported barnase was not exportability but the turnover rate of the barnase variant. The yield of a stabilized mutant was up to 50% higher than that of the wild type. This suggests that exporting a protein to the periplasm and using protein engineering to enhance the stability can be combined as a strategy to optimize the production of recombinant proteins.

Bacillus↗

Randomized radiostereometric study comparing osteogenic protein-1 (BMP-7) and autograft bone in human noninstrumented posterolateral lumbar fusion: 2002 Volvo Award in clinical studies.

STUDY DESIGN: Randomized efficacy trial comparing two types of noninstrumented posterolateral fusion between L5 and S1 in patients with L5 spondylolysis and vertebral slip less than 50%, as evaluated by radiostereometric analysis. OBJECTIVE: To determine whether osteogenic protein-1 (BMP-7) in the OP-1 Implant yields better stabilizing bony fusion than autograft bone. SUMMARY OF BACKGROUND DATA: Animal studies of osteoinductive proteins in noninstrumented posterolateral fusions have shown high fusion rates. No similar conclusive study on humans has been performed. METHODS: For this study, 20 patients were randomized to fusion with either OP-1 Implant or autograft bone from the iliac crest, 10 in each group. The patients were instructed to keep the trunk straight for 5 months after surgery with the aid of a soft lumbar brace. At surgery 0.8-mm metallic markers were positioned in L5 and the sacrum, enabling radiostereometric follow-up analysis during 1 year. The three-dimensional vertebral movements, as measured by radiostereometric analysis induced by positional change from supine posture to standing and sitting, were calculated with an accuracy of 0.5 to 0.7 mm and 0.5 degrees to 2.0 degrees. Conventional radiography was added. RESULTS: No significant difference was noted between the radiostereometric and radiographic results of fusion with the OP-1 Implant and fusion with autograft bone. There was a significant relation between reduced vertebral movements and better bone formation. No adverse effects of the OP-1 Implant occurred. Persistent minor pain at the iliac crest was noticed in one patient. CONCLUSIONS: There was no significant difference between the two fusion versions. Thus, the OP-1 Implant did not yield better stabilizing bony fusion than autograft bone.

Adult↗

Production of yellow fever 17DD vaccine virus in primary culture of chicken embryo fibroblasts: yields, thermo and genetic stability, attenuation and immunogenicity.

While a good vaccine against yellow fever (YF) virus has been available for decades, the basic technology for the production of YF vaccine in chicken embryos has remained substantially unchanged since the 1940s. Here we describe the highly efficient and economic production of the 17DD strain of YF virus in chicken embryo fibroblast (CEF) cell cultures with viral titers ranging from 6.3 to 6.7 log10PFU/mL. Thermostability of two different formulations (5 and 50-dose vials) of the CEF vaccine virus was found to be as high as the current vaccines retaining the minimal titer required for YF 17D vaccines. The production passage in CEF did not lead to the selection of genetic variants as shown by nucleotide sequence analyses of the CEF-derived vaccine lots or the sequence of viruses recovered from monkeys experimentally inoculated with the CEF virus. YF 17DD virus produced in CEF was also indistinguishable from its seed lot virus parent in terms of plaque size and immunogenicity in mice and monkeys. Comparison of the CEF virus and the seed lot virus made in chicken embryo in the internationally accepted monkey neurovirulence test (MNVT) revealed a higher clinical score for the former. The differences in central nervous system (CNS) histological scores for monkeys inoculated with the chicken embryo and experimental CEF vaccines were at the borderline level of statistical significance. These data warrant further studies on the monkey attenuation of other batches of CEF-derived vaccines.

Animals↗

Ozonolysis of alpha-pinene and beta-pinene: kinetics and mechanism.

A combined quantum-chemical and RRKM/ME (ME--master equation) approach is employed to investigate the structures, energetics, and kinetics of intermediate and stable species, and the yields of stabilized carbonyl oxides and OH radicals from the alpha-pinene and beta-pinene ozonolysis reactions. The cycloaddition of O(3) is highly exothermic, with the reaction energies of 55.1 and 51.1 kcal mol(-1) for alpha- and beta-pinenes, respectively. Cleavage of primary ozonides yields carbonyl oxides with the barrier height of 12.2-17.5 kcal mol(-1). For the prompt reactions of carbonyl oxides from alpha- and beta-pinene ozonolysis, H migration to hydroperoxides represents the dominant pathway over ring closure to dioxiranes. The kinetic calculations indicate a significant portion of stabilization for alpha- and beta-carbonyl oxides. The yields of stabilized carbonyl oxides are estimated to be 0.34 for alpha-pinene and 0.22 for beta-pinene. The applicability of theoretical methods for investigation of oxidation reactions of large hydrocarbon molecules is demonstrated.

Bicyclic Monoterpenes↗