bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward a framework for sulfoproteomics: Synthesis and characterization of sulfotyrosine‐containing peptides
Authors: Seibert Christoph , Sakmar Thomas P. 
Published: August 2007

AbstractTyrosine sulfation is one of the most common post‐translational modifications in secreted and transmembrane proteins and a key modulator of extracellular protein‐protein interactions. Several proteins known to be tyrosine sulfated play important roles in physiological processes, and in some cases a direct link between protein function and tyrosine sulfation has been established. In blood coagulation, tyrosine sulfation of factor VIII is required for efficient binding of von Willebrand factor; in leukocyte adhesion, tyrosine sulfation of the P‐selectin glycoprotein ligand‐1 mediates high‐affinity binding to P‐selectin; and in leukocyte chemotaxis, tyrosine sulfation of chemokine receptors is required for optimal interaction with chemokine ligands. Furthermore, tyrosine sulfation has been implicated in several infectious diseases. In particular, tyrosine sulfation of the HIV‐1 co‐receptor CCR5 is required for viral entry into host cells and tyrosine sulfation of the Duffy antigen/receptor for chemokines is crucial for erythrocyte invasion by the malaria parasite plasmodium vivax. Despite increasing interest in tyrosine sulfation in recent years, the sulfoproteome still remains largely unexplored. To date, only a relatively small number of sulfotyrosine‐containing peptides and proteins have been identified, and a specific role for tyrosine sulfation has not been established for most of these. Here, we provide an overview of the biology and enzymology of tyrosine sulfation and discuss recent developments in preparative and analytical methods that are central to sulfoproteome research. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 459–477, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprintversion. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley. com
Evidence of species succession during chlorobenzene biodegradation
Authors: Baptista I.I.R. , Zhou N.Y. , Emanuelsson E.A.C. , Peeva L.G. , Leak D.J. , Mantalaris A. , Livingston A.G. 
Published: August 2007

AbstractWe have previously reported the disappearance of a specific strain degrading chlorobenzene from a functionally stable bioreactor. In the present work, we investigated this species succession and isolated a new dominant strain, identified as Pandoraea pnomenusa sp. strain MCB032. A specific 16S rRNA‐targeted oligonucleotide probe was designed and validated to identify strain MCB032 using fluorescence in situ hybridisation (FISH). The results confirmed the presence of strain MCB032 in samples collected over time, and showed that it was primarily located within the biofilm. Denaturing gradient gel electrophoresis (DGGE) provided evidence that the species succession occurred early in the operating period. The application of these biomolecular tools highlighted the remarkable stability of this new strain during the 15 months of reactor operation. The succession was attributed to the competitive kinetic behaviour of strain MCB032, which exhibited faster growth (µmax = 0.34 h−1) and higher substrate affinity (Ks = 0.35 mg L−1) than strain JS150. Finally, this study contributed to the characterisation of the recently established Pandoraea genus, an emerging group in the biodegradation field. Biotechnol. Bioeng. 2008;99: 68–74. © 2007 Wiley Periodicals, Inc.
A semicontinuous 3‐column countercurrent solvent gradient purification (MCSGP) process
Authors: Aumann Lars , Morbidelli Massimo 
Published: August 2007

AbstractThe recently developed continuous Multicolumn Countercurrent Solvent Gradient Purification (MCSGP) Process has been reduced to a fully equivalent semicontinuous setup with only three chromatographic columns and three gradient pump modules. Actually the 3‐column MCSGP unit can even achieve better performance than the original 6‐column process due to an additional degree of freedom, that is a different switching time for the “batch lane” and the “interconnected lane.” Experimental results for the 3‐column MCSGP unit of the purification of an industrial multicomponent peptide mixture containing 46% of Calcitonin on a reversed phase resin are compared with model simulations. It is concluded, that the model is well suited to predict the system behavior and therefore to design its optimal operating conditions. Biotechnol. Bioeng. 2008;99: 728–733. © 2007 Wiley Periodicals, Inc.
A study of the influence of yeast cell debris on protein and α‐glucosidase adsorption at various zones within the expanded bed using In‐Bed sampling
Authors: Balasundaram B. , Harrison S.T.L. , Li J. , Chase H.A. 
Published: August 2007

AbstractExpanded bed adsorption chromatography is used to capture products directly from unclarified feedstocks, thus combining solid–liquid separation, product concentration and preliminary purification into a single step. However, when non‐specific ion‐exchangers are used as the adsorbent in the expanded bed, there is the possibility that electrostatic interactions of cells or cell debris with the adsorbent may interfere with the adsorption of soluble products. These interactions depend on the particle size of the cell debris and its surface charge, which in turn depend on the extent of disruption used to release the intracellular products. The interactions occurring during expanded bed adsorption between the anionic ion‐exchanger STREAMLINE DEAE and particulate yeast homogenates obtained by high pressure homogenisation at different intensities of disruption achieved by operating at different pressures were studied, while maintaining all other parameters constant. In‐bed sampling from the expanded bed using ports fitted up the height of expanded bed was used to study the retention of yeast cells and cell debris within the bed and its influence on the adsorption of total soluble protein and α‐glucosidase within various zones of the expanded bed. The retention of the biomass present in the homogenate obtained at a lower intensity of disruption was found to be high at the lower end of the column (17% from 13.8 MPa sample compared to 1% from 41.4 MPa sample). This interaction of the particulate material with the adsorbent was found to reduce the dynamic binding capacity of the adsorbent for total soluble protein from 3.6 mg/mL adsorbent for 41.4 MPa sample to 3.0 mg/mL adsorbent for 13.8 MPa sample. The adsorption of α‐glucosidase was found to increase with an increase in the concentration of the enzyme in the feed, which increased with the intensity of disruption. Selective adsorption of 6,732 U α‐glucosidase per mg of total protein bound, was noticed for the feedstock prepared at a higher disruption intensity at 41.4 MPa compared to adsorption of 1,262 U/mg of total protein bound for that prepared at 13.8 MPa. The selective adsorption of α‐glucosidase due to its high concentration together with simultaneous high specific activity of the enzyme in the feed indicated the significance of selective release of enzymes during microbial cell disruption for efficient expanded bed adsorption processes. Biotechnol. Bioeng. 2008;99: 614–624. © 2007 Wiley Periodicals, Inc.
Detection of chrysotile asbestos by using a chrysotile‐binding protein
Authors: Kuroda Akio , Nishimura Tomoki , Ishida Takenori , Hirota Ryuichi , Nomura Kazutaka 
Published: August 2007

AbstractIn the current studies, we found that the DksA protein from Escherichia coli binds strongly to chrysotile, which is the most commonly used form of asbestos. We developed a convenient colorimetric assay for chrysotile using a fusion of DksA and alkaline phosphatase along with 5‐bromo‐4‐chloro‐3‐indolyl‐phosphate and nitro blue tetrazolium as substrates. Also, using a fusion of DksA and green‐fluorescent protein, we were able to detect chrysotile by fluorescence microscopy. Biotechnol. Bioeng. 2008;99: 285–289. © 2007 Wiley Periodicals, Inc.
Production and separation of manganese peroxidase from heme amended yeast cultures
Authors: Jiang Fei , Kongsaeree Puapong , Charron Rose , Lajoie Curtis , Xu Haowen , Scott Gary , Kelly Christine 
Published: August 2007

AbstractA method for the production and concentration of the lignin‐degrading enzyme, manganese peroxidase (rMnP), was developed using the yeast Pichia pastoris in high cell density, fed‐batch cultivations. A gene encoding manganese peroxidase (mnp1) from the white‐rot fungus Phanerochaete chrysosporium was cloned into a protease deficient (pep4−) strain of the methylotrophic yeast P. pastoris. Heme is an important cofactor for active rMnP production, and amendment of yeast cultures with heme increased active rMnP concentrations. In both shake‐flasks and fed‐batch bioreactors, the relationship between heme concentration and rMnP activity was logarithmic, with increasing heme concentrations resulting in progressively lesser increases in enzyme activity. Scale‐up from shake‐flasks to 2 L fed‐batch cultivations increased rMnP activities from 200 U/L to 2,500 U/L, with addition of 0.1 g/L heme (added heme per liquid volume) at the beginning of the fed‐batch phase resulting in higher enzyme activities than addition at the beginning of the batch phase. A combination of centrifugation, acetone precipitation, dialysis, and freeze drying was found to be effective for concentrating the rMnP from 2,500 U/L in the P. pastoris bioreactor culture to 30,000 U/L in 0.1 M potassium phosphate buffer pH 6. The rMnP recovery yield was 60% and the purity was 1–4%. By using 0.1 g/L heme during the fed‐batch cultivation, the heme content of the final enzyme preparation could be reduced by 97%, and had sufficiently high rMnP activity and low enough color to be suitable for pulp bleaching experiments. Biotechnol. Bioeng. 2008;99: 540–549. © 2007 Wiley Periodicals, Inc.
Redesigning the substrate specificity of ω‐aminotransferase for the kinetic resolution of aliphatic chiral amines
Authors: Cho Byung‐Kwan , Park Hyung‐Yeon , Seo Joo‐Hyun , Kim Juhan , Kang Taek‐Jin , Lee Bon‐Su , Kim Byung‐Gee 
Published: August 2007

AbstractSubstrate specificity of the ω‐aminotransferase obtained from Vibrio fluvialis (ω‐ATVf) was rationally redesigned for the kinetic resolution of aliphatic chiral amines. ω‐ATVf showed unique substrate specificity toward aromatic amines with a high enantioselectivity (E > 100) for (S)‐enantiomers. However, the substrate specificity of this enzyme was much narrower toward aliphatic amines. To overcome the narrow substrate specificity toward aliphatic amines, we redesigned the substrate specificity of ω‐ATVf using homology modeling and the substrate structure‐ activity relationship. The homology model and the substrate structure‐activity relationship showed that the active site of ω‐ATVf consists of one large substrate‐binding site and another small substrate‐binding site. The key determinant in the small substrate‐binding site was D25, whose role was expected to mask R415 and to generate the electrostatic repulsion with the substrate's α‐carboxylate group. In the large substrate‐binding site, R256 was predicted to recognize the α‐carboxylate group of substrate thus obeying the dual substrate recognition mechanism of aminotransferase subgroup II enzymes. Among the several amino acid residues in the large substrate‐binding site, W57 and W147, with their bulky side chains, were expected to restrict the recognition of aliphatic amines. Two mutant enzymes, W57G and W147G, showed significant changes in their substrate specificity such that they catalyzed transamination of a broad range of aliphatic amines without losing the original activities toward aromatic amines and enantioselectivity. Biotechnol. Bioeng. 2008;99: 275–284. © 2007 Wiley Periodicals, Inc.
Development of a simple and rapid method for producing non‐fucosylated oligomannose containing antibodies with increased effector function
Authors: Zhou Qun , Shankara Srinivas , Roy Andre , Qiu Huawei , Estes Scott , McVie‐Wylie Alison , Culm‐Merdek Kerry , Park Anna , Pan Clark , Edmunds Tim 
Published: August 2007

AbstractGlycosylation in the Fc region of antibodies has been shown to play an important role in antibody function. In the current study, glycosylation of human monoclonal antibodies was metabolically modulated using a potent α‐mannosidase I inhibitor, kifunensine, resulting in the production of antibodies with oligomannose‐type N‐glycans. Growing Chinese hamster ovary cells for 11 days in batch culture with a single treatment of kifunensine was sufficient to elicit this effect without any significant impact on cell viability or antibody production. Antibodies expressed in the presence of kifunensine at a concentration as low as 60 ng/mL contained mainly oligomannose‐type glycans and demonstrated increased ADCC activity and affinity for FcγRIIIA, but reduced C1q binding. Although the kifunensine‐mediated shift to oligomannose‐type glycans could, in theory, result in rapid clearance of the antibody through increased mannose receptor binding, the serum levels of antibody in mice were not significantly altered up to 168 h following injection. The use of kifunensine provides a simple and rapid method for the production of antibodies with increased ADCC without the time‐consuming need to re‐engineer either the antibody molecule or the host cell line. Biotechnol. Bioeng. 2008;99: 652–665. © 2007 Wiley Periodicals, Inc.
Cells for bioartificial liver devices: The human hepatoma‐derived cell line C3A produces urea but does not detoxify ammonia
Authors: Mavri‐Damelin Demetra , Damelin Leonard H. , Eaton Simon , Rees Myrddin , Selden Clare , Hodgson Humphrey J.F. 
Published: August 2007

AbstractExtrahepatic bioartificial liver devices should provide an intact urea cycle to detoxify ammonia. The C3A cell line, a subclone of the hepatoma‐derived HepG2 cell line, is currently used in this context as it produces urea, and this has been assumed to be reflective of ammonia detoxification via a functional urea cycle. However, based on our previous findings of perturbed urea‐cycle function in the non‐urea producing HepG2 cell line, we hypothesized that the urea produced by C3A cells was via a urea cycle‐independent mechanism, namely, due to arginase II activity, and therefore would not detoxify ammonia. Urea was quantified using 15N‐ammonium chloride metabolic labelling with gas chromatography–mass spectrometry. Gene expression was determined by real‐time reverse transcriptase‐PCR, protein expression by western blotting, and functional activities with radiolabelling enzyme assays. Arginase inhibition studies used Nω‐hydroxy‐nor‐L‐arginine. Urea was detected in C3A conditioned medium; however, 15N‐ammonium chloride‐labelling indicated that 15N‐ammonia was not incorporated into 15N‐labelled urea. Further, gene expression of two urea cycle genes, ornithine transcarbamylase and arginase I, were completely absent. In contrast, arginase II mRNA and protein was expressed at high levels in C3A cells and was inhibited by Nω‐hydroxy‐nor‐L‐arginine, which prevented urea production, thereby indicating a urea cycle‐independent pathway. The urea cycle is non‐functional in C3A cells, and their urea production is solely due to the presence of arginase II, which therefore cannot provide ammonia detoxification in a bioartificial liver system. This emphasizes the continued requirement for developing a component capable of a full repertoire of liver function. Biotechnol. Bioeng. 2008;99: 644–651. © 2007 Wiley Periodicals, Inc.
Genetic engineering of a lysosomal enzyme fusion protein for targeted delivery across the human blood‐brain barrier
Authors: Boado Ruben J. , Zhang Yun , Zhang Yufeng , Xia Chun‐fang , Wang Yuntao , Pardridge William M. 
Published: August 2007

AbstractMucopolysaccharidosis Type I, Hurler's Syndrome, is a lysosomal storage disorder that affects the brain. The missing enzyme, α‐L‐iduronidase (IDUA), does not cross the blood‐brain barrier (BBB). To enable BBB transport of the enzyme, human IDUA was fused to the carboxyl terminus of the heavy chain of a chimeric monoclonal antibody (MAb) to the human insulin receptor (HIR). The HIRMAb crosses the BBB on the endogenous insulin receptor, and acts as a molecular Trojan horse to ferry into brain the IDUA. Transfection of COS cells resulted in high levels of IDUA enzyme activity both in the medium and in the intracellular space. The size of the fusion heavy chain, as measured with Western blotting and antibodies to either human IDUA or human IgG, was increased about 80 kDa, relative to the size of the heavy chain of the parent HIRMAb. The IDUA enzyme specific activity of the affinity purified HIRMAb‐IDUA fusion protein was 363 ± 37 U/µg protein, which is comparable to specific activity of recombinant IDUA. The accumulation of glycosoaminoglycans in Hurler fibroblasts was decreased 70% by treatment with the HIRMAb‐IDUA fusion protein. Confocal microscopy showed targeting of the fusion protein to the lysosome. The HIRMAb‐IDUA fusion protein bound with high affinity to the HIR, and was rapidly transported into the brain of the adult Rhesus monkey following intravenous administration. The HIRMAb‐IDUA fusion protein is a new treatment for Hurler's syndrome, which has been specifically engineered to cross the human BBB. Biotechnol. Bioeng. 2008;99: 475–484. © 2007 Wiley Periodicals, Inc.
Large‐scale production of endotoxin‐free plasmids for transient expression in mammalian cell culture
Authors: Rozkov Aleksei , Larsson Bert , Gillström Stefan , Björnestedt Robert , Schmidt Stefan R. 
Published: August 2007

AbstractTransient expression of recombinant proteins in mammalian cell culture in a 100‐L scale requires a large quantity of plasmid that is very labour intensive to achieve with shake flask cultures and commercially available plasmid purification kits. In this paper we describe a process for plasmid production in 100‐mg scale. The fermentation is carried out in a 4‐L fed‐batch culture with a minimal medium. The detection of the end of batch and triggering the exponential (0.1 h−1) feed profile was unattended and controlled by Multi‐fermenter Control System. A restricted specific growth rate in fed‐batch culture increased the specific plasmid yield compared to batch cultures with minimal and rich media. This together with high biomass concentration (68–107 g L−1 wet weight) achieves high volumetric yields of plasmid (95–277 mg L−1 depending on the construct). The purification process consisted of alkaline lysis, lysate clarification and ultrafiltration, two‐phase extraction with Triton X‐114 for endotoxin removal, anion‐exchange chromatography as a polishing step, ultrafiltration and sterile filtration. Both fermentation and purification processes were used without optimisation for production of four plasmids yielding from 39 to 163 mg of plasmids with endotoxin content of 2.5 EU mg−1 or less. Biotechnol. Bioeng. 2008;99: 557–566. © 2007 Wiley Periodicals, Inc.
The bactericidal effect of ultraviolet and visible light on Escherichia coli
Authors: Vermeulen Natasha , Keeler Werden J. , Nandakumar Kanavillil , Leung Kam Tin 
Published: August 2007

AbstractThe bactericidal radiation dosages at specific wavelengths in the ultraviolet (UV)–visible spectrum are not well documented. Such information is important for the development of new monochromatic bactericidal devices to be operated at different wavelengths. In this study, radiation dosages required to cause mortality of an Escherichia coli strain, ATCC 25922, at various wavelengths between 250 and 532 nm in the UV and visible spectrum were determined. Radiation at 265 nm in the UV region was most efficient in killing the E. coli cells and 100% mortality was achieved at a dose of 1.17 log mJ/cm2. In the visible spectrum, the radiation dosages required for a one‐log reduction of the E. coli cell density at 458 and 488 nm were 5.5 and 6.9 log mJ/cm2, respectively. However, at 515 and 532 nm, significant killing was not observed at radiation dosage up to 7 log mJ/cm2. Based on the cell survival data at various radiation dosages between 250 and 488 nm, a predictive equation for the survival of E. coli cells is derived, namely log(S/S0) =  −(1.089 × 107 e−0.0633λ)D. The symbols, S0, S, λ, and D, represent initial cell density, cell density after irradiation, wavelength of the radiation and radiation dosage, respectively. The proportion of the surviving E. coli cells decreases exponentially with the increase in radiation dosage at a given wavelength. In addition, the radiation dose required for killing a certain fraction of the E. coli cells increases exponentially as the wavelength of radiation increases. Bioeng. 2008;99: 550–556. © 2007 Wiley Periodicals, Inc.
Accelerated cell line development using two‐color fluorescence activated cell sorting to select highly expressing antibody‐producing clones
Authors: Sleiman Robert J. , Gray Peter P. , McCall Martin N. , Codamo Joe , Sunstrom Noelle‐Ann S. 
Published: August 2007

AbstractThe success of engineered monoclonal antibodies as biopharmaceuticals has generated considerable interest in strategies designed to accelerate development of antibody expressing cell lines. Stable mammalian cell lines that express therapeutic antibodies at high levels typically take 6–12 months to develop. Here we describe a novel method to accelerate selection of cells expressing recombinant proteins (e.g., antibodies) using multiparameter fluorescence activated cell sorting (FACS) in association with dual intracellular autofluorescent reporter proteins. The method is co‐factor‐independent and does not require complex sample preparation. Chinese hamster ovary (CHO) clones expressing high levels of recombinant antibody were selected on the basis of a two‐color FACS sorting strategy using heavy and light chain‐specific fluorescent reporter proteins. We were able to establish within 12 weeks of transfection cell lines with greater than a 38‐fold increase in antibody production when compared to the pool from which they were isolated, following a single round of FACS. The method provides a robust strategy to accelerate selection and characterization of clones and builds a foundation for a predictive model of specific productivity based upon on two‐color fluorescence. Biotechnol. Bioeng. 2008;99: 578–587. © 2007 Wiley Periodicals, Inc.
Anti‐Carbohydrate Antibodies Elicited by Polyvalent Display on a Viral Scaffold
Authors: Kaltgrad Eiton , Sen Gupta Sayam , Punna Sreenivas , Huang Cheng‐Yuan , Chang Aileen , Wong Chi‐Huey , Finn M. G. , Blixt Ola 
Published: August 2007

AbstractTetra‐ and hexasaccharides were arrayed on the exterior surface of cowpea mosaic virus by using a copper‐catalyzed azide–alkyne cycloaddition reaction. Inoculation of chickens with these virus conjugates gave rise to large quantities of polyclonal anti‐glycan IgY antibodies that displayed excellent avidity and specificity on analysis with printed glycan microarrays. Avian IgY antibodies are produced in significantly higher yield than is possible for mouse or rabbit IgG, and exhibit reduced cross reactivity with native mammalian proteins. For a tri‐LacNAc antigen, affinity purification against immobilized mono‐LacNAc was necessary to provide a set of antibodies with specific binding properties. Comparable performance was observed for the virus‐based polyclonal versus a commercial monoclonal antibody raised against the globo‐H tetrasaccharide; this highlights the utility of the glycan microarray for both quality control and rapid in‐depth analysis. Virus–carbohydrate conjugates are promising candidates for development in diagnostic and immunotherapeutic applications.