bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behavior of Aromatic Compounds Contained in Kraft Mill Effluents Treated by an Aerated Lagoon
Authors: Chamorro S. , Xavier C. R. , Vidal G. 
Published: October 2005

AbstractKraft mill effluents were biologically treated in an aerated lagoon (AL) (3.4 L) to evaluate the behavior of aromatic compounds by UV‐vis spectroscopy. Under aerobic conditions, biological oxygen demand (BOD5) removal was between 84% and 95%, whereas soluble chemical oxygen demand (CODs) removal ranged between 40% and 60%. A slight increase was observed in the VIS436/CODs relationship (0.101–0.110), indicating that color reduction was less than the total organic matter reduction expressed by CODs. Additionally, low values of UV254/UV280 (1.23–1.12) indicate the presence of lignin‐derived compounds in the aerobic effluent relationship. Ultrafiltration (UF) analysis shows that color was concentrated in the molecular weight fraction larger than 10 000 Da. The recalcitrant fraction was found to be resistant to further biodegradation, even under optimized microbiological conditions.
Engineered Saccharomycescerevisiae Strain BioS‐OS1/2, for the Detection of Oxidative Stress
Authors: Jayaraman Muralidharan , Radhika V. , Bamne Mikhil N. , Ramos Ross , Briggs Rita , Dhanasekaran Danny N. 
Published: October 2005

AbstractOne of the major stress factors during space and high‐altitude flight is the oxidative damage caused by the release of reactive oxygen intermediates (ROIs) in human tissues. ROIs are released in response to several stress factors including radiation in space. Since ROIs contribute to several pathological conditions, there has been a great interest in developing a biosensor that can monitor the impact of ROIs on biological systems. Toward this goal, we sought to engineer a yeast stain that can monitor oxidative stress and be easily integrated into a biosensor platform. Saccharomyces cerevisiae respond to hyperoxidative stress by activating the expression of many proteins including the transcription factor, Yap1. Activated Yap1 primarily binds to the Yap‐1 response elements in the promoters of genes that combat oxidative stress. Based on these observations, we genetically altered the Yap‐1 pathway in the YCR094W BY4742 strain of S. cerevisiae by fusing the YREs in the promoter region of TRX2 gene to a cDNA‐insert encoding green fluorescent protein (GFP). Exposure of this engineered yeast strain BioS‐OS1 to varying levels of oxidative stress, as generated by different concentrations of H2O2 or diamide, elicits robust expression of GFP that can be monitored by the fluorescence of GFP by as early as 1 h. BioS‐OS1 can detect a H2O2 concentration from 300 μM onward. We also show that the signaling strength of the strain can be increased by engineering multiple YREs in the upstream of the cDNA‐insert encoding GFP. Thus, the results presented here demonstrate that the engineered BioS‐OS yeast strain can detect ROI‐generating oxidative stress and validate the use of this prototypic strain for the development of a biosensor to detect and monitor oxidative stress factors during space and high altitude flights.
Production of GFP and Glucoamylase by Recombinant Aspergillusniger: Effects of Fermentation Conditions on Fungal Morphology and Protein Secretion
Authors: Talabardon Mylene , Yang Shang‐Tian 
Published: October 2005

AbstractThe effect of filamentous fungal morphology on heterologous protein secretion was investigated using the recombinant Aspergillus niger strain AB4.1[pgpdAGLAGFP], which contained the gene coded for the GLA‐GFP (glucoamylase‐green fluorescence protein) fusion protein. Three culturing systems were studied to develop different morphological forms of the fungus. Free‐cell cultures in conventional stirred‐tank bioreactors grew in pellet form with various sizes depending on culturing conditions. Cells immobilized on cotton cloth grew in mycelial form in a rotating fibrous bed (RFB) and a static fibrous bed (SFB) bioreactors. The expression of the fusion protein was growth‐associated and dependent on the fungal morphology. Immobilized cells produced 10‐fold more GFP and glucoamylase than well‐oxygenated free‐cell pellets. In free‐cell cultures, excretion of the fusion protein occurred mainly from cell autolysis, when oxygen or nutrient were depleted, whereas protein secretion took place from the beginning of the fermentation in immobilized‐cell cultures. Also, protein secretion was found to be strongly dependent on morphology. Small pellets of a 1‐mm size secreted 82% of GFP produced, whereas 43% of GFP remained intracellular in larger pellets of 5 mm. Complete secretion of GFP was obtained with cells immobilized on the fibrous matrix. The improvement in heterologous protein synthesis and secretion can be attributed to the filamentous mycelial morphology since protein secretion occurred predominantly at the tips of growing hyphae. Secretion of proteases occurred mainly in the stationary phase or when cell autolysis were induced by nutrient depletion and was not dependent on morphology, although immobilizing the cells also reduced protease activity. The RFB bioreactor gave the best fermentation performance because of its ability to control the cell morphology that was amenable to efficient oxygen transfer and protein secretion.
An Approximate Solution for a Transient Two‐Phase Stirred Tank Bioreactor with Nonlinear Kinetics
Authors: Valdés‐Parada Francisco J. , Álvarez‐Ramírez José , Ochoa‐Tapia J. Alberto 
Published: October 2005

AbstractThe derivation of an approximate solution method for models of a continuous stirred tank bioreactor where the reaction takes place in pellets suspended in a well‐mixed fluid is presented. It is assumed that the reaction follows a Michaelis‐Menten‐type kinetics. Analytic solution of the differential equations is obtained by expanding the reaction rate expression at pellet surface concentration using Taylor series. The concept of a pelletapos;s dead zone is incorporated; improving the predictions and avoiding negative values of the reagent concentration. The results include the concentration expressions obtained for (a) the steady state, (b) the transient case, imposing the quasi‐steady‐state assumption for the pellet equation, and (c) the complete solution of the approximate transient problem. The convenience of the approximate method is assessed by comparison of the predictions with the ones obtained from the numerical solution of the original problem. The differences are in general quite acceptable.
Cytoplasmic Overexpression, Folding, and Processing of Penicillin Acylase Precursor in Escherichiacoli
Authors: Xu Yali , Hsieh Ming‐Yi , Narayanan Niju , Anderson William A. , Scharer Jeno M. , Moo‐Young Murray , Chou C. Perry 
Published: October 2005

AbstractPenicillin acylase (PAC) precursor, proPAC, was overproduced in a soluble or insoluble form in the cytoplasm of Escherichia coli through the expression of the leader‐less pac gene (ll‐pac) devoid of the coding region for the signal peptide of PAC. Also, a portion of the overexpressed proPAC was further processed to form mature PAC, indicating that the posttranslational processing steps for PAC maturation can occur in both the periplasm and the cytoplasm of E. coli. The cultivation performance for ll‐pac expression was limited by several factors, including (1) misfolding of proPAC, resulting in the aggregation of insoluble proPAC as inclusion bodies, (2) intracellular proteolysis, leading to the degradation of the overexpressed gene products, and (3) inefficient PAC maturation, limiting the formation of active PAC. The effect of coexpression of various cytoplasmic chaperones, including trigger factor, GroEL/ES, DnaK/J‐GrpE, and their combinations, on ll‐pac expression was investigated. Intracellular proteolysis of the overexpressed gene products could be prevented by coexpression of GroEL/ES. On the other hand, coexpression of trigger factor appeared to be able to facilitate the folding of soluble proPAC and to improve PAC maturation. The roles of trigger factor and GroEL/ES could be coordinated to significantly improve ll‐pac expression performance. DnaK/J‐GrpE had an effect for solublization of proPAC and perhaps, similar to trigger factor, for improving PAC maturation. The ll‐pac expression performance was also significantly improved through the simultaneous coexpression of DnaK/J‐GrpE and GroEL/ES. The results of the study suggest that the folding and/or processing of proPAC could be a major issue limiting the overproduction of PAC in E. coli and the bottleneck could be eliminated through the coexpression of appropriate chaperone(s).
Heuristic Optimization of Antibody Production by Chinese Hamster Ovary Cells
Authors: Sandadi Sandeepa , Ensari Semsi , Kearns Brian 
Published: October 2005

AbstractLarge‐scale production of monoclonal antibodies necessitates the development of a commercially viable process using the appropriate bioreactors, culture medium, and optimal feeding strategies. In the development of feeding strategies for higher antibody titers it is critical to assess the effects of limiting substrates on cell culture longevity and antibody production. In this study, glucose andl‐glutamine were identified as limiting substrates and their effects on culture longevity and antibody production were evaluated in small‐scale experiments. The results suggested that an optimal feeding strategy should account for the osmolality profile of the culture. The heuristic approach taken to optimize the antibody production showed that the fed‐batch cultivation is superior to batch culture and maintaining low osmolality during growth phase increases cumulative viable cell density and thus leads to higher final antibody titer.
Medium Term Planning of Biopharmaceutical Manufacture using Mathematical Programming
Authors: Lakhdar Kais , Zhou Yuhong , Savery James , Titchener‐Hooker Nigel J. , Papageorgiou Lazaros G. 
Published: October 2005

AbstractRegulatory pressures and capacity constraints are forcing the biopharmaceutical industry to consider employing multiproduct manufacturing facilities running on a campaign basis. The need for such flexible and cost‐effective manufacture poses a significant challenge for planning and scheduling. This paper reviews the problem of planning and scheduling of biopharmaceutical manufacture and presents a methodology for the planning of multiproduct biopharmaceutical manufacturing facilities. The problem is formulated as a mixed integer linear program (MILP) to represent the relevant decisions required within the planning process and is tested on two typical biopharmaceutical industry planning problems. The proposed formulation is compared with an industrial rule based approach, which it outperforms in terms of profitability. The results indicate that the developed formulation offers an effective representation of the planning problem and would be a useful decision tool for manufacturers in the biopharmaceutical industry particularly at times of limited manufacturing capacity.
Effects of Sulfuric Acid Loading and Residence Time on the Composition of Sugarcane Bagasse Hydrolysate and Its Use as a Source of Xylose for Xylitol Bioproduction
Authors: Silva Silvio S. , Matos Zuzel R. , Carvalho Walter 
Published: October 2005

AbstractA 22 full factorial design was employed to evaluate the effects of sulfuric acid loading and residence time on the composition of sugarcane bagasse hydrolysate obtained in a 250‐L reactor. The acid loading and the residence time were varied from 70 to 130 mg acid per gram of dry bagasse and from 10 to 30 min, respectively, while the temperature (121 °C) and the bagasse loading (10%) were kept constant. Both the sulfuric acid loading and the residence time influenced the concentrations of xylose and inhibitors in the hydrolysate. The highest xylose concentration (22.71 g/L) was achieved when using an acid loading of 130 mg/g and a residence time of 30 min. These conditions also led to increased concentrations of inhibiting byproducts in the hydrolysate. All of the hydrolysates were vacuum‐concentrated to increase the xylose concentration, detoxified by pH alteration and adsorption into activated charcoal, and used for xylitol bioproduction in a stirred tank reactor. Neither the least (70 mg/g, 10 min) nor the most severe (130 mg/g, 30 min) hydrolysis conditions led to the best xylitol production (37.5 g/L), productivity (0.85 g/L h), and yield (0.78 g/g).
Transient Effects of Overexpressing Anthranilate Synthase α and β Subunits in Catharanthusroseus Hairy Roots
Authors: Peebles Christie A. M. , Hong Seung‐Beom , Gibson Susan I. , Shanks Jacqueline V. , San Ka‐Yiu 
Published: October 2005

AbstractCatharanthus roseus produces two economically valuable anticancer drugs, vinblastine and vincristine. These drugs are members of the terpenoid indole alkaloids and accumulate in small quantities within the plant; thus these two drugs are expensive to produce. Metabolic engineering efforts have focused on increasing the alkaloids in this pathway through various means such as elicitation, precursor feeding, and gene overexpression. Recently we successfully expressed Arabidopsis genes encoding a feedback‐insensitive anthranilate synthase α subunit under the control of the glucocorticoid‐inducible promoter system and the anthranilate synthase β subunit under the control of a constitutive promoter in C. roseus hairy roots. In this work we look at the transient behaviors of terpenoid indole alkaloids over a 72 h induction period in late exponential growth phase cultures. Upon induction, the tryptophan, tryptamine, and ajmalicine pools accumulated over 72 h. In contrast, the lochnericine, hörhammericine, and tabersonine pools decreased and leveled out over the 72 h induction period. Visible changes within the individual compounds usually took from 4 to 12 h.
Functional food science and defence against reactive oxidative species
Authors: Diplock A. T. , Charuleux J.-L. , Crozier-Willi G. , Kok F. J. , Rice-Evans C. , Roberfroid M. , Stahl W. , Viña-Ribes J. 
Published: October 2005

AbstractThis paper assesses critically the science base that underpins the argument that oxidative damage is a significant causative factor in the development of human diseases and that antioxidants are capable of preventing or ameliorating these disease processes. The assessment has been carried out under a number of headings, and some recommendations for future research are made based on the present day knowledge base.
GARSA: genomic analysis resources for sequence annotation
Authors: Dávila Alberto M. R. , Lorenzini Daniel M. , Mendes Pablo N. , Satake Thiago S. , Sousa Gabriel R. , Campos Linair M. , Mazzoni Camila J. , Wagner Glauber , Pires Paulo F. , Grisard Edmundo C. , Cavalcanti Maria C. R. , Campos Maria Luiza M. 
Published: October 2005

Abstract
Summary: Growth of genome data and analysis possibilities have brought new levels of difficulty for scientists to understand, integrate and deal with all this ever-increasing information. In this scenario, GARSA has been conceived aiming to facilitate the tasks of integrating, analyzing and presenting genomic information from several bioinformatics tools and genomic databases, in a flexible way. GARSA is a user-friendly web-based system designed to analyze genomic data in the context of a pipeline. EST and GGS data can be analyzed using the system since it accepts (1) chromatograms, (2) download of sequences from GenBank, (3) Fasta files stored locally or (4) a combination of all three. Quality evaluation of chromatograms, vector removing and clusterization are easily performed as part of the pipeline. A number of local and customizable Blast and CDD analyses can be performed as well as Interpro, complemented with phylogeny analyses. GARSA is being used for the analyses of Trypanosoma vivax (GSS and EST), Trypanosoma rangeli (GSS, EST and ORESTES), Bothrops jararaca (EST), Piaractus mesopotamicus (EST) and Lutzomyia longipalpis (EST).
Availability: The GARSA system is freely available under GPL license (). For download requests visit or contact Dr Alberto Dávila.
Contact: davila@fiocruz.br
Discovering hidden viral piracy
Authors: Kim Eddo , Kliger Yossef 
Published: October 2005

Abstract
Motivation: Viruses and developers of anti-inflammatory therapies share a common interest in proteins that manipulate the immune response. Large double-stranded DNA viruses acquire host proteins to evade host defense mechanisms. Hence, viral pirated proteins may have a therapeutic potential. Although dozens of viral piracy events have already been identified, we hypothesized that sequence divergence impedes the discovery of many others.
Results: We developed a method to assess the number of viral/human homologs and discovered that at least 917 highly diverged homologs are hidden in low-similarity alignment hits that are usually ignored. However, these low-similarity homologs are masked by many false alignment hits. We therefore applied a filtering method to increase the proportion of viral/human homologous proteins. The homologous proteins we found may facilitate functional annotation of viral and human proteins. Furthermore, some of these proteins play a key role in immune modulation and are therefore therapeutic protein candidates.
Contact: kliger@compugen.co.il
The gene expression signature of relapse in paediatric acute lymphoblastic leukaemia: implications for mechanisms of therapy failure
Authors: Beesley Alex H. , Cummings Aaron J. , Freitas Joseph R. , Hoffmann Katrin , Firth Martin J. , Ford Jette , de Klerk Nicolas H. , Kees Ursula R. 
Published: October 2005

SummaryDespite significant improvements in the treatment of childhood acute lymphoblastic leukaemia (ALL), the prognosis for relapsing patients remains poor. The aim of this study was to generate a transcriptional profile of relapsed ALL to increase our understanding of the mechanisms involved in therapy failure. RNA was extracted from 11 pairs of cryopreserved pre‐B ALL bone marrow specimens taken from the same patients at diagnosis and relapse, and analysed using HG‐U133A microarrays. Relapse specimens overexpressed genes that are involved with cell growth and proliferation, in keeping with their aggressive phenotype. When tested in 72 independent specimens of pre‐B ALL and T‐ALL, the identified genes could successfully differentiate between diagnosis and relapse in either lineage, indicating the existence of relapse mechanisms common to both. These genes have functions relevant for oncogenesis, drug resistance and metastasis, but are not related to classical multidrug‐resistance pathways. Increased expression of the top‐ranked gene (BSG) at diagnosis was significantly associated with adverse outcome. Several chromosomal loci, including 19p13, were identified as potential hotspots for aberrant gene expression in relapsed ALL. Our results provide evidence for a link between drug resistance and the microenvironment that has previously only been considered in the context of solid tumour biology.
Infections with human herpesvirus 6 variant B delay platelet engraftment after allogeneic haematopoietic stem cell transplantation
Authors: Radonić Aleksandar , Oswald Olivia , Thulke Stefanie , Brockhaus Nina , Nitsche Andreas , Siegert Wolfgang , Schetelig Johannes 
Published: October 2005

SummaryThe clinical significance of human herpesvirus (HHV‐6) infections after allogeneic stem cell transplantation (SCT) remains controversial. We analysed cryoconserved plasma samples from 82 patients after allogeneic SCT by quantitative polymerase chain reaction for HHV‐6 variants A and B. Platelet engraftment was delayed in patients with HHV‐6B infections but not with HHV‐6A infections detected before day +28. In multivariate analysis early HHV‐6B infections and the type of conditioning were associated with platelet engraftment. In conclusion, the two variants of HHV‐6 should be studied separately; early infections with HHV‐6B may contribute to delayed platelet engraftment after allogeneic SCT.
Clone‐specific responses in leaf phenolics of willows exposed to enhanced UVB radiation and drought stress
Authors: Turtola Satu , Rousi Matti , Pusenius Jyrki , Yamaji Keiko , Heiska Susanne , Tirkkonen Veijo , Meier Beat , Julkunen‐Tiitto Riitta 
Published: October 2005

AbstractThe effects of enhanced UVB radiation and drought stress on willow secondary phenolics were studied using the leaves of 8‐week‐old micropropagated plantlets from interspecific hybrids (Salix myrsinites L. ×S. myrsinifolia Salisb.) and pure species (S. myrsinifolia). The plantlets were subjected for 4 weeks to two levels of UVB radiation (ambient, enhanced) and two levels of watering (well‐watered, drought‐stressed) according to a 2 × 2 factorial design. Enhanced UVB radiation increased the total concentration of flavonoids and phenolic acids in all plantlets, while the total concentration of salicylates remained unaffected. Drought stress reduced the total concentration of salicylates and phenolic acids in S. myrsinifolia plantlets, while in hybrids only phenolic acids were affected. The response of phenolic acids to enhanced UVB in drought‐stressed plantlets was different from that in well‐watered ones, indicating that drought stress limited the accumulation of phenolic acids under enhanced UVB radiation. Flavonoids increased in response to enhanced UVB radiation in drought‐stressed plantlets, although drought caused serious physiological stress on growth. There were significant differences between hybrid and S. myrsinifolia plantlets with respect to the composition of phenolics and between families and clones with respect to their concentration. In addition, the response of salicylates, flavonoids and phenolic acids to enhanced UVB and drought stress was clone‐specific, which may indicate that climatic changes will alter the genetic composition of northern forests.
Glutamine depletion potentiates leucocyte‐dependent inflammatory events induced by carrageenan or Clostridium difficile toxin A in rats
Authors: Nascimento Silvia B. , Sousa Romualdo B. , Martins Marcos Jullian B. , Souza Gomes Antoniella , Souza Marcellus Henrique L. P. , Guerrant Richard L. , Cunha Fernando Q. , Ribeiro Ronaldo A. , Brito Gerly A. C. 
Published: October 2005

SummaryThis research investigated the effect of glutamine (Gln) depletion on leucocyte‐dependent inflammatory events. Rats were treated intraperitoneally, 16 hr prior to the peak of every parameter evaluated, with either 0·9% NaCl, methionine‐sulphoximine (MSO, an inhibitor of endogenous Gln synthesis, 25 mg/kg) or with MSO + Gln (MSO as above plus Gln 3 g/kg in three doses). MSO‐induced Gln depletion increased paw oedema induced both by carrageenan (Cg) and by Clostridium difficile toxin A (TxA) (66·2% and 45·5%, respectively; P < 0·05). In dextran‐injected animals, oedema and myeloperoxidase (MPO) activity were not modified by Gln depletion. In Cg‐treated paws, Gln depletion increased MPO activity by 44% (P < 0·05), interleukin‐1β (IL‐1β) and tumour necrosis factor‐α (TNF‐α) concentrations by 47% and 52%, respectively (P < 0·05), and immunostaining for TNF‐α in paw tissue. In TxA‐injected paws, Gln depletion increased MPO activity (46%; P < 0·05). Gln depletion increased Cg‐ and TxA‐induced neutrophil migration to subcutaneous air pouches by 56% and 77% (P < 0·05), respectively, but did not affect migration induced by N‐formyl‐methionyl‐leucyl‐phenylalanine (fMLP). Gln infusions reversed all the effects of MSO. Leucocyte counts did not differ between groups. Gln depletion potentiates acute inflammation, possibly by increasing neutrophil migration through resident cell activation and production of IL‐1β and TNF‐α. Gln supplementation reverses these effects and may be useful during inflammatory catabolic stress.