bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protosilencers as building blocks for heterochromatin
Authors: Fourel Geneviève , Lebrun Eléonore , Gilson Eric 
Published: September 2002

AbstractDNA repetitions may provoke heterochromatinization. We explore here a model in which multiple cis‐acting sequences that display no silencing activity on their own (protosilencers) may cooperate to establish and maintain a heterochromatin domain efficiently. Protosilencers, first defined in budding yeast, have now been found in a wide range of genomes where they appear to stabilize and to extend the propagation of heterochromatin domains. Strikingly, isolated or moderately repeated protosilencers can also be found in promoters where they participate in transcriptional activation and have insulation functions. This suggests that the proper juxtaposition of a threshold number of protosilencers converts them from neutral or transactivating elements into ones that nucleate heterochromatin. Interactions might be transient or permanent, and are likely to occur over distances by looping. This model provides a conceptual framework for as varied phenomena as telomere‐driven silencing in Drosophila, X inactivation in mammals, and rDNA silencing in S. cerevisiae. It may also account for the silencing that occurs when multiple copies of a transgene are inserted in tandem. BioEssays 24:828–835, 2002. © 2002 Wiley Periodicals, Inc.
Beyond structure: do intermediate filaments modulate cell signalling?
Authors: Paramio Jesus M. , Jorcano José L. 
Published: September 2002

AbstractIntermediate filament (IF) proteins form the largest family of cytoskeletal proteins in mammalian cells. The function of these proteins has long been thought to be only structural. However, this single function does not explain their diverse tissue‐ and differentiation‐specific expression patterns. Evidence is now emerging that IF also act as an important framework for the modulation and control of essential cell processes, in particular, signal transduction events. Here, we review the most recent developments in this growing and exciting new field. BioEssays 24:836–844, 2002. © 2002 Wiley Periodicals, Inc.
Nucleotide sequence‐based typing of bacteria and the impact of automation
Authors: Clarke Stuart C. 
Published: September 2002

AbstractDNA‐based typing methods are increasingly important for the characterisation of bacteria. They are used to monitor the epidemiology of pathogens with public health significance and also to help understand the evolution and population biology of bacteria. However, these methods require accuracy and reproducibility and are often of a high‐throughput nature. Laboratory automation is therefore the key to the successful implementation of such methods. This review describes the impact of automation on DNA‐based typing methods, particularly multi‐locus sequence typing (MLST), and the method components that can be automated. BioEssays 24:858–862, 2002. © 2002 Wiley Periodicals, Inc.
Canonical and non‐canonical Wnt signaling pathways in Caenorhabditis elegans: variations on a common signaling theme
Authors: Korswagen Hendrik C. 
Published: September 2002

AbstractWnt glycoproteins are signaling molecules that control a wide range of developmental processes in organisms ranging from the simple metazoan Hydra to vertebrates. Wnt signaling also plays a key role in the development of the nematode C. elegans, and is involved in cell fate specification and determination of cell polarity and cell migration. Surprisingly, the first genetic studies of Wnt signaling in C. elegans revealed major differences with the established (canonical) Wnt signaling pathways of Drosophila and vertebrates. Thus, the Wnt‐dependent induction of endoderm in the early embryo and the specification of several asymmetric cell divisions during larval development are mediated by as yet novel Wnt signaling pathways that repress, rather than activate the TCF/LEF‐1 transcription factor POP‐1. Recently, however, it has been shown that, in addition to these divergent Wnt pathways, C. elegans also has a canonical Wnt pathway that converts POP‐1 into an activator and controls the expression of several homeobox genes. Interestingly, these different Wnt pathways use distinct β‐catenins to control POP‐1 function: the endoderm induction pathway requires the β‐catenin WRM‐1 and parallel input from a mitogen‐activated kinase (MAPK) pathway to downregulate POP‐1, whereas the canonical Wnt pathway employs the β‐catenin BAR‐1 to activate Wnt target gene expression. BioEssays 24:801–810, 2002. © 2002 Wiley Periodicals, Inc.
What can humans learn from flies about adenomatous polyposis coli?
Authors: Barth Angela I.M. , Nelson W. James 
Published: September 2002

AbstractSomatic or inherited mutations in the adenomatous polyposis coli (APC) gene are a frequent cause of colorectal cancer in humans. APC protein has an important tumor suppression function to reduce cellular levels of the signaling protein β‐catenin and, thereby, inhibit β‐catenin and T‐cell‐factor‐mediated gene expression. In addition, APC protein binds to microtubules in vertebrate cells and localizes to actin‐rich adherens junctions in epithelial cells of the fruit fly Drosophila (Fig. 1). Very little is known, however, about the function of these cytoskeletal associations. Recently, Hamada and Bienz have described a potential role for Drosophila E‐APC in cellular adhesion,1 which offers new clues to APC function in embryonic development, and potentially colorectal adenoma formation and tumor progression in humans. BioEssays 24:771–774, 2002. © 2002 Wiley Periodicals, Inc.
Non‐stop decay—a new mRNA surveillance pathway
Authors: Vasudevan Shobha , Peltz Stuart W. , Wilusz Carol J. 
Published: September 2002

AbstractGene expression is an inherently complex process and errors often occur during the transcription and processing of mRNAs. Several surveillance mechanisms have evolved to check the fidelity at each step of mRNA manufacture. Two recent reports describe the identification of a novel pathway in eukaryotes that recognizes and degrades mRNAs that lack a stop codon.1,2 The non‐stop decay mechanism releases ribosomes stalled at the 3′ end of a mRNA and stimulates the exosome to rapidly degrade the transcript. BioEssays 24:785–788, 2002. © 2002 Wiley Periodicals, Inc.
Fourier transform IR study of aggregational behavior of N‐acetyl‐L‐ and N‐butyloxycarbonyl‐L‐glutamic acid oligomeric benzyl esters in dioxane and benzene: β‐Turn → antiparallel β‐sheet transition
Authors: Okabayashi Hirofumi , Ishida Makoto , Tamaoki Harushiko , Masuda Hideki , O'Connor Charmian J. 
Published: September 2002

AbstractOligomeric N‐acetyl‐L‐glutamic acid benzyl esters (ANpZ) with exact residue numbers (Np = 2, 3, 4, and 5) and N‐butyloxycarbonyl‐L‐glutamic acid benzyl esters (BOCNpZ) with exact residue numbers (Np = 4, 5, 6, and 8) are synthesized by a stepwise procedure in a liquid phase. The aggregational behavior of these oligomeric molecules in dioxane and benzene is examined by Fourier transform IR spectra. In particular, the concentration dependence of the IR spectra for the ANpZ solutions with Np values of 4 (A4Z) and 5 (A5Z) shows that the predominant antiparallel β‐sheet structure is stabilized above the critical aggregation concentration (cac), while other conformations including β‐turns may coexist below the cac. This fact provides evidence that aggregation induces the conformational transition from other conformers (probably β‐turns) to an antiparallel β‐sheet form. The IR results for the A3Z and A2Z solutions indicate that specific conformers (β‐turns), which are different from the β‐sheet structure, may be preferentially stabilized upon aggregation. Thus, the critical residue number of the ANpZ oligopeptides, which is essential for formation of a rodlike aggregate in dioxane and benzene, is 4 or 5. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 65: 129–141, 2002
Effects of aminooxy analogues of biogenic polyamines on aggregation and stability of calf thymus DNA
Authors: Ramírez F. J. , Thomas T. J. , Antony T. , Ruiz‐Chica J. , Thomas T. 
Published: September 2002

AbstractThe effect of a series of aminooxy analogues of the biogenic polyamines spermidine and spermine on the conformation of calf thymus DNA is studied. These new molecules are isosteric and charge insufficient analogues that are suitable to study the roles of both charge distribution and structural requirements in the molecular physiology of the biogenic polyamines. They are also evidenced as useful tools to inhibit polyamine biosynthesis and cell growth. Circular dichroism (CD) spectra of solutions containing DNA and the aminooxy analogues at different concentrations (100–1000 μM) and different pH values, (5–7.5) are recorded. We use both sonicated and highly polymerized calf thymus DNA. The CD spectra of sonicated DNA showed the formation of Ψ‐DNA, a highly ordered aggregated structure similar to liquid crystals, in the presence of the aminooxy analogues. Aggregation induced by an aminooxy derivative of spermine is followed by DNA collapse when increasing the polyamine concentration. The features of Ψ‐DNA are not detected for highly polymerized DNA. Temperature melting measurements support a high degree of structural order of the aggregates. The CD experiments indicate that dications are unable to induce major changes on the macromolecular structure of DNA. In addition, aggregation is only observed when the trimethylene moiety is present between two adjacent positive charges. The observed differences among the CD spectra of DNA solutions with different aminooxy derivatives of spermidine indicate different roles for different amino groups of this biogenic polyamine when interacting with DNA. Our results support the idea that aminooxy analogues can be used as good models in studying the physiological functions of biogenic polyamines. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 65: 148–157, 2002
Multinuclear NMR and FTIR studies of new polyoxaalkyl esters of lasalocid and their complexes with lithium and sodium cations
Authors: Pankiewicz Radosław , Schroeder Grzegorz , Gierczyk Błażej , Brzezinski Bogumił , Bartl Franz 
Published: September 2002

AbstractThree new polyoxaalkyl esters of lasalocid are synthesized. Their ability to form complexes with Li+ and Na+ cations is studied using multinuclear NMR methods, FTIR spectroscopy in the middle and far IR regions, and mass spectrometry. It is found that lasalocid esters form only 1:1 complexes with the metal cations. The results of the NMR study in pyridine show that the polyoxaalkyl chain of the ester does not influence the complex formation of the lasalocid part of the esters. The reason for this is the competition of the pyridine molecules in the complexation process of metal cations. In chloroform the properties of the complex formation have changed and the oxaalkyl chain plays an important role within the complexation process, as demonstrated by the dependence of the respective continuous absorptions in the far IR region on the length of the oxaalkyl chain (i.e., on the number of the oxygen atoms in the chain). The modifications of the lasalocid molecule influences the complexation of the metal cation and probably the interactions with the membrane. An increase in antibiotic activity is found as a consequence of these changed interactions. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 65: 95–110, 2002
Conformational studies of wheat flour high relative molecular mass glutenin subunits by circular dichroism spectroscopy
Authors: Fisichella S. , Alberghina G. , Amato M. E. , Fichera M. , Mantarro D. , Palermo A. , Savarino A. , Scarlata G. 
Published: September 2002

AbstractConformational studies of 1Dx2, 1Bx7, and 1Dy12 high relative molecular mass glutenin subunits, extracted from Alisei 1 flour, are reported. Circular dichroism (CD) spectroscopy is employed to study their conformational polymorphism induced by urea and by urea in the presence of 1% sodium dodecyl sulfate (SDS). The CD spectra indicate that SDS promotes ordered structures. The addition of urea to the SDS‐acetate solution of 1Dx2, 1Bx7, and 1Dy12 subunits eliminates the effect of SDS. Its addition to the acetate solution of proteins induces conformational transitions to form a poly‐L‐proline II‐like structure. All the changes induced by urea follow a multistep transition process that is typical of proteins consisting of different domains. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 65: 142–147, 2002
Spin trapping study of reactive oxygen species formation during bopindolol peroxidation
Authors: Kruk Irena , Michalska Teresa , Kladna Aleksandra , Aboul‐Enein Hassan Y. 
Published: September 2002

AbstractThe generation of singlet molecular oxygen (1O2) and hydroxyl radicals (HO ·) during peroxidation of bopindolol in the presence of Co(II) ions was studied using electron spin resonance (ESR) and spectrophotometry methods. 2,2,6,6‐Tetramethyl‐4‐piperidone and 5,5‐dimethyl‐1‐pyrroline‐1‐oxide were used as traps. The spectrophotometry determination of 1O2 was based on bleaching of p‐nitrosodimethylaniline (RNO), which was caused by the product of the reaction of 1O2 with imidazole and was followed by monitoring the decrease in optical density at 440 nm. The effect of 1O2 quenchers and oxygen free radical scavengers on the ESR signal and the bleaching of RNO was studied. The data presented here give new evidence for generation of the reactive oxygen species during peroxidation of bopindolol. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 65: 89–94, 2002
Production of L(+)‐lactic acid from glucose and starch by immobilized cells of Rhizopus oryzae in a rotating fibrous bed bioreactor
Authors: Tay Abdullatif , Yang Shang‐Tian 
Published: September 2002

AbstractA rotating fibrous‐bed bioreactor (RFB) was developed for fermentation to produce L(+)‐lactic acid from glucose and cornstarch by Rhizopus oryzae. Fungal mycelia were immobilized on cotton cloth in the RFB for a prolonged period to study the fermentation kinetics and process stability. The pH and dissolved oxygen concentration (DO) were found to have significant effects on lactic acid productivity and yield, with pH 6 and 90% DO being the optimal conditions. A high lactic acid yield of 90% (w/w) and productivity of 2.5 g/L·h (467 g/h·m2) was obtained from glucose in fed‐batch fermentation. When cornstarch was used as the substrate, the lactic acid yield was close to 100% (w/w) and the productivity was 1.65 g/L·h (300 g/h·m2). The highest concentration of lactic acid achieved in these fed‐batch fermentations was 127 g/L. The immobilized‐cells fermentation in the RFB gave a virtually cell‐free fermentation broth and provided many advantages over conventional fermentation processes, especially those with freely suspended fungal cells. Without immobilization with the cotton cloth, mycelia grew everywhere in the fermentor and caused serious problems in reactor control and operation and consequently the fermentation was poor in lactic acid production. Oxygen transfer in the RFB was also studied and the volumetric oxygen transfer coefficients under various aeration and agitation conditions were determined and then used to estimate the oxygen transfer rate and uptake rate during the fermentation. The results showed that the oxygen uptake rate increased with increasing DO, indicating that oxygen transfer was limited by the diffusion inside the mycelial layer. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 1–12, 2002.
Controlled enzymatic removal of damaging casein layers on medieval wall paintings
Authors: Beutel Sascha , Klein Kerstin , Knobbe Gabi , Königfeld Peter , Petersen Karin , Ulber Roland , Scheper Thomas 
Published: September 2002

AbstractA new, gentle enzymatic method was developed for a controlled removal of casein layers from medieval wall paintings. These casein layers were applied over the last 60 years on wall paintings in order to decrease substantial damage due to a peeling off of the frescoes from the roughcast surface due to environmental effects. However, due to the aging of the casein layers (at 40–50 years), a more drastic peeling occurred and the danger of total destruction of the wall paintings is severe. Thus, screening was performed to find the most suitable enzyme for casein digestion. Alcalase 2.5 DX L was the most appropriate enzyme for an effective proteolysis reaction. The enzyme was immobilized on functionalized cellulose membrane. A membrane pad system with immobilized enzymes was developed which could be pressed on the casein layers on the wall painting. A controlled removal of the casein layers by proteolytic digestion was observed and it was possible to continuously wash off the hydrolyzed casein fragments from the wall painting surface by an aqueous carbonate buffer flowing through the membrane pad. The removal and the digestion was monitored by reverse HPLC. Additionally, an on‐line monitoring system was set up in order to continuously follow the casein layer removal and the digestion procedure directly on the wall painting. This technique is based on noninvasive 2D‐fluorescence monitoring. Optical fiber systems were used to continuously monitor the fluorescence intensity of casein‐bound tryptophan. The off‐line data were verified with the on‐line 2D‐fluorescence data. Based on the scientific result an appropriate technique for the controlled enzymatic removal of damaging casein layers on the surface of medieval wall paintings using immobilized enzyme is now available. It is now applied to remove such casein layers from medieval wall paintings in the Allerheiligen‐Kapelle Cloister, Wienhausen, Germany, and the St. Alexander Kirche, Wildeshausen, Germany. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 13–21, 2002.
Recovery and separation of cell lysate proteins using hydrogels guided by aqueous two‐phase extraction principles
Authors: Putka Christopher S. , Gehrke Stevin H. , Willis Mike , Stafford David , Bryant John 
Published: September 2002

AbstractThe addition of poly(ethylene glycol) and salts to clarified cell lysates of Thiosphaera pantotropha increases sorption of microbial proteins into dextran hydrogels, consistent with the thermodynamics of aqueous two‐phase extraction. Addition of 12 wt% PEG‐10,000 to the lysate increased total sorption of protein by the dextran gel from 5.2 mg/g dextran to 37 mg/g; addition of either 0.1 M potassium iodide or tetrabutylammonium fluoride along with PEG to the lysate increased protein sorption to more than 63 mg/g, a 12‐fold increase. SDS‐PAGE demonstrated that the type of salt added controls which proteins are absorbed by the gel. Previously demonstrated only with model solutions, these results suggest another approach to recovery and separation strategies for proteins produced by fermentation. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 139–143, 2002.
Development of a large‐scale biocalorimeter to monitor and control bioprocesses
Authors: Voisard D. , Pugeaud P. , Kumar A. R. , Jenny K. , Jayaraman K. , Marison I. W. , von Stockar U. 
Published: September 2002

AbstractCalorimetry has shown real potential at bench‐scale for chemical and biochemical processes. The aim of this work was therefore to scale‐up the system by adaptation of a standard commercially available 300‐L pilot‐scale bioreactor. To achieve this, all heat flows entering or leaving the bioreactor were identified and the necessary instrumentation implemented to enable on‐line monitoring and dynamic heat balance estimation. Providing that the signals are sufficiently precise, such a heat balance would enable calculation of the heat released or taken up during an operational (bio)process. Two electrical Wattmeters were developed, the first for determination of the power consumption by the stirrer motor and the second for determination of the power released by an internal calibration heater. Experiments were designed to optimize the temperature controller of the bioreactor such that it was sufficiently rapid so as to enable the heat accumulation terms to be neglected. Further calibration experiments were designed to correlate the measured stirring power to frictional heat losses of the stirrer into the reaction mass. This allows the quantitative measurement of all background heat flows and the on‐line quantitative calculation of the (bio)process power. Three test fermentations were then performed with B. sphaericus 1593M, a spore‐forming bacterium pathogenic to mosquitoes. A first batch culture was performed on a complex medium, to enable optimization of the calorimeter system. A second batch culture, on defined medium containing three carbon sources, was used to show the fast, accurate response of the heat signal and the ability to perfectly monitor the different growth phases associated with growth on mixed substrates, in particular when carbon sources became depleted. A maximum heat output of 1100 W was measured at the end of the log‐phase. A fed‐batch culture on the same defined medium was then carried out with the feed rate controlled as a function of the calorimeter signal. A maximum heat output of 2250 W was measured at the end of the first log‐phase. This work demonstrates that real‐time quantitative calorimetry is not only possible at pilot‐scale, but could be readily applied at even larger scales. The technique requires simple, readily available devices for determination of the few necessary heat flows, making it a robust, cost‐effective technique for process development and routine monitoring and control of production processes. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 125–138, 2002
Optimization of recombinant protein expression level in Escherichia coli by flow cytometry and cell sorting
Authors: Soriano Elena , Borth Nicole , Katinger Hermann , Mattanovich Diethard 
Published: September 2002

AbstractOverexpression of recombinant proteins in Escherichia coli often leads to a severe growth retardation of the host cells. The phage T7 promoter ϕ10 in a pET vector was utilized to express human superoxide dismutase. Induction with IPTG lead to an increase in protein content and cell size and a termination of cell division, due to the deviation of the general metabolic fluxes from all cellular processes to plasmid maintenance and foreign protein synthesis. To generate promoter mutants which are better tolerated by the host cells we constructed a random mutation library by PCR with degenerated primers in a part of the promoter involved in the binding to the RNA polymerase and the initiation of transcription. This library was sorted by flow cytometry for cells with a lower total protein content as an indicator for continued cell replication and hence a less severe stress situation. The clones obtained had a similar SOD production compared to the original strain, but were able to reach higher densities in a batch culture, which resulted in a higher total yield. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 93–99, 2002.