bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence‐specific recognition of DNA by hydrophobic, alanine‐rich mutants of the basic region/leucine zipper motif investigated by fluorescence anisotropy
Authors: Bird Gregory H. , Lajmi Ajay R. , Shin Jumi A. 
Published: October 2002

AbstractWe generated minimalist proteins capable of sequence‐specific, high‐affinity binding of DNA to probe how proteins are used and can be used to recognize DNA. In order to quantify binding affinities and specificities in our protein–DNA system, we used fluorescence anisotropy to measure in situ the thermodynamics of binding of alanine‐rich mutants of the GCN4 basic region/leucine zipper (bZIP) domain to DNA duplexes containing target sites AP‐1 (5′‐TGACTCA‐3′) or ATF/CREB (5′‐TGACGTCA‐3′). We simplified the α‐helical bZIP molecular recognition scaffold by alanine substitution: 4A, 11A, and 18A contain four, eleven, and eighteen alanine mutations in their DNA‐binding basic regions, respectively. DNase I footprinting analysis demonstrates that all bZIP mutants retain the sequence‐specific DNA‐binding function of native GCN4 bZIP. Titration of fluorescein‐labeled oligonucleotide duplexes with increasing amounts of protein yielded low nanomolar dissociation constants for all bZIP mutants in complex with the AP‐1 and ATF/CREB sites: binding to the nonspecific control duplex was > 1000‐fold weaker. Remarkably, the most heavily mutated protein 18A, containing 24 alanines in its 27‐residue basic region, still binds AP‐1 and ATF/CREB with dissociation constants of 15 and 7.8 nM, respectively. Similarly, wild‐type bZIP binds these sites with Kd values of 9.1 and 14 nM. 11A also displays low nanomolar dissociation constants for AP‐1 and ATF/CREB, while 4A binds these sites with ∼ 10‐fold weaker Kd values. Thus, both DNA‐binding specificity and affinity are maintained in all our bZIP derivatives. This Ala‐rich scaffold may be useful in design and synthesis of small α‐helical proteins with desired DNA‐recognition properties capable of serving as therapeutics targeting transcription. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 10–20, 2002
Effect of electrical charges and fields on injury and viability of airborne bacteria
Authors: Mainelis Gediminas , Górny Rafał L. , Reponen Tiina , Trunov Mikhaylo , Grinshpun Sergey A. , Baron Paul , Yadav Jagjit , Willeke Klaus 
Published: October 2002

AbstractIn this study, the effects of the electric charges and fields on the viability of airborne microorganisms were investigated. The electric charges of different magnitude and polarity were imparted on airborne microbial cells by a means of induction charging. The airborne microorganisms carrying different electric charge levels were then extracted by an electric mobility analyzer and collected using a microbial sampler. It was found that the viability of Pseudomonas fluorescens bacteria, used as a model for sensitive bacteria, carrying a net charge from 4100 negative to 30 positive elementary charges ranged between 40% and 60%; the viability of the cells carrying >2700 positive charges was below 1.5%. In contrast, the viability of the stress‐resistant spores of Bacillus subtilis var. niger (used as simulant of anthrax‐causing Bacillus anthracis spores when testing bioaerosol sensors in various studies), was not affected by the amount of electric charges on the spores. Because bacterial cells depend on their membrane potential for basic metabolic activities, drastic changes occurring in the membrane potential during aerosolization and the local electric fields induced by the imposed charges appeared to affect the sensitive cells' viability. These findings facilitate applications of electric charging for environmental control purposes involving sterilization of bacterial cells by imposing high electric charges on them. The findings from this study can also be used in the development of new bioaerosol sampling methods based on electrostatic principles. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 79: 229–241, 2002.
Advantages of using non‐isothermal bioreactors for the enzymatic synthesis of antibiotics: The penicillin G acylase as enzyme model
Authors: Travascio P. , Zito E. , De Maio A. , Schroën C. G. P. H. , Durante D. , De Luca P. , Bencivenga U. , Mita D. G. 
Published: October 2002

AbstractA new hydrophobic and catalytic membrane was prepared by immobilizing Penicillin G acylase (PGA, EC.3.5.1.11) from E. coli on a nylon membrane, chemically grafted with butylmethacrylate (BMA). Hexamethylenediamine (HMDA) and glutaraldehyde (Glu) were used as a spacer and coupling agent, respectively. PGA was used for the enzymatic synthesis of cephalexin, using D(‐)‐phenylglycine methyl ester (PGME) and 7‐amino‐3‐deacetoxycephalosporanic acid (7‐ADCA) as substrates. Several factors affecting this reaction, such as pH, temperature, and concentrations of substrates were investigated. The results indicated good enzyme‐binding efficiency of the pre‐treated membrane, and an increased stability of the immobilized PGA towards pH and temperature. Calculation of the activation energies showed that cephalexin production by the immobilized biocatalyst was limited by diffusion, resulting in a decrease of enzyme activity and substrate affinity. Temperature gradients were employed as a way to reduce the effects of diffusion limitation. Cephalexin was found to linearly increase with the applied temperature gradient. A temperature difference of about 3°C across the catalytic membrane resulted into a cephalexin synthesis increase of 100% with a 50% reduction of the production times. The advantage of using non‐isothermal bioreactors in biotechnological processes, including pharmaceutical applications, is also discussed. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 79: 334–346, 2002.
Rapid sampling for analysis of in vivo kinetics using the BioScope: A system for continuous‐pulse experiments
Authors: Visser Diana , van Zuylen Gertan A. , van Dam Jan C. , Oudshoorn Arthur , Eman Michael R. , Ras Cor , van Gulik Walter M. , Frank Johannes , van Dedem Gijs W. K. , Heijnen Joseph J. 
Published: October 2002

AbstractIn this article we present a novel device, the BioScope, which allows elucidation of in vivo kinetics of microbial metabolism via perturbation experiments. The perturbations are carried out according to the continuous‐flow method. The BioScope consists of oxygen permeable silicon tubing, connected to the fermentor, through which the broth flows at constant velocity. The tubing has a special geometry (serpentine channel) to ensure plug flow. After leaving the fermentor, the broth is mixed with a small flow of perturbing agent. This represents the start of the perturbation. The broth is sampled at different locations along the tubing, corresponding to different incubation times. The maximal incubation time is 69 s; the minimally possible time interval between the samples is 3–4 s. Compared to conventional approaches, in which the perturbation is carried out in the fermentor, the BioScope offers a number of advantages. (1) A large number of different perturbation experiments can be carried out on the same day, because the physiological state of the fermentor is not perturbed. (2) In vivo kinetics during fed‐batch experiments and in large‐scale reactors can be investigated. (3) All metabolites of interest can be measured using samples obtained in a single experiment, because the volume of the samples is unlimited. (4) The amount of perturbing agent spent is minimal, because only a small volume of broth is perturbed. (5) The system is completely automated. Several system properties, including plug‐flow characteristics, mixing, oxygen and carbon dioxide transfer rates, the quenching time, and the reproducibility have been explored, with satisfactory results. Responses of several glycolytic intermediates in Saccharomyces cerevisiae to a glucose pulse, measured using a conventional approach are compared to results obtained with the BioScope. The agreement between the results demonstrates that the BioScope is indeed a promising device for studying in vivo kinetics. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 79: 674–681, 2002.
Integrated bioprocessing in Saccharomyces cerevisiae using green fluorescent protein as a fusion partner
Authors: Li Jincai , Xu Haixin , Herber Wayne K. , Bentley William E. , Rao Govind 
Published: October 2002

AbstractIn this study, we examine the use of green fluorescent protein (GFP) for monitoring a hexokinase (HXK)–GFP fusion protein in Saccharomyces cerevisiae for various events including expression, degradation, purification, and localization. The fusion, HXK‐EK‐GFP‐6 × His, was constructed where the histidine tag (6 × His) would allow for convenient affinity purification, and the enterokinase (EK) cleavage site would be used for separation of HXK from GFP after affinity purification. Our results showed that both HXK and GFP remained active in the fusion and, more importantly, that there was a linear correlation between HXK activity and GFP fluorescence. Enterokinase cleavage studies revealed that both GFP fluorescence intensity and HXK activity remained unchanged after separation of the fusion proteins, which indicated that fusion of GFP did not cause structural alteration of HXK and thus did not affect the enzymatic activity of HXK. We also found that degradation of the fusion protein occurred, and that degradation was limited to HXK with GFP remaining intact in the fusion. Confocal microscopy studies showed that while GFP was distributed evenly in the yeast cytosol, HXK‐GFP fusion followed the correct localization of HXK, which resulted in a di‐localization of both cytosol and the nucleus. GFP proved to be a useful fusion partner that may lead to the possibility of integrating the bioprocesses by quantitatively following the entire process visually. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 79: 682–693, 2002.
Restorative justice innovations in Canada
Authors: Wilson Robin J. , Huculak Bria , McWhinnie Andrew 
Published: October 2002

AbstractAs many jurisdictions move towards more retributive measures as a means to address public discontent with crime, a parallel movement has developed in regard to restorative justice. This article presents three restorative initiatives currently in use in Canada. Each initiative addresses offender behavior and community engagement at a different point in the justice continuum. The use of Sentencing Circles is an example of how restorative justice principles can be instituted at the front end, prior to an offender becoming lodged in the system. The Restorative Justice Options to Parole Suspension project demonstrates how community engagement can assist in preventing offenders from being returned to the system once they have achieved conditional release. The Circles of Support and Accountability project has enlisted the support of professionally supported volunteers in the community reintegration of high‐risk sexual offenders. These initiatives are presented within a framework of effective correctional interventions and increased empowerment for a variety of stakeholders. Copyright © 2002 John Wiley & Sons, Ltd.
Procedures based on simulation and hardware for a computer architecture course
Authors: González E. J. , Alayón S. , Piñeiro J. D. , Sánchez J. L. , Estévez J. I. , Sigut J. F. , Moreno L. 
Published: October 2002

AbstractIn this study, a procedure planning for a Computer Architecture Course that tries to create a balance between simulation and laboratory procedures is presented. For this planning, we use hardware implementation for parts of this subject that require careful dedication because of its complexity: interconnection networks and parallel processing. On the other hand, we use simulation packages for the teaching of pipelined and vectorial processors. © 2002 Wiley Periodicals, Inc. Comput Appl Eng Educ 10: 11–17, 2002; Published online in Wiley InterScience (www.interscience.wiley.com.); DOI 10.1002/cae.10012
Abciximab administration and clinical outcomes after percutaneous intervention for in‐stent restenosis
Authors: Moustapha Ali , Assali Abid R. , Sdringola Stefano , Yusuf S. Wamique , Vaughn William K. , Fish R. David , Schroth George W. , Krajcer Zvonimir , Rosales Oscar R. , Smalling Richard W. , Anderson H. Vernon 
Published: October 2002

AbstractAbciximab therapy improves clinical outcomes after percutaneous interventions for de novo coronary artery disease. We sought to determine whether clinical outcomes after percutaneous intervention for in‐stent restenosis are affected by abciximab administration. Between January 1996 and July 1999, 322 consecutive patients underwent percutaneous intervention for in‐stent restenosis; 157 patients received abciximab and 165 patients were treated without abciximab based on operator discretion. Baseline clinical and angiographic variables and type of percutaneous intervention were recorded. Follow‐up information was obtained and clinical endpoints were recorded. A multivariate analysis was performed to determine the independent variables associated with adverse clinical outcomes. Baseline clinical and angiographic variables were similar in both groups. Patients who received abciximab were more likely to be treated with rotational atherectomy and less likely to have only balloon angioplasty or repeat stenting. Mean follow‐up duration was 19 ± 12 months. There were no significant differences in the incidence of angina/myocardial infarction (29% vs. 30%; P = 0.9), target vessel revascularization (18% vs. 21%; P = 0.5), death (8% vs. 7%; P = 0.4), or major adverse cardiovascular events (38% vs. 39%; P = 0.9) in both groups. Abciximab administration was not an independent variable associated with adverse outcomes. In this observational study, clinical outcomes after percutaneous intervention for in‐stent restenosis did not seem to be affected by abciximab administration. Randomized trials are needed to identify the role of platelet glycoprotein IIb/IIIa inhibitors in the management of in‐stent restenosis. Cathet Cardiovasc Intervent 2002;56:184–187. © 2002 Wiley‐Liss, Inc.
IntraStent double‐strut LD: Collapse and recoil following use in postoperative stenoses
Authors: Recto Michael R. , Grifka Ronald G. 
Published: October 2002

AbstractWe describe the use of the Intratherapeutics IntraStent in two postoperative patients, its collapse and recoil following deployment, and subsequent transcatheter correction. Cathet Cardiovasc Intervent 2002;56:254–261. © 2002 Wiley‐Liss, Inc.
Femoropopliteal occlusive disease: Diagnosis, indications for treatment, and results of interventional therapy
Authors: Silver Mitchell J. , Ansel Gary M. 
Published: October 2002

AbstractThe relative role of percutaneous therapy versus bypass surgery for femoropopliteal occlusive disease (FPD) represents an area of great controversy in the field of vascular medicine. This controversy is complicated by the very dynamic therapeutic options that continue to be introduced, particularly on the endovascular side. The purpose of this review is to provide an overview of the current diagnostic modalities available to characterize the level and degree of vascular insufficiency and summarize the currently available endovascular therapeutic options with their clinical role and outcomes. Finally, future therapeutic advances that will soon be evaluated in clinical trials will be discussed. Cathet Cardiovasc Intervent 2002;56:555–561. © 2002 Wiley‐Liss, Inc.
Use of a pigtail catheter to engage a difficult internal mammary artery
Authors: Lapp Harald , Haltern Georg , Kranz Thomas , Boerrigter Guido , Horlitz Mark , Klein Michael , Krakau Ingo , Guelker Hartmut 
Published: October 2002

AbstractIncreasing use of bilateral internal mammary arteries for coronary surgery will increase the number of interventions in these grafts. Such interventions may be technically challenging because of often tortuous and angulated vessels. We describe a technique to intubate an acutely angulated right internal mammary artery that was inaccessible with conventional catheters. Cathet Cardiovasc Intervent 2002;56:489–491. © 2002 Wiley‐Liss, Inc.
Anterograde balloon valvuloplasty for the treatment of neonatal critical valvar aortic stenosis
Authors: Peuster Matthias , Fink Christoph , Schoof Stefan , Schnakenburg Christian Von , Hausdorf Gerd 
Published: October 2002

AbstractWe report our experience with anterograde balloon valvuloplasty in 17 neonates treated between November 1996 and June 2001 for critical aortic stenosis. Patients with hypoplastic left heart syndrome were excluded. Anterograde balloon valvoplasty of the aortic valve was possible in all 17 patients. The mean peak systolic gradient prior to cardiac catheterization was 73 mm Hg (range, 30–117 mm Hg) and decreased to 37 mm Hg (range, 21–60 mm Hg) after the dilation. Aortic regurgitation after balloon valvoplasty was absent or mild in 14/17 patients, moderate in 2 patients, and severe in 1 patient. There was no mortality or echocardiographic evidence for aortic cusp perforation or mitral regurgitation associated with the procedure. Redilation was necessary in 3/17 patients. Two patients are awaiting elective Ross operation. One patient with endocardial fibroelastosis died at 11 months of age. Anterograde balloon valvoplasty can be safely and effectively performed to palliate neonates with critical aortic valve stenosis. Cathet Cardiovasc Intervent 2002;56:516–520. © 2002 Wiley‐Liss, Inc.
Hypoplastic left heart syndrome with intact atrial septum: Levoatriocardinal vein stent placement as a bridge to surgery
Authors: Vance Michael S. 
Published: October 2002

AbstractInfants with hypoplastic left heart syndrome, an intact atrial septum and pulmonary venous hypertension, are critically ill and have a poor prognosis. This case describes relief of severe pulmonary edema in such a patient by stent placement in a stenotic levoatriocardinal vein, with subsequent successful surgical palliation. Cathet Cardiovasc Intervent 2002;57:85–87. © 2002 Wiley‐Liss, Inc.
Constrained least squares methods for estimating reaction rate constants from spectroscopic data
Authors: Bijlsma Sabina , Boelens Hans F. M. , Hoefsloot Huub C. J. , Smilde Age K. 
Published: October 2002

AbstractModel errors, experimental errors and instrumental noise influence the accuracy of reaction rate constant estimates obtained from spectral data recorded in time during a chemical reaction. In order to improve the accuracy, which can be divided into the precision and bias of reaction rate constant estimates, constraints can be used within the estimation procedure. The impact of different constraints on the accuracy of reaction rate constant estimates has been investigated using classical curve resolution (CCR). Different types of constraints can be used in CCR. For example, if pure spectra of reacting absorbing species are known in advance, this knowledge can be used explicitly. Also, the fact that pure spectra of reacting absorbing species are non‐negative is a constraint that can be used in CCR. Experimental data have been obtained from UV‐vis spectra taken in time of a biochemical reaction. From the experimental data, reaction rate constants and pure spectra were estimated with and without implementation of constraints in CCR. Because only the precision of reaction rate constant estimates could be investigated using the experimental data, simulations were set up that were similar to the experimental data in order to additionally investigate the bias of reaction rate constant estimates. From the results of the simulated data it is concluded that the use of constraints does not result self‐evidently in an improvement in the accuracy of rate constant estimates. Guidelines for using constraints are given. Copyright © 2002 John Wiley & Sons, Ltd.
Overlapping antisense transcription in the human genome
Authors: Fahey M. E. , Moore T. F. , Higgins D. G. 
Published: October 2002

AbstractAccumulating evidence indicates an important role for non‐coding RNA molecules
in eukaryotic cell regulation. A small number of coding and non‐coding overlapping
antisense transcripts (OATs) in eukaryotes have been reported, some of which
regulate expression of the corresponding sense transcript. The prevalence
of this phenomenon is unknown, but there may be an enrichment of such transcripts
at imprinted gene loci. Taking a bioinformatics approach, we systematically
searched a human mRNA database (RefSeq) for complementary regions that might facilitate
pairing with other transcripts. We report 56 pairs of overlapping transcripts,
in which each member of the pair is transcribed from the same locus. This
allows us to make an estimate of 1000 for the minimum number of such transcript
pairs in the entire human genome. This is a surprisingly large number of overlapping
gene pairs and, clearly, some of the overlaps may not be functionally significant.
Nonetheless, this may indicate an important general role for overlapping antisense
control in gene regulation. EST databases were also investigated in order
to address the prevalence of cases of imprinted genes with associated non‐coding
overlapping, antisense transcripts. However, EST databases were found to be
completely inappropriate for this purpose. Copyright © 2002 John Wiley
& Sons, Ltd.
Cytoplasmic dynein/dynactin mediates the assembly of aggresomes
Authors: Johnston Jennifer A. , Illing Michelle E. , Kopito Ron R. 
Published: October 2002

AbstractAggresomes are pericentrosomal cytoplasmic structures into which aggregated, ubiquitinated, misfolded proteins are sequestered. Misfolded proteins accumulate in aggresomes when the capacity of the intracellular protein degradation machinery is exceeded. Previously, we demonstrated that an intact microtubule cytoskeleton is required for the aggresome formation [Johnston et al., 1998: J. Cell Biol. 143:1883–1898]. In this study, we have investigated the involvement of microtubules (MT) and MT motors in this process. Induction of aggresomes containing misfolded ΔF508 CFTR is accompanied by a redistribution of the retrograde motor cytoplasmic dynein that colocalizes with aggresomal markers. Coexpression of the p50 (dynamitin) subunit of the dynein/dynactin complex prevents the formation of aggresomes, even in the presence of proteasome inhibitors. Using in vitro microtubule binding assays in conjunction with immunogold electron microscopy, our data demonstrate that misfolded ΔF508 CFTR associate with microtubules. We conclude that cytoplasmic dynein/dynactin is responsible for the directed transport of misfolded protein into aggresomes. The implications of these findings with respect to the pathogenesis of neurodegenerative disease are discussed. Cell Motil. Cytoskeleton 53:26–38, 2002. © 2002 Wiley‐Liss, Inc.