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Results for “protocol optimization”

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PubMed1993

Drug delivery optimization through Bayesian networks: an application to erythropoietin therapy in uremic anemia.

This paper describes how Bayesian networks can be used in combination with compartmental models to plan recombinant human erythropoietin delivery in the treatment of anemia of chronic uremic patients. Past measurements of hemoglobin concentration in a patient during the therapy can be exploited to adjust the parameters of a compartmental model of erythropoiesis. This adaptive process provides more accurate patient-specific predictions, and hence a more rational dosage planning. Inferences are performed by using a stochastic simulation algorithm called Gibbs sampling. We describe a drug delivery optimization protocol based on our approach. Some results obtained on real data are presented.

Adult↗

PubMed2000

Cryopreservation of seabream (Sparus aurata) spermatozoa.

The aim of this research was to optimize protocols for freezing spermatozoa of seabream (Sparus aurata). All the phases of the cryopreservation procedure (sampling, choosing the cryoprotective extender, cooling, freezing, and thawing) were studied in relation to the species of spermatozoa under examination, so as to be able to restore on thawing the morphological and physiological characteristics of fresh semen. Seabream spermatozoa were collected by stripping and transported to the laboratory chilled (0-2 degrees C). Five cryoprotectants, dimethyl sulfoxide (Me(2)SO), ethylene glycol (EG), 1,2-propylene glycol (PG), glycerol, and methanol, were tested at concentrations between 5 and 15% by volume to evaluate their effect on the motility of semen exposed for up to 30 min at 26 degrees C. The less toxic cryoprotectants, 10% EG, 10% PG, and 5% Me(2)SO, respectively, were added to 1% NaCl to formulate the extenders for freezing. The semen was diluted 1:6 with the extender, inserted into 0.25-ml plastic straws by Pasteur pipette, and frozen using a cooling rate of either 10 or 15 degrees C/min to -150 degrees C followed by transfer and storage in liquid nitrogen (-196 degrees C). The straws were thawed at 15 degrees C/s. On thawing, the best motility was obtained with 5% Me(2)SO, although both 10% PG and EG showed good results; no differences were found between the two freezing gradients, although semen frozen with the 10 degrees C/min gradient showed a slightly higher and more prolonged motility.

Animals↗

PubMed2001

Microarray-based analysis of early development in Xenopus laevis.

In order to examine transcriptional regulation globally, during early vertebrate embryonic development, we have prepared Xenopus laevis cDNA microarrays. These prototype embryonic arrays contain 864 sequenced gastrula cDNA. In order to analyze and store array data, a microarray analysis pipeline was developed and integrated with sequence analysis and annotation tools. In three independent experimental settings, we demonstrate the power of these global approaches and provide optimized protocols for their application to molecular embryology. In the first set, by comparing maternal versus zygotic transcription, we document groups of genes that are temporally regulated. This analytical approach resulted in the discovery of novel temporally regulated genes. In the second, we examine changes in gene expression spatially during development by comparing dorsal and ventral mesoderm dissected from early gastrula embryos. We have discovered novel genes with spatial enrichment from these experiments. Finally, we use the prototype microarray to examine transcriptional responses from embryonic explants treated with activin. We selected genes (two of which are novel) regulated by activin for further characterization. All results obtained by the arrays were independently tested by RT-PCR or by in situ hybridization to provide a direct assessment of the accuracy and reproducibility of these approaches in the context of molecular embryology.

Animals↗

PubMed2002

Validation of an ex vivo Xenopus liver slice bioassay for environmental estrogens and estrogen mimics.

A sensitive ex vivo bioassay for detecting environmental estrogens and estrogen mimics was developed using Xenopus liver slice culture. Vitellogenin synthesis by these cultures was used as biomarker for estrogenic activity of environmental water samples. Sensitization of the assay for estrogens and mimics was accomplished by employing tissue from animals after in vivo preexposure to estrogen. Effects of various tissue culture factors were investigated in order to obtain optimum conditions for the bioassay. It was found that endogenous vitellogenin and/or estrogen could be "washed out" of cultures and that not only uncontaminated males but also estrogen-pretreated males and females can successfully be used as bioindicators. Estrogenicity was detected, using the ex vivo Xenopus liver slice culture assay, in sewage effluent, lake water, and dam water. This article presents an optimized protocol for effective estrogen detection in environmental water samples.

Animals↗

PubMed2002

Analysis of shuffled gene libraries.

In vitro recombination of homologous genes (family shuffling) has been proposed as an effective search strategy for laboratory evolution of genes and proteins. Few data are available, however, on the composition of shuffled gene libraries, from which one could assess the efficiency of recombination and optimize protocols. Here, probe hybridization is used in a macroarray format to analyze chimeric DNA libraries created by DNA shuffling. Characterization of hundreds of shuffled genes encoding dioxygenases has elucidated important biases in the shuffling reaction. As expected, crossovers are favored in regions of high sequence identity. A sequence-based model of homologous recombination that captures this observed bias was formulated using the experimental results. The chimeric genes were found to show biases in the incorporation of sequences from certain parents, even before selection. Statistically different patterns of parental incorporation in genes expressing functional proteins can help to identify key sequence-function relationships.

Base Sequence↗

PubMed1995

Xenobiotic metabolizing enzyme activities and viability are well preserved in EDTA-isolated rat liver parenchymal cells after cryopreservation.

Rat liver parenchymal cells (PC) were isolated by EDTA perfusion and were purified by a subsequent Percoll centrifugation. The isolated PC had a viability of 95%, as judged by trypan blue exclusion. Freshly isolated PC were cryopreserved with an optimized protocol in a computer-controlled freezer. After thawing, the PC still retained a viability of 89%. The activities of representative xenobiotic metabolizing enzymes were compared between freshly isolated and cryopreserved PC after thawing. The cytochrome P450 content and the cytochrome P450 2C11 isoenzyme activity, determined by hydroxylation of testosterone in intact cells, were not affected by the cryopreservation. The following phase II enzyme activities were also well maintained after cryopreservation: Phenol sulfotransferase (92%), 1-naphthol UDP-glucuronosyl transferase (95%), soluble epoxide hydrolase (87%), and glutathione S-transferase (88%), determined with broad spectrum substrate 1-chloro-2,4-dinitrobenzene. However, there was a significant decrease in plating efficiency between freshly isolated (86%) and cryopreserved (57%) PC when they were cultured. The initial quality of the freshly isolated PC is decisive for the success of cryopreservation. These results support the use of cryopreserved PC in pharmacology and toxicology with the aim to reduce the number of experimental animals used.

Animal Testing Alternatives↗

PubMed2002

Repeated cycles of alternate administration of fludarabine and Zidovudine plus Didanosine inhibits murine AIDS and reduces proviral DNA content in lymph nodes to undetectable levels.

The results of the combined use of Fludarabine, an anticancer agent that may be able to target latently infected cells, and conventional antiretroviral therapy (AZT+DDI) in a murine model of AIDS, i.e., LP-BM5 infection, are reported. Eighty percent of infected mice, treated with four cycles of alternate administration of Fludarabine and AZT+DDI, showed undetectable levels of proviral DNA in lymph nodes. After 8 weeks of treatment interruption, the infected/treated animals, although still alive at a time when all untreated animals had succumbed to the infection, showed disease progression and reappearance of proviral DNA in lymph nodes. The retrospective analysis of proviral DNA content in spleen and bone marrow at the end of the fourth cycle of treatment revealed a low but detectable amount of BM5d proviral DNA. We thus concluded that the spleen and bone marrow may be less sensitive to lympholitic drugs and therefore act as viral reservoirs in LP-BM5 infection. This study suggests that optimized protocols of alternate administration of cytolytic and antiretroviral drugs may represent a useful strategy to eradicate retroviral infections.

Animals↗

PubMed1995

Measuring resistance to phagocytosis of group A and G streptococci: comparison of direct bactericidal assay and flow cytometry.

M protein is thought to contribute to the ability of non-opsonized group A and group G streptococci (GAS and GGS, respectively) to resist phagocytosis by polymorphonuclear leukocytes. In previous studies, correlation between M protein expression and phagocytosis was determined by incubating these pathogens in human blood and comparing colony-forming bacterial counts prior to and after exposure to blood (direct bactericidal assay; DBA). Here, we report the application of flow cytometry to measure GAS and GGS resistance to phagocytosis. The results of the assays were in complete agreement with those from DBAs. Nevertheless, flow cytometry was regarded as superior to DBA because of its speed and potential uses for quantitative studies. In addition, the use of anti-CD11b monoclonal antibody for granulocyte staining guaranteed a non-compromized granulocyte function. The optimized protocol for flow cytometry presented here could be utilized to directly measure the involvement of individual protein types in bacterial resistance to phagocytosis.

Blood Bactericidal Activity↗

PubMed1990

Measurement of cerebral blood flow with a bolus of oxygen-15-labelled water: comparison of dynamic and integral methods.

A method is presented for the measurement of cerebral blood flow (CBF) with a bolus of water labelled with oxygen 15. The method, which has been evaluated in normal volunteers, is based on Kety's model, with two additional parameters to account for the difference in the time of tracer arrival in the radial and carotid arteries ("delay") and for dispersion of the tracer in the body and/or blood counting systems. It combines the advantages of: (i) dynamic data collection for estimation of delay and dispersion; (ii) robustness and linearity of CBF estimates with an integral method; and (iii) simplicity of continuous external monitoring of arterial blood radioactivity, particularly with repeated measurements. An optimized protocol is proposed for routine applications in neurological and neurophysiological studies.

Adult↗

PubMed1983

The control issue in biofeedback training.

Well-delineated models and procedural descriptions are noticeably missing from the clinical biofeedback literature dealing with the training of physiological self-control. As a consequence, optimal protocols for the assessment and training of self-control of physiological functions have not eventuated. The present article reviews evidence suggesting that researchers have (a) confused self-control training, assessment, and measurement of tonic response levels, (b) neglected to determine the degree of acquired physiological self-control, and (c) failed to report the relationship between level of acquired physiological control and clinical outcome. The article also proposes an assessment and training paradigm that may be useful in reducing these methodological problems in future biofeedback research.

Arousal↗

PubMed1992

Survival of human oocytes cryopreserved with or without the cumulus in 1,2-propanediol.

BACKGROUND: Although cryopreservation of human preembryos has been carried out with success, the cryostorage of oocytes, which pose fewer controversial moral, ethical, and legal problems has been much less successful. Various attempts to cryopreserve human oocytes have been mostly unsuccessful and the search for an optimal protocol for oocyte cryopreservation remains elusive. We therefore undertook this study to determine the effect of oocyte cryostorage in 1,2-propanediol. METHOD: Mature human oocytes with or without their cumuli were cryopreserved in precooled 1,2-propanediol, then thawed and inseminated with sperms for in vitro fertilization. The outcome of insemination and subsequent embryonic development were also recorded and compared. RESULTS: Postthaw cryosurvival rate was significantly better when cryostorage was carried out with the oocyte cumulus intact as compared to those oocytes denuded of their cumuli (54 versus 27%, respectively; P < 0.05). Eight (44%) of 18 surviving postthaw oocytes with intact cumuli were fertilized normally, with cleavage in six, as compared to two (25%) and one, respectively, of those denuded of their cumulus prior to cryostorage. Development to the blastocyst stage was achieved in three embryos derived from oocytes with an intact cumulus at cryostorage. CONCLUSION: We conclude that 1,2-propanediol can be used with success in oocyte cryopreservation, although the issue of parthenogenecity is still to be resolved. Oocyte's with intact cumulus survive cryostorage better than those without it.

Adult↗

PubMed1987

Establishment of primary cell cultures: experiences with 155 cell strains.

Cell culture systems allow the examination of cell populations in a functional state. To simulate in vivo conditions as closely as possible freshly established cell strains are superior to permanent cell lines. Different aspects for the establishment of primary cell cultures obtained from various tissues are compared: Disintegration, culture media supplemented with basal additions, special supplements (growth factors, hormones), and attachment factors. The proliferation rates of the attained cell strains were evaluated by determination of cell doubling times. Procedures for how to obtain a relatively high plating efficiency (approx. 70% in our series of 219 attempts) of primary growth in vitro are described: (1) Mechanical disintegration is superior to enzymatic digestion. If mechanical treatment alone did not produce a sufficient number of viable cells, additional digestion with collagenase/dispase revealed a higher number of proliferating primary cultures than with trypsin. (2) Proliferation of cell cultures from normal and tumorous tissues of epithelial origin was superior in Leibovitz L 15 medium (58 of 87 (67%) cases). Cultures from mesenchymal tissues and tumors were found to have shortest cell doubling times in MEM and RPMI 1640 (16 of 23 (70%) cases). The media were supplemented with the basal additions indicated. (3) In approx. 30% of the cases special supplements like growth factors or hormones increased cell replication, although they were almost always not essential for cell growth. (4) Attachment factors only rarely contributed to the initiation of primary monolayer cultures. The application of various culture conditions does not lead to a protocol optimal for all tissues, for all probes of the same type of tumor, or for all tumor specimens of unique differentiation.

Cell Adhesion↗

PubMed2000

Muscle glycogen recovery after exercise measured by 13C-magnetic resonance spectroscopy in humans: effect of nutritional solutions.

The rate of glycogen resynthesis in human skeletal muscle after glycogen-depleting exercise is known to depend on carbohydrate intake and is reported to reach a plateau after an adequate amount of carbohydrate (CHO) consumption. Efforts to maximize the rate of glycogen storage by changing the type and form of CHO, as well as by adding proteins or lipids have yielded inconsistent results. The objective of this study was to assess whether isocaloric addition of proteins and arginine to a CHO diet in the first 4 h after an endurance exercise would increase the rate of glycogen synthesis. The CHO solution, given twice at a 2 h interval according to earlier optimized protocols, contained 1.7 g CHO/kg(body weieght) The effects of this solution were compared to those of an isocaloric solution containing 1.2 g CHO/kg(body weight) plus 0.5 g protein/kg(body weight) (including 5 g arginine). Glycogen was measured in quadriceps muscle in vivo with natural abundance 13C-magnetic resonance spectroscopy before exercise and twice after exercise, before and at the end of a 4-h period following the intake of one of the solutions. Eight subjects took part in a randomized cross-over trial separated by at least 1 week. Glycogen synthesis was found to be significantly increased with both regimes compared to a zero-caloric placebo diet, but no significant difference in glycogen resynthesis was found between the CHO-only diet and the one supplemented by proteins and arginine. It is estimated that significance would have been reached for an increase of 34%, while the effectively measured synthesis rates only differed by 5%.

Adult↗

PubMed1994

Polybrene/DMSO-assisted gene transfer. Generating stable transfectants with nanogram amounts of DNA.

Polybrene/DMSO-assisted gene transfer is a simple and versatile transfection strategy capable of producing high numbers of stable transfectants from adherent monolayer cultures with low (nanogram) quantities of exogenous DNA. The procedure involves two stages: adsorption and internalization. The former is mediated by polybrene (a polycation polymer) and favors the uniform coating of target cells with polybrene-DNA complexes. Following adsorption, the cells are permeabilized by a brief exposure to dimethyl sulfoxide (DMSO) to facilitate the uptake of DNA complexes. Diverse cell types can be exposed to a wide range of polybrene concentrations without adverse effects. By contrast, the key determinant of success is the DMSO permeabilization regime, which must be configured independently for each cell line. Protocols optimized for gene transfer in murine and human fibroblasts are presented along with a guide for the rapid optimization of the method. The advantages and limitations of the method are also discussed.

3T3 Cells↗

PubMedDate not supplied

Factors enhancing Agrobacterium tumefaciens-mediated gene transfer in peanut (Arachis hypogaea L.).

Parameters enhancing Agrobacterium-mediated transfer of foreign genes to peanut (Arachis hypogaea L.) cells were investigated. An intron-containing beta-glucuronidase uidA (gusA) gene under the transcriptional control of CaMV 35S promoter served as a reporter. Transformation frequency was evaluated by scoring the number of sectors expressing GUS activity on leaf and epicotyl explants. The 'Valencia Select' market type cv. New Mexico was more amenable to Agrobacterium transformation than the 'runner' market type cultivars tested (Florunner, Georgia Runner, Sunrunner, or South Runner). The disarmed Agrobacterium tumefaciens strain EHA101 was superior in facilitating the transfer of uidA gene to peanut cells compared to the disarmed strain C58. Rinsing of explants in half-strength Murashige-Skoog (MS) media prior to infection by Agrobacterium significantly increased the transformation efficiency. The use of cocultivation media containing high auxin [1.0 or 2.5 mg/l (4.53 micromolar or 11.31 micromolar) 2,4-D] and low cytokinin [0.25 or 0.5 mg/l (1.0 micromolar or 2.0 micromolar) BA] promoted higher transformation than either hormone-free or thidiazuron-containing medium. The polarity of the epicotyl during cocultivation was important; explants incubated in an inverted (vertically) manner followed by a vertically upright position resulted in improved transformation and shoot regeneration frequencies. Preculture of explants in MS basal medium or with 2.5 mg thidiazuron per l prior to infection drastically decreased the number of transformed zones. The optimized protocol was used to obtain transient transformation frequencies ranging from 12% to 36% for leaf explants, 15% to 42% for epicotyls. Initial evidence of transformation was obtained by polymerase chain reaction and subsequently confirmed by Southern analysis of regenerated plants.

Agrobacterium tumefaciens↗

PubMed1994

Genetic transformation of plants by protoplast electroporation.

This article describes an optimized protocol for the electroporation of tobacco mesophyll protoplasts together with notes and data on the effects of various parameters and suggestions for work with protoplasts of other species. In this protocol, electroporation is achieved by means of electrical pulses from a high-voltage, capacitive-discharge unit. Procedures are described for measurement of protoplast viability with Evan's blue, the detection of transient expression of CAT and GUS gene plasmid constructs, and for the recovery of stable transformants based on selection for kanamycin resistance.

Cell Survival↗

PubMed2002

Biochemical response after 3-d conformal radiotherapy of localized prostate cancer to a total dose of 66 gy 4-year results.

BACKGROUND: Since the introduction of 3-D conformal radiotherapy (CRT) doses of </= 70 Gy have been used in many European countries. In this analysis, the impact of a short-term neoadjuvant hormonal treatment in combination with CRT to a moderate dose level of 66 Gy was examined. PATIENTS AND METHODS: From January 1994 to February 1999 397 patients were treated for carcinoma of the prostate. In 279 patients a definitive curative treatment (T1 = 38, T2 = 165, T3 = 50, Tx = 11) with or without androgen deprivation was performed. 164 patients with radiotherapy of the prostate +/- seminal vesicles to a total dose of 66 Gy (n = 109) alone or in combination with a short-term hormonal treatment (n = 55) were included in this analysis. Biochemical relapse was defined as three rising PSA values or reintroduction of hormonal treatment. A low-risk subgroup was defined for patients with maximum serum PSA level </= 10 and cT</=2 and G</=2, all other patients were summarized as high-risk patients. RESULTS: The median follow-up of alive patients was 40 months (12-72 months). There was a total of 29/164 deaths, two were cause-specific and 27 were considered unrelated to prostate cancer. The 4-year rates of no biochemical evidence of disease for all patients was 58%. For the high-risk group the 4-year rates could be improved with borderline significance from 35% to 66% (p = 0.057) by additional neoadjuvant hormonal treatment. In contrast for the low-risk group no significant improvement was observed: 73% and 82%, respectively (p = 0.5). CONCLUSION: Especially in high-risk patients doses </= 70 Gy for radiotherapy alone seem not to be sufficient for curative treatment. Additional hormonal treatment and doses >/= 70 Gy should be considered. As a consequence of our earlier analysis a prospective multicenter treatment optimization protocol has been initiated in 1999. The protocol includes a risk-adapted dose increase from 70 Gy in low-risk patients to 74 Gy in high-risk patients including short-term androgen ablation.

Adenocarcinoma↗

PubMed1997

[MR angiography of thoracic blood vessels].

Through the introduction of newly invented high-performance gradient systems to MRI, which enable for echoplanar imaging (EPI), also magnetic resonance angiography (MRA) has gained an entirely new field of applications and techniques. Ultrafast imaging techniques in MRA allow the investigation of larger vascular areas within a single breath-hold-period. Artifacts like motion induced signal misregistrations, dephasing or saturation of the vascular signal are minimized by extremely short echo times. The technique thus requires the intravenous application of a contrast media bolus, usually a gadolinium compound, which is in standard clinical use. Coordination of the bolus injection and the timing of the data acquisition is crucial for optimal results. The first pass evaluation of the contrast media resembles CTA to a certain extend. Due to the fast measurement and the high contrast in contrast-enhanced MRA (CE-MRA) new applications and indications are developed like MRA of the pulmonary vessels. The paper offers considerations and trials for optimization of thoracical CE-MRA. Besides parameter constellation also bolus-optimization is described with respect to the dedicated anatomical premises. Investigations on volunteers and on patients build a basis for suggestions of optimized CE-MRA procedures. To date, a final estimation of the clinical value of the new technique cannot be given since ongoing improvements change the optimal protocol frequently and the potential of further developments is high.

Adolescent↗