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PubMed1996

Optimization of restriction fragment length polymorphism and single strand conformation polymorphism analysis for the detection of point mutations of ras oncogenes in paraffin-embedded tissues.

69 samples of formalin-fixed and paraffin-embedded tumor tissues (colon carcinomas n = 15, colon adenomas n = 15, transitional cell carcinomas of the urinary bladder n = 17, transitional cell papillomas of the urinary bladder n = 22) were investigated for point mutations of ras oncogenes using polymerase chain reaction (PCR) and nested-PCR followed by restriction fragment length polymorphism (RFLP) and single strand conformation polymorphism (SSCP), respectively. Results were proved by sequence analysis. Nested-PCR combined with SSCP analysis revealed five mutations of the Ki-ras oncogenes in five colon tumors. RFLP analysis revealed one point mutation in one sample of invasive transitional cell carcinomas. Using optimized PCR protocols, the methods described are applicable to paraffin- embedded tissues and offer a tool for mutation analysis in retrospective and prospective studies.

Base Sequence↗

PubMed1996

Measuring the potency of pulp mill effluents for induction of hepatic mixed-function oxygenase activity in fish.

A bioassay protocol was optimized for measuring the potency of effluents or waterborne chemicals for inducing mixed-function oxygenase (MFO) activity of rainbow trout (Oncorhynchus mykiss). Measurements of ethoxyresorufin O-deethylase (EROD) can be made with an established endpoint assay using large volumes of reagents and tissue. However, a new kinetic microplate assay offers significant savings in time, reagents, and sample volumes. Data are distributed lognormally and must be log transformed before statistical analyses. EROD activity increases with exposure time to pulp mill effluent, and a 4-d exposure provides a near-maximal response. Optimum fish size conforms to standard practices in fish toxicology; loading rates should not exceed 1 g of fish per liter of test solution per day. Feed should be withheld from test fish 48 h before testing to reduce the variance of measured activity, and anaesthetizing fish with MS-222 does not affect their response to MFO inducers. Pulp mill effluents do not lose their potency during 2-3 wk of exposure at temperatures ranging from -20 to 13 degrees C, whether stored in plastic or glass. Steel containers were associated with slight losses in potency. Bioassays of MFO induction in fish exposed to liquid effluents are practical and conform to standard practice for testing the lethality of waterbone chemicals. The results are sufficiently precise that differences among means based on live fish per treatment can be discriminated statistically when activity changes by threefold or more.

Analysis of Variance↗

PubMed1996

[Neuroimaging and epilepsy].

The objective of magnetic resonance neuroimaging is to define the structural changes responsible for epileptogenic lesions and to rule out the presence of dual pathology when partial epileptic seizures are being studied. To this end, the individualization and optimization of protocols and sequences is indispensable. Structural images must be complemented by clinical evidence and function studies (EEG, SPECT, PET) in order to determine whether the structural lesion is responsible for the seizure and might eventually be excised. Spectroscopy provides biochemical information that is somewhat comparable to that obtained by biopsy of the epileptogenic zone. Spectroscopic images in the near future will provide clear "blind" views of these zones. Functional magnetic resonance images will presumably be of great help in the management of these patients.

Arteriovenous Malformations↗

PubMed1997

Efficient in vivo marking of primary CD4+ T lymphocytes in nonhuman primates using a gibbon ape leukemia virus-derived retroviral vector.

High efficiency retroviral-mediated gene transfer to rhesus CD4+ peripheral blood lymphocytes (PBL) was accomplished using an optimized transduction protocol using a gibbon ape leukemia virus (GaLV) envelope-containing packaging cell line PG13. Engineered CD4+ PBL were administered to three nonmyeloablated animals in three or four separate infusions over 9 months. Polymerase chain reaction (PCR) demonstrated in vivo reconstitution of the genetically engineered CD4+ PBL at levels between 1% and 10% of the circulating leukocytes. This level of gene marking indicates that up to 30% of endogenous circulating CD4+ cells can be genetically engineered. The high levels of marked lymphocytes persist for the first 3 weeks following reinfusion then decline to < or = 0.1% over the next 21 weeks. Lymph node (LN) biopsies were performed to determine if the engineered CD4+ lymphocytes could traffic to lymphoid tissues. Marked lymphocytes were detected in LN biopsies 100 days following reinfusion of the transduced cells. Expression of retroviral vector-derived sequences was detected by reverse transcriptase (RT)-PCR analysis from CD4-enriched lymphocytes that were activated by culturing in the presence of recombinant interleukin-2 (rlL-2). A humoral immune response to fetal bovine serum (FBS) was detected in all animals following the second administration of the culture expanded CD4+ lymphocytes. No antibody response was detected to the neomycin-resistance (Neo(R)) transgene, the murine retroviral group-specific antigen (gag), or GaLV envelope (env) proteins.

Animals↗

PubMed1997

New treatment regimens in organophosphate (diazinon) and carbamate (methomyl) insecticide-induced toxicosis in fowl.

The objective of this work was to determine optimal treatment regimens for organophosphate (OP) or carbamate insecticide toxicoses in fowl using the antidotes atropine sulfate and pralidoxime chloride (2-PAM). Broiler chicks in treatment groups, each comprising 3 replicates of 6-7 birds/replicate, were gavaged on a body weight (BW) basis with the OP and carbamate insecticides, diazinon and methomyl, respectively, at lethal dosages. Treatment groups were injected with either or both of the antidotes at various dosages as soon as clinical signs appeared. Birds appearing healthy 24 h thereafter were regarded as having been treated successfully. At a dosage of 100 mg/kg BW, atropine was mildly toxic and at 200 mg/kg 2-PAM was severely toxic (but not lethal), whereas at dosages of 50 and 100 mg/kg BW, respectively, the antidotes were at their most effective. With diazinon, atropine alone was only partially effective (12/20 survivors), whereas 2-PAM was extremely efficacious. (20/20 survivors); the combination of the 2 antidotes at 2 dosages was slightly less effective (19/20 survivors) than 2-PAM alone. For methomyl toxicity, atropine was largely successful (18/20 survivors), whereas 2-PAM was mostly unsuccessful (10/20 survivors); the combination at high dosage was less effective (15/20 survivors) than atropine alone, but at a low dosage the combination was the most successful (20/20 survivors). The results indicate that anticholinesterase insecticide toxicoses in fowl should not be treated according to textbook recommendations, and antidotal dosage with atropine should be up to 100 times greater than is commonly recommended. The specific cause of the toxicoses should ideally be determined before treatment is given, but as this is often unknown, a combination of antidotes may be the optimal treatment protocol.

Animals↗

PubMed1998

Revised FIGO staging system for gestational trophoblastic tumors. Recommendations regarding therapy.

OBJECTIVE: To evaluate the revised International Federation of Gynecology and Obstetrics (FIGO) staging system for gestational trophoblastic tumors (GTT) and to recommend therapy. STUDY DESIGN: Review of the literature regarding the development of the FIGO staging system, the World Health Organization (WHO) prognostic scoring system and Hammond's clinical classification for GTT plus analysis of response to single-agent chemotherapy in 546 patients treated at the New England Trophoblastic Disease Center. RESULTS: The revised FIGO staging system appears to successfully combine anatomic staging and a prognostic clinical classification. The revised FIGO staging system reliably predicts treatment outcome and therefore can be used to help select optimal treatment protocols. CONCLUSION: The revised FIGO staging system is capable of predicting patients who respond poorly to single-agent chemotherapy, appears to reliably predict outcome and therefore can be used to help select appropriate treatment protocols.

Antimetabolites, Antineoplastic↗

PubMed1998

The management of acute fractures involving the distal radio-ulnar joint and distal ulna.

The acute management of fractures involving the distal radio-ulnar joint and distal ulna is controversial. The primary goal is recognition and differentiation between stable and unstable fracture patterns. Although an operative approach is adopted in the treatment of these injuries, the optimal management protocol awaits good prospective randomized studies.

Humans↗

PubMed1998

Report of the Sinus Consensus Conference of 1996.

Retrospective data from sinus floor augmentation bone grafts were collected from 38 surgeons for 1007 sinus grafts that involved the placement of 2997 implants over a 10-year period, with the majority of the implants followed for 3 years or more postrestoration. There were 229 implant failures reported. Various root-form implants and grafting modalities were used. A consensus conference was organized to evaluate the data and reach a consensus on optimal treatment protocols. The complete database demonstrated a 90.0% success rate for implants placed in sinus grafts with at least 3 years of function. Differences in grafting materials, implant surfaces, and timing protocols were statistically analyzed. However, the database was so multivariate and multifactorial that it was difficult to draw definitive conclusions; these must await controlled prospective studies. The consensus conference therefore developed and voted on multiple consensus statements derived by committee review for bone graft materials, type of implants, timing for implant placement, failure analysis, radiographic analysis, indications/contraindications, prosthetics, and nomenclature. Several consensus statements were obtained, the most significant being that the sinus graft should now be considered a highly predictable and effective therapeutic modality.

Bone Substitutes↗

PubMed1998

Delivery of therapeutic doses of radioiodine using bispecific antibody-targeted bivalent haptens.

UNLABELLED: Two-step pretargeting strategies have been designed to deliver radioisotopes to tumors more selectively than directly labeled antibodies or fragments. In this article, we compare quantitatively the potential of these strategies for the radioimmunotherapy of solid tumors. METHODS: Direct targeting was performed using iodine-labeled IgG and F(ab')2. As two-step strategies, we used the sequential injection of anti-CEA x anti-DTPA-In bispecific F(ab')2 (BsF(ab')2) and monovalent and bivalent DTPA derivatives labeled with iodine. The biodistribution of iodine in nude mice grafted with the LS174T human colorectal carcinoma was monitored in time and used for calculating radiation doses. RESULTS: In agreement with earlier studies, the IgG was more effective for delivering a radiation dose to the tumor than the F(ab')2 (7.8 versus 0.76 Gy/MBq, respectively) and both were moderately selective with respect to normal tissues (tumor:blood of 2.9 and 1.7, respectively). At their MTD, they should deliver 86 and 34 Gy, respectively, to the tumor. Using a nM-affinity DTPA-In bivalent hapten, the two-step protocol was optimized by varying the dosage of the BsF(ab')2, the stoichiometry of the reagents and the pretargeting time. The saturation of the tumor was obtained by injecting 5 nmol (500 microg) of BsF(ab')2. The pretargeted BsF(ab')2 was saturated by the injection of 0.5 mol of bivalent hapten per mole of antibody. With a 48-hr pretargeting time, the selectivity of the irradiation of the tumor was optimized (tumor:blood of 7.8) but only at the price of a lower efficiency (0.35 versus 0.86 Gy/MBq, 48-hr and 20-hr pretargeting time, respectively). Attempts to increase selectivity by using a microM-affinity DTPA-Y bivalent hapten or by chasing excess circulating radiolabeled hapten with an excess of unlabeled hapten also reduced tumor exposure. The use of a monovalent hapten resulted in both lower efficiency and selectivity. However, the two-step pretargeting of high-affinity bivalent hapten (Affinity Enhancement System, AES) should deliver 30-60 Gy to the tumor with less than 9 Gy to the blood in tumor-bearing mice. CONCLUSION: Radioimmunotherapy with AES is predicted to be as efficient and with lower hematological toxicity than direct targeting.

Animals↗

PubMed1998

Antagonistic effects of systemic interleukin 2 on immune Tcell-mediated graft-versus-leukemia reactivity.

This study demonstrates that systemic interleukin 2 (IL-2) can decrease the homing of syngeneic immune T cells to the target organ of metastases and accelerate unwanted side effects of allogeneic immune T cells. As a tumor system, we used the well-characterized highly aggressive DBA/2 mouse leukemia ESb and its less aggressive adhesion variant, ESb-MP. Systemic IL-2 treatment was performed with recombinant human interleukin-2 (Proleukin), which was slowly released via an implanted osmotic pump or was modified with polyethylene glycol (PEG-IL-2) to achieve constant plasma levels. Allogeneic B10.D2 antitumor immune spleen cells (ISPL cells) exerted strong graft-versus-leukemia (GvL) reactivity after adoptive transfer into late-stage ESb-MP tumor-bearing DBA/2 mice. Mls(a) superantigen-reactive vbeta6 donor T cells were not eliminated or tolerized by in vivo priming with the tumor cells and were present in active proliferation in liver infiltrates. When exogenous PEG-IL-2 or Proleukin was applied in addition to ISPL cells in such mice, the strong GvL-mediated protective immunity was converted into a fatal graft-versus-host disease. IL-2 treatment alone had no toxic effect and caused a moderate protection effect in the absence of an effect on local tumor growth. Potentiation of GvH reactivity of B10.D2 ISPL by PEG-IL-2 was proven in non-tumor-bearing DBA/2 mice, in which graft-versus-host disease was characterized by: (a) heavy hepatic lymphocytic infiltration, (b) irreversible increase of serum glutamate-oxalacetate-transaminase and glutamate-pyruvate-transaminase levels, (c) weight loss, and (d) death. Antagonistic effects of systemic IL-2 on GvL were observed with syngeneic DBA/2 anti-ESb immune peritoneal effector cells (PECs). There was a detrimental effect of systemic IL-2 on liver target organ infiltration by immune T cells causing, at day 6 after transfer, a drop from 20-30 CD4 or CD8 T cells per liver lobule in the PEC group to <5 in the PEC plus IL-2 group. The results emphasize the importance of a better understanding of IL-2 function in vivo and of its interaction with immune cell function to improve protocols for optimal application in the clinic to achieve maximal GvL effects.

Animals↗

PubMed1998

Construction of a quantitative PCR system to determine expression of tumor associated antigen.

Cancer immunotherapy is a strategy for cancer treatment by induction of anti tumor responses. The identification of candidate tumor associated antigens (TAA) suggested their potential use as immunogens for vaccination studies. Quantification of a TAA expression by cancerous cells is an important factor in determination of induced immune response efficiency against tumors and thus enables us to devise optimal immunotherapy protocol to cure cancer. The quantitative polymerase chain reaction (PCR) enables us to compare the TAA expression in highly metastatic tumor clones with that in less metastatic ones and in normal cells. It allows us to gain more insight into genome rearrangements that occur in malignant transformation as well as broaden our knowledge about tumor cell gene expression regulation. One of the peptides isolated previously in our lab from a murine lung carcinoma is the mutated Connexin 37 (cx37), a gap-junction protein. Research is underway to determine the expression level of the TAA in various Lewis lung carcinoma cells. This evaluation is achieved by means of quantitative PCR. A quantitative PCR experiment includes preparation of a control template, which is added in known amounts together with the target template in a series of amplification reactions. The control template uses the same primers as the target sequence, yet their PCR products differ in size so as to be distinguishable. Two methods were used to produce this control template. The first one included specific deletion of a sequence of approximately 100 bp that lay between the two primers, insertion of the new template into a plasmid vector, transformation of competent bacteria, detection of transformed bacterial colonies and isolation of the plasmid DNA in a large quantity. The non-mutated, deleted Connexin 37 cDNA was also isolated from bacteria and used for another experiment aimed at producing deleted, mutated Connexin 37 cDNA by means of primer mutagenesis. (Fig. 5, Ref 8.)

Animals↗

PubMed1999

Progression detection of stage I nonseminomatous testis cancer on surveillance: implications for the followup protocol.

PURPOSE: To optimize followup in patients with stage I nonseminomatous testis cancer on surveillance we evaluated the contribution of each followup modality to the detection of progression as well as morbidity and mortality outcomes. MATERIALS AND METHODS: After orchiectomy 170 patients with clinical stage I nonseminoma were prospectively placed on a surveillance protocol. History, physical examination, serum tumor markers, abdominal and pelvic computerized tomography (CT), and chest x-ray were used for followup. The number of failures, methods and timing of progression detection, treatments required, mortality rate and subsequent contralateral primary tumors were recorded. RESULTS: The 170 surveillance patients were followed a median of 6.3 years. Within 2 years (median 6.9 months) postoperatively 48 patients (28.2%) had disease progression. History, physical examination, markers, CT and chest radiography provided the initial evidence of progression in 18 (37.5%), 34 (70.8%), 34 (70.8%), and 4 (8.3%) patients, respectively. Each modality was the only indicator of failure in 2 (4.2%), 4 (8.3%), 10 (20.8%) and 0 cases, respectively. Of the 170 patients 122 (71.8%) required no additional treatment beyond orchiectomy, 26 (15.3%) received 1 and 22 (12.9%) underwent more than 1 therapeutic modality. Only 1 patient (0.6%) died of disease. Contralateral tumors developed in 5 cases (2.9%) therapeutic a mean of 8.1 years after orchiectomy. CONCLUSIONS: In stage I nonseminoma patients, surveillance history, physical examination, tumor markers and abdominopelvic CT are necessary components of the followup protocol. Removal of routine chest x-ray from the protocol would not have changed progression detection. The initial surveillance visit must occur by 2 months postoperatively. Patients should be followed beyond 5 years and likely for life in addition to regular patient self-examination.

Adolescent↗

PubMed2000

[Various spiral CT protocols and their significance in the diagnosis of aortic dissections: results of a prospective study].

PURPOSE: Development of an optimized Spiral CT protocol type for the diagnosis of aortic dissections. MATERIAL AND METHODS: 121 consecutive CT examinations applying 5 different protocol types were blindly read by two experienced radiologists and then compared with: (a) 45 biplane transesophageal echocardiographies (TEE), (b) 52 transthoracic echocardiographies (TTE), (c) 52 operative findings and, furthermore, related to the clinical course over at least six months in 79 patients. RESULTS: The sensitivity of the spiral computed tomography for detection of dissection was 97% (biplane TEE: 88%), the specificity 100% (biplane TEE: 91%). In 15% dissections with atypical origin and entries (mid-portion of the aortic arch, distal thoracic aorta, etc.) were found. The optimal CT-protocol was the one with a combination of two separate but adjacent spiral scans achieving high spatial resolution for the aortic arch and enough spatial resection for the residual aorta (1. helical scan 3 mm collimation, pitch 2. 2. helical scan 5 mm collimation and pitch 2, 130 ml contrast medium at 5 ml/s) with a classification accuracy of 100%, visualization of entries of 100%, reentries of 100% (40% direct, 60% indirect). The identification of the ostia of the aortic branches were: supraaortic 93%, visceral 100%, left renal artery 100%, right renal artery 93%, iliac 64%. The CT angiography, designed as aortic arch angiography, showed a good contrast in the aortic arch vessels (79-86%) and the visceral vessels too (91%). CONCLUSION: Thoracic CT angiography can be used as gold standard in the primary evaluation of aortic dissections.

Adolescent↗

PubMed2005

Optimization of a simple, automatable extraction method to recover sufficient DNA from low copy number DNA samples for generation of short tandem repeat profiles.

AIM: To develop an automated, high throughput extraction protocol in order to produce database eligible profiles from fingerprints and other low copy number (LCN) DNA sources. METHODS: Extraction of either purified control DNA or buccal cells, for example, with commercial kits was compared to extraction with a simple digestion buffer and a subsequent concentration and purification. Results were evaluated based on the amount of DNA recovered and the completeness of the DNA profiles produced. RESULTS: Simple procedures with fewer steps were superior to commercial kits, such as DNA IQ (Promega, Madison, WI, USA) and QiaAmp (Qiagen, Valencia, CA, USA), and other protocols with many manipulations. The optimized protocol included a thirty-minute incubation with 0.01% SDS and proteinase K at 56 degrees C, followed by an incubation at 100 degrees C for 10 minutes. Concentration of the extract and removal of the SDS was accomplished with a Microcon 100 (Millipore, Bedford, MA, USA), which can be assembled into a 96 well plate, the Microcon-96 Retentate Assembly Plate (Millipore) for automation. The addition of 1 ng Poly A RNA to the Microcon significantly improved DNA recovery. CONCLUSION: A one-step sample digestion followed by sample concentration/purification minimized sample loss and maximized amplification input. Moreover, this methodology can be easily adapted for automation. Implementation of this protocol, due to the numerous potential sources of LCN DNA samples, will enhance the recovery of biological evidence from crime scenes and may be a source of database profiles.

Automation↗

PubMed2002

Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis.

BACKGROUND: T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. RESULTS: Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3-3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification. CONCLUSION: T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays.

Journal Article↗

PubMed2025

Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing.

BACKGROUND: The respiratory microbiome, which comprises bacteria, fungi, and viruses, plays a crucial role in respiratory health and disease. However, its study is limited by the low microbial biomass in respiratory samples and the dominance of host RNA. Metatranscriptomics offers comprehensive insights into active microbial communities and their interactions with the host but requires optimized RNA extraction protocols for robust and unbiased analysis. This study evaluated two RNA extraction kits—one employing chemical lysis (CL) and another combining chemical and mechanical lysis (CML)—to determine their effectiveness for metatranscriptomic analysis of respiratory samples. RESULTS: The CML protocol significantly increased double-stranded DNA (dsDNA) library yields, leading to higher sequencing read counts for both sample types (p < 0.0001). The read length was unaffected by the lysis protocol for the BAL and NPS samples. Taxonomic profiling revealed that CML enhanced the detection of robust microorganisms, such as gram-positive bacteria and fungi, without compromising viral detection. CONCLUSIONS: The CML protocol demonstrated superior recovery of genetic material, particularly for fungi and gram-positive bacteria, making it better suited for comprehensive metatranscriptomic analyses. These findings underscore the need for tailored RNA extraction strategies on the basis of sample type and research objectives. Optimized metatranscriptomic protocols are pivotal for advancing our understanding of the respiratory microbiome and its role in health and disease.

Microbiota↗

PubMed2006

Randomized clinical trial assessing the effect of Doppler-optimized fluid management on outcome after elective colorectal resection.

BACKGROUND: Protocolized fluid administration using oesophageal Doppler monitoring may improve the postoperative outcome in patients undergoing surgery. METHODS: A total of 108 patients undergoing elective colorectal resection were recruited into a double-blind prospective randomized controlled trial. An oesophageal Doppler probe was placed in all patients. The control group received perioperative fluid at the discretion of the anaesthetist, whereas the intervention group received additional colloid boluses based on Doppler assessment. Primary outcome was length of postoperative hospital stay. Secondary outcomes were morbidity, return of gastrointestinal function and cytokine markers of the systemic inflammatory response. Standard preoperative and postoperative management was used in all patients. RESULTS: Demographic and surgical details were similar in the two groups. Aortic flow time, stroke volume, cardiac output and cardiac index during the intraoperative period were higher in the intervention group (P<0.050). The intervention group had a reduced postoperative hospital stay (7 versus 9 days in the control group; P=0.005), fewer intermediate or major postoperative complications (2 versus 15 percent; P=0.043) and tolerated diet earlier (2 versus 4 days; P=0.029). There was a reduced rise in perioperative level of the cytokine interleukin 6 in the intervention group (P=0.039). CONCLUSION: A protocol-based fluid optimization programme using intraoperative oesophageal Doppler monitoring leads to a shorter hospital stay and decreased morbidity in patients undergoing elective colorectal resection.

Aged↗

PubMed2003

Optimization of high-density cDNA-microarray protocols by 'design of experiments'.

Expression analysis using microarray technology implies a complex experimental procedure with a large number of parameters affecting the final result. We have demonstrated that optimization of such a complex protocol can be far better handled using design of experiments (DOE) than by working on a single parameter at a time. Based on the results of a screening design, we developed a spotting buffer composed of formamide, betaine and nitrocellulose. This buffer provides a 2-fold increase in signal-to-background ratio compared to 3x SSC. Comparison to seven other buffers tested on 10 different substrates revealed it had the highest sensitivity. DNA dissolved in this buffer can be spotted on epoxysilane-coated microscope slides at a density of up to 70 000 spots per slide. A second DOE approach characterized the RNA labeling process with regard to the concentration of fluorescent dyes, dNTPs and reverse transcriptase. Adjust ments of the concentrations of dNTPs, as well as reverse transcriptase, towards the optimum, produced an improvement in the performance of the labeling procedure by a factor of 3 (Cy3) and 10 (Cy5). These results demonstrate that the process of establishing a stable expression profiling protocol and its further optimization can be significantly shortened and improved by DOE.

Buffers↗