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Laser-based detectors in chromatographic analysis.

Advances in detection technology have been a vital part of the development of microscale chromatographic techniques. Separation techniques such as microbore liquid chromatography impose severe constraints on the permissible volume of detector cells. The use of lasers to construct a new generation of chromatographic detectors has satisfied the need for low volume detection and high sensitivity. The unique properties of laser radiation have been used to advantage in designing new approaches to the detection of optical absorbance through fluorescence emission and thermal effects. New approaches to monitoring refractive index changes and optical rotation have also been developed. Together, the combination of microscale-separation techniques and highly sensitive detection provide a powerful tool for analysing small quantities of samples. Yet, there are practical limitations arising from the cost and complexity of much of the instrumentation reported to date, as well as the difficulties of preparing small samples for analysis which have limited the wide-scale application of these methods to solve practical problems. Recent advances in laser technology such as the advent of diode lasers may be useful in overcoming some of these limitations.

Chromatography↗

Phosphorescent platinum/palladium coproporphyrins for time-resolved luminescence microscopy.

Streptavidin and antibodies were labeled with phosphorescent platinum and palladium coproporphyrin. The optimal conjugates were selected on the basis of spectroscopic analysis (molar extinction coefficient, quantum yield, lifetime) and using ELISA assays to determine the retention of biological activity and immunospecificity. They were subsequently tested for the detection of prostate-specific antigen, glucagon, human androgen receptor, p53, and glutathione transferase in strongly autofluorescent tissues. Furthermore, platinum and palladium coproporphyrin-labeled dUTPs were synthesized for the enzymatic labeling of DNA probes. Porphyrin-labeled DNA probes and porphyrin-labeled streptavidin conjugates were evaluated for DNA in situ hybridization on metaphase spreads, using direct and indirect methods, respectively. The developed in situ detection technology is shown to be applicable not only in mammals but also in plants. A modular- based time-resolved microscope was constructed and used for the evaluation of porphyrin-stained samples. The time-resolved module was found suitable for detection of antigens and DNA targets in an autofluorescent environment. Higher image contrasts were generally obtained in comparison with conventional detection systems (e.g., fourfold improvement in detection of glutathione transferase).

Acyltransferases↗

High throughput genotyping technologies for pharmacogenomics.

Genetic differences between individuals play a role in determining susceptibility to diseases as well as in drug response. The challenge today is first to discover the range of genetic variability in the human population and then to define the particular gene variants, or alleles, that contribute to clinically important outcomes. Consequently, high throughput, automated methods are being developed that allow rapid scoring of microsatellite alleles and single nucleotide polymorphisms (SNPs). Many detection technologies are being used to accomplish this goal, including electrophoresis, standard fluorescence, fluorescence polarization, fluorescence resonance energy transfer, and mass spectrometry. SNP alleles may be distinguished by any one of several methods, including single nucleotide primer extension, allele-specific hybridization, allele-specific primer extension, oligonucleotide ligation assay, and invasive signal amplification. Newer methods require less sample manipulation, increase sensitivity, allow more flexibility, and decrease reagent costs. Recent developments show promise for continuing these trends by combining amplification and detection steps and providing flexible, miniaturized platforms for genotyping.

Automation↗

Fluorescence readouts in HTS: no gain without pain?

Fluorescence-based detection technologies are frequently applied in biological testing, due to their unique advantages in setting up homogeneous, sensitive assays in miniaturized formats. However, the wide application of these readouts has highlighted challenges in reagent design and problems with interference from biological reagents and compounds. Here, we summarize the current application of fluorescence-based detection methodologies, focusing on the problems faced by assay developers and on solutions to reduce false positive and negative results in fluorescence-based HTS.

Calmodulin-Binding Proteins↗

Radioimmunoguided surgery in primary colorectal carcinoma: an intraoperative prognostic tool and adjuvant to traditional staging.

BACKGROUND: The prognostic value of traditional staging classification for colorectal cancer has changed little since Dukes created the first staging scheme. Some patients with known metastatic disease are long-term survivors, while other patients with local disease die early. New intraoperative cancer detection technology, the radioimmunoguided surgery (RIGS) system, is being studied as a tool to aid in prediction of patient outcome. PATIENTS AND METHODS: Thirty-one patients with primary colorectal cancer were injected with the monoclonal antibody CC49, which was radiolabeled with iodine 125 (125I). A hand-held gamma-detecting probe was used at surgery to detect the radiolabeled antibody. Patients were classified as to the presence or absence of 125I-CC49-positive residual tissue at the close of surgery. Patient survival was analyzed. RESULTS: Follow-up ranged from 30 to 54 months. Survival of 11 stage I or II patients was longer than in 20 stage III or IV patients (P = 0.019). All 14 patients cleared of RIGS-positive tissue were alive at last follow-up, while 15 of 17 RIGS-positive patients died of their disease (P < 0.0001). CONCLUSIONS: The RIGS system used during surgery provides the surgeon with immediate prognostic information on patients with colorectal cancer and supplements traditional pathologic staging.

Adult↗

The chemical-biological interface: developments in automated and miniaturised screening technology.

The rapidly changing developments in genomics and combinatorial chemistry, generating new drug targets and large numbers of compounds, have caused a revolution in high-throughput screening technologies. Key to this revolution has been the introduction of robotics and automation, together with new biological assay technologies (e.g., homogeneous time resolved fluorescence). With ever increasing workloads, together with economic and logistical constraints, miniaturisation is rapidly becoming essential for the future of high-throughput screening and combinatorial chemistry. This is evident from the introduction of high-density microtitre plates, small volume liquid handling robots and associated detection technology.

Automation↗

A systematic review and lessons learned from early lung cancer detection trials using low-dose computed tomography of the chest.

BACKGROUND: Computed tomography (CT) screening of the chest has shown promise for early detection of lung cancer, but evidence for a reduction in lung cancer mortality by CT screening is not available. METHODS: We reviewed 208 articles to synthesize available evidence for efficacy of CT screening in detecting potentially curative stages of lung cancer and for evidence in reducing lung cancer mortality. Other outcomes of interest included detection rate of cancer and of suspicious lesions, histology and stage of cancer at detection, screening-related morbidity, and the identification of populations uniquely suited for CT screening. We identified eight papers that reported the outcomes for CT of the chest in lung cancer screening. RESULTS: Since none of the studies utilized a control group, quantitative pooling was not done. In two studies, both CT and chest radiography (CXR) were used as screening tools in the same cohorts. A total of 19,107 subjects were screened using CT. The detected prevalence rate for lung cancer ranged from 0.40% to 13.6% and was a function of the subjects' age and smoking history. CT screening resulted in a 3-fold higher detection rate and a 5-fold increase in the rate of resectable cancers compared to CXR. Data on lung cancer and overall mortality and screening-related morbidity and mortality were incomplete. CT screening resulted in selective detection of adenocarcinomas with an approximately 2- to 3-fold oversampling of this histologic subtype. The positive predictive value of CT screening was highest for subjects in the 8th decade of life, and it was virtually nil for those in their 5th decade. CONCLUSIONS: Evidence regarding lung cancer screening by CT shows that this technology detects earlier-stage and smaller lung cancers with greater frequency than other screening methods. To date, no trials have demonstrated that CT screening leads to a reduction in lung cancer mortality. Until mortality trials are completed, low-dose CT screening should be considered an investigative tool rather than the standard of care.

Humans↗

[Ultrastructural diagnosis of early neoplasia in man].

Recent progress in cancer detection technology has resulted in the increasing need for pathological diagnosis of small cancers at their early stage of development. Electron microscopy of early cancers may reveal ultrastructural markers characteristic of certain cell lineage and help classify these cancers in terms of aberration in differentiation of neoplastic cells. Furthermore, electron microscopy of early cancers may detect certain cellular gene products at cellular as well as subcellular levels, and help understand the process of malignant progression in situ of transformed cells.

Diagnosis, Differential↗

Protein micro- and macroarrays: digitizing the proteome.

The early applications of microarrays and detection technologies have been centered on DNA-based applications. The application of array technologies to proteomics is now occurring at a rapid rate. Numerous researchers have begun to develop technologies for the creation of microarrays of protein-based screening tools. The stability of antibody molecules when bound to surfaces has made antibody arrays a starting point for proteomic microarray technology. To minimize disadvantages due to size and availability, some researchers have instead opted for antibody fragments, antibody mimics or phage display technology to create libraries for protein chips. Even further removed from antibodies are libraries of aptamers, which are single-stranded oligonucleotides that express high affinity for protein molecules. A variation on the theme of protein chips arrayed with antibody mimics or other protein capture ligand is that of affinity MS where the protein chips are directly placed in a mass spectrometer for detection. Other approaches include the creation of intact protein microarrays directly on glass slides or chips. Although many of the proteins may likely be denatured, successful screening has been demonstrated. The investigation of protein-protein interactions has formed the basis of a technique called yeast two-hybrid. In this method, yeast "bait" proteins can be probed with other yeast "prey" proteins fused to DNA binding domains. Although the current interpretation of protein arrays emphasizes microarray grids of proteins or ligands on glass slides or chips, 2-D gels are technically macroarrays of authentic proteins. In an innovative departure from the traditional concept of protein chips, some researchers are implementing microfluidic printing of arrayed chemistries on individual protein spots blotted onto membranes. Other researchers are using in-jet printing technology to create protein microarrays on chips. The rapid growth of proteomics and the active climate for new technology is driving a new generation of companies and academic efforts that are developing novel protein microarray techniques for the future.

Protein Array Analysis↗

Walking activity at estrus and subsequent fertility in dairy cows.

Poor detection of estrus, still a major problem in the dairy industry, has prompted the development of electronic estrous detection technologies. One of the features of estrous behavior is a marked increase in walking activity. The objectives of the present study were to evaluate the effects of various management factors on walking activity increase at estrus, and the relationship between this trait and fertility. Data from 5883 artificial inseminations (AI) conducted in two high-producing dairy herds were analyzed. Detection of estrus was performed using a pedometer system. Of the total AI investigated, 2072 (35.2%) resulted in pregnancy. The following data were recorded for each animal at AI: herd, lactation number, milk production (average for the 3 days prior to AI), lactation stage (early, mid, and late lactation), previous estrous synchronization (cloprostenol or progesterone releasing intravaginal device [PRID] for animals showing estrus within 7 days of treatment), season (warm versus cool period), insemination number following parturition, inseminating bull, inseminator, and pedometer measurements. Variables were screened for associations with walking activity by analysis of variance (ANOVA) through generalized linear model procedures (PROC GLM). Increased parity and milk production, and insemination during the warm period were associated with lower pedometer measurements. No significant effects of the herd, estrous synchronization, and lactation stage were observed. The link between walking activity and fertility was determined by applying logistic regression models. We detected no significant effects of herd, milk production, estrous synchronization, lactation stage, and inseminator on pregnancy rate. A higher lactation and insemination number, and insemination during the warm period were negatively correlated with the pregnancy rate. The likelihood of pregnancy was greater when semen from one of the bulls was used and when physical activity at estrus was increased. Our findings indicate that cow and management factors contribute intensely to walking activity at estrus, and also reveal a close link between increased walking activity and fertility.

Animals↗

Microarray-based detection of genetic heterogeneity, antimicrobial resistance, and the viable but nonculturable state in human pathogenic Vibrio spp.

The morbidity and mortality associated with Vibrio-mediated waterborne diseases necessitates the development of sensitive detection technologies that are able to elucidate the identity, potential pathogenicity, susceptibility, and viability of contaminating bacteria in a timely manner. For this purpose, we have designed a single multiplex PCR assay to simultaneously amplify 95 diagnostic regions (encompassing species/serogroup-specific, antimicrobial resistance, and known toxin markers) and combined it with a long oligonucleotide microarray to create a platform capable of rapidly detecting and discriminating the major human pathogenic species from the genus Vibrio: V. cholerae, V. parahaemolyticus, V. vulnificus, and V. mimicus. We were able to validate this strategy by testing 100 geographically and temporally distributed isolates and observed an excellent concordance between species- and serotype-level microarray-based identification and traditional typing methods. In addition to accurate identification, the microarray simultaneously provided evidence of antibiotic resistance genes and mobile genetic elements, such as sulfamethoxazole-trimethoprim constins and class I integrons, and common toxin (ctxAB, rtxA, hap, hlyA, tl, tdh, trh, vvhA, vlly, and vmhA) and pathogenicity (tcpA, type III secretion system) genes that are associated with pathogenic Vibrio. The versatility of this method was further underscored by its ability to detect the expression of known toxin and virulence genes from potentially harmful viable but nonculturable organisms. The results suggest that this molecular identification method provides rapid and definitive information that would be of value in epidemiological, environmental, and health risk assessment surveillance.

Anti-Infective Agents↗

In-process monitoring of protein purification with thin film silicon sensor technology.

We have developed a rapid and sensitive thin film assay for in-process monitoring of target protein purification. This novel biosensor method provides rapid (5-min) visual evaluation of column purification fractions. The method can be used to monitor the efficiency of purification and potential loss of protein if the column binding capacity is exceeded. The eluted fractions containing the highest yield of target protein can be quickly identified, pooled, and processed. This convenient platform, known as the SILAS product, is a thin-film detection technology in which specific molecular interactions are transduced into visible color changes based on changes in the optical thickness of layers on a silicon surface. The results are interpreted without instrumentation. Proteins eluted from a purification column are adsorbed to the assay surface, and the ligand of interest (target) can be identified with specific binding reagents. Here we demonstrate two protein purification applications for the SILAS technology product: monitoring antibody elution from a Protein G column and evaluating the efficiency of purification of a glutathione-S-transferase (GST)-tagged recombinant protein through each step of the purification process.

Animals↗

Detection and prevention of uterine cancer.

The two major uterine cancers, squamous carcinoma of the cervix and adenocarcinoma of the endometrium, are highly vulnerable to detection technology and, therefore, secondary prevention. High risk groups for each have been defined, cancer precursors described, i.e., dysplasia of the cervix and adenomatous hyperplasia of the endometrium, and efficient screening methods made available. For the cervical tumor cytologic testing is most appropriate, while histologic screening is more efficient for endometrial precursor lesions. The strategies of approach of these accessible tumors are models for detection and prevention methods elsewhere in the body and we should exploit them to virtual eradication of these uterine tumors.

Carcinoma↗

Mass allele detection (MAD) of rare 5-HT1A structural variants with allele-specific amplification and electrochemiluminescent detection.

A strategy is described that exploits allele-specific amplification (ASA-PCR) and electrochemiluminescence (ECL) detection technology to rapidly and cheaply screen large numbers of DNAs arranged in pooled matrices in order to identify individual nucleotide sequence variants. To demonstrate this strategy, a large genomic DNA collection was screened for two nucleotide variants in the 5-HT1A serotonin receptor gene and individual heterozygotes were identified. Conversion of two SSCP variants to allele-specific PCR polymorphisms was accomplished, and PCR product capture and ECL detection were enabled by the covalent addition of biotin to allele-specific PCR primers and ruthenium to the nonspecific PCR primer. A two-level DNA pooling strategy was used to reduce the number of individual PCR reactions required. Pooling experiments established that ASA-PCR with ECL detection is sufficiently sensitive to reproducibly detect a single specific allele in the presence of a 40-fold excess of genomic DNA from individuals negative for the specific allele. The detection sensitivity of the ECL device and the design of the pooled DNA arrays reduced the number of PCRs required to detect the rare individuals with the variant sequences by approximately 90%. This strategy is called mass allele detection (MAD).

Alleles↗

A novel separation-free assay technique for serum antibodies using antibody bridging assay principle and two-photon excitation fluorometry.

A new technique for separation-free detection of antigen-specific antibodies is presented. The new technique employs antibody bridging assay principle and the recently developed ArcDia TPX fluorescence detection technology. According to the assay scheme, antibody molecules from the sample bind with one arm to an antigen on polymer microspheres and with the other arm to a fluorescently labeled secondary antigen reagent. Consequently, fluorescent immunocomplexes are formed on the surface of microspheres in proportion to the concentration of the analyte in the sample. The fluorescence signal from individual microspheres is measured by means of two-photon excited fluorescence detection. In order to demonstrate the applicability of the new assay technique, an assay for anti-adenovirus antibodies was constructed. The function of the assay method was tested both with monoclonal anti-adenovirus antibody preparation (standard analyte), and with positive serum samples. Standard class-specific ELISA was used as a reference method. The new assay method provides comparable sensitivity and precision, and wider dynamic range for IgG antibodies than the ELISA method. The standard curve showed linear response (R(2)=0.999) with a dynamic range of three orders of magnitude, detection limit (mean+3S.D.) of 8 pM, and intra-assay signal precision of 5%. Applicability of the new method for clinical serodiagnostics is discussed.

Animals↗

Recommendations for microbial source tracking: lessons from a methods comparison study.

The methods comparison study described in accompanying manuscripts demonstrated the potential value of microbial source tracking (MST) techniques, but also identified a need for method refinement. This paper provides three classes of recommendations to improve MST technology: optimization, development and evaluation. Optimization recommendations focus on library-dependent methods and include improved selection of restriction enzymes or antibiotics, better definition of appropriate library size, selection of target species and choice of statistical pattern-matching algorithms. Methods development recommendations focus on identifying new genomic targets and quantification procedures for library-independent methods. Longer-term methods development recommendations include integration of microarrays and other direct pathogen detection technology with MST. Studies defining host specificity and population dynamics should aid selection of target species during methods development. Evaluation recommendations include enhancements that should be incorporated into future methods comparison studies, along with studies to assess the value of MST results for risk characterization.

Animals↗

A novel method using edge detection for signal extraction from cDNA microarray image analysis.

Gene expression analyses by probes of hybridization from mRNA to cDNA targets arrayed on membranes or activated glass surfaces have revolutionized the way of profiling mega level gene expression. The main remaining problems however are sensitivity of detection, reproducibility and data processing. During processing of microarray images, especially irregularities of spot position and shape could generate significant errors: small regions of signal spots can be mis-included into background area and vice versa. Here we report a novel method to eliminate such obstacles by sensing their edges. Application of edge detection technology on separating spots from the background decreases the probability of the errors and gives more accurate information about the states of spots such as the pixel number, degree of fragmentation, width and height of spot, and circumference of spot. Such information can be used for the quality control of cDNA microarray experiments and filtering of low quality spots. We analyzed the cDNA microarray image that contains 10,368 genes using edge detection and compared the result with that of conventional method which draws circle around the spot.

DNA, Complementary↗

The molecular genetic basis and diagnosis of familial hypercholesterolemia in Denmark.

Normal function of the hepatic low-density lipoprotein (LDL) receptor is obligate for normal levels of plasma LDL cholesterol. The LDL receptor regulates the concentration of plasma LDL cholesterol by internalizing apolipoprotein B-100- and apolipoprotein E-containing lipoproteins by receptor-mediated endocytosis. Mutations in the gene encoding the LDL receptor protein give rise to one of the most common classical autosomal dominant inherited disorders in man, familial hypercholesterolemia (FH). The estimated prevalence of heterozygous FH is 0.2% (1:500) in most populations of the world including the Danish. Worldwide, an estimated ten million people are afflicted with FH and in Denmark there are approximately 10,000 subjects with heterozygous FH. Persons with heterozygous FH are characterized by a severely elevated concentration of LDL cholesterol in plasma starting in early childhood, tendon xanthomas and a markedly increased risk of premature coronary heart disease (CHD). Adequate control of plasma LDL cholesterol levels can be achieved in most patients with heterozygous FH, and to a lesser extent in the very rare cases with homozygous FH, using combinations of diet, drug therapy and selective LDL-apheresis. So, it is very important that physicians be aware of this relatively common disorder since there is good evidence that early diagnosis and cholesterol-lowering therapy will delay or even prevent CHD in persons with FH. A large majority of these persons, however, are still not diagnosed or adequately treated. It is believed that the diagnostic abilities molecular biology has to offer will provide the impetus for correcting this situation. The aims of the studies behind the present thesis, therefore, were to obtain important knowledge about current mutation detection technology, prevalence and spectrum of LDL receptor gene mutations in Denmark, methods to evaluate pathogenicity of LDL receptor gene mutations, relationship between FH genotype-phenotype, and clinical versus DNA diagnosis in the Danish FH population. Among different relative laborious and expensive scanning methods for unknown gene mutations we have shown that the polymerase chain reaction (PCR) single-strand conformation polymorphism (SSCP) analysis is a highly efficient and sensitive technique for detection of mutations in the 18 exons including intronic splice-site sequences and the promoter region of the LDL receptor gene, reserving DNA sequencing to the exons revealing variant SSCP patterns. Southern blot analysis or long distance PCR analysis are necessary to identify large gene re-arrangements in the LDL receptor gene in FH patients in whom SSCP analysis did not reveal any smaller sequence alterations. Worldwide, about 700 different mutations in the LDL receptor gene have been reported and in the Danish FH population we have so far identified 60 different mutations localized throughout the LDL receptor gene. In certain populations a small number of mutations predominate due to founder effects. The spectrum of LDL receptor mutations in Danish FH patients is intermediate between such specific founder populations with 5 predominant mutations (W23X, W66G, W556S, 313 + 1G-->A, 1846-1G-->A) accounting for about 40-50% of FH. These frequent mutations can easily and inexpensively be tested for by specific PCR based assays using restriction enzyme cleavage. Future analysis of LDL receptor mutations in heterozygous FH subjects, therefore, should be based on the mutational spectrum present in each relevant specific subset. Most mutations in the LDL receptor gene cause the classical heterozygous form of FH, but a small proportion seem to result in mild or moderate forms of autosomal, dominantly inherited hypercholesterolemia. Differentiation between harmless sequence variations and disease-causing mutations is not always easy without additional work. We have experienced that large re-arrangements, frame-shift and nonsense mutations obviously are pathogenic, but full pathogenicity should not be ascribed to missense mutations and small in-frame deletions, e.g. the N543H and 2393del9 mutations, unless in vitro gene expression in eukaryotic cells have been studied, or to splice-site mutations, e.g. the 1592 + 5G-->A mutation, before mRNA studies in patient cells have been performed. The cumulated LDL cholesterol exposure, mainly determined by the defect LDL receptor, plays a crucial role for the clinical manifestation of FH. The phenotypic expression of homozygous FH appears to be dominated by the consequences of the LDL receptor gene mutations. In heterozygous FH, however, the underlying mutational LDL receptor type determines only to a much lesser extent, if any, the variable phenotypic expression as seen in Danish patients. Extreme low fat dietary habits or major gene interactions may influence the lipid profile and the excess cardiovascular mortality observed in heterozygous FH, whereas minor gene determinants do not seem to play any significant role. The clinical diagnosis of heterozygous FH should be based on an elevated plasma LDL cholesterol concentration above the 95th percentiles for the general population together with either the presence of tendon xanthomas or an autosomal dominant transmission of hypercholesterolemia in the family or a child with hypercholesterolemia. Our studies illustrate clearly that molecular genetics can strengthen an equivocal clinical diagnosis and assist decision-making in diagnosis and tracing family members. If demonstration of a pathogenic mutation in the LDL receptor gene fails, other causes of autosomal dominant inherited hypercholesterolemia should be sought. Familial defective apolipoprotein B (FDB) caused by the R3500Q apolipoprotein B gene mutation may mimic FH but the clinical course, however, is often milder than that seen in patients with LDL receptor gene mutations. A newly discovered third major locus at chromosome 1 may also be of future diagnostic importance although the exact gene remains to be identified. The overall molecular genetic knowledge obtained about FH in Denmark forms the basis for the implementation and use of molecular genetic diagnostics of FH in daily clinical practice.

Apolipoproteins↗