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PubMed2002

Technologies for individual genotyping: detection of genetic polymorphisms in drug targets and disease genes.

Genetic variations have been associated with a predisposition to common diseases and individual variations in drug responses. Identification and genotyping a vast number of genetic polymorphisms in large populations are increasingly important for disease gene identification and pharmacogenetics. Commonly used gel electrophoresis-based genotyping methods for known polymorphisms include polymerase chain reaction (PCR) coupled with restriction fragment-length polymorphism analysis, allele-specific amplification, and oligonucleotide ligation assay. Fluorescent dye-based DNA fragmentation has been extensively used for high-throughput microsatellite or short tandem-repeat genotyping. TaqMan and molecular beacon genotyping are commonly used homogeneous solution hybridization technologies. Because of the ease of experimental assay design, single nucleotide polymorphism (SNP) genotyping methods based on single-base extension are in rapid development, such as fluorescence homogenous assays, pyrosequencing and mass spectrometry. Non-PCR based genotyping assays such as Invader trade mark assays are promised to genotype directly from genomic DNA without the requirement of PCR amplification. The DNA microarray is a solid phase genotyping format that is rapidly developing for parallel genotyping of a large number of SNPs simultaneously. Advanced technologies to identify genetic polymorphisms rapidly, accurately, and cost effectively will fundamentally change the practice of medicine by allowing physicians to prescribe medicine based on a patient's genetic make-up.

Alleles↗
PubMed2006

Advanced imaging and technology in gastrointestinal neoplasia: summary of the AGA-NCI Symposium October 4-5, 2004.

Imaging and other advanced technologies for detection of gastrointestinal cancers are undergoing a major revolution on several fronts. This is facilitated by convergence of key technologies including advanced endoscopic-detection systems, more specific contrast agents, rapid and high-resolution cross-sectional imaging, and miniaturization of construction systems for making all imaging equipment smaller and less invasive. This convergence is occurring along traditional translational research pathways (clinical medicine-molecular biology) as well as nontraditional lines (clinical medicine-optical physics/engineering and molecular biology-optical physics/engineering). These new efforts are producing a wide array of technologies aimed at improving detection, classification, and monitoring of gastrointestinal neoplasia, especially for colorectal and esophageal cancer because of easier accessibility. A critical goal is to detect lesions at their premalignant stages, thereby permitting meaningful intervention. Inspired by these advances, the American Gastroenterological Association and the National Cancer Institute sponsored a symposium held in Bethesda, MD, from October 4-5, 2004, bringing together leading investigators with diverse backgrounds in imaging technology. The aims of this symposium were to summarize the state of the art and priorities for research in the coming decade in the field of imaging and advanced technology for gastrointestinal neoplasia. In this overview, we summarize the salient results of that symposium. The initial sections discuss the major technologies in each area of endoluminal imaging and molecular imaging followed by applications to specific diseases such as Barrett's esophagus and colon neoplasia. Each section focuses on the current state of the art then lists major priorities for research in the field.

Barrett Esophagus↗
PubMed2003

New biochip technology for label-free detection of pathogens and their toxins.

microSERS is a new biochip technology that uses surface-enhanced Raman scattering (SERS) microscopy for label-free transduction. The biochip itself comprises pixels of capture biomolecules immobilized on a SERS-active metal surface. Once the biochip has been exposed to the sample and the capture biomolecules have selectively bound their ligands, a Raman microscope is used to collect SERS fingerprints from the pixels on the chip. SERS, like other whole-organism fingerprinting techniques, is very specific. Our initial studies have shown that the Gram-positive Listeria and Gram-negative Legionella bacteria, Bacillus spores and Cryptosporidium oocysts can often be identified at the subspecies/strain level on the basis of SERS fingerprints collected from single organisms. Therefore, pathogens can be individually identified by microSERS, even when organisms that cross-react with the capture biomolecules are present in a sample. Moreover, the SERS fingerprint reflects the physiological state of a bacterial cell, e.g., when pathogenic Listeria and Legionella were cultured under conditions known to affect virulence, their SERS fingerprints changed significantly. Similarly, nonviable (e.g., heat- or UV-killed) microorganisms could be differentiated from their viable counterparts by SERS fingerprinting. Finally, microSERS is also capable of the sensitive and highly specific detection of toxins. Toxins that comprised as little as 0.02% by weight of the biomolecule-toxin complex produced strong, unique fingerprints when spectra collected from the complexes were subtracted from the spectra of the uncomplexed biomolecules. For example, aflatoxins B(1) and G(1) could be detected and individually identified when biochips bearing pixels of antibody or enzyme capture biomolecules were incubated in samples containing one or both aflatoxins, and the spectra were then collected for 20 s from an area of the biomolecule pixel approximately 1 microm in diameter. In the future, we plan to investigate the use of hyperspectral imaging Raman microscopy for collecting fingerprints from all the pixels on the biochip, individually yet simultaneously, to enable the rapid detection of diverse pathogens and their toxins in a sample, using a single biochip.

Aflatoxins↗
PubMed2002

Single-tube genotyping of MBL-2 polymorphisms using melting temperature analysis.

Recently several authors correlated MBL-2 gene polymorphisms with different pathologies and there is a growing interest for MBL-2 genotyping in a large number of individuals. We have developed a single-tube, rapid, economic, and fully automated melting temperature analysis screening method, based on ABI 7700 Sequence Detection System technology and SYBR Green I chemistry, for the detection of three polymorphisms (exon 1, codons 52, 54, 57) in the MBL-2 gene. We also developed an electronic sheet for the automatic calling of different genotypes, based on the analysis of the first derivative of ABI 7700 raw data.

Carrier Proteins↗
PubMed2002

Overview: Signal production and detection.

Studies of signal production and detection are complicated by the diverse modalities used by animals, constraints of human signal perception, and limitations of a controlled laboratory environment. These complications can be addressed by creative approaches to studying anatomical adaptations for signal production and detection, innovative technology, and careful studies of signal production and detection in the field. These solutions should overcome the perceptual limitations of researchers as they explore Umwelten in other species.

Animal Communication↗
PubMed2001

Differentiation of mammographically suspicious lesions: evaluation of breast ultrasound, MRI mammography and electrical impedance scanning as adjunctive technologies in breast cancer detection.

AIM: Various modalities are used as an adjunct to mammography for differentiation of potentially suspicious breast lesions. Electrical impedance scanning (EIS) is a new technique based upon the principle that cancer cells exhibit altered local dielectric properties and thus show measurably higher conductivity values. The accuracy of differentiation of benign and malignant breast lesions was evaluated to determine whether EIS duplicates or supplements the results obtainable from ultrasound (US) or magnetic resonance imaging (MRI). MATERIALS AND METHODS: One hundred mammographically suspicious lesions were examined using US, MRI and EIS. Definitive histology was acquired through either lesion biopsy or surgical excision. RESULTS: Fifty of 62 malignant lesions were correctly identified using EIS (81% overall sensitivity), 24/38 benign lesions were correctly identified as benign (63% specificity). Negative predictive value and positive predictive value of 67 and 78% were observed, respectively. kappa-factor evaluation revealed a value of 0.82 between MRI and EIS and 0.62 between US and EIS. CONCLUSIONS: EIS may be a valuable adjunct for differentiation of suspicious mammographic lesions. Based upon the calculated kappa-factor, EIS results supplement US examinations. Artifacts (superficial skin lesions, poor contact, air bubbles) currently result in the high false-positive rate of EIS.

Breast Neoplasms↗
PubMedDate not supplied

MR-based technology for in vivo detection, characterization, and quantification of pathology of relapsing-remitting multiple sclerosis.

In relapsing-remitting (RR) multiple sclerosis (MS), conventional magnetic resonance (MR) imaging (MRI) has proved to be a valuable tool to assess the lesion burden and activity over time. However, conventional MRI cannot characterize and quantify the tissue damage within and outside such lesions and only can provide some gross measures reflecting the presence of irreversible tissue damage, such as the load of T1 "black holes" and the severity of brain or cord atrophy. Other MR-based techniques, including cell-specific imaging, magnetization transfer (MT) MRI (MT-MRI), diffusion-weighted (DW) MRI (DW-MRI), proton magnetic resonance spectroscopy (1H-MRS), and functional MRI (fMRI), have the potential to overcome this limitation and, consequently, to provide additional information about the nature and the extent of MS tissue damage, which would inevitably remain undetected when only a conventional MRI is obtained. Cell-specific imaging should result in a better definition of the cellular mechanisms associated with MS inflammation. Metrics derived from MT- and DW-MRI can quantify the structural changes occurring within and outside lesions visible on conventional MRI scans. 1H-MRS could add information on the biochemical nature of such changes. fMRI is a promising technique to assess the mechanisms of cortical reorganization, which may limit the consequences of an MS-related injury. The application of these MR techniques to the study of RRMS is likely to provide useful insights into the pathophysiology of this disease and to improve our ability to assess the efficacy of experimental treatments.

Biopsy, Needle↗
PubMed2003

[The application of RAPD technology in genetic diversity detection of Jute].

The fingerprints of 10 species including 27 accessions in genus Corchorus were investigated with the technique of RAPD. Twenty-five primers were screened from 119 random primers, and a total of 329 DNA fragments were amplified ranging from 0.3-3.0 kb, 253 (87.78%), which were polymorphic. The average number of DNA band produced by each primer was 13.16. UPGMA cluster analysis and Nei's similarity coefficients were carried out and a dendrogram was constructed using software Biol D++. The results showed as follows: (1) There were abundant genetic diversities among 15 wild species and 12 cultivated species in Corchorus with genetic similarity coefficients ranging from 0.49-0.98. (2) The accessions could be clustered into three groups at cultivated species, and their close wild species were obviously different from wild species genetically. (3) At the level of D = 0.850, 27 accessions of Jute could be classified into ten groups, including C. sestuans, C. tridens, C. fascicularis, C. psendo-olitorius, C. psendo-capsularis, C. tilacutaris, Tian Jute (untitled), C. capsularis, C. olitorius and C. uriticifolius. Among which C. capsularis presented closer relationship with C. olitorius and further relationship with C. uriticifolius. The results matched well with that of the morphologic classification. (4) According to the molecular cluster tree, C. uritifolius, Chinese Tina Jute (untitled) and C. aestuans were at the basic level, revealing that these three species could be the primary wild species of Jute. (5) The tree also showed that C. tilacularis 21C from Africa could be a ecological subspecies of C. tilacularis, whilst niannian cai, ma cai and zhu cai collected different ecological types of C. aestuans, C. capsularis from Hainan was a close wild species of round fruit Jute cultivated species, and three species of C. olitorius collected from zhangpu, Henan and Mali were close wild species of long fruit Jute cultivated species. (6) within two cultivated species, the genetic similarity coefficients in round fruit cultivated species was higher than that of in long fruit cultivated species.

Corchorus↗
PubMed2003

[Application of ISSR technology in genetic diversity detection of jute].

The genetic diversity among 27 accessions of Corchorus, including 10 Jute species, was investigated with ISSR technique. 283 DNA bands were amplified with 25 ISSR primers, among which, 263 (92.85%) were polymorphic, with 10.48 bands per primer in average. A further systemic cluster analysis indicated that the accessions could be clustered into three groups, and the group II (including two cultispecies and their close wild species) was obviously genetically different from the groups I and III (including eight wild species). Moreover, 16 accessions in group II presented a higher intraspecific genetic resemblance, while 11 accessions among groups I & III showed an abundant interspecific genetic diversity. After synthesized the relevant findings of morphology and DNA classification, it's found that C. urticifolius could be one of the original wild species, C. tilaculariszic was a variation of C. tilaculari, and Tian Jute could be an untitled wild species.

DNA Fingerprinting↗
PubMed1994

[Use of nuclear medicine technology (radionuclide venography) in detecting a case of suspected ileofemoral phlebothrombosis].

We reviewed a complex nuclear medical method's application for investigating venous circulation of lower extremities--radionuclide venography (RVG) in explaining a case of suspective ileofemoral thrombosis. Suffering from pain and swelling of the right leg, patient T.J. wanted a checkup. After the physical examination, vascular surgeon suspected phlebothrombosis of the right ileofemoral region and immediately sent her to have a radionuclide venography (RVG) (because by Doppler-ultrasonography certain data confirming presence of thrombus in the pelvic region couldn't be gained). On the basis of gathered results vascular surgeon can make a final diagnosis (phlebothrombosis of the right vein femoralis), so that in this case flebography was not necessary. Although performing RVG is complex and requires engagement of experts of different profiles, gathered data are valuable because they cover the shortage of existing diagnostic methods which are most often used in routine work (Doppler-ultrasonography and phlebography). Applying RVG phlebography can be avoided in all patients who are not expected to have operative treatment, and in cases where thrombosis is suspected in deep veins of pelvis, RVG can be performed right away, without Doppler ultrasonography.

Adult↗
PubMed2005

Diagnosis of extrapulmonary tuberculosis by smear, culture, and PCR using universal sample processing technology.

Definitive and rapid diagnosis of extrapulmonary tuberculosis is challenging since conventional techniques have limitations. We have developed a universal sample processing (USP) technology for detecting mycobacteria in clinical specimens. In this study, this technology was evaluated blindly on 99 extrapulmonary specimens collected from 87 patients. USP-processed specimens were submitted to smear microscopy for detection of acid-fast bacilli (AFB), culture, and two PCR tests targeting devR (Rv3133c) and IS6110 gene sequences. On the basis of clinical characteristics, histology and cytology, conventional microbiology results, and response to antitubercular therapy, 68 patients were diagnosed with tuberculosis. Although USP smear and culture were significantly superior to conventional microbiology, which was not optimized (P < 0.0001), these approaches fell short of PCR tests (P < 0.0001). The low yields by smear and culture are attributed to the paucibacillary load in the specimens. The highest sensitivity in PCR was achieved when devR and IS6110 test results were combined; the sensitivity and specificity values were 83 and 93.8%, 87.5 and 100%, and 66.7 and 75%, respectively, in pleural fluid, needle-biopsied pleural tissue, and lymph node specimens. In conclusion, the application of USP technology, together with clinicopathological characteristics, promises to improve the accuracy and confidence of extrapulmonary tuberculosis diagnosis.

Adult↗