SEARCH · PubMed Health

Results for “IDENTIFICATION”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,171 records · Page 65Linked to original sources

PubMed1999

Identification of five species of the Anopheles dirus complex from Thailand, using allele-specific polymerase chain reaction.

The Anopheles dirus complex of mosquitoes contains some of the most important vectors of malaria in Southeast Asia. To distinguish five species of the complex that occur in Thailand, a method using the polymerase chain reaction (PCR) was developed. The method utilizes allele-specific amplification to detect fixed differences between the species in the DNA sequence of the ribosomal DNA internal transcribed spacer 2. Primers were designed to amplify fragments of diagnostic length from the DNA of the different species. The method was tested on 179 mosquitoes of the An. dirus complex from many parts of Thailand and shown to be effective. Every specimen was unambiguously identified as species A, B, C, D or F (i.e. An. dirus s.s. species B, C, D or An. nemophilous, respectively) by the PCR method, with confirmation of 58/61 identifications from polytene chromosome characteristics. For the other three specimens (3/44 from Kanchanaburi 5 locality), there was disagreement between the PCR and chromosomal methods of species identification (probably due to errors in the chromosomal identifications). Primers can be combined in a single PCR reaction providing a rapid, sensitive and straightforward method of species identification. Only small quantities of DNA are required, leaving most of the mosquito to be used for other analyses.

Alleles↗

PubMed1999

Identification of roots of woody species using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis

Within the last two decades, substantial progress has been made in understanding seed-bank dynamics and the contribution of the soil seed bank to a postdisturbance plant community. There has been relatively little progress, however, in understanding perennial bud-bank dynamics and the contribution of the soil bud bank to secondary succession. This lack of information is due primarily to the inability to reliably identify roots, rhizomes and lignotubers that lie dormant beneath the soil surface. This investigation addressed the issue of identification of below-ground woody structures. The first objective was to develop a method that used molecular tools to identify woody plant species from subsoil tissue samples. The second objective was to develop a key in which molecular markers served as criteria for the identification and differentiation of selected tree and shrub species common to the mountains of northeast Oregon and southeast Washington. Application of restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified rbcL appears to be a reliable method to identify and differentiate 15 plants to the genus level. Two restriction enzymes, DpnII and HhaI, provided restriction site polymorphisms in the PCR product. The fragment number and length were used to develop an identification key. However, plants not analysed in this 'exploratory key' might share the same banding patterns, resulting in a false identification of unknowns.

Journal Article↗

PubMed2001

Molecular identification of fine roots of trees from the Alps: reliable and fast DNA extraction and PCR-RFLP analyses of plastid DNA.

Fine roots of trees are intensively used as indicators to assess soil alterations, e.g. those owing to atmospheric inputs of acidifying substances, but their identification to species with morphological criteria is difficult. In this study, we established molecular techniques in order to identify fine roots of the 30 most common tree species of the Alps. We developed a protocol for efficient isolation of DNA from fine roots with extraction of DNA in the presence of polyvinylpyrrolidone (PVP) and polyvinylpolypyrrolidone (PVPP). The trnL (UAA) intron of plastid DNA was used as a marker for fine root identification. We amplified and sequenced this intron with plant universal primers. The size of the sequences ranged from 444 to 672 bp. A synoptic key for species identification was designed on the basis of restriction fragment patterns predicted from sequence data. Using the restriction enzyme TaqI as key enzyme, and where necessary HinfI, RsaI and CfoI, 16 taxa, including Picea abies, Larix decidua, Abies alba, and Fagus sylvatica, the dominant tree species of the Alpine region could be identified by agarose gel electrophoresis of restriction fragments. Fourteen taxa could be identified to the genus level, among them Quercus, Salix and Populus species. In a field study, conducted in a 20 x 30 m plot of a mixed forest with five tree species, fine roots of 43 out of 46 samples were identified and their distributions were mapped. These results demonstrate the utility of our DNA extraction method and of the trnL intron for the identification of fine tree roots.

DNA, Plant↗

PubMed2003

Comparative evaluation of three chromogenic agars for detection and rapid identification of aerobic Gram-negative bacteria in the normal intestinal microflora.

OBJECTIVE: To compare three different chromogenic agars and MacConkey agar for the detection of aerobic Gram-negative bacteria in the normal intestinal microflora and to assess the accuracy of the chromogenic agars for the direct identification of Escherichia coli. METHODS: A total of 164 Gram-negative clinical isolates (E. coli, Proteus, Klebsiella, Enterobacter, Morganella and Pseudomonas species) and 30 stool specimens were inoculated in parallel on four media: Chromagar E. coli/Coliform, Chromogenic urinary tract infection UTI medium, CHROMagar Orientation and MacConkey agar. All colonies that differed by color and/or morphology were selected for further identification by VITEK 1 and/or API 20E from each medium. RESULTS: On E. coli/Coliform agar five out of 32 (16%) E. coli strains failed to produce the color as described by the manufacturer. No remarkable discrepancies were found for the other clinical isolates. There was no significant difference in detection rate (DR) of aerobic Gram-negative bacteria in stool specimens between the different chromogenic agars and MacConkey agar. The overall DR was about 84%, and varied from 100% for monomicrobial specimens to 33% for polymicrobial specimens. The positive predictive values (PPV) for the direct identification of E. coli on Chromagar E. coli/Coliform, Chromogenic UTI medium and CHROMagar Orientation were 1.00, 0.93 and 0.93, respectively. The negative predictive values (NPV) were 0.53, 0.68 and 0.69, respectively. CONCLUSION: Chromogenic UTI medium and CHROMagar Orientation are the preferred media because of the higher NPV. The high PPV of these agars allows accurate and rapid identification of E. coli.

Agar↗

PubMed1999

Development of a m-PCR assay for simultaneous identification of Campylobacter jejuni and C. coli.

Multiplex PCR assay (m-PCR) with three sets of primers was developed for simultaneous identification of Campylobacter jejuni and C. coli. Poultry faecal samples were enriched in Preston broth for 24 h and streaking on selective media was performed before and after enrichment. m-PCR was applied on bacterial cultures harvested from media plates. The data showed a selective effect of Preston broth which favoured the growth of C. coli. Identification of the species by the hippurate hydrolysis test and by the m-PCR was performed on 294 isolates of Campylobacter. The efficiency of the identification by the biochemical test is only 34% in comparison to 100% efficiency with the PCR. The use of our m-PCR in combination with the culture method allowed reliable detection and identification of C. jejuni and C. coli within 3-4 d.

Animals↗

PubMed1994

The routine use of Rh-negative reagent red cells for the identification of anti-D and the detection of non-D red cell antibodies.

BACKGROUND: Before 1987, fewer than 50 patients per year at the authors' laboratory had a positive antibody detection test due to antepartum Rhesus immunoprophylaxis. However, after 1987, a marked increase was observed in the number of patients who had received Rh immune globulin (RhIG) during pregnancy as part of routine antepartum Rh immunoprophylaxis. In anticipation that an increased use of RhIG during pregnancy would increase the number of patients in whom anti-D was detected by this laboratory, a protocol was developed to abbreviate the process required to identify anti-D. Although this protocol was adopted primarily to address an anticipated increase in antenatal RhIG usage in women, it was also applied to alloimmunized Rh-negative males. STUDY DESIGN AND METHODS: When an Rh-negative patient (male or female) had a reactive screening test for unexpected antibodies and met certain other criteria, the patient's serum was tested with a three-vial set of Rh-negative reagent red cells (Rh-negative screening RBCs), instead of with panels of typed RBCs (panel RBCs), for the identification of anti-D or the detection of non-D antibodies. If the serum under test did not agglutinate or hemolyze Rh-negative screening RBCs, anti-D was identified and no further testing was performed. If the serum agglutinated or hemolyzed Rh-negative screening RBCs, conventional testing with panel RBCs was done to determine the antibody specificity. RESULTS: Rh-negative patients (n = 1174) who had reactive screening tests for unexpected antibodies were tested with Rh-negative screening RBCs; 1079 were found to have anti-D as a single antibody. Seven of these patients subsequently developed a non-D alloantibody, after transfusion or pregnancy, and one patient had anti-C that escaped detection at the time of initial testing with Rh-negative RBCs (a false-negative result). Ninety-two patients had anti-D in combination with a non-D antibody, and three patients had a non-D antibody but not anti-D. Use of the anti-D identification protocol actually reduced the laboratory workload by 176 College of American Pathologists workload units per month, in spite of a marked increase in the number of patients in whom anti-D was detected. No hemolytic transfusion reaction was attributed to the abbreviation of anti-D identification. CONCLUSION: The identification of anti-D may be abbreviated without jeopardizing patient safety. Such a protocol can reduce laboratory workload and might be particularly appealing to health care facilities that perform antibody detection testing on large numbers of Rh-negative pregnant women, especially if antepartum RhIG is administered routinely.

Erythrocytes↗

PubMedDate not supplied

Assessment of PCR for routine identification of species of the Mycoplasma mycoides cluster in ruminants.

DNA amplification techniques offer considerable promise for the identification of Mycoplasma mycoides cluster members. They avoid antigenic cross-reactivity and variability that hamper serological methods. Many sets of primers, specific of these different members and of Mycoplasma putrefaciens, have been proposed. To assess the reliability of some of these PCR tests in routine laboratory diagnostic use, 230 field strains supposed to belong to this group were simultaneously identified by PCR and an antigenic method. The results were well correlated to antigenic identification for M. putrefaciens, but PCR failed to identify respectively 74% and 52% of M. mycoides subsp. mycoides Large Colony type and M. capricolum subsp. capricolum strains. Any identification of M. mycoides subsp. mycoides Small Colony type must be confirmed by two different tests. Difficulties in defining the M. species bovine serogroup 7 were also encountered with both the PCR and immunological methods. The occurrence of putative variable antigen(s) on the mycoplasma surface may explain part of the identification difficulties encountered with the immunological methods.

Acholeplasma↗

PubMed2004

Presliding friction identification based upon the Maxwell Slip model structure.

The problem of presliding friction identification based upon the Maxwell Slip model structure, which is capable of accounting for the presliding hysteresis with nonlocal memory, is considered. The model structure's basic properties are examined, based upon which a priori identifiability is established, the role of initial conditions on identification is investigated, and the necessary and sufficient conditions for a posteriori identifiability are derived. Using them, guidelines for excitation signal design are also formulated. Building upon these results, two new methods, referred to as Dynamic Linear Regression (DLR) and NonLinear Regression (NLR), are postulated for presliding friction identification. Both may be thought of as different extensions of the conventional Linear Regression (LR) method that uses threshold preassignment: The DLR by introducing extra dynamics in the form of a vector finite impulse response filter, and the NLR by relaxing threshold preassignment through a special nonlinear regression procedure. The effectiveness of both methods is assessed via Monte Carlo experiments and identification based upon laboratory signals. The results indicate that both methods achieve significant improvements over the LR. The DLR offers the highest accuracy, with the NLR striking a very good balance between accuracy and parametric complexity.

Journal Article↗

PubMed2003

Species identification and strain differentiation of dermatophyte fungi using polymerase chain reaction amplification and restriction enzyme analysis.

BACKGROUND: Standard biochemical tests, microscopy, colony characteristics, and mating tests have conventionally been used for the identification of dermatophytes species, but these methods of identification are costly, time-consuming, and require special skills. OBJECTIVE: Our purpose was to identify a method that enables rapid species identification and strain differentiation of dermatophyte fungi. METHODS: We chose 4 restriction enzymes (BsYiI, DdeI, HinfI, and MvaI) that could produce different fragment patterns after enzyme digestion according to species or strain. We performed enzyme digestions after polymerase chain reaction amplification of internal transcribed spacer region and identified different restriction fragment length polymorphisms (RFLP) according to species and strains. RESULTS: All the species included in this study could be easily differentiated using any combination of 2 different restriction enzymes except Trichophyton rubrum and T raubitschekii, which produced identical digestion patterns after all 4 restriction enzyme digestions. In the case of T mentagrophytes, MvaI and DdeI each produced 2 distinct RFLP patterns. CONCLUSION: This study showed that internal transcribed spacer region analysis using polymerase chain reaction-RFLP through DdeI and MvaI is useful for rapid identification of the majority of dermatophytes species. However, there were 2 different band patterns by DdeI and MvaI restriction enzyme digestion and no correlations between morphologic types and RFLP patterns in T mentagrophytes.

Arthrodermataceae↗

PubMed2002

Use of technetium-99m tin colloid for sentinel lymph node identification in non-small cell lung cancer.

BACKGROUND: To test the reliability of sentinel lymph node identification in non-small cell lung cancer, sentinel nodes were localized with a radioactive colloid in patients undergoing surgery. METHODS: Forty-six patients with non-small cell lung cancer undergoing curative resection with mediastinal lymph node dissection were examined. The day before surgery, technetium-99m ((99m)Tc) tin colloid was injected into the peritumoral region. At operation, the radioactivity of the lymph nodes was counted with a handheld gamma counter before (in vivo) and after (ex vivo) dissection. Lymph nodes with an ex vivo radioactive count more than 10 times the background value were identified as sentinel nodes. The correlation between the in vivo and ex vivo results was examined. RESULTS: Lymphoscintigraphy revealed that it took longer than 6 hours for sufficient (99m)Tc tin colloid to reach the sentinel nodes. Sentinel nodes could be identified in 40 patients (87%). Patients whose sentinel nodes could not be identified had a significantly lower ratio of forced expiratory volume in 1 second to forced vital capacity than did those with identifiable sentinel nodes (P =.03). No false-negative sentinel nodes were detected in 14 patients with N1 or N2 disease (0%). In the hilar lymph node stations, the lobar lymph nodes were most frequently identified as sentinel nodes (as often as 85% of the time). Fourteen patients (35%) had sentinel nodes in the mediastinum, the distribution of which depended on the lobe. In vivo and ex vivo counting showed 88% concurrence for the identification of sentinel nodes in mediastinal lymph node stations. CONCLUSION: The identification of sentinel nodes with (99m)Tc tin colloid is a reliable method of establishing the first site of nodal metastasis in non- small cell lung cancer. Sentinel nodes could be hardly identified in patients with a low ratio of forced expiratory volume in 1 second to forced vital capacity because of such conditions as chronic obstructive pulmonary disease. In vivo identification of sentinel nodes in the mediastinum could be useful approach to guide mediastinal lymph node sampling or dissection.

Adult↗

PubMed1999

Identification of gender in domestic-cat faces with and without training: perceptual learning of a natural categorization task.

Three experiments were conducted to determine whether human observers could identify the gender of 40 domestic cats (20 female, 20 male) depicted in individual color photographs. In experiment 1a, observers performed at chance for photographs depicting whole cats, cat heads (bodies occluded), and cat bodies (heads occluded). Experiment 1b showed that chance performance was also obtained when the photographs were full-face close-ups of the cats. Experiment 2a revealed that even with gender-identification training on 30 (15 female, 15 male) of the 40 face close-ups, observers were unable to generalize their training to reliably identify the gender of the 10 remaining test faces (5 female, 5 male). However, experiment 2b showed that gender-identification training with the 14 most accurately identified faces from experiment 1b (7 female, 7 male) was successful in raising gender identification of the 10 test faces above chance. Experiments 3a and 3b extended this facilitative effect of gender-identification training to a population of animal-care workers. The findings indicate that, with appropriate training, human observers can identify the gender of cat faces at an above-chance level. A perceptual category learning account emphasizing the on-line formation of differentiated male versus female prototypes during training is offered as an explanation of the findings.

Adolescent↗

PubMed2004

Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation.

MS-based proteomics usually involves the fragmentation of tryptic peptides (tandem MS or MS(2)) and their identification by searching protein sequence databases. In ion trap instruments fragments can be further fragmented and analyzed, a process termed MS/MS/MS or MS(3). Here, we report that efficient ion capture in a linear ion trap leads to MS(3) acquisition times and spectra quality similar to those for MS(2) experiments with conventional 3D ion traps. Fragmentation of N- or C-terminal ions resulted in informative and low-background spectra, even at subfemtomol levels of peptide. Typically C-terminal ions are chosen for further fragmentation, and the MS(3) spectrum greatly constrains the C-terminal amino acids of the peptide sequence. MS(3) spectra allow resolution of ambiguities in identification, a crucial problem in proteomics. Because of the sensitivity and rapid scan rates of the linear ion trap, several MS(3) spectra per peptide can be obtained even when sequencing very complex mixtures. We calculate the probability that an experimental MS(3) spectrum originates from fragmentation of a given N- or C-terminal ion of a peptide under consideration. This MS(3) identification score can be combined with the MS(2) scores of the precursor peptide from existing search engines. When MS(3) is performed on the linear ion trap-Fourier transform mass spectrometer combination, accurate peptide masses further increase confidence in peptide identification.

Algorithms↗

PubMed2006

In vivo identification of ribonucleoprotein-RNA interactions.

To understand the role of RNA-binding proteins (RBPs) in the regulation of gene expression, methods are needed for the in vivo identification of RNA-protein interactions. We have developed the peptide nucleic acid (PNA)-assisted identification of RBP technology to enable the identification of proteins that complex with a target RNA in vivo. Specific regions of the 3' and 5' UTRs of ankylosis mRNA were targeted by antisense PNAs transported into cortical neurons by the cell-penetrating peptide transportan 10. An array of proteins was isolated in complex with or near the targeted regions of the ankylosis mRNA through UV-induced crosslinking of the annealed PNA-RNA-RBP complex. The first evidence for pharmacological modulation of these specific protein-RNA associations was observed. These data show that the PNA-assisted identification of the RBP technique is a reliable method to rapidly identify proteins interacting in vivo with the target RNA.

Amino Acids↗

PubMed1996

Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels.

The function of many of the uncharacterized open reading frames discovered by genomic sequencing can be determined at the level of expressed gene products, the proteome. However, identifying the cognate gene from minute amounts of protein has been one of the major problems in molecular biology. Using yeast as an example, we demonstrate here that mass spectrometric protein identification is a general solution to this problem given a completely sequenced genome. As a first screen, our strategy uses automated laser desorption ionization mass spectrometry of the peptide mixtures produced by in-gel tryptic digestion of a protein. Up to 90% of proteins are identified by searching sequence data bases by lists of peptide masses obtained with high accuracy. The remaining proteins are identified by partially sequencing several peptides of the unseparated mixture by nanoelectrospray tandem mass spectrometry followed by data base searching with multiple peptide sequence tags. In blind trials, the method led to unambiguous identification in all cases. In the largest individual protein identification project to date, a total of 150 gel spots-many of them at subpicomole amounts-were successfully analyzed, greatly enlarging a yeast two-dimensional gel data base. More than 32 proteins were novel and matched to previously uncharacterized open reading frames in the yeast genome. This study establishes that mass spectrometry provides the required throughput, the certainty of identification, and the general applicability to serve as the method of choice to connect genome and proteome.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2005

Rapid and sensitive identification of major histocompatibility complex class I-associated tumor peptides by Nano-LC MALDI MS/MS.

Identification of major histocompatibility complex (MHC)-associated peptides recognized by T-lymphocytes is a crucial prerequisite for the detection and manipulation of specific immune responses in cancer, viral infections, and autoimmune diseases. Unfortunately immunogenic peptides are less abundant species present in highly complex mixtures of MHC-extracted material. Most peptide identification strategies use microcapillary LC coupled to nano-ESI MS/MS in a challenging on-line approach. Alternatively MALDI PSD analysis has been applied for this purpose. We report here on the first off-line combination of nanoscale (nano) LC and MALDI TOF/TOF MS/MS for the identification of naturally processed MHC peptide ligands. These peptides were acid-eluted from human leukocyte antigen (HLA)-A2, HLA-A3, and HLA-B/-C complexes separately isolated from a renal cell carcinoma cell lysate using HLA allele-specific antibodies. After reversed-phase HPLC, peptides were further fractionated via nano-LC. This additional separation step provided a substantial increase in the number of detectable candidate species within the complex peptide pools. MALDI MS/MS analysis on nano-LC-separated material was then sufficiently sensitive to rapidly identify more than 30 novel HLA-presented peptide ligands. Peptide sequences contained perfect anchor amino acid residues described previously for HLA-A2, HLA-A3, and HLA-B7. The most promising candidate for a T-cell epitope is an HLA-B7-binding nonamer peptide derived from the tumor-associated gene NY-BR-16. To demonstrate the sensitivity of our approach we characterized peptides binding to HLA-C molecules that are usually expressed at the cell surface at approximately only 10% the levels of HLA-A or HLA-B. In fact, multiple renal cell carcinoma peptides were identified that contained anchor amino acid residues of HLA-Cw5 and HLA-Cw7. We conclude that the nano-LC MALDI MS/MS approach is a sensitive tool for the rapid and automated identification of MHC-associated tumor peptides.

Amino Acid Sequence↗

PubMed2006

Universal metrics for quality assessment of protein identifications by mass spectrometry.

Increasing numbers of large proteomic datasets are becoming available. As attempts are made to interpret these datasets and integrate them with other forms of genomic data, researchers are becoming more aware of the importance of data quality with respect to protein identification. We present three simple and universal metrics that describe different aspects of the quality of protein identifications by peptide mass fingerprinting. Hit ratio gives an indication of the signal-to-noise ratio in a mass spectrum, mass coverage measures the amount of protein sequence matched, and excess of limit-digested peptides reflects the completeness of the digestion that precedes the peptide mass fingerprinting. Receiver-operating characteristic plots show that the novel metric, excess of limit-digested peptides, can discriminate between correct and random matches more accurately than search score when validating the results from a state-of-the-art protein identification software system (Mascot) especially when combined with the two other metrics, hit ratio and mass coverage. Recommendations are made regarding the use of the metrics when reporting protein identification experiments.

Mass Spectrometry↗

PubMed2006

Stable isotope tagging of epitopes: a highly selective strategy for the identification of major histocompatibility complex class I-associated peptides induced upon viral infection.

Identification of peptides presented in major histocompatibility complex (MHC) class I molecules after viral infection is of strategic importance for vaccine development. Until recently, mass spectrometric identification of virus-induced peptides was based on comparative analysis of peptide pools isolated from uninfected and virus-infected cells. Here we report on a powerful strategy aiming at the rapid, unambiguous identification of naturally processed MHC class I-associated peptides, which are induced by viral infection. The methodology, stable isotope tagging of epitopes (SITE), is based on metabolic labeling of endogenously synthesized proteins during infection. This is accomplished by culturing virus-infected cells with stable isotope-labeled amino acids that are expected to be anchor residues (i.e. residues of the peptide that have amino acid side chains that bind into pockets lining the peptide-binding groove of the MHC class I molecule) for the human leukocyte antigen allele of interest. Subsequently these cells are mixed with an equal number of non-infected cells, which are cultured in normal medium. Finally peptides are acid-eluted from immunoprecipitated MHC molecules and subjected to two-dimensional nanoscale LC-MS analysis. Virus-induced peptides are identified through computer-assisted detection of characteristic, binomially distributed ratios of labeled and unlabeled molecules. Using this approach we identified novel measles virus and respiratory syncytial virus epitopes as well as infection-induced self-peptides in several cell types, showing that SITE is a unique and versatile method for unequivocal identification of disease-related MHC class I epitopes.

Amino Acid Sequence↗

PubMed2002

Utility of olfactory identification test for diagnosing Chinese patients with Alzheimer's disease.

The present study examined the utility of two tests, the olfactory identification test and the olfactory threshold test, in detecting dementia of the Alzheimer's type in Chinese patients in Hong Kong. The olfactory identification test developed by Murphy, Anderson, and Markinson (1994) was utilized with some modifications of odor stimuli suitable for the Chinese culture. Results showed that patients with Alzheimer's disease (AD) identified significantly fewer odors and had significantly higher olfactory threshold than their age- and education-matched normal control subjects. With the cut-off point of 5 identified odors (out of 6), the olfactory identification test yielded a sensitivity of 83% in discriminating AD patients from normal controls which was consistent with that reported by Morgan, Nordin, and Murphy (1995). Thus, the present results suggested that the olfactory identification test could be applied cross-culturally for identifying patients with dementia of the Alzheimer's type.

Aged↗