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PubMed2005

Multigenic families and proteomics: extended protein characterization as a tool for paralog gene identification.

In classical proteomic studies, the searches in protein databases lead mostly to the identification of protein functions by homology due to the non-exhaustiveness of the protein databases. The quality of the identification depends on the studied organism, its complexity and its representation in the protein databases. Nevertheless, this basic function identification is insufficient for certain applications namely for the development of RNA-based gene-silencing strategies, commonly termed RNA interference (RNAi) in animals and post-transcriptional gene silencing (PTGS) in plants, that require an unambiguous identification of the targeted gene sequence. A PTGS strategy was considered in the study of the infection of Oryza sativa by the Rice Yellow Mottle Virus (RYMV). It is suspected that the RYMV recruits host proteins after its entry into plant cells to form a complex facilitating virus multiplication and spreading. The protein partners of this complex were identified by a classical proteomic approach, nano liquid chromatography tandem mass spectrometry. Among the identified proteins, several were retained for a PTGS strategy. Nevertheless most of the protein candidates appear to be members of multigenic families for which all paralog genes are not present in protein databases. Thus the identification of the real expressed paralog gene with classical protein database searches is impossible. Consequently, as the genome contains all genes and thus all paralog genes, a whole genome search strategy was developed to determine the specific expressed paralog gene. With this approach, the identification of peptides matching only a single gene, called discriminant peptides, allows definitive proof of the expression of this identified gene. This strategy has several requirements: (i) a genome completely sequenced and accessible; (ii) high protein sequence coverage. In the present work, through three examples, we report and validate for the first time a genome database search strategy to specifically identify paralog genes belonging to multigenic families expressed under specific conditions.

Chaperonin 60↗
PubMed1996

Guessing strategies, aging, and bias effects in perceptual identification.

In the typical single-stimulus perceptual identification task, accuracy is improved by prior study of test words, a repetition priming benefit. There is also a cost, inasmuch as previously studied words are likely to be produced (incorrectly) as responses if the test word is orthographically similar but not identical to a studied word. In two-alternative forced-choice perceptual identification, a test word is flashed and followed by two alternatives, one of which is the correct response. When the two alternatives are orthographically similar, test words identical to previously studied items are identified more accurately than new words (a benefit) but tests words orthographically similar to studied words are identified less accurately than new words (a cost). Ratcliff and McKoon (in press) argue that these are bias effects that arise in the decision stage of word identification. We report five experiments that examined the alternative hypothesis that these bias effects arise from postperceptual guessing strategies. In single-stimulus perceptual identification, repetition priming benefits were equally great for young and older adults who claimed to use deliberate guessing strategies and those who did not (Experiment 1). In contrast, only groups of young and older people who claimed to deliberately guess studied words in a two-alternative forced-choice task (Experiments 2 and 5) showed reliable benefits and costs. Costs and benefits were abolished in the two-alternative forced-choice task when a very long study list was used, presumably because the increased retrieval burden made the use of deliberate guessing strategies less attractive (Experiment 3). Under conditions similar to those of Experiment 3, repetition priming was observed in single-stimulus perceptual identification (Experiment 4). These results are consistent with the view that costs and benefits in the forced-choice perceptual identification task arise from deliberate guessing strategies but that those in the single-stimulus task do not. The possibility that the observed relationship between strategy reports and priming effects reflects erroneous postexperimental assessments of strategies by participants is also considered.

Adolescent↗
PubMed1998

Word-identification priming for ignored and attended words.

Three experiments examined contributions of study phase awareness of word identity to subsequent word-identification priming by manipulating visual attention to words at study. In Experiment 1, word-identification priming was reduced for ignored relative to attended words, even though ignored words were identified sufficiently to produce negative priming in the study phase. Word-identification priming was also reduced after color naming relative to emotional valence rating (Experiment 2) or word reading (Experiment 3), even though an effect of emotional valence upon color naming (Experiment 2) indicated that words were identified at study. Thus, word-identification priming was reduced even when word identification occurred at study. Word-identification priming may depend on awareness of word identity at the time of study.

Adolescent↗
PubMed2001

Development of a latex agglutination test for rapid identification of Escherichia coli.

Escherichia coli, one of the most important human pathogens, is usually identified by a battery of biochemical tests that require overnight incubation. For rapid identification of Escherichia coli, a latex agglutination test (LAT) was developed. Rabbits were immunized with cell-surface antigens extracted from Escherichia coli CCRC 15481 with 4 M urea, and the affinity-purified antibodies were used to coat latex particles for the identification of the bacterium. The following gram-negative bacteria were used to evaluate the LAT: Escherichia coli (n = 761), Enterobacteriaceae other than Escherichia coli (n = 632), Aeromonas spp. (n = 21), Pseudomonas spp. (n = 75), Vibrio spp. (n = 18), and other bacteria (n = 64). The LAT had a sensitivity and specificity of 99.2 and 93.3%, respectively. If the LAT was used in conjunction with the tests of indole production or lactose fermentation, the specificity values for the identification of Escherichia coli increased from 93.3 to 98.8 and 98.7%, respectively. If the LAT, indole production, and lactose fermentation were used together for the identification of Escherichia coli, the sensitivity and specificity were 94 and 99.7%, respectively. Lactose fermentation could be detected by observing the colonies grown on selective media (e.g. MacConkey agar), and indole production could be analyzed simply by the spot indole test. Strains producing negative reactions (i.e. not identified as Escherichia coli) should be processed by the conventional procedures for identification. The present protocol integrating the LAT, indole production, and lactose fermentation for the identification of Escherichia coli offers considerable savings of time, manpower, and cost.

Animals↗
PubMed2005

Pyridinium-based ionic liquid matrices can improve the identification of proteins by peptide mass-fingerprint analysis with matrix-assisted laser desorption/ionization mass spectrometry.

Matrix-assisted laser desorption/ionization mass spectrometry has become an indispensable tool for identification of proteins by peptide mass-fingerprint analysis. Selection of the matrix, addition of matrix additives, and sample-preparation techniques are known to affect the quality of the spectra and hence protein identification. We investigated the effect of pyridine as matrix additive for the commonly used crystalline matrix alpha-cyano-4-hydroxycinnamic acid (CCA), forming a pyridinium based ionic liquid matrix, on the mass spectra of synthetic peptides and tryptic protein digests. Beside the equimolar mixture of CCA and pyridine, the effect of addition of substoichiometric amounts of the base to the acid was tested. Optimum results in terms of signal-to-noise ratios, reduction of chemical noise, and reduced formation of alkali adducts and matrix clusters were observed for the matrix CCA-pyridine in the molar ratio 2:1. The optimized ionic liquid matrix was used for identification of tryptic digests of six model proteins and for identification of a protein extracted from a two-dimensional gel with the proteome of the bacterium Corynebacterium glutamicum, and shown to facilitate protein identification, yielding higher scores and increased sequence coverage compared with pure CCA. Thus CCA-Py 2:1 is a potential alternative for identification and characterization of proteins by peptide mass-fingerprint analysis.

Corynebacterium glutamicum↗
PubMed2005

Impact of axillary nodal metastases on lymphatic mapping and sentinel lymph node identification rate in patients with early stage breast cancer.

PURPOSE: The aim of this study was to define the impact of the presence of axillary nodal metastases on lymphatic mapping and sentinel lymph node (SLN) identification rate in patients with early breast cancer. METHODS: Two hundred and forty-six lymphatic mapping procedures were performed with both labelled nanocolloid and blue dye, followed by SLN biopsy and/or complete axillary dissection. The following parameters were recorded: patient's age, tumour laterality and location, tumour size, tumour histology, tumour stage, tumour grade, lymphovascular invasion, radiotracer injection site (subdermal-peritumoural/peri-areolar), SLN visualisation at lymphoscintigraphy, SLN metastases (presence/absence, size) and other axillary metastases (presence/absence, number). Discriminant analysis was used to analyse the data. RESULTS: SLNs were identified by labelled nanocolloid alone in 94.7% of tumours, by blue dye alone in 93.5% and by the combined technique in 99.2%. Discriminant analysis showed the gamma probe SLN identification rate to be significantly limited by the presence of axillary nodal metastases. In particular, the size of SLN metastases and the number of other axillary metastases were the most important variables in reducing the gamma probe SLN identification rate (p = 0.004 and p = 0.002, respectively). On the other hand, high tumour grade was the only parameter limiting the blue dye SLN identification rate. CONCLUSION: The accuracy of lymphatic mapping with labelled nanocolloid is limited by the presence of axillary nodal metastases, and particularly by the degree of SLN tumoural invasion and the presence and number of other axillary nodal metastases. Neither of these elements seems to interfere with the blue dye identification rate. The combination of the two tracers maximises the SLN identification rate.

Adult↗
PubMed2003

Identification of sentinel lymph nodes in colon cancer depends on the amount of dye injected relative to tumor size.

Recent studies have shown that the sentinel lymph node (SLN) procedure might improve staging in colon cancer. However, low SLN identification and high false negative rates have also been reported. In a two-institution study, the SLN procedure with isosulfan blue 1% was performed according to a standardized protocol in 31 patients with open resections for colon cancer. Data were collected prospectively. The database was analyzed retrospectively to determine factors contributing to a low identification rate. The SLN identification rate was 87% and the false negative rate was 50%. Successful SLN identification was significantly associated with application of higher volumes of dye relative to the tumor diameter ( p = 0.04) and more frequent tumor localization in the sigmoid colon ( p = 0.04) as compared to missing SLN identification. The tumor diameter was not significantly different in the two groups. Sentinel lymph node identification in colon cancer depends on the amount of dye injected relative to the tumor size. Application of only 1 ml of dye-the amount generally recommended in the literature-is not sufficient in large tumors.

Aged↗
PubMed2000

The application of dental methods of identification to human burn victims in a mass disaster.

This paper deals with the usefulness of dental identification in the case of 28 human burn victims of a bus accident in Spain. Postmortem forensic procedures for identification were used including general external examination, routine photographs and radiographs and complementary biological methods. Dental identification was also used and a description of the method is presented. Dental identification was established in 57% of the cases. When victims were less than 20 years of age, the success rate of identification by dental methods was higher (76% of victims in this age group). The assessment of dental age allowed the establishment of identity of four victims. We recommend that dental procedures be used in human identification after mass disasters. Odontological and radiographic procedures are powerful methods when dealing with burn victims.

Accidents, Traffic↗
PubMed2006

Eyewitness identification accuracy and response latency.

Eyewitness identification research has reliably shown that accurate identifications are faster than inaccurate identifications. Recently, D. Dunning and S. Perretta (2002) claimed that an identification latency of 10-12 s not only best discriminates between accurate and inaccurate identifications but also produces extremely high accuracy rates, approaching 90%. Consistent with predictions from recognition memory theory, however, we show that the optimum time boundary varies with overall response latency under manipulations of retention interval and nominal lineup size, and that the accuracy rate inside the optimum time boundary is much less impressive than previously reported. We outline directions for clarifying the accuracy and latency relationship to assist the reliable diagnosis of identification accuracy.

Analysis of Variance↗
PubMed2004

Alternative approaches to the definition and identification of learning disabilities: some questions and answers.

Recent consensus reports concur in suggesting major changes in the federal regulatory approach to the identification of learning disabilities (LD). These reports recommend abandoning the IQ-discrepancy model and the use of IQ tests for identification, and also recommend incorporation of response to instruction (RTI) as one of the identification criteria. These changes are also recommended to states in the current reauthorization of the U.S. Individuals with Disabilities in Education Act (IDEA). While not mandatory, states that follow these recommendations will experience major changes in identification and treatment of students served under the LD category. This paper reviews the basis for these recommendations, summarizing four recent consensus group reports on special education that concur in suggesting these changes. Seventeen commonly asked questions about these changes are presented, with responses. In order to ensure adequate instruction for students with LD, it is essential that identification practices focus on assessments that are directly related to instruction, that any services for students who are struggling prioritize intervention over eligibility, and that special education be permitted to focus more on results and outcomes and less on eligibility and process. Identification models that incorporate RTI represent a shift in special education toward the goals of better achievement and behavioral outcomes for students identified with LD, as well as those students at risk for LD.

Child↗
PubMed1985

Identification and assessment of hazardous compounds in drinking water.

The identification of organic chemicals in drinking water and their assessment in terms of potential hazardous effects are two very different but closely associated tasks. In relation to both continuous low-level background contamination and specific, often high-level, contamination due to pollution incidents, the identification of contaminants is a pre-requisite to evaluation of significant hazards. Even in the case of the rapidly developing short-term bio-assays which are applied to water to indicate a potential genotoxic hazard (for example Ames tests), identification of the active chemicals is becoming a major factor in the further assessment of the response. Techniques for the identification of low concentrations of organic chemicals in drinking water have developed remarkably since the early 1970s and methods based upon gas chromatography-mass spectrometry (GC-MS) have revolutionised qualitative analysis of water. Such techniques are limited to "volatile" chemicals and these usually constitute a small fraction of the total organic material in water. However, in recent years there have been promising developments in techniques for "non-volatile" chemicals in water. Such techniques include combined high-performance liquid chromatography-mass spectrometry (HPLC-MS) and a variety of MS methods, involving, for example, field desorption, fast atom bombardment and thermospray ionisation techniques. In the paper identification techniques in general are reviewed and likely future developments outlined. The assessment of hazards associated with chemicals identified in drinking and related waters usually centres upon toxicology - an applied science which involves numerous disciplines. The paper examines the toxicological information needed, the quality and deployment of such information and discusses future research needs. Application of short-term bio-assays to drinking water is a developing area and one which is closely involved with, and to some extent dependent on, powerful methods of identification. Recent developments are discussed.

Animals↗
PubMed1993

Congenital hearing disability--epidemiology and identification: a comparison between two health authority districts.

The objective of the present study was to describe some epidemiological aspects of congenital/early acquired (i.e. in the neonatal period) hearing disability (CEHD) in children born between 1980 and 1990, living in two separate health authority districts, i.e. the Copenhagen City/County; in addition, to evaluate the age at identification of the children, the persons raising suspicion of the hearing loss and the pattern of referral; finally, to compare some epidemiological aspects and the age at identification of similarly defined cohorts of children, born 1970-80. Thus the evaluation can be considered as an audit of the primary health care sector concerning children with CEHD. An identical prevalence rate of CEHD was demonstrated, i.e. 1.5/1000 with a better ear hearing level average at 0.5-4 kHz > or = 25 dB (BEHL 0.5-4 kHz) in both regions and unchanged from 1970-80. The median age at identification in the total cohort was 16/18 months in the City/County, respectively, demonstrating a significantly earlier identification of at-risk children in the County with the opposite pattern in the City. The parents were the first to raise suspicion of their child's hearing disability in 50%/57% in the City/County and only minor differences in the pattern of referral was found in the two regions. The frequency of at-risk children among parents/professionals who first suspected the CEHD showed no significant differences; however, the BEHL 0.5-4 kHz in the children was poorer in the group of parents who first raised the suspicion when compared with the group of professionals. Thus the BEHL 0.5-4 kHz is of significance for the age at identification and for the person raising the suspicion of CEHD. Although an improvement in the early identification of CEHD has taken place, when comparing the 1970-80 cohort and 1980-90 cohort, it is concluded that children with CEHD are identified with a substantial delay and that the line of information both concerning high-risk criteria and general information should be continued and intensified towards both parents and professionals.

Age Factors↗
PubMed2006

Simultaneous species identification and detection of methicillin resistance in staphylococci using triplex real-time PCR assay.

For rapid identification of methicillin-resistant Staphylococcus aureus, molecular methods are generally targeting mecA and species-specific genes. Sa442 DNA fragment is a popular species-specific target. However, recently, there have been few reports on S. aureus isolates that are negative for Sa442 fragment; therefore, use of single gene or DNA-fragment-specific polymerase chain reaction (PCR) for identification of microbial isolate may result in misidentification. This study includes CoA gene in parallel with Sa442 marker for identification of S. aureus. This further improves the specificity of the assay by checking for 2 determinants simultaneously for the identification of S. aureus and can prevent misidentification of S. aureus isolates lacking Sa442 DNA fragment. In this study, the newly developed triplex real-time PCR assay was compared with a quadruplex conventional gel-based PCR assay using the same primer sets in both assays. The dual-labeled TaqMan probes (ProOligo, France) for these primers were specifically designed and used in a real-time PCR assay. The clinical isolates (n = 152) were subjected to both PCR assays. The results obtained from both assays proved that the primer and probe sets were 100% sensitive and 100% specific for identification of S. aureus and detection of methicillin resistance. This triplex real-time PCR assay represents a rapid and powerful method for S. aureus identification and detection of methicillin resistance.

Coenzyme A↗
PubMed2005

Intelligent dental identification system (IDIS) in forensic medicine.

This study reports the design and development of the intelligent dental identification system (IDIS), including its efficiency and reliability. Five hundred patients were randomly selected from the Dental Department at Police General Hospital in Thailand to create a population of 3000 known subjects. From the original 500 patients, 100 were randomly selected to create a sample of 1000 unidentifiable subjects (400 subjects with completeness and possible alterations of dental information corresponding to natural occurrences and general dental treatments after the last clinical examination, such as missing teeth, dental caries, dental restorations, and dental prosthetics, 100 subjects with completeness and no alteration of dental information, 500 subjects with incompleteness and no alteration of dental information). Attempts were made to identify the unknown subjects utilizing IDIS. The use of IDIS advanced method resulted in consistent outstanding identification in the range of 82.61-100% with minimal error 0-1.19%. The results of this study indicate that IDIS can be used to support dental identification. It supports not only all types of dentitions: primary, mixed, and permanent but also for incomplete and altered dental information. IDIS is particularly useful in providing the huge quantity and redundancy of related documentation associated with forensic odontology. As a computerized system, IDIS can reduce the time required for identification and store dental digital images with many processing features. Furthermore, IDIS establishes enhancements of documental dental record with odontogram and identification codes, electrical dental record with dental database system, and identification methods and algorithms. IDIS was conceptualized based on the guidelines and standards of the American Board of Forensic Odontology (ABFO) and International Criminal Police Organization (INTERPOL).

Adolescent↗
PubMed2005

ApoE gene and familial risk of Alzheimer's disease as predictors of odour identification in older adults.

The study examined odour identification ability in healthy older adults at increased risk for developing Alzheimer's disease (AD). We recruited a sample (n = 24) of siblings related to probable AD cases and an age-matched control sample (n = 47). All participants were genotyped for the presence of the ApoE epsilon4 allele. Performance on a simple olfactory task of odour identification was compared according to positive family history of AD and ApoE epsilon4 status. The sibling group showed an odour identification deficit compared to the control group. Whilst there was no independent influence of ApoE epsilon4 status on odour identification, there was a significant interaction between positive family history and ApoE epsilon4 status. Sibling epsilon4 carriers showed the greatest odour identification deficit and their performance was significantly poorer than both the sibling non-epsilon4 carrier and control epsilon4 carrier groups. Odour identification deficits like those reported here are considered to be early cognitive markers of incipient AD. In this respect, these findings support the need to both monitor individuals at increased risk of the disease and introduce olfactory-mediated cognitive tasks into the diagnostic setting.

Age Factors↗
PubMed2004

Phonetic perceptual identification by native- and second-language speakers differentially activates brain regions involved with acoustic phonetic processing and those involved with articulatory-auditory/orosensory internal models.

This experiment investigates neural processes underlying perceptual identification of the same phonemes for native- and second-language speakers. A model is proposed implicating the use of articulatory-auditory and articulatory-orosensory mappings to facilitate perceptual identification under conditions in which the phonetic contrast is ambiguous, as in the case of second-language speakers. In contrast, native-language speakers are predicted to use auditory-based phonetic representations to a greater extent for perceptual identification than second-language speakers. The English /r-l/ phonetic contrast, although easy for native English speakers, is extremely difficult for native Japanese speakers who learned English as a second language after childhood. Twenty-two native English and twenty-two native Japanese speakers participated in this study. While undergoing event-related fMRI, subjects were aurally presented with syllables starting with a /r/, /l/, or a vowel and were required to rapidly identify the phoneme perceived by pushing one of three buttons with the left thumb. Consistent with the proposed model, the results show greater activity for second- over native-language speakers during perceptual identification of /r/ and /l/ relative to vowels in brain regions implicated with instantiating forward and inverse articulatory-auditory articulatory-orosensory models [Broca's area, anterior insula, anterior superior temporal sulcus/gyrus (STS/G), planum temporale (PT), superior temporal parietal area (Stp), SMG, and cerebellum]. The results further show that activity in brain regions implicated with instantiating these internal models is correlated with better /r/ and /l/ identification performance for second-language speakers. Greater activity found for native-language speakers especially in the anterior STG/S for /r/ and /l/ perceptual identification is consistent with the hypothesis that native-language speakers use auditory phonetic representations more extensively than second-language speakers.

Adult↗
PubMed2006

Associations between olfactory identification and verbal memory in patients with schizophrenia, first-degree relatives, and non-psychiatric controls.

OBJECTIVE: Olfactory identification deficits and verbal memory impairments may represent trait markers for schizophrenia. The aims of this study were to: (1) assess olfactory identification in patients, first-degree relatives, and non-psychiatric controls, (2) determine differences in verbal memory functioning in these three groups, and (3) study correlations between olfactory identification and three specific verbal memory domains. METHOD: A total of 106 participants-41 patients with schizophrenia or related disorders, 27 relatives, and 38 controls-were assessed with the University of Pennsylvania Smell Identification Test (UPSIT) and the Wechsler Memory Scale-Third Edition. Linear mixed models, accounting for clustering within families and relevant covariates, were used to compare scores across groups and to examine associations between olfactory identification ability and the three verbal memory domains. RESULTS: A group effect was apparent for all four measures, and relatives scored midway between patients and controls on all three memory domains. UPSIT scores were significantly correlated with all three forms of verbal memory. Age, verbal working memory, and auditory recognition delayed memory were independently predictive of UPSIT scores. CONCLUSIONS: Impairments in olfactory identification and verbal memory appear to represent two correlated risk markers for schizophrenia, and frontal-temporal deficits likely account for both impairments.

Adult↗
PubMed2006

Raman microspectroscopy as an identification tool within the phylogenetically homogeneous 'Bacillus subtilis' group.

Vibrational methods have multiple advantages compared to more classic, chemotaxonomic and even molecular microbial tools for the identification of bacteria. Nevertheless, their definite breakthrough in diagnostic microbiology laboratories is determined by their identification potential. This paper reports on the profound evaluation of Raman spectroscopy to identify closely related species by means of 68 Bacillus strains that are assigned or closely related to the phylogenetically homogeneous 'Bacillus subtilis'-group (sensu stricto). These strains were chosen to represent biological variation within the selected species and to create a realistic view on the possibilities of this technique The evaluation resulted in 49/54 correct identifications at the species level for intern and 15/19 for extern testing. The correct identification of strains, which were not represented in the training set, supports the potential as an identification tool within the 'B. subtilis group'. Considering the vague borderline between the species studied, Raman spectroscopy can be regarded here as a promising application for identifications at the species level.

Bacillus subtilis↗