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At least 127 records · Page 7Linked to original sources
PubMed2006

Identification of a potent botulinum neurotoxin a protease inhibitor using in situ lead identification chemistry.

[reaction: see text] Botulinum neurotoxins (BoNTs), etiological agents of the deadly food poisoning disease botulism, are the most toxic proteins currently known. By using in situ lead identification chemistry, we have uncovered the first class of inhibitors that displays nanomolar potency. From a 15 microM lead compound, structure-activity relationship studies were performed granting the most potent BoNT/A inhibitor reported to date that displays an inhibition constant of 300 nM.

Botulinum Toxins, Type A↗
PubMed2004

The Smell Identification Test as a measure of olfactory identification ability in schizophrenia and healthy populations: a Rasch psychometric study.

This study examines University of Pennsylvania Smell Identification Test (UPSIT; R. L. Doty, 1995) performance in 133 controls and 54 chronic, medicated outpatients with schizophrenia (SZ) using item-response theory modeling. Results show that UPSIT items contribute to 1 factor, cover a range of 8 standard errors of measurement, and articulate 3 ability levels. Although it is not difficult enough to discriminate among persons of above-average ability, the test has diagnostic utility in detecting moderate impairment. Independent of item difficulty, 13 items differentiate patients from controls. When 45 patients and 45 controls were matched on gender and age, patient accuracy remained significantly reduced. The findings support the test's utility and demonstrate how traditional data analysis is insensitive to complexities in test performance.

Adult↗
PubMed1999

A novel human hepatic organic anion transporting polypeptide (OATP2). Identification of a liver-specific human organic anion transporting polypeptide and identification of rat and human hydroxymethylglutaryl-CoA reductase inhibitor transporters.

A novel human organic transporter, OATP2, has been identified that transports taurocholic acid, the adrenal androgen dehydroepiandrosterone sulfate, and thyroid hormone, as well as the hydroxymethylglutaryl-CoA reductase inhibitor, pravastatin. OATP2 is expressed exclusively in liver in contrast to all other known transporter subtypes that are found in both hepatic and nonhepatic tissues. OATP2 is considerably diverged from other family members, sharing only 42% sequence identity with the four other subtypes. Furthermore, unlike other subtypes, OATP2 did not transport digoxin or aldosterone. The rat isoform oatp1 was also shown to transport pravastatin, whereas other members of the OATP family, i.e. rat oatp2, human OATP, and the prostaglandin transporter, did not. Cis-inhibition studies indicate that both OATP2 and roatp1 also transport other statins including lovastatin, simvastatin, and atorvastatin. In summary, OATP2 is a novel organic anion transport protein that has overlapping but not identical substrate specificities with each of the other subtypes and, with its liver-specific expression, represents a functionally distinct OATP isoform. Furthermore, the identification of oatp1 and OATP2 as pravastatin transporters suggests that they are responsible for the hepatic uptake of this liver-specific hydroxymethylglutaryl-CoA reductase inhibitor in rat and man.

Amino Acid Sequence↗
PubMed1978

Comparison of a commercial identification kit and conventional biochemical tests used for the identification of enteric gram-negative rods.

A comparison between 11 Minitek biochemical tests and corresponding conventional tubed media was undertaken with 1,089 isolates of enteric gram-negative rods. Overall correlation between Minitek and conventional biochemicals was 97.4%. Minitek proved to be a time- and space-saving miniaturized biochemical system that can be used effectively for the identification of enteric gram-negative rods.

Bacteriological Techniques↗
PubMed1997

Allele identification using immobilized mismatch binding protein: detection and identification of antibiotic-resistant bacteria and determination of sheep susceptibility to scrapie.

A novel method for detection and identification of specific alleles has been developed utilizing immobilized mismatch binding protein (IMBP). The assay involves the use of biotin-labeled probes, which are prepared by PCR amplification of cloned fragments with known sequence. The use of probes avoids many of the problems associated with the extreme sensitivity of IMBP assays to errors in PCR amplification. The method can be used to monitor PCR fidelity and to genotype both diploid and haploid organisms and has been used to distinguish rifampicin-sensitive and -resistant strains of Mycobacterium tuberculosis and to detect and distinguish two alleles of the sheep prion protein gene involved in susceptibility to scrapie.

Alleles↗
PubMed1999

New method for automatic identification identification and typing of single and multiple superimposed human papillomavirus sequences.

This study of specimens of human papillomaviruses (HPV) through HPV-specific polymerase chain reaction (PCR), followed by direct sequencing, resulted in 11% (38/354) superimposed HPV sequences, signifying coinfection with more than one HPV type. To address the diagnostic problem that these superimposed ("degenerated," overlapping) sequences pose, the authors created a papillomavirus database in Microsoft Excel (Microsoft Corporation, Redmond, WA, U.S.A.) and Corel Quattro Pro 9 (Corel Corporation, Ottawa, Ontario, Canada) formats, retrievable from http://www2.crosswinds.net/ -crosswindswatson/index.html. This sequence database is simultaneously a search and comparison tool for quick (several seconds) typing of HPV from regular and "degenerated" sequencing results. Some of the advantages of the method are as follows: (1) superimposed HPV sequences that differ in length could be readily identified from a single input; (2) the search is restricted to the currently known 127 PV types, which speeds up the typing; (3) the most common HPV sequencing artifacts are included for quick detection; (4) there is no proprietary code and the database could be easily improved; (5) HPV sequence identification does not require internet connection; and (6) new HPV types could be easily detected. This method allowed resolution of all but 1 of 354 HPV-positive specimens. From 38 superimposed HPV sequences, this method identified one known HPV type (3 specimens), two HPV types (30 specimens) and three HPV types (4 specimens).

DNA Primers↗
PubMed2002

A possible pitfall in the identification of Burkholderia mallei using molecular identification systems based on the sequence of the flagellin fliC gene.

Amotile Burkholderia mallei and motile Burkholderia pseudomallei display a high similarity with regard to phenotype and clinical syndromes, glanders and melioidosis. The aim of this study was to establish a fast and reliable molecular method for identification and differentiation. Despite amotility, the gene of the filament forming flagellin (fliC) could be completely sequenced in two B. mallei strains. Only one mutation was identified discriminating between B. mallei and B. pseudomallei. A polymerase chain reaction-restriction fragment length polymorphism assay was designed making use of the absence of an AvaII recognition site in B. mallei. All seven B. mallei, 12 out of 15 B. pseudomallei and 36 closely related apathogenic Burkholderia thailandensis strains were identified correctly. However, in three B. pseudomallei strains a point mutation at gene position 798 (G to C) disrupted the AvaII site. Therefore, molecular systems based on the fliC sequence can be used for a reliable proof of strains of the three species but not for the differentiation of B. mallei and B. pseudomallei isolates.

Base Sequence↗
PubMed1989

Parathyroid identification by ultrasonically guided aspiration cytology. Is correct cytological identification possible?

Reliable parathyroid identification is necessary before percutaneous inactivation of parathyroid tumours is carried out. Aspiration cytology is one of the methods used for this purpose. Some, but not all, investigators have found it difficult or impossible to make a cytological distinction between thyroid and parathyroid cells. In a blind morphological study of 16 parathyroid and 16 thyroid aspirations the specificity of a cytological diagnosis of parathyroid cells was 100%. The sensitivity of the same diagnosis was 9/16 = 56% if only certain diagnosis of parathyroid cells was considered, but 14/16 = 88% if also diagnoses of "probably parathyroid cells" were considered.

Biopsy, Needle↗
PubMed2025

Accurate serotype identification of Streptococcus pneumoniae using nanopore Cas9-targeted serotype identification (nCATSerotyping).

Streptococcus pneumoniae (pneumococcus) is a leading cause of community-acquired pneumonia and invasive diseases, particularly among children and the elderly. The introduction of pneumococcal conjugate vaccines has significantly reduced invasive pneumococcal disease, but the prevalence of non-vaccine serotypes and newly emerging serotypes is increasing globally. Thus, accurate serotyping is essential for epidemiological surveillance and the development of next-generation multivalent pneumococcal vaccines. Conventional serotyping methods, including multiplex polymerase chain reaction (mPCR), monoclonal antibody (mAb) assays, and Quellung reaction using rabbit antisera, are limited by serotype coverage and cross-reactivity, making the detection of new or emerging serotypes challenging. In this study, we developed a nanopore Cas9-targeted serotyping (nCATSerotyping) platform, which employs Cas9-mediated enrichment of the capsular polysaccharide synthesis locus followed by Oxford Nanopore sequencing. Applying this method to 276 clinical pneumococcal isolates collected in South Korea (2018-2020), we achieved a serotyping success rate of 97.10% (268/276), significantly outperforming conventional methods such as mAb and mPCR, which identified only 76.45% (211/276) of isolates. Whole-genome sequencing of the remaining eight non-typeable isolates revealed them to be non-pneumococcal (oral streptococci), confirming 100% accuracy for S. pneumoniae serotyping. Importantly, our method identified emerging and underrepresented serotypes, including serotype 13 and null capsule clade strains. nCATSerotyping offers a rapid, accurate, and comprehensive solution for pneumococcal serotyping, with significant advantages in identifying novel and non-typeable strains. This scalable platform will be a valuable tool for global serotype surveillance and next-generation multivalent pneumococcal vaccine development.IMPORTANCEAccurate pneumococcal serotyping is critical for vaccine development and epidemiological surveillance, particularly as non-vaccine serotypes emerge following widespread pneumococcal conjugate vaccine implementation. Current serotyping methods face significant limitations in coverage and accuracy, identifying around 76% of pneumococcal isolates and failing to detect emerging serotypes like serotype 13 and null capsule clades. The nanopore Cas9-targeted serotyping platform addresses these critical gaps by achieving 100% serotyping accuracy for confirmed Streptococcus pneumoniae isolates while identifying previously undetectable strains that conventional methods missed. This comprehensive approach is essential for monitoring vaccine effectiveness, understanding serotype replacement patterns, and informing next-generation vaccine development strategies. Furthermore, the identification of misclassified oral streptococci highlights the diagnostic precision needed for accurate pneumococcal surveillance, ensuring that epidemiological data accurately reflect true pneumococcal disease burden and serotype distribution patterns.

Streptococcus pneumoniae↗
PubMed1987

Comparison of rapid identification method and conventional substrates for identification of Corynebacterium group JK isolates.

In an effort to identify Corynebacterium group JK isolates rapidly, Rapid Identification Method (RIM series; Austin Biological Laboratories, Inc., Austin, Tex.) substrates were tested in parallel with conventional substrates. RIM reactions agreed with conventional substrate results, respectively, as follows: urea, 38 of 38; nitrate, 35 of 38; glucose, 35 of 38; maltose, 28 of 38; sucrose, 37 of 38; and o-nitrophenyl-beta-D-galactopyranoside, 24 of 26. As a supplement to initial screening tests, the RIM tests offer a rapid method for identifying group JK isolates.

Bacteriological Techniques↗
PubMed1996

Rapid species identification of "Streptococcus milleri" strains by line blot hybridization: identification of a distinct 16S rRNA population closely related to Streptococcus constellatus.

A collection of 399 "Streptococcus milleri" strains were identified to the species level by the use of a line blot assay. Their PCR-amplified partial 16S rRNA gene sequences were hybridized with species-specific 5'-biotinylated oligonucleotide probes homologous to the bp 213 to 231 regions of the 16S rRNA gene sequences of the type strains Streptococcus anginosus ATCC 33397, Streptococcus constellatus ATCC 27823, and Streptococcus intermedius ATCC 27335. The hybridization results were compared with the reference phenotypic identification method data (R. A. Whiley, H. Fraser, J. M. Hardie, and D. Beighton, J. Clin. Microbiol. 28:1497-1501, 1990). Most strains (357 of 399 [89.5%]) reacted unambiguously with only one probe. However, 42 of the 399 strains (10.5%) reacted with both the S. constellatus- and S. intermedius-specific probes; 41 of them were phenotypically identified as S. constellatus. These dually reactive strains hybridized with a 5'-biotinylated probe based on the bp 213 to 231 region of the 16S rRNA gene sequence of one of two species. Analysis of the 5' ends of the 16S rRNA gene sequences (487 bp) demonstrated that the dually reactive strains represent a distinct rRNA population sharing 98.1% sequence similarity with S. constellatus. Phenotypic consistency between the dually reactive strains and the S. constellatus strains was not demonstrated. Line blot hybridization proved to be a simple and inexpensive method to screen large numbers of strains for genetic relatedness, and it allowed the detection of a distinct 16S rRNA type within the "S. milleri" group.

Bacterial Typing Techniques↗
PubMed1997

Identification of Staphylococcus species and subspecies by the chaperonin 60 gene identification method and reverse checkerboard hybridization.

A previous study (S. H. Goh et al., J. Clin. Microbiol. 34:818-823, 1996) demonstrated that a 600-bp region of the chaperonin 60 (Cpn60) genes from various bacterial isolates could be amplified by PCR with a pair of degenerate primers and that the products could be used as species-specific probes for Staphylococcus aureus, S. epidermidis, S. haemolyticus, S. lugdunensis, S. saprophyticus, and S. schleiferi. To further validate the utility of bacterial Cpn60 genes as universal targets for bacterial identification (ID), reverse checkerboard chemiluminescent hybridization experiments were performed with DNA probes from 34 different Staphylococcus species and subspecies. With the exception of probes from the Cpn60 genes of S. intermedius and S. delphini, which cross hybridized, all were species specific. Two subspecies of both S. capitis and S. cohnii were differentiated from one another, while DNAs from the two S. schleiferi subspecies cross hybridized. When 40 known Staphylococcus isolates were tested in a blind experiment by the Cpn60 gene method, 36 strains, representing six species and one subspecies (S. sciuri, S. caseolyticus, S. hominis, S. warneri, S. hyicus, S. haemolyticus, and S. capitis subsp. ureolyticus), were correctly identified. DNA from the four remaining isolates, known to be S. hyicus bovine strains, failed to hybridize to DNA from the S. hyicus target strain or any other Staphylococcus species. However, DNAs from these S. hyicus isolates did cross hybridize with each other. New DNA sequence data and evidence from previous studies suggest some genetic divergence between the two groups of S. hyicus isolates. Our results demonstrate that this Cpn60 gene-based ID method has the potential to be a basic method for bacterial ID. Studies are in progress to further validate the utility of this Cpn60 gene system for ID of Staphylococcus and other genera, including those of slow-growing microorganisms.

Animals↗
PubMed1998

Streptococcus iniae, a human and animal pathogen: specific identification by the chaperonin 60 gene identification method.

It was recently reported that Streptococcus iniae, a bacterial pathogen of aquatic animals, can cause serious disease in humans. Using the chaperonin 60 (Cpn60) gene identification method with reverse checkerboard hybridization and chemiluminescent detection, we identified correctly each of 12 S. iniae samples among 34 aerobic gram-positive isolates from animal and clinical human sources.

Animals↗
PubMed2005

An optimization method for the identification of minimal sets of discriminating gene markers: application to cultivar identification in wheat.

A potentially large number of molecular markers are available for identifying genotypes in various species. For wheat, cultivar identity is an important determinant for end-use segregation and for payment of end-point royalties and grower premiums. A number of dominant DNA markers, that give either a positive or negative response, have been developed previously for wheat cultivar identification. This paper gives a method for identifying minimal marker sets for a given cultivar group, for example those grown in a specific geographical zone. It is based on an integer linear programming formulation of the problem, and can find all minimal marker sets for the group if required. The paper then describes the production of two software packages, GGDS and GGIP, that incorporate this methodology. Various practical issues are also discussed. These packages enable the rapid selection of minimal marker sets for the efficient discrimination of any sample set where the marker responses of the samples are known. They are already being used by the Australian wheat industry.

Algorithms↗
PubMed2000

Identification of a substrate for Pkn2, a protein Ser/Thr kinase from Myxococcus xanthus by a novel method for substrate identification.

Eukaryotic cells contain a large number of protein Ser/ Thr kinases, which play important roles in signal transduction required for cell proliferation, differentiation, and stress response and adaptation. It is also known that some prokaryotes contain a family of protein Ser/Thr kinases. A major challenge in the characterization of these kinases is how to identify their specific substrates. Here we developed such a method using a protein Ser/Thr kinase, Pkn2 from Myxococcus xanthus, a Gram-negative soil bacterium. When Pkn2 is inducibly expressed in E. coli, cells are unable to form colonies on agar plates. This lethal effect of Pkn2 was eliminated in an inactive Pkn2 mutant in which the highly conserved Lys residue was changed to Asn, indicating that phosphorylation of a cellular protein(s) in E. coli resulted in growth arrest. Several clones from an E. coli genomic library were found to suppress the lethal effect when co-expressed with pkn2. Four out of seven multi-copy suppressors were identified to encode HU, (3 for HUalpha and 1 for HUB) a histone-like DNA binding protein. Purified HUalpha was found to be specifically phosphorylated by Pkn2 at Thr-59, and the phosphorylated HUalpha became unable to bind to DNA, suggesting that the phosphorylation of endogenous HU proteins by Pkn2 contributed at least in part to the lethal effect in E. coli. The present method termed the STEK method (Suppressors of Toxic Effects of Kinases) may be widely used for the substrate identification not only for prokaryotic protein Ser/Thr kinases but also for eukaryotic kinases.

Bacterial Proteins↗
PubMed2001

Toxicity identification of metals: development of toxicity identification fingerprints.

The ecotoxicological and chemical response of five metals (Cd, Cr, Cu, Ni, and Zn) to selective fractionation techniques was assessed using the organism Daphnia magna. The metals Cu and Zn revealed similar toxicity patterns, showing an increased toxicity when lowering the pH, a marked reduction in toxicity after addition of ethylenediaminetetraacetic acid (EDTA). Similar toxicity reductions were obtained by passing the metal solutions over ion exchangers, activated charcoal, and filtration/solid-phase extraction units at neutral and basic pHs. The discrimination between Cu- and Zn-toxicity occurred in the oxidant reduction test, i.e., Zn toxicity was not affected by the addition of Na2S2O3, while Cu toxicity was strongly reduced. A second cluster was formed by Cd and Ni. The toxicity of both metals markedly decreased in the EDTA, ion exchangers, activated charcoal, filtration, and solid-phase extraction tests at high pHs. Discrimination between the toxicity of both metals was accomplished with the graduated pH test, in which a pH-independent toxicity response was found for Ni while the toxicity of Cd increased at lower pHs. Compared with the other metals, a very distinct toxicity pattern for Cr was observed. From the applied fractionation techniques, only the graduated pH and the anion resin tests resulted in a marked change in Cr toxicity. The produced toxicity patterns for each individual metal could therefore be used as fingerprints (i.e., toxicity identification fingerprints) in order to identify the toxicity caused by individual metals for D. magna.

Algorithms↗
PubMed2003

Smoking status identification: two managed care organizations' experiences with a pilot project to implement identification systems in independent practice associations.

OBJECTIVE: To determine whether managed care organizations (MCOs) can effectively promote the sustained use of smoking status identification systems among independent practice associations. STUDY DESIGN: Quasi-experimental design measuring smoking status documentation before and after an intervention. METHODS: A chart review of the MCOs' patients at 4 participating primary care clinics determined the baseline for smoking status documentation before intervention. Baseline data were unavailable from a fifth participating clinic. Two quality improvement personnel were sent by the MCOs to help the clinics chose and implement a system for identifying smoking status. All of the clinics chose a sticker system. The change in smoking status documentation was assessed by chart reviews of patients enrolled in the MCOs who were seen during the period between 3 and 16 months after implementation of the system. RESULTS: Following the intervention, a significant increase in smoking status documentation was noted among participating clinics. The proportion of patients whose smoking status was identified and documented by any method increased from 50% to 87% (P < .01) at the 4 clinics with baseline data. By clinic, the increase varied from 6% to 60%. The sticker system was the method by which most patients' smoking status was documented (77%). There were no controls, so the influence of outside factors, including a regional smoking cessation campaign that coincided with this study, cannot be quantified. CONCLUSIONS: Managed care organizations may be an effective change agent for implementing the guidelines for tobacco use and dependence treatment.

Blue Cross Blue Shield Insurance Plans↗
PubMed2003

Secure de-identification and re-identification.

Today's healthcare organizations have both an ethical and legal responsibility for protecting patient privacy. However, the HIPAA privacy rule allows for the release of de-identified patient data for certain purposes. Secure encryption technology can be used to encrypt patient identified data so only the owners of the original data can re-identify the patient. It further allows consistent de-identification over episodic collection events.

Computer Security↗