A new cost-effective staining method for rapid identification of Cryptococcus

AbstractAn innovative approach for the rapid identification of wood species is presented. By combining X-ray fluorescence spectrometry with convolutional neural network machine learning, 48 different wood specimens were clearly differentiated and identified with a 99% accuracy. Wood species identification is imperative to assess illegally logged and transported lumber. Alternative options for identification can be time consuming and require some level of sampling. This non-invasive technique offers a viable, cost-effective alternative to rapidly and accurately identify timber in efforts to support environmental protection laws and regulations.

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Rapid Identification of Potential Drug Candidates from Multi-Million Compounds’ Repositories. Combination of 2D Similarity Search with 3D Ligand/Structure Based Methods and In Vitro Screening

Molecules ◽

10.3390/molecules26185593 ◽

2021 ◽

Vol 26 (18) ◽

pp. 5593

Author(s):

Katalin Szilágyi ◽

Beáta Flachner ◽

István Hajdú ◽

Mária Szaszkó ◽

Krisztina Dobi ◽

...

Keyword(s):

Similarity Search ◽

Pharmacophore Model ◽

Cost Effective ◽

Rapid Identification ◽

Drug Candidates ◽

Hit Rate ◽

Physico Chemical ◽

Cost Effective Approach ◽

3D Methods

Rapid in silico selection of target focused libraries from commercial repositories is an attractive and cost-effective approach in early drug discovery. If structures of active compounds are available, rapid 2D similarity search can be performed on multimillion compounds’ databases. This approach can be combined with physico-chemical parameter and diversity filtering, bioisosteric replacements, and fragment-based approaches for performing a first round biological screening. Our objectives were to investigate the combination of 2D similarity search with various 3D ligand and structure-based methods for hit expansion and validation, in order to increase the hit rate and novelty. In the present account, six case studies are described and the efficiency of mixing is evaluated. While sequentially combined 2D/3D similarity approach increases the hit rate significantly, sequential combination of 2D similarity with pharmacophore model or 3D docking enriched the resulting focused library with novel chemotypes. Parallel integrated approaches allowed the comparison of the various 2D and 3D methods and revealed that 2D similarity-based and 3D ligand and structure-based techniques are often complementary, and their combinations represent a powerful synergy. Finally, the lessons we learnt including the advantages and pitfalls of the described approaches are discussed.

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Cost-effective, clinically relevant method for rapid identification of beta-hemolytic streptococci and enterococci.

Journal of Clinical Microbiology ◽

10.1128/jcm.33.5.1154-1157.1995 ◽

1995 ◽

Vol 33 (5) ◽

pp. 1154-1157 ◽

Cited By ~ 4

Author(s):

R Kirby ◽

K L Ruoff

Keyword(s):

Cost Effective ◽

Rapid Identification

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Urea-Fibrinogen Slide Coagulase Test – A Simple Alternative Method for the Rapid Identification of Staphylococcus aureus

Journal of Gandaki Medical College-Nepal ◽

10.3126/jgmcn.v10i1.17903 ◽

2017 ◽

Vol 10 (1) ◽

pp. 5-10

Author(s):

Binita Koirala Sharma ◽

S Gokhale ◽

K Sharma

Keyword(s):

Staphylococcus Aureus ◽

Sensitivity And Specificity ◽

Reference Method ◽

Cost Effective ◽

Rapid Identification ◽

Accurate Identification ◽

Predictive Values ◽

Negative Results ◽

Animal Pathogens ◽

Sensitivity Specificity

Introduction: The accurate identification of Staphylococcus aureus clinical isolates requires a series of tests. Morphological features and slide coagulase test are two criteria on which S. aureus are identified. Resort to tube coagulase test is sought when results of slide coagulase test are equivocal or doubtful. Both coagulase tests detect the enzymes that convert fibrinogen into fibrin. Human, rabbit or sheep pooled plasma is used as substrate for both tests. Slide coagulase test is simpler and faster as compared to tube coagulase test. The plasma could be carrier of many human and animal pathogens like HIV, HBV, HCV etc. Storage of plasma for longer duration is fraught with chances of contamination. Improperly stored plasma can lead to false positive or negative results. Citrated plasma may be unsuitable for this test if contaminated with citrate utilizing bacteria. Considering the role of S. aureus as a common etiological agent in nosocomial and community infections, there is a need of implementing rapid, easy and cost-effective phenotypic test.Objectives: Considering the disadvantages and risks associated with fresh plasma, this study aims to launch for safer, more reliable substitute with longer shelf life that may provide reliable results for prompt identification of S. aureus by slide coagulase test.Methods: The present work evaluates slide coagulase test (SCT), and urea fibrinogen slide coagulase test (UF-SCT) for S. aureus detection considering Tube coagulase test (TCT) as the reference method. Sensitivity, specificity, positive predictive value and negative predictive values of SCT and UF-SCT were calculated using TCT as gold standard. Results: A total of 150 staphylococcal isolates from different clinical specimens ere selected for the evaluation of coagulase tests. All the specimens were subjected to SCT, UF-SCT and TCT. The UF-SCT showed better sensitivity (95.04%), specificity (100%), PPV (100%), and NPV (82.85%) with reference to TCT. UF-SCT showed similar sensitivity and specificity to SCT. None of the isolates were negative in UF-SCT and positive in SCT. Since UF-SCT does not incorporate plasma directly and at the same time has a very good sensitivity and specificity, it is recommended that UF-SCT could replace SCT for identification of S. aureus.Conclusion: The findings of present study shall encourage laboratories to use the urea-fibrinogen slide coagulase test routinely for the rapid identification of S aureus.Journal of Gandaki Medical College Vol. 10, No. 1, 2017, Page: 5-10

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Differentiation of Salmonella enterica Serovars and Strains in Cultures and Food Using Infrared Spectroscopic and Microspectroscopic Techniques Combined with Soft Independent Modeling of Class Analogy Pattern Recognition Analysis

Journal of Food Protection ◽

10.4315/0362-028x-71.11.2249 ◽

2008 ◽

Vol 71 (11) ◽

pp. 2249-2256 ◽

Cited By ~ 18

Author(s):

ANNEGRET MÄNNIG ◽

NATHAN A. BALDAUF ◽

LUIS A. RODRIGUEZ-ROMO ◽

AHMED E. YOUSEF ◽

LUIS E. RODRÍGUEZ-SAONA

Keyword(s):

Ir Spectroscopy ◽

Disease Outbreaks ◽

Cost Effective ◽

Rapid Identification ◽

Multivariate Statistical ◽

Salmonella Serovars ◽

Bacterial Lipopolysaccharides ◽

Multiple Strains ◽

Membrane Components ◽

Ir Spectroscopic

Detection of pathogenic microorganisms in food is often a tedious and time-consuming exercise. Developing rapid and cost-effective techniques for identifying pathogens to subspecies is critical for tracking causes of foodborne disease outbreaks. The objective of this study was to develop a method for rapid identification and differentiation of Salmonella serovars and strains within these serovars through isolation on hydrophobic grid membrane filters (HGMFs), examination by infrared (IR) spectroscopy and microspectroscopy, and data analysis by multivariate statistical techniques. Salmonella serovars (Anatum, Enteritidis, Heidelberg, Kentucky, Muenchen, and Typhimurium), most of which were represented by multiple strains, were grown in tryptic soy broth (24 h at 42°C), diluted to 102 to 103 CFU/ml, and filtered using HGMFs. The membranes were incubated on Miller-Mallinson agar (24 h at 42°C), and typical Salmonella colonies were sonicated in 50% acetonitrile and centrifuged. Resulting pellets were vacuum dried on a ZnSe crystal and analyzed using IR spectroscopy. Alternatively, the membranes containing Salmonella growth were removed from the agar, vacuum dried, and colonies were analyzed directly by IR microspectroscopy. Soft independent modeling of class analogy (SIMCA) models were developed from spectra. The method was validated by analyzing Salmonella-inoculated tomato juice, eggs, milk, and chicken. Salmonella serovars exhibited distinctive and reproducible spectra in the fingerprint region (1,200 to 900 cm−1) of the IR spectrum. SIMCA permitted distinguishing Salmonella strains from each other through differences in bacterial lipopolysaccharides and other membrane components. The model correctly predicted Salmonella in foods at serovar (100%) and strain (90%) levels. Isolation of Salmonella on HGMF and selective agar followed by IR spectroscopic analysis resulted in rapid and efficient isolation, identification, and differentiation of Salmonella serovars and strains.

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Mid Infrared Acousto-Optical Tunable Filter-Spectrometer for Rapid Identification of Black Plastics from Automobile Construction

Journal of Near Infrared Spectroscopy ◽

10.1255/jnirs.184 ◽

1998 ◽

Vol 6 (A) ◽

pp. A149-A151 ◽

Cited By ~ 3

Author(s):

F. Kowol ◽

M. Oleimeulen ◽

H. Freitag ◽

T. Huth-Fehre

Keyword(s):

Consumer Goods ◽

Cost Effective ◽

Rapid Identification ◽

Tunable Filter ◽

Mid Infrared ◽

Plastic Recycling ◽

Plastic Type ◽

Essential Question ◽

Ft Ir ◽

Automobile Construction

Black plastics are common compounds of many technical devices and consumer goods. A well known example is the usage in automobile construction. Plastic recycling is gaining more and more importance, with fast plastic type identification being an essential question. This article presents a cost-effective and rugged alternative to FT-IR techniques, based on an acousto-optical tunable filter spectrometer, which is able to master the special difficulties in the recognition of black plastics.

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Rapid Identification of Plasma DNA Samples with Increased ctDNA Levels by a Modified FAST-SeqS Approach

Clinical Chemistry ◽

10.1373/clinchem.2014.234286 ◽

2015 ◽

Vol 61 (6) ◽

pp. 838-849 ◽

Cited By ~ 59

Author(s):

Jelena Belic ◽

Marina Koch ◽

Peter Ulz ◽

Martina Auer ◽

Teresa Gerhalter ◽

...

Keyword(s):

Screening Method ◽

Cost Effective ◽

Maternal Blood ◽

Circulating Tumor Dna ◽

Rapid Identification ◽

Plasma Samples ◽

Plasma Dna ◽

Aneuploidy Screening ◽

Z Scores ◽

Tumor Genome

Abstract BACKGROUND Recent progress in the analysis of cell-free DNA fragments [cell-free circulating tumor DNA (ctDNA)] now allows monitoring of tumor genomes by noninvasive means. However, previous studies with plasma DNA from patients with cancer demonstrated highly variable allele frequencies of ctDNA. The comprehensive analysis of tumor genomes is greatly facilitated when plasma DNA has increased amounts of ctDNA. Therefore, a fast and cost-effective prescreening method to identify such plasma samples without previous knowledge about alterations in the respective tumor genome could assist in the selection of samples suitable for further extensive qualitative analysis. METHODS We adapted the recently described Fast Aneuploidy Screening Test-Sequencing System (FAST-SeqS) method, which was originally established as a simple, effective, noninvasive screening method for fetal aneuploidy from maternal blood. RESULTS We show that our modified FAST-SeqS method (mFAST-SeqS) can be used as a prescreening tool for an estimation of ctDNA percentage. With a combined evaluation of genome-wide and chromosome arm–specific z-scores from dilution series with cell line DNA and by comparisons of plasma-Seq profiles with data from mFAST-SeqS, we established a detection limit of ≥10% mutant alleles. Plasma samples with an mFAST-SeqS z-score >5 showed results that were highly concordant with those of copy number profiles obtained from our previously described plasma-Seq approach. CONCLUSIONS Advantages of this approach include the speed and cost-effectiveness of the assay and that no prior knowledge about the genetic composition of tumor samples is necessary to identify plasma DNA samples with >10% ctDNA content.

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Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome-specific KASP genotyping assays

10.1101/633842 ◽

2019 ◽

Author(s):

Surbhi Grewal ◽

Stella Hubbart-Edwards ◽

Caiyun Yang ◽

Urmila Devi ◽

Lauren Baker ◽

...

Keyword(s):

Cost Effective ◽

Single Copy ◽

Rapid Identification ◽

Wild Relatives ◽

Introgression Lines ◽

Wheat Genome ◽

Wild Relative ◽

Backcross Population ◽

Biotic Stresses ◽

Specific Pcr

SummaryFor future food security it is important that wheat, one of the most widely consumed crops in the world, can survive the threat of abiotic and biotic stresses. New genetic variation is currently being introduced into wheat through introgressions from its wild relatives. For trait discovery, it is necessary that each introgression is homozygous and hence stable. Breeding programs rely on efficient genotyping platforms for marker-assisted selection (MAS). Recently, single nucleotide polymorphism (SNP) based markers have been made available on high-throughput Axiom® SNP genotyping arrays. However, these arrays are inflexible in their design and sample numbers, making their use unsuitable for long-term MAS. SNPs can potentially be converted into Kompetitive allele-specific PCR (KASP™) assays which are comparatively cost-effective and efficient for low-density genotyping of introgression lines. However, due to the polyploid nature of wheat, KASP assays for homoeologous SNPs can have difficulty in distinguishing between heterozygous and homozygous hybrid lines in a backcross population. To identify co-dominant SNPs, that can differentiate between heterozygotes and homozygotes, we PCR-amplified and sequenced genomic DNA from potential single-copy regions of the wheat genome and compared them to orthologous copies from different wild relatives. A panel of 620 chromosome-specific KASP assays have been developed that allow rapid detection of wild relative segments and provide information on their homozygosity and site of introgression in the wheat genome. A set of 90 chromosome-nonspecific assays was also produced that can be used for genotyping introgression lines. These multipurpose KASP assays represent a powerful tool for wheat breeders worldwide.

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Suitability of Passive Integrated Transponder Tags for Marking Live Animals for Trade.

Wildlife Research ◽

10.1071/wr9950767 ◽

1995 ◽

Vol 22 (6) ◽

pp. 767 ◽

Cited By ~ 5

Author(s):

WJ Freeland ◽

K Fry

Keyword(s):

Cost Effective ◽

Rapid Identification ◽

Pit Tag ◽

Passive Integrated Transponder ◽

Reliable Identification ◽

Pit Tags ◽

Technological Improvements ◽

Animal Trade ◽

Passive Integrated Transponder Tags ◽

Environmental Interference

Passive Integrated Transponder (PIT) tags were subject to a series of experimental manipulations designed to simulate conditions operating during the course of trade in animals. Experiments were designed to determine the effects of tag-wand angle of orientation, various barriers between tags and wands and different wand-readers on the distance at which a reading could be made. The distances at which readings can be made are subject to influences by all three variables. The effect of tag-wand angle of orientation is likely to be trivial under most circumstances. Of more importance to the utility of PIT tags for animal trade is environmental interference, particularly that due to metallic barriers (plate or mesh). Different wand-readers produce idiosyncratic results in relation to orientation of the tag and wand and type of barrier. Implantation of tags in cane toads (Bufo marinus) indicates that tags are long lived and reliable. Loss of tags from the toads was relatively rare and probably due to error during the insertion of tags. PIT tags proved resistant to preservation in formalin or ethanol, and to the decomposition of animals in which they had been inserted. Tags inserted into 14 species of Australian mammal provided reliable identification of individuals, and were lost only from species that fly (bats) or are arboreal and glide (a petaurid marsupial). PIT tags are outstandingly reliable and provide for rapid identification of individual animals. Limitations to the use of PIT tags in trade in animals are the inability to conduct readings from a distance (>50mm), and their vulnerability to environmental interference. Technological improvements in taglscannerlreader design may improve the distance from which readings may be made, and cages could possibly be designed in ways that minimise environmental interference. Until these developments have occurred, the PIT tag does not provide cost-effective improvements in the ability to identify animals used in trade.

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A Streamlined Approach to Rapidly Detect SARS-CoV-2 Infection Avoiding RNA Extraction: Workflow Validation

Disease Markers ◽

10.1155/2020/8869424 ◽

2020 ◽

Vol 2020 ◽

pp. 1-5

Author(s):

Catia Mio ◽

Adriana Cifù ◽

Stefania Marzinotto ◽

Natascha Bergamin ◽

Chiara Caldana ◽

...

Keyword(s):

Large Scale ◽

Rna Extraction ◽

Cost Effective ◽

Extraction Methods ◽

Rapid Identification ◽

Proteinase K ◽

Rt Pcr ◽

Isolation Method ◽

Pcr Assay ◽

Sensitivity Specificity

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly spread worldwide from the beginning of 2020. The presence of viral RNA in samples by nucleic acid (NA) molecular analysis is the only method available to diagnose COVID-19 disease and to assess patients’ viral load. Since the demand for laboratory reagents has increased, there has been a worldwide shortage of RNA extraction kits. We, therefore, developed a fast and cost-effective viral genome isolation method that, combined with quantitative RT-PCR assay, detects SARS-CoV-2 RNA in patient samples. The method relies on the addition of Proteinase K followed by a controlled heat-shock incubation and, then, E gene evaluation by RT-qPCR. It was validated for sensitivity, specificity, linearity, reproducibility, and precision. It detects as low as 10 viral copies/sample, is rapid, and has been characterized in 60 COVID-19-infected patients. Compared to automated extraction methods, our pretreatment guarantees the same positivity rate with the advantage of shortening the time of the analysis and reducing its cost. This is a rapid workflow meant to aid the healthcare system in the rapid identification of infected patients, such as during a pathogen-related outbreak. For its intrinsic characteristics, this workflow is suitable for large-scale screenings.

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