NIL: large-scale detection of large-variance clones

2021 ◽  
Author(s):  
Tasuku Nakagawa ◽  
Yoshiki Higo ◽  
Shinji Kusumoto
Keyword(s):  
Large Scale ◽  
Scale Detection

scholarly journals Recombinant polypeptide of Mycobacterium leprae as a potential tool for serological detection of leprosy

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Marcelo dos Santos Barbosa ◽  
Iara Beatriz Andrade de Sousa ◽  
Simone Simionatto ◽  
Sibele Borsuk ◽  
Silvana Beutinger Marchioro
Keyword(s):  
Large Scale ◽  
Mycobacterium Leprae ◽  
Detection Methods ◽  
Recombinant Polypeptide ◽  
Cell Reactivity ◽  
Tertiary Structures ◽  
Leprosy Patients ◽  
T Cell Reactivity ◽  
Prevention Methods ◽  
Scale Detection

AbstractCurrent prevention methods for the transmission of Mycobacterium leprae, the causative agent of leprosy, are inadequate as suggested by the rate of new leprosy cases reported. Simple large-scale detection methods for M. leprae infection are crucial for early detection of leprosy and disease control. The present study investigates the production and seroreactivity of a recombinant polypeptide composed of various M. leprae protein epitopes. The structural and physicochemical parameters of this construction were assessed using in silico tools. Parameters like subcellular localization, presence of signal peptide, primary, secondary, and tertiary structures, and 3D model were ascertained using several bioinformatics tools. The resultant purified recombinant polypeptide, designated rMLP15, is composed of 15 peptides from six selected M. leprae proteins (ML1358, ML2055, ML0885, ML1811, ML1812, and ML1214) that induce T cell reactivity in leprosy patients from different hyperendemic regions. Using rMLP15 as the antigen, sera from 24 positive patients and 14 healthy controls were evaluated for reactivity via ELISA. ELISA-rMLP15 was able to diagnose 79.17% of leprosy patients with a specificity of 92.86%. rMLP15 was also able to detect the multibacillary and paucibacillary patients in the same proportions, a desirable addition in the leprosy diagnosis. These results summarily indicate the utility of the recombinant protein rMLP15 in the diagnosis of leprosy and the future development of a viable screening test.

scholarly journals DNA Melting Analysis for Detection of Single Nucleotide Polymorphisms

2001 ◽  
Vol 47 (4) ◽  
pp. 635-644 ◽  
Author(s):  
Robert H Lipsky ◽  
Chiara M Mazzanti ◽  
Joseph G Rudolph ◽  
Ke Xu ◽  
Gopal Vyas ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Large Scale ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Dna Melting ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Efficient System ◽  
Gradient Gel Electrophoresis ◽  
Melting Analysis ◽  
Scale Detection

Abstract Background: Several methods for detection of single nucleotide polymorphisms (SNPs; e.g., denaturing gradient gel electrophoresis and denaturing HPLC) are indirectly based on the principle of differential melting of heteroduplex DNA. We present a method for detecting SNPs that is directly based on this principle. Methods: We used a double-stranded DNA-specific fluorescent dye, SYBR Green I (SYBR) in an efficient system (PE 7700 Sequence Detector) in which DNA melting was controlled and monitored in a 96-well plate format. We measured the decrease in fluorescence intensity that accompanied DNA duplex denaturation, evaluating the effects of fragment length, dye concentration, DNA concentration, and sequence context using four naturally occurring polymorphisms (three SNPs and a single-base deletion/insertion). Results: DNA melting analysis (DM) was used successfully for variant detection, and we also discovered two previously unknown SNPs by this approach. Concentrations of DNA amplicons were readily monitored by SYBR fluorescence, and DNA amplicon concentrations were highly reproducible, with a CV of 2.6%. We readily detected differences in the melting temperature between homoduplex and heteroduplex fragments 15–167 bp in length and differing by only a single nucleotide substitution. Conclusions: The efficiency and sensitivity of DMA make it highly suitable for the large-scale detection of sequence variants.

HUME: large-scale detection of causal genetic factors of adverse drug reactions

2018 ◽  
Vol 34 (24) ◽  
pp. 4274-4283 ◽  
Author(s):  
Mehrdad Mansouri ◽  
Bowei Yuan ◽  
Colin J D Ross ◽  
Bruce C Carleton ◽  
Martin Ester
Keyword(s):  
Adverse Drug Reactions ◽  
Large Scale ◽  
Genetic Factors ◽  
Drug Reactions ◽  
Scale Detection

scholarly journals Evaluation of a competitive inhibition ELISA based on the recombinant protein tSAG1 to detect anti–Neospora caninum antibodies in cattle

2020 ◽  
Vol 32 (3) ◽  
pp. 401-408
Author(s):  
María B. Novoa ◽  
Beatriz S. Valentini ◽  
Macarena Sarli ◽  
Susana M. Torioni-de-Echaide ◽  
María E. Primo ◽  
...  
Keyword(s):  
Large Scale ◽  
Competitive Inhibition ◽  
Neospora Caninum ◽  
Management Strategies ◽  
Protozoan Parasite ◽  
Economic Losses ◽  
Serum Samples ◽  
Beef Cow ◽  
Inhibition Elisa ◽  
Scale Detection

Neospora caninum is a protozoan parasite that causes abortion and important economic losses in cattle worldwide. There are no treatments or vaccines available; disease control is based on diagnosis and herd management strategies. We developed, validated, and evaluated under field conditions a competitive inhibition ELISA based on the truncated SAG1 protein (tSAG1), expressed in Escherichia coli, and the RafNeo5 monoclonal antibody (ciELISAtSAG1). A criterion based on the 3-y sequential serologic analysis of 230 dairy cows by IFAT was used as the gold standard. The assay was validated using 860 serum samples from cows that were consistently positive or negative by IFAT throughout the study period. ciELISAtSAG1 was then used to evaluate the prevalence of neosporosis in 16 beef cow herds (22 samples per herd, 352 total samples). The results were compared with those from IFAT and a commercial cELISA (cELISAVMRD). The ciELISAtSAG1 cutoff was ≥ 29%I, with a diagnostic sensitivity of 98.7% (95% CI = 96.8–99.7%) and a diagnostic specificity of 97.9% (95% CI = 96.4–99.0%). Concordance among IFAT, cELISAVMRD, and ciELISAtSAG1 was 90.3%. The agreement (κ) between ciELISAtSAG1 and the other 2 tests was ≥ 0.81. The overall prevalence of neosporosis in the 16 beef herds was 30% (range: 5–60%). The ciELISAtSAG1 could be useful for large-scale detection of anti– N. caninum antibodies in cattle and seroepidemiologic investigations, given its appropriate sensitivity and specificity, and the simplicity of production.

scholarly journals Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

2010 ◽  
Vol 38 (14) ◽  
pp. 4755-4767 ◽  
Author(s):  
Ernesto Picardi ◽  
David S. Horner ◽  
Matteo Chiara ◽  
Riccardo Schiavon ◽  
Giorgio Valle ◽  
...  
Keyword(s):  
Rna Editing ◽  
Deep Sequencing ◽  
Large Scale ◽  
Rna Deep Sequencing ◽  
Scale Detection

scholarly journals Spatiotemporal identification of druggable binding sites using deep learning

2020 ◽  
Author(s):  
Igor Kozlovskii ◽  
Petr Popov
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Large Scale ◽  
Specific Binding ◽  
Three Dimensional ◽  
Growth Factor Receptor ◽  
Protein Binding Sites ◽  
Binding Site Identification ◽  
Scale Detection

Identification of novel protein binding sites expands «druggable genome» and opens new opportunities for drug discovery. Generally, presence or absence of a binding site depends on the three-dimensional conformation of a protein, making binding site identification resemble to object detection problem in computer vision. Here we introduce a computational approach for the large-scale detection of protein binding sites, named BiteNet, that considers protein conformations as the 3D-images, binding sites as the objects on these images to detect, and conformational ensembles of proteins as the 3D-videos to analyze. BiteNet is suitable for spatiotemporal detection of hard-to-spot allosteric binding sites, as we showed for conformation-specific binding site of the epidermal growth factor receptor, oligomer-specific binding site of the ion channel, and binding sites in G protein-coupled receptors. BiteNet outperforms state-of-the-art methods both in terms of accuracy and speed, taking about 1.5 minute to analyze 1000 conformations of a protein with 2000 atoms. BiteNet is available at https://github.com/i-Molecule/bitenet.

scholarly journals Large scale detection of half-flats in CAT(0)-spaces

2010 ◽  
Vol 59 (2) ◽  
pp. 395-416
Author(s):  
Stefano Francaviglia ◽  
Jean-Francois Lafont
Keyword(s):  
Large Scale ◽  
Scale Detection
Sign in / Sign up

Export Citation Format

Share Document