SG186987A1 - Nucleic acids for multiplex organism detection and methods of use and making the same - Google Patents
Nucleic acids for multiplex organism detection and methods of use and making the same Download PDFInfo
- Publication number
- SG186987A1 SG186987A1 SG2013001573A SG2013001573A SG186987A1 SG 186987 A1 SG186987 A1 SG 186987A1 SG 2013001573 A SG2013001573 A SG 2013001573A SG 2013001573 A SG2013001573 A SG 2013001573A SG 186987 A1 SG186987 A1 SG 186987A1
- Authority
- SG
- Singapore
- Prior art keywords
- probe
- mixture
- sequence
- probes
- target
- Prior art date
Links
- 238000000034 method Methods 0.000 title claims abstract description 156
- 150000007523 nucleic acids Chemical class 0.000 title claims description 86
- 102000039446 nucleic acids Human genes 0.000 title claims description 78
- 108020004707 nucleic acids Proteins 0.000 title claims description 78
- 238000001514 detection method Methods 0.000 title abstract description 30
- 239000000523 sample Substances 0.000 claims abstract description 924
- 239000000203 mixture Substances 0.000 claims abstract description 160
- 244000052769 pathogen Species 0.000 claims abstract description 52
- 125000003729 nucleotide group Chemical group 0.000 claims description 123
- 239000002773 nucleotide Substances 0.000 claims description 121
- 238000012163 sequencing technique Methods 0.000 claims description 101
- 241000282414 Homo sapiens Species 0.000 claims description 56
- 238000012360 testing method Methods 0.000 claims description 48
- 230000007717 exclusion Effects 0.000 claims description 38
- 238000009396 hybridization Methods 0.000 claims description 37
- 230000035772 mutation Effects 0.000 claims description 32
- 230000001717 pathogenic effect Effects 0.000 claims description 26
- 108091034117 Oligonucleotide Proteins 0.000 claims description 24
- 108091093088 Amplicon Proteins 0.000 claims description 15
- 241000894007 species Species 0.000 claims description 13
- 239000012472 biological sample Substances 0.000 claims description 11
- 241000894006 Bacteria Species 0.000 claims description 10
- 108091028043 Nucleic acid sequence Proteins 0.000 claims description 10
- 241000700605 Viruses Species 0.000 claims description 10
- 230000001419 dependent effect Effects 0.000 claims description 10
- 241000206602 Eukaryota Species 0.000 claims description 9
- 101710163270 Nuclease Proteins 0.000 claims description 9
- 238000003776 cleavage reaction Methods 0.000 claims description 9
- 230000007017 scission Effects 0.000 claims description 9
- 241000233866 Fungi Species 0.000 claims description 8
- 238000011282 treatment Methods 0.000 claims description 8
- 241000124008 Mammalia Species 0.000 claims description 7
- 238000004519 manufacturing process Methods 0.000 claims description 6
- 108091008146 restriction endonucleases Proteins 0.000 claims description 6
- 238000001574 biopsy Methods 0.000 claims description 4
- 102000054765 polymorphisms of proteins Human genes 0.000 claims description 4
- 230000003115 biocidal effect Effects 0.000 claims description 3
- 239000003153 chemical reaction reagent Substances 0.000 claims description 3
- 238000003780 insertion Methods 0.000 claims description 3
- 230000037431 insertion Effects 0.000 claims description 3
- 238000002493 microarray Methods 0.000 claims description 3
- 230000001225 therapeutic effect Effects 0.000 claims description 3
- 239000003053 toxin Substances 0.000 claims description 3
- 231100000765 toxin Toxicity 0.000 claims description 3
- 108010042407 Endonucleases Proteins 0.000 claims description 2
- 238000012217 deletion Methods 0.000 claims description 2
- 230000037430 deletion Effects 0.000 claims description 2
- 230000003252 repetitive effect Effects 0.000 claims description 2
- 238000007400 DNA extraction Methods 0.000 claims 1
- 102000004533 Endonucleases Human genes 0.000 claims 1
- 241000617156 archaeon Species 0.000 claims 1
- 238000011321 prophylaxis Methods 0.000 claims 1
- 108700026220 vif Genes Proteins 0.000 claims 1
- 108020004711 Nucleic Acid Probes Proteins 0.000 abstract description 10
- 239000002853 nucleic acid probe Substances 0.000 abstract description 10
- 230000003321 amplification Effects 0.000 description 70
- 238000003199 nucleic acid amplification method Methods 0.000 description 70
- 239000007795 chemical reaction product Substances 0.000 description 63
- 108020004414 DNA Proteins 0.000 description 58
- 238000006243 chemical reaction Methods 0.000 description 55
- 239000000047 product Substances 0.000 description 33
- 238000002844 melting Methods 0.000 description 31
- 230000008018 melting Effects 0.000 description 31
- 210000000349 chromosome Anatomy 0.000 description 25
- 238000003752 polymerase chain reaction Methods 0.000 description 24
- 230000000295 complement effect Effects 0.000 description 23
- 239000011159 matrix material Substances 0.000 description 23
- 238000004458 analytical method Methods 0.000 description 22
- 230000008569 process Effects 0.000 description 22
- 241000588724 Escherichia coli Species 0.000 description 18
- 108090000623 proteins and genes Proteins 0.000 description 18
- 241000725303 Human immunodeficiency virus Species 0.000 description 15
- 241001138501 Salmonella enterica Species 0.000 description 15
- 208000019206 urinary tract infection Diseases 0.000 description 15
- 102000010029 Homer Scaffolding Proteins Human genes 0.000 description 14
- 108010077223 Homer Scaffolding Proteins Proteins 0.000 description 14
- 102000053602 DNA Human genes 0.000 description 13
- 238000012545 processing Methods 0.000 description 13
- 241000588770 Proteus mirabilis Species 0.000 description 12
- 238000013461 design Methods 0.000 description 12
- 201000008827 tuberculosis Diseases 0.000 description 12
- 108060002716 Exonuclease Proteins 0.000 description 11
- 102000013165 exonuclease Human genes 0.000 description 11
- YBJHBAHKTGYVGT-ZKWXMUAHSA-N (+)-Biotin Chemical compound N1C(=O)N[C@@H]2[C@H](CCCCC(=O)O)SC[C@@H]21 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 0.000 description 10
- 102000004190 Enzymes Human genes 0.000 description 10
- 108090000790 Enzymes Proteins 0.000 description 10
- 241000588747 Klebsiella pneumoniae Species 0.000 description 10
- 108090000364 Ligases Proteins 0.000 description 10
- 102000003960 Ligases Human genes 0.000 description 10
- 238000003556 assay Methods 0.000 description 10
- -1 swabs) Substances 0.000 description 10
- 230000003612 virological effect Effects 0.000 description 10
- 208000035657 Abasia Diseases 0.000 description 9
- 241001147691 Staphylococcus saprophyticus Species 0.000 description 9
- 230000015572 biosynthetic process Effects 0.000 description 9
- 210000004369 blood Anatomy 0.000 description 9
- 239000008280 blood Substances 0.000 description 9
- 238000003786 synthesis reaction Methods 0.000 description 9
- 241000222122 Candida albicans Species 0.000 description 8
- 241000193998 Streptococcus pneumoniae Species 0.000 description 8
- 238000001914 filtration Methods 0.000 description 8
- 230000006870 function Effects 0.000 description 8
- 150000002240 furans Chemical class 0.000 description 8
- 206010059866 Drug resistance Diseases 0.000 description 7
- 241001472782 Proteus penneri Species 0.000 description 7
- 229940095731 candida albicans Drugs 0.000 description 7
- 238000011049 filling Methods 0.000 description 7
- 239000012634 fragment Substances 0.000 description 7
- 208000015181 infectious disease Diseases 0.000 description 7
- 238000007481 next generation sequencing Methods 0.000 description 7
- 102000040430 polynucleotide Human genes 0.000 description 7
- 108091033319 polynucleotide Proteins 0.000 description 7
- 230000002441 reversible effect Effects 0.000 description 7
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 7
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 6
- 108010063905 Ampligase Proteins 0.000 description 6
- 241000203069 Archaea Species 0.000 description 6
- 241000193163 Clostridioides difficile Species 0.000 description 6
- 241000191967 Staphylococcus aureus Species 0.000 description 6
- 230000001580 bacterial effect Effects 0.000 description 6
- 229960002685 biotin Drugs 0.000 description 6
- 239000011616 biotin Substances 0.000 description 6
- 239000000872 buffer Substances 0.000 description 6
- 238000004422 calculation algorithm Methods 0.000 description 6
- 238000010586 diagram Methods 0.000 description 6
- 238000003205 genotyping method Methods 0.000 description 6
- 239000000463 material Substances 0.000 description 6
- 239000013610 patient sample Substances 0.000 description 6
- 238000012216 screening Methods 0.000 description 6
- 239000000243 solution Substances 0.000 description 6
- 229940031000 streptococcus pneumoniae Drugs 0.000 description 6
- 108010014303 DNA-directed DNA polymerase Proteins 0.000 description 5
- 102000016928 DNA-directed DNA polymerase Human genes 0.000 description 5
- 241000588748 Klebsiella Species 0.000 description 5
- 241000725643 Respiratory syncytial virus Species 0.000 description 5
- 101710084578 Short neurotoxin 1 Proteins 0.000 description 5
- 101710182532 Toxin a Proteins 0.000 description 5
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 description 5
- 238000013459 approach Methods 0.000 description 5
- 235000020958 biotin Nutrition 0.000 description 5
- 230000000903 blocking effect Effects 0.000 description 5
- 230000007423 decrease Effects 0.000 description 5
- 201000010099 disease Diseases 0.000 description 5
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 5
- 230000000694 effects Effects 0.000 description 5
- 230000001404 mediated effect Effects 0.000 description 5
- 230000000813 microbial effect Effects 0.000 description 5
- 239000002157 polynucleotide Substances 0.000 description 5
- 238000007480 sanger sequencing Methods 0.000 description 5
- 239000011734 sodium Substances 0.000 description 5
- 210000001519 tissue Anatomy 0.000 description 5
- 108091032955 Bacterial small RNA Proteins 0.000 description 4
- ZRALSGWEFCBTJO-UHFFFAOYSA-N Guanidine Chemical compound NC(N)=N ZRALSGWEFCBTJO-UHFFFAOYSA-N 0.000 description 4
- 241000606768 Haemophilus influenzae Species 0.000 description 4
- 241001014264 Klebsiella variicola Species 0.000 description 4
- 241001465754 Metazoa Species 0.000 description 4
- 241000588769 Proteus <enterobacteria> Species 0.000 description 4
- 241000589517 Pseudomonas aeruginosa Species 0.000 description 4
- 241000607142 Salmonella Species 0.000 description 4
- 241000935255 Ureaplasma parvum Species 0.000 description 4
- 238000003491 array Methods 0.000 description 4
- 210000004027 cell Anatomy 0.000 description 4
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 4
- 238000007418 data mining Methods 0.000 description 4
- 238000005516 engineering process Methods 0.000 description 4
- 238000010348 incorporation Methods 0.000 description 4
- 230000001965 increasing effect Effects 0.000 description 4
- 230000000977 initiatory effect Effects 0.000 description 4
- 230000000241 respiratory effect Effects 0.000 description 4
- 230000000717 retained effect Effects 0.000 description 4
- 229920000936 Agarose Polymers 0.000 description 3
- 241000589876 Campylobacter Species 0.000 description 3
- 201000007336 Cryptococcosis Diseases 0.000 description 3
- 241000221204 Cryptococcus neoformans Species 0.000 description 3
- 230000007067 DNA methylation Effects 0.000 description 3
- 241000709661 Enterovirus Species 0.000 description 3
- 108091092584 GDNA Proteins 0.000 description 3
- 241000700588 Human alphaherpesvirus 1 Species 0.000 description 3
- 241000701074 Human alphaherpesvirus 2 Species 0.000 description 3
- 201000009906 Meningitis Diseases 0.000 description 3
- 241000588653 Neisseria Species 0.000 description 3
- 241000191940 Staphylococcus Species 0.000 description 3
- 241000202921 Ureaplasma urealyticum Species 0.000 description 3
- 235000015107 ale Nutrition 0.000 description 3
- 230000008901 benefit Effects 0.000 description 3
- 210000001175 cerebrospinal fluid Anatomy 0.000 description 3
- 230000008859 change Effects 0.000 description 3
- 239000002299 complementary DNA Substances 0.000 description 3
- 238000012258 culturing Methods 0.000 description 3
- 230000029087 digestion Effects 0.000 description 3
- 239000000539 dimer Substances 0.000 description 3
- 238000006073 displacement reaction Methods 0.000 description 3
- 238000009826 distribution Methods 0.000 description 3
- 229940079593 drug Drugs 0.000 description 3
- 239000003814 drug Substances 0.000 description 3
- 239000000839 emulsion Substances 0.000 description 3
- 230000002538 fungal effect Effects 0.000 description 3
- 239000000499 gel Substances 0.000 description 3
- 238000011534 incubation Methods 0.000 description 3
- 230000003993 interaction Effects 0.000 description 3
- 230000011987 methylation Effects 0.000 description 3
- 238000007069 methylation reaction Methods 0.000 description 3
- 238000012175 pyrosequencing Methods 0.000 description 3
- 238000011002 quantification Methods 0.000 description 3
- 239000002096 quantum dot Substances 0.000 description 3
- 238000009781 safety test method Methods 0.000 description 3
- 230000035945 sensitivity Effects 0.000 description 3
- 238000004088 simulation Methods 0.000 description 3
- 239000002689 soil Substances 0.000 description 3
- 238000007619 statistical method Methods 0.000 description 3
- 238000003860 storage Methods 0.000 description 3
- 230000002123 temporal effect Effects 0.000 description 3
- 231100000041 toxicology testing Toxicity 0.000 description 3
- 238000010200 validation analysis Methods 0.000 description 3
- 108020000946 Bacterial DNA Proteins 0.000 description 2
- 241000222120 Candida <Saccharomycetales> Species 0.000 description 2
- 241001647372 Chlamydia pneumoniae Species 0.000 description 2
- 241000423301 Clostridioides difficile 630 Species 0.000 description 2
- 241000223205 Coccidioides immitis Species 0.000 description 2
- 241000711573 Coronaviridae Species 0.000 description 2
- 241000223935 Cryptosporidium Species 0.000 description 2
- 108090000695 Cytokines Proteins 0.000 description 2
- 241000588914 Enterobacter Species 0.000 description 2
- 241000194033 Enterococcus Species 0.000 description 2
- 241000194031 Enterococcus faecium Species 0.000 description 2
- 241000192125 Firmicutes Species 0.000 description 2
- ZHNUHDYFZUAESO-UHFFFAOYSA-N Formamide Chemical compound NC=O ZHNUHDYFZUAESO-UHFFFAOYSA-N 0.000 description 2
- 208000005176 Hepatitis C Diseases 0.000 description 2
- 101000876829 Homo sapiens Protein C-ets-1 Proteins 0.000 description 2
- 241000701044 Human gammaherpesvirus 4 Species 0.000 description 2
- 241000701027 Human herpesvirus 6 Species 0.000 description 2
- 241000829111 Human polyomavirus 1 Species 0.000 description 2
- 102000002698 KIR Receptors Human genes 0.000 description 2
- 108010043610 KIR Receptors Proteins 0.000 description 2
- 241000589242 Legionella pneumophila Species 0.000 description 2
- 241000186781 Listeria Species 0.000 description 2
- 241000186779 Listeria monocytogenes Species 0.000 description 2
- 108700011259 MicroRNAs Proteins 0.000 description 2
- 101150101095 Mmp12 gene Proteins 0.000 description 2
- 241000711386 Mumps virus Species 0.000 description 2
- 241000187479 Mycobacterium tuberculosis Species 0.000 description 2
- 241000204031 Mycoplasma Species 0.000 description 2
- 241000202934 Mycoplasma pneumoniae Species 0.000 description 2
- CHJJGSNFBQVOTG-UHFFFAOYSA-N N-methyl-guanidine Natural products CNC(N)=N CHJJGSNFBQVOTG-UHFFFAOYSA-N 0.000 description 2
- 208000002606 Paramyxoviridae Infections Diseases 0.000 description 2
- 102100035251 Protein C-ets-1 Human genes 0.000 description 2
- 241000589516 Pseudomonas Species 0.000 description 2
- 102000006382 Ribonucleases Human genes 0.000 description 2
- 108010083644 Ribonucleases Proteins 0.000 description 2
- 241000315672 SARS coronavirus Species 0.000 description 2
- 241000961587 Secoviridae Species 0.000 description 2
- 241000295644 Staphylococcaceae Species 0.000 description 2
- 108010090804 Streptavidin Proteins 0.000 description 2
- 108010006785 Taq Polymerase Proteins 0.000 description 2
- 241000223109 Trypanosoma cruzi Species 0.000 description 2
- 241000607734 Yersinia <bacteria> Species 0.000 description 2
- 239000002253 acid Substances 0.000 description 2
- 230000001413 cellular effect Effects 0.000 description 2
- 125000003636 chemical group Chemical group 0.000 description 2
- MYSWGUAQZAJSOK-UHFFFAOYSA-N ciprofloxacin Chemical compound C12=CC(N3CCNCC3)=C(F)C=C2C(=O)C(C(=O)O)=CN1C1CC1 MYSWGUAQZAJSOK-UHFFFAOYSA-N 0.000 description 2
- 238000010367 cloning Methods 0.000 description 2
- 239000000356 contaminant Substances 0.000 description 2
- 238000011109 contamination Methods 0.000 description 2
- 238000012864 cross contamination Methods 0.000 description 2
- 229940104302 cytosine Drugs 0.000 description 2
- 230000002950 deficient Effects 0.000 description 2
- 238000012938 design process Methods 0.000 description 2
- 238000002405 diagnostic procedure Methods 0.000 description 2
- SWSQBOPZIKWTGO-UHFFFAOYSA-N dimethylaminoamidine Natural products CN(C)C(N)=N SWSQBOPZIKWTGO-UHFFFAOYSA-N 0.000 description 2
- 230000002255 enzymatic effect Effects 0.000 description 2
- 238000011156 evaluation Methods 0.000 description 2
- 238000002474 experimental method Methods 0.000 description 2
- 210000003608 fece Anatomy 0.000 description 2
- 238000002866 fluorescence resonance energy transfer Methods 0.000 description 2
- 208000002672 hepatitis B Diseases 0.000 description 2
- 101150024289 hly gene Proteins 0.000 description 2
- 229920001519 homopolymer Polymers 0.000 description 2
- QAOWNCQODCNURD-UHFFFAOYSA-M hydrogensulfate Chemical compound OS([O-])(=O)=O QAOWNCQODCNURD-UHFFFAOYSA-M 0.000 description 2
- 125000002887 hydroxy group Chemical group [H]O* 0.000 description 2
- 238000000126 in silico method Methods 0.000 description 2
- 239000012678 infectious agent Substances 0.000 description 2
- 230000002458 infectious effect Effects 0.000 description 2
- 238000011901 isothermal amplification Methods 0.000 description 2
- 229940115932 legionella pneumophila Drugs 0.000 description 2
- 235000019689 luncheon sausage Nutrition 0.000 description 2
- 239000003550 marker Substances 0.000 description 2
- 238000002156 mixing Methods 0.000 description 2
- 230000004048 modification Effects 0.000 description 2
- 238000012986 modification Methods 0.000 description 2
- 238000012544 monitoring process Methods 0.000 description 2
- 238000007837 multiplex assay Methods 0.000 description 2
- 229940013390 mycoplasma pneumoniae Drugs 0.000 description 2
- 230000007918 pathogenicity Effects 0.000 description 2
- 230000002186 photoactivation Effects 0.000 description 2
- 238000011176 pooling Methods 0.000 description 2
- 238000002360 preparation method Methods 0.000 description 2
- 102000004169 proteins and genes Human genes 0.000 description 2
- 238000000746 purification Methods 0.000 description 2
- 238000003753 real-time PCR Methods 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- JQXXHWHPUNPDRT-WLSIYKJHSA-N rifampicin Chemical compound O([C@](C1=O)(C)O/C=C/[C@@H]([C@H]([C@@H](OC(C)=O)[C@H](C)[C@H](O)[C@H](C)[C@@H](O)[C@@H](C)\C=C\C=C(C)/C(=O)NC=2C(O)=C3C([O-])=C4C)C)OC)C4=C1C3=C(O)C=2\C=N\N1CC[NH+](C)CC1 JQXXHWHPUNPDRT-WLSIYKJHSA-N 0.000 description 2
- 229960001225 rifampicin Drugs 0.000 description 2
- 150000003384 small molecules Chemical class 0.000 description 2
- 239000000126 substance Substances 0.000 description 2
- 239000000758 substrate Substances 0.000 description 2
- 238000012706 support-vector machine Methods 0.000 description 2
- 101150032575 tcdA gene Proteins 0.000 description 2
- 239000001226 triphosphate Substances 0.000 description 2
- 235000011178 triphosphate Nutrition 0.000 description 2
- 241000701161 unidentified adenovirus Species 0.000 description 2
- 241000712461 unidentified influenza virus Species 0.000 description 2
- 210000002700 urine Anatomy 0.000 description 2
- 230000001018 virulence Effects 0.000 description 2
- RLLPVAHGXHCWKJ-IEBWSBKVSA-N (3-phenoxyphenyl)methyl (1s,3s)-3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropane-1-carboxylate Chemical compound CC1(C)[C@H](C=C(Cl)Cl)[C@@H]1C(=O)OCC1=CC=CC(OC=2C=CC=CC=2)=C1 RLLPVAHGXHCWKJ-IEBWSBKVSA-N 0.000 description 1
- 108020004465 16S ribosomal RNA Proteins 0.000 description 1
- JCLFHZLOKITRCE-UHFFFAOYSA-N 4-pentoxyphenol Chemical compound CCCCCOC1=CC=C(O)C=C1 JCLFHZLOKITRCE-UHFFFAOYSA-N 0.000 description 1
- BSFODEXXVBBYOC-UHFFFAOYSA-N 8-[4-(dimethylamino)butan-2-ylamino]quinolin-6-ol Chemical compound C1=CN=C2C(NC(CCN(C)C)C)=CC(O)=CC2=C1 BSFODEXXVBBYOC-UHFFFAOYSA-N 0.000 description 1
- 241000251468 Actinopterygii Species 0.000 description 1
- 241000701242 Adenoviridae Species 0.000 description 1
- 241000607534 Aeromonas Species 0.000 description 1
- 241000606828 Aggregatibacter aphrophilus Species 0.000 description 1
- 241000175213 Alloherpesviridae Species 0.000 description 1
- 241000839461 Alphaendornavirus Species 0.000 description 1
- 241000961634 Alphaflexiviridae Species 0.000 description 1
- 241001135756 Alphaproteobacteria Species 0.000 description 1
- 241001339993 Anelloviridae Species 0.000 description 1
- 241000243790 Angiostrongylus cantonensis Species 0.000 description 1
- 241001156002 Anthonomus pomorum Species 0.000 description 1
- 241000224482 Apicomplexa Species 0.000 description 1
- 102100021569 Apoptosis regulator Bcl-2 Human genes 0.000 description 1
- 241000205054 Archaeoglobales Species 0.000 description 1
- 241000712892 Arenaviridae Species 0.000 description 1
- 241001292006 Arteriviridae Species 0.000 description 1
- 241000235349 Ascomycota Species 0.000 description 1
- 241000157873 Ascoviridae Species 0.000 description 1
- 241000977261 Asfarviridae Species 0.000 description 1
- 241000228212 Aspergillus Species 0.000 description 1
- 241001225321 Aspergillus fumigatus Species 0.000 description 1
- 241001533362 Astroviridae Species 0.000 description 1
- 241000271566 Aves Species 0.000 description 1
- 108091012583 BCL2 Proteins 0.000 description 1
- 108700020463 BRCA1 Proteins 0.000 description 1
- 102000036365 BRCA1 Human genes 0.000 description 1
- 101150072950 BRCA1 gene Proteins 0.000 description 1
- 241000193833 Bacillales Species 0.000 description 1
- 241000606125 Bacteroides Species 0.000 description 1
- 241000605059 Bacteroidetes Species 0.000 description 1
- 241000701412 Baculoviridae Species 0.000 description 1
- 241001533460 Barnaviridae Species 0.000 description 1
- 241001279892 Benyvirus Species 0.000 description 1
- 241001135755 Betaproteobacteria Species 0.000 description 1
- 241001340646 Bicaudaviridae Species 0.000 description 1
- 241000702628 Birnaviridae Species 0.000 description 1
- LSNNMFCWUKXFEE-UHFFFAOYSA-M Bisulfite Chemical compound OS([O-])=O LSNNMFCWUKXFEE-UHFFFAOYSA-M 0.000 description 1
- 241000228405 Blastomyces dermatitidis Species 0.000 description 1
- 241000588807 Bordetella Species 0.000 description 1
- 241000776207 Bornaviridae Species 0.000 description 1
- 241000589969 Borreliella burgdorferi Species 0.000 description 1
- 241000283690 Bos taurus Species 0.000 description 1
- 241001533462 Bromoviridae Species 0.000 description 1
- 241001453380 Burkholderia Species 0.000 description 1
- 241000589513 Burkholderia cepacia Species 0.000 description 1
- 239000008000 CHES buffer Substances 0.000 description 1
- 241000714198 Caliciviridae Species 0.000 description 1
- 241000282465 Canis Species 0.000 description 1
- 241000520666 Carmotetraviridae Species 0.000 description 1
- 241001137855 Caudovirales Species 0.000 description 1
- 241001115395 Caulimoviridae Species 0.000 description 1
- 240000008365 Celosia argentea Species 0.000 description 1
- 235000000722 Celosia argentea Nutrition 0.000 description 1
- 241001218361 Cheravirus Species 0.000 description 1
- 241000606161 Chlamydia Species 0.000 description 1
- 241001185363 Chlamydiae Species 0.000 description 1
- 241000191368 Chlorobi Species 0.000 description 1
- 241001060419 Chrysoviridae Species 0.000 description 1
- 241001533399 Circoviridae Species 0.000 description 1
- 241000588923 Citrobacter Species 0.000 description 1
- 241000588917 Citrobacter koseri Species 0.000 description 1
- 241000207199 Citrus Species 0.000 description 1
- 241000973027 Closteroviridae Species 0.000 description 1
- 241001112696 Clostridia Species 0.000 description 1
- 241001112695 Clostridiales Species 0.000 description 1
- 241001522796 Clostridioides difficile CD196 Species 0.000 description 1
- 241000193403 Clostridium Species 0.000 description 1
- 241000193155 Clostridium botulinum Species 0.000 description 1
- 108010065152 Coagulase Proteins 0.000 description 1
- 208000003322 Coinfection Diseases 0.000 description 1
- 208000035473 Communicable disease Diseases 0.000 description 1
- 108091035707 Consensus sequence Proteins 0.000 description 1
- 241000701520 Corticoviridae Species 0.000 description 1
- 241000186227 Corynebacterium diphtheriae Species 0.000 description 1
- 108091029523 CpG island Proteins 0.000 description 1
- 241001137853 Crenarchaeota Species 0.000 description 1
- 241000192700 Cyanobacteria Species 0.000 description 1
- 108010076010 Cystathionine beta-lyase Proteins 0.000 description 1
- 241000702221 Cystoviridae Species 0.000 description 1
- 102000004127 Cytokines Human genes 0.000 description 1
- HMFHBZSHGGEWLO-SOOFDHNKSA-N D-ribofuranose Chemical group OC[C@H]1OC(O)[C@H](O)[C@@H]1O HMFHBZSHGGEWLO-SOOFDHNKSA-N 0.000 description 1
- 108010061982 DNA Ligases Proteins 0.000 description 1
- 102000012410 DNA Ligases Human genes 0.000 description 1
- 108010017826 DNA Polymerase I Proteins 0.000 description 1
- 102000004594 DNA Polymerase I Human genes 0.000 description 1
- 108010008286 DNA nucleotidylexotransferase Proteins 0.000 description 1
- 102100029764 DNA-directed DNA/RNA polymerase mu Human genes 0.000 description 1
- 241001135761 Deltaproteobacteria Species 0.000 description 1
- 241001533413 Deltavirus Species 0.000 description 1
- AHCYMLUZIRLXAA-SHYZEUOFSA-N Deoxyuridine 5'-triphosphate Chemical compound O1[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)C[C@@H]1N1C(=O)NC(=O)C=C1 AHCYMLUZIRLXAA-SHYZEUOFSA-N 0.000 description 1
- 241000188738 Desulfurococcales Species 0.000 description 1
- 241000615461 Dicistroviridae Species 0.000 description 1
- 241000224460 Diplomonadida Species 0.000 description 1
- 102100035813 E3 ubiquitin-protein ligase CBL Human genes 0.000 description 1
- 108050002772 E3 ubiquitin-protein ligase Mdm2 Proteins 0.000 description 1
- 102000012199 E3 ubiquitin-protein ligase Mdm2 Human genes 0.000 description 1
- 102000001301 EGF receptor Human genes 0.000 description 1
- 102100031780 Endonuclease Human genes 0.000 description 1
- 241000305071 Enterobacterales Species 0.000 description 1
- 241000588921 Enterobacteriaceae Species 0.000 description 1
- 241000194032 Enterococcus faecalis Species 0.000 description 1
- 241001148568 Epsilonproteobacteria Species 0.000 description 1
- 241000283073 Equus caballus Species 0.000 description 1
- 241001646719 Escherichia coli O157:H7 Species 0.000 description 1
- 108700024394 Exon Proteins 0.000 description 1
- 102100037091 Exonuclease V Human genes 0.000 description 1
- 108050006542 Exonuclease V Proteins 0.000 description 1
- 241000282324 Felis Species 0.000 description 1
- 241000711950 Filoviridae Species 0.000 description 1
- 241000710781 Flaviviridae Species 0.000 description 1
- YLQBMQCUIZJEEH-UHFFFAOYSA-N Furan Chemical group C=1C=COC=1 YLQBMQCUIZJEEH-UHFFFAOYSA-N 0.000 description 1
- 241000723722 Furovirus Species 0.000 description 1
- 241000701367 Fuselloviridae Species 0.000 description 1
- 102100024165 G1/S-specific cyclin-D1 Human genes 0.000 description 1
- 102100029974 GTPase HRas Human genes 0.000 description 1
- 102100039788 GTPase NRas Human genes 0.000 description 1
- 241000192128 Gammaproteobacteria Species 0.000 description 1
- 241000702463 Geminiviridae Species 0.000 description 1
- 241000224466 Giardia Species 0.000 description 1
- 241000224467 Giardia intestinalis Species 0.000 description 1
- 241001136687 Globuloviridae Species 0.000 description 1
- 241001276383 Gnathostoma spinigerum Species 0.000 description 1
- 241000205038 Halobacteriales Species 0.000 description 1
- 101710154606 Hemagglutinin Proteins 0.000 description 1
- 241000700739 Hepadnaviridae Species 0.000 description 1
- 241001122120 Hepeviridae Species 0.000 description 1
- 241000175212 Herpesvirales Species 0.000 description 1
- 241000700586 Herpesviridae Species 0.000 description 1
- 101710121996 Hexon protein p72 Proteins 0.000 description 1
- 241000228404 Histoplasma capsulatum Species 0.000 description 1
- 241000282412 Homo Species 0.000 description 1
- 101000851181 Homo sapiens Epidermal growth factor receptor Proteins 0.000 description 1
- 101000980756 Homo sapiens G1/S-specific cyclin-D1 Proteins 0.000 description 1
- 101000584633 Homo sapiens GTPase HRas Proteins 0.000 description 1
- 101000744505 Homo sapiens GTPase NRas Proteins 0.000 description 1
- 101001064870 Homo sapiens Lon protease homolog, mitochondrial Proteins 0.000 description 1
- 101000916644 Homo sapiens Macrophage colony-stimulating factor 1 receptor Proteins 0.000 description 1
- 101001030211 Homo sapiens Myc proto-oncogene protein Proteins 0.000 description 1
- 101000585703 Homo sapiens Protein L-Myc Proteins 0.000 description 1
- 101000573199 Homo sapiens Protein PML Proteins 0.000 description 1
- 101000857677 Homo sapiens Runt-related transcription factor 1 Proteins 0.000 description 1
- 101000739160 Homo sapiens Secretoglobin family 3A member 1 Proteins 0.000 description 1
- 101000595531 Homo sapiens Serine/threonine-protein kinase pim-1 Proteins 0.000 description 1
- 101000891113 Homo sapiens T-cell acute lymphocytic leukemia protein 1 Proteins 0.000 description 1
- 101000800488 Homo sapiens T-cell leukemia homeobox protein 1 Proteins 0.000 description 1
- 101000837626 Homo sapiens Thyroid hormone receptor alpha Proteins 0.000 description 1
- 101000813738 Homo sapiens Transcription factor ETV6 Proteins 0.000 description 1
- 101000823316 Homo sapiens Tyrosine-protein kinase ABL1 Proteins 0.000 description 1
- 101000912503 Homo sapiens Tyrosine-protein kinase Fgr Proteins 0.000 description 1
- 241000724309 Hordeivirus Species 0.000 description 1
- 241000701085 Human alphaherpesvirus 3 Species 0.000 description 1
- 241000713772 Human immunodeficiency virus 1 Species 0.000 description 1
- 241000701806 Human papillomavirus Species 0.000 description 1
- 241001533448 Hypoviridae Species 0.000 description 1
- 101150005343 INHA gene Proteins 0.000 description 1
- 241001533403 Idaeovirus Species 0.000 description 1
- 241000615454 Iflavirus Species 0.000 description 1
- DGAQECJNVWCQMB-PUAWFVPOSA-M Ilexoside XXIX Chemical compound C[C@@H]1CC[C@@]2(CC[C@@]3(C(=CC[C@H]4[C@]3(CC[C@@H]5[C@@]4(CC[C@@H](C5(C)C)OS(=O)(=O)[O-])C)C)[C@@H]2[C@]1(C)O)C)C(=O)O[C@H]6[C@@H]([C@H]([C@@H]([C@H](O6)CO)O)O)O.[Na+] DGAQECJNVWCQMB-PUAWFVPOSA-M 0.000 description 1
- 241000702394 Inoviridae Species 0.000 description 1
- 108010061833 Integrases Proteins 0.000 description 1
- 108090001005 Interleukin-6 Proteins 0.000 description 1
- 241000701377 Iridoviridae Species 0.000 description 1
- 241000764238 Isis Species 0.000 description 1
- 241000701460 JC polyomavirus Species 0.000 description 1
- 241000222712 Kinetoplastida Species 0.000 description 1
- 206010061259 Klebsiella infection Diseases 0.000 description 1
- 208000024233 Klebsiella infectious disease Diseases 0.000 description 1
- 241001112724 Lactobacillales Species 0.000 description 1
- 241000186673 Lactobacillus delbrueckii Species 0.000 description 1
- 240000002605 Lactobacillus helveticus Species 0.000 description 1
- 235000013967 Lactobacillus helveticus Nutrition 0.000 description 1
- 101100460473 Lactococcus lactis subsp. lactis nisP gene Proteins 0.000 description 1
- 101710128836 Large T antigen Proteins 0.000 description 1
- 241000589248 Legionella Species 0.000 description 1
- 241000714210 Leviviridae Species 0.000 description 1
- 241000701365 Lipothrixviridae Species 0.000 description 1
- 241000253097 Luteoviridae Species 0.000 description 1
- 241000712899 Lymphocytic choriomeningitis mammarenavirus Species 0.000 description 1
- 108700012912 MYCN Proteins 0.000 description 1
- 101150022024 MYCN gene Proteins 0.000 description 1
- 102100028198 Macrophage colony-stimulating factor 1 receptor Human genes 0.000 description 1
- 101710125418 Major capsid protein Proteins 0.000 description 1
- 241000175209 Malacoherpesviridae Species 0.000 description 1
- 241001661687 Marnaviridae Species 0.000 description 1
- 238000007476 Maximum Likelihood Methods 0.000 description 1
- 241000203067 Methanobacteriales Species 0.000 description 1
- 241000203361 Methanococcales Species 0.000 description 1
- 241000959683 Methanopyrales Species 0.000 description 1
- 241000359380 Methanosarcinales Species 0.000 description 1
- RJQXTJLFIWVMTO-TYNCELHUSA-N Methicillin Chemical compound COC1=CC=CC(OC)=C1C(=O)N[C@@H]1C(=O)N2[C@@H](C(O)=O)C(C)(C)S[C@@H]21 RJQXTJLFIWVMTO-TYNCELHUSA-N 0.000 description 1
- 108060004795 Methyltransferase Proteins 0.000 description 1
- 241000243190 Microsporidia Species 0.000 description 1
- 241000702318 Microviridae Species 0.000 description 1
- 241000186187 Mimiviridae Species 0.000 description 1
- 241000711513 Mononegavirales Species 0.000 description 1
- 241000588621 Moraxella Species 0.000 description 1
- 241000588655 Moraxella catarrhalis Species 0.000 description 1
- 102100025725 Mothers against decapentaplegic homolog 4 Human genes 0.000 description 1
- 101100128278 Mus musculus Lins1 gene Proteins 0.000 description 1
- 101100107522 Mus musculus Slc1a5 gene Proteins 0.000 description 1
- 102100038895 Myc proto-oncogene protein Human genes 0.000 description 1
- 241000545499 Mycobacterium avium-intracellulare Species 0.000 description 1
- 241001646722 Mycobacterium tuberculosis CDC1551 Species 0.000 description 1
- 241000385073 Mycobacterium tuberculosis F11 Species 0.000 description 1
- 241001049988 Mycobacterium tuberculosis H37Ra Species 0.000 description 1
- 241001646725 Mycobacterium tuberculosis H37Rv Species 0.000 description 1
- 108700035964 Mycobacterium tuberculosis HsaD Proteins 0.000 description 1
- 241001580620 Mycobacterium tuberculosis KZN 1435 Species 0.000 description 1
- 241000701553 Myoviridae Species 0.000 description 1
- 108700026495 N-Myc Proto-Oncogene Proteins 0.000 description 1
- MKWKNSIESPFAQN-UHFFFAOYSA-N N-cyclohexyl-2-aminoethanesulfonic acid Chemical compound OS(=O)(=O)CCNC1CCCCC1 MKWKNSIESPFAQN-UHFFFAOYSA-N 0.000 description 1
- 102100030124 N-myc proto-oncogene protein Human genes 0.000 description 1
- 241000224438 Naegleria fowleri Species 0.000 description 1
- 241001437658 Nanoarchaeota Species 0.000 description 1
- 241001336717 Nanoviridae Species 0.000 description 1
- 241001112477 Narnaviridae Species 0.000 description 1
- 241000588652 Neisseria gonorrhoeae Species 0.000 description 1
- 241000588650 Neisseria meningitidis Species 0.000 description 1
- 241000244206 Nematoda Species 0.000 description 1
- 102000005348 Neuraminidase Human genes 0.000 description 1
- 108010006232 Neuraminidase Proteins 0.000 description 1
- 241001292005 Nidovirales Species 0.000 description 1
- 241001484257 Nimaviridae Species 0.000 description 1
- 241000723741 Nodaviridae Species 0.000 description 1
- GFRROZIJVHUSKZ-FXGMSQOLSA-N OS I Natural products C[C@@H]1O[C@@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@@H](OC[C@@H](O)[C@@H](O)[C@@H](O)CO)[C@@H]2NC(=O)C)[C@H](O)[C@H](O)[C@H]1O GFRROZIJVHUSKZ-FXGMSQOLSA-N 0.000 description 1
- 240000007182 Ochroma pyramidale Species 0.000 description 1
- 101150101537 Olah gene Proteins 0.000 description 1
- 108020005187 Oligonucleotide Probes Proteins 0.000 description 1
- 108700020796 Oncogene Proteins 0.000 description 1
- 102000043276 Oncogene Human genes 0.000 description 1
- 241000015083 Ophiovirus Species 0.000 description 1
- 241000712464 Orthomyxoviridae Species 0.000 description 1
- 240000007594 Oryza sativa Species 0.000 description 1
- 235000007164 Oryza sativa Nutrition 0.000 description 1
- 241001112506 Ourmiavirus Species 0.000 description 1
- 101710093908 Outer capsid protein VP4 Proteins 0.000 description 1
- 101710135467 Outer capsid protein sigma-1 Proteins 0.000 description 1
- 238000012408 PCR amplification Methods 0.000 description 1
- 238000002944 PCR assay Methods 0.000 description 1
- 229910019142 PO4 Inorganic materials 0.000 description 1
- 241001631646 Papillomaviridae Species 0.000 description 1
- 241000711504 Paramyxoviridae Species 0.000 description 1
- 241000710936 Partitiviridae Species 0.000 description 1
- 241000701945 Parvoviridae Species 0.000 description 1
- 241000606860 Pasteurella Species 0.000 description 1
- 241000264850 Pecluvirus Species 0.000 description 1
- 108091005804 Peptidases Proteins 0.000 description 1
- 108091093037 Peptide nucleic acid Proteins 0.000 description 1
- 241000150350 Peribunyaviridae Species 0.000 description 1
- 201000005702 Pertussis Diseases 0.000 description 1
- 241001326562 Pezizomycotina Species 0.000 description 1
- 241000701253 Phycodnaviridae Species 0.000 description 1
- ZYFVNVRFVHJEIU-UHFFFAOYSA-N PicoGreen Chemical compound CN(C)CCCN(CCCN(C)C)C1=CC(=CC2=[N+](C3=CC=CC=C3S2)C)C2=CC=CC=C2N1C1=CC=CC=C1 ZYFVNVRFVHJEIU-UHFFFAOYSA-N 0.000 description 1
- 241001144416 Picornavirales Species 0.000 description 1
- 241000709664 Picornaviridae Species 0.000 description 1
- 241000701369 Plasmaviridae Species 0.000 description 1
- 241000702072 Podoviridae Species 0.000 description 1
- 241000701374 Polydnaviridae Species 0.000 description 1
- 241001631648 Polyomaviridae Species 0.000 description 1
- 241001112830 Pomovirus Species 0.000 description 1
- 241001533393 Potyviridae Species 0.000 description 1
- 241000700625 Poxviridae Species 0.000 description 1
- 241000288906 Primates Species 0.000 description 1
- 239000004365 Protease Substances 0.000 description 1
- 101710176177 Protein A56 Proteins 0.000 description 1
- 102100030128 Protein L-Myc Human genes 0.000 description 1
- 102100026375 Protein PML Human genes 0.000 description 1
- 208000022274 Proteus Infections Diseases 0.000 description 1
- 208000011501 Proteus infectious disease Diseases 0.000 description 1
- 241000576783 Providencia alcalifaciens Species 0.000 description 1
- 241000588777 Providencia rettgeri Species 0.000 description 1
- 241000043392 Providencia rustigianii Species 0.000 description 1
- 241000205156 Pyrococcus furiosus Species 0.000 description 1
- 108010009460 RNA Polymerase II Proteins 0.000 description 1
- 241000702247 Reoviridae Species 0.000 description 1
- 241000712907 Retroviridae Species 0.000 description 1
- 102100037486 Reverse transcriptase/ribonuclease H Human genes 0.000 description 1
- 241000711931 Rhabdoviridae Species 0.000 description 1
- PYMYPHUHKUWMLA-LMVFSUKVSA-N Ribose Natural products OC[C@@H](O)[C@@H](O)[C@@H](O)C=O PYMYPHUHKUWMLA-LMVFSUKVSA-N 0.000 description 1
- 241000606651 Rickettsiales Species 0.000 description 1
- 241000283984 Rodentia Species 0.000 description 1
- 241001534527 Roniviridae Species 0.000 description 1
- 241000040592 Rudiviridae Species 0.000 description 1
- 102100025373 Runt-related transcription factor 1 Human genes 0.000 description 1
- 101150019443 SMAD4 gene Proteins 0.000 description 1
- 241001326564 Saccharomycotina Species 0.000 description 1
- 241001596272 Sadwavirus Species 0.000 description 1
- 241000607356 Salmonella enterica subsp. arizonae Species 0.000 description 1
- 241000789939 Salmonella enterica subsp. enterica serovar Agona str. SL483 Species 0.000 description 1
- 241001617476 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 Species 0.000 description 1
- 241000125693 Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853 Species 0.000 description 1
- 241000458510 Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 Species 0.000 description 1
- 241000458513 Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 Species 0.000 description 1
- 241000789937 Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 Species 0.000 description 1
- 241001340628 Salmonella enterica subsp. enterica serovar Newport str. SL254 Species 0.000 description 1
- 241000531795 Salmonella enterica subsp. enterica serovar Paratyphi A Species 0.000 description 1
- 241001175683 Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 Species 0.000 description 1
- 241000242340 Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7 Species 0.000 description 1
- 241001551912 Salmonella enterica subsp. enterica serovar Paratyphi C str. RKS4594 Species 0.000 description 1
- 241000671018 Salmonella enterica subsp. enterica serovar Schwarzengrund Species 0.000 description 1
- 241000225553 Salmonella enterica subsp. enterica serovar Typhi str. CT18 Species 0.000 description 1
- 241001248470 Salmonella enterica subsp. enterica serovar Typhi str. Ty2 Species 0.000 description 1
- 241001053778 Salterprovirus Species 0.000 description 1
- 101000702553 Schistosoma mansoni Antigen Sm21.7 Proteins 0.000 description 1
- 101000714192 Schistosoma mansoni Tegument antigen Proteins 0.000 description 1
- 241001326539 Schizosaccharomycetes Species 0.000 description 1
- 102100037268 Secretoglobin family 3A member 1 Human genes 0.000 description 1
- 206010040047 Sepsis Diseases 0.000 description 1
- 238000012300 Sequence Analysis Methods 0.000 description 1
- 102100036077 Serine/threonine-protein kinase pim-1 Human genes 0.000 description 1
- 241000607720 Serratia Species 0.000 description 1
- 241000607768 Shigella Species 0.000 description 1
- 241000607760 Shigella sonnei Species 0.000 description 1
- 108020004682 Single-Stranded DNA Proteins 0.000 description 1
- 241000702202 Siphoviridae Species 0.000 description 1
- 108700031298 Smad4 Proteins 0.000 description 1
- 241000710119 Sobemovirus Species 0.000 description 1
- 241000589970 Spirochaetales Species 0.000 description 1
- 241000191963 Staphylococcus epidermidis Species 0.000 description 1
- 241001466451 Stramenopiles Species 0.000 description 1
- 201000005010 Streptococcus pneumonia Diseases 0.000 description 1
- 241000273172 Streptococcus pneumoniae 70585 Species 0.000 description 1
- 241000823701 Streptococcus pneumoniae ATCC 700669 Species 0.000 description 1
- 241000727755 Streptococcus pneumoniae CGSP14 Species 0.000 description 1
- 241000130810 Streptococcus pneumoniae D39 Species 0.000 description 1
- 241000674319 Streptococcus pneumoniae G54 Species 0.000 description 1
- 241000271750 Streptococcus pneumoniae Hungary19A-6 Species 0.000 description 1
- 241000273161 Streptococcus pneumoniae JJA Species 0.000 description 1
- 241000273164 Streptococcus pneumoniae P1031 Species 0.000 description 1
- 241000694196 Streptococcus pneumoniae R6 Species 0.000 description 1
- 241000683224 Streptococcus pneumoniae TIGR4 Species 0.000 description 1
- 241000271753 Streptococcus pneumoniae Taiwan19F-14 Species 0.000 description 1
- 241000193996 Streptococcus pyogenes Species 0.000 description 1
- 241000205074 Sulfolobales Species 0.000 description 1
- 102100040365 T-cell acute lymphocytic leukemia protein 1 Human genes 0.000 description 1
- 102100033111 T-cell leukemia homeobox protein 1 Human genes 0.000 description 1
- 241000701521 Tectiviridae Species 0.000 description 1
- 241000724318 Tenuivirus Species 0.000 description 1
- 241000204969 Thermococcales Species 0.000 description 1
- 241000204668 Thermoplasmatales Species 0.000 description 1
- 241000205177 Thermoproteales Species 0.000 description 1
- 102100028702 Thyroid hormone receptor alpha Human genes 0.000 description 1
- 241000723848 Tobamovirus Species 0.000 description 1
- 241000723717 Tobravirus Species 0.000 description 1
- 241000710924 Togaviridae Species 0.000 description 1
- 241001533336 Tombusviridae Species 0.000 description 1
- 241000710915 Totiviridae Species 0.000 description 1
- 102100039580 Transcription factor ETV6 Human genes 0.000 description 1
- 241000242541 Trematoda Species 0.000 description 1
- 241000589884 Treponema pallidum Species 0.000 description 1
- 239000007983 Tris buffer Substances 0.000 description 1
- 108060008682 Tumor Necrosis Factor Proteins 0.000 description 1
- 102000044209 Tumor Suppressor Genes Human genes 0.000 description 1
- 108700025716 Tumor Suppressor Genes Proteins 0.000 description 1
- 102100040247 Tumor necrosis factor Human genes 0.000 description 1
- 241001059845 Tymoviridae Species 0.000 description 1
- 102100022596 Tyrosine-protein kinase ABL1 Human genes 0.000 description 1
- 102100026150 Tyrosine-protein kinase Fgr Human genes 0.000 description 1
- 241001533358 Umbravirus Species 0.000 description 1
- 241000202898 Ureaplasma Species 0.000 description 1
- 206010046367 Ureaplasma infections Diseases 0.000 description 1
- 208000025833 Ureaplasma urethritis Diseases 0.000 description 1
- 241000607598 Vibrio Species 0.000 description 1
- 241000607626 Vibrio cholerae Species 0.000 description 1
- 108020005202 Viral DNA Proteins 0.000 description 1
- 241000520892 Xanthomonas axonopodis Species 0.000 description 1
- 241000204362 Xylella fastidiosa Species 0.000 description 1
- 241000607447 Yersinia enterocolitica Species 0.000 description 1
- 241000607477 Yersinia pseudotuberculosis Species 0.000 description 1
- 241000758405 Zoopagomycotina Species 0.000 description 1
- 230000005856 abnormality Effects 0.000 description 1
- 150000007513 acids Chemical class 0.000 description 1
- 239000008186 active pharmaceutical agent Substances 0.000 description 1
- 229940092980 adalat Drugs 0.000 description 1
- 230000006978 adaptation Effects 0.000 description 1
- 108700010877 adenoviridae proteins Proteins 0.000 description 1
- 238000001261 affinity purification Methods 0.000 description 1
- 239000011543 agarose gel Substances 0.000 description 1
- 239000004191 allura red AC Substances 0.000 description 1
- HMFHBZSHGGEWLO-UHFFFAOYSA-N alpha-D-Furanose-Ribose Natural products OCC1OC(O)C(O)C1O HMFHBZSHGGEWLO-UHFFFAOYSA-N 0.000 description 1
- 125000003277 amino group Chemical group 0.000 description 1
- 239000003242 anti bacterial agent Substances 0.000 description 1
- 229940088710 antibiotic agent Drugs 0.000 description 1
- 230000014102 antigen processing and presentation of exogenous peptide antigen via MHC class I Effects 0.000 description 1
- 239000007864 aqueous solution Substances 0.000 description 1
- 238000013528 artificial neural network Methods 0.000 description 1
- 239000002956 ash Substances 0.000 description 1
- 101150090348 atpC gene Proteins 0.000 description 1
- 230000003190 augmentative effect Effects 0.000 description 1
- 238000003287 bathing Methods 0.000 description 1
- 238000013476 bayesian approach Methods 0.000 description 1
- 235000013405 beer Nutrition 0.000 description 1
- 101150035306 bexA gene Proteins 0.000 description 1
- 229960000074 biopharmaceutical Drugs 0.000 description 1
- 229920001222 biopolymer Polymers 0.000 description 1
- 238000001369 bisulfite sequencing Methods 0.000 description 1
- 230000036770 blood supply Effects 0.000 description 1
- 210000000988 bone and bone Anatomy 0.000 description 1
- 244000309464 bull Species 0.000 description 1
- 238000004364 calculation method Methods 0.000 description 1
- 238000011088 calibration curve Methods 0.000 description 1
- 229910052799 carbon Inorganic materials 0.000 description 1
- 238000004113 cell culture Methods 0.000 description 1
- 238000002512 chemotherapy Methods 0.000 description 1
- 229960003405 ciprofloxacin Drugs 0.000 description 1
- 235000020971 citrus fruits Nutrition 0.000 description 1
- 201000003486 coccidioidomycosis Diseases 0.000 description 1
- 230000001427 coherent effect Effects 0.000 description 1
- 210000003022 colostrum Anatomy 0.000 description 1
- 235000021277 colostrum Nutrition 0.000 description 1
- 230000000052 comparative effect Effects 0.000 description 1
- 238000000205 computational method Methods 0.000 description 1
- 210000002808 connective tissue Anatomy 0.000 description 1
- 230000001276 controlling effect Effects 0.000 description 1
- 238000012937 correction Methods 0.000 description 1
- 230000008878 coupling Effects 0.000 description 1
- 238000010168 coupling process Methods 0.000 description 1
- 238000005859 coupling reaction Methods 0.000 description 1
- 101150059761 ctrA gene Proteins 0.000 description 1
- 230000001351 cycling effect Effects 0.000 description 1
- SPTYHKZRPFATHJ-HYZXJONISA-N dT6 Chemical compound O=C1NC(=O)C(C)=CN1[C@@H]1O[C@H](COP(O)(=O)O[C@@H]2[C@H](O[C@H](C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=O)O[C@@H]2[C@H](O[C@H](C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=O)O[C@@H]2[C@H](O[C@H](C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=O)O[C@@H]2[C@H](O[C@H](C2)N2C(NC(=O)C(C)=C2)=O)COP(O)(=O)O[C@@H]2[C@H](O[C@H](C2)N2C(NC(=O)C(C)=C2)=O)CO)[C@@H](O)C1 SPTYHKZRPFATHJ-HYZXJONISA-N 0.000 description 1
- 230000003247 decreasing effect Effects 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 230000018109 developmental process Effects 0.000 description 1
- 238000010790 dilution Methods 0.000 description 1
- 239000012895 dilution Substances 0.000 description 1
- 238000006471 dimerization reaction Methods 0.000 description 1
- 206010013023 diphtheria Diseases 0.000 description 1
- 238000009510 drug design Methods 0.000 description 1
- 235000013601 eggs Nutrition 0.000 description 1
- 210000001900 endoderm Anatomy 0.000 description 1
- 230000002708 enhancing effect Effects 0.000 description 1
- 229940032049 enterococcus faecalis Drugs 0.000 description 1
- 230000000369 enteropathogenic effect Effects 0.000 description 1
- 230000000688 enterotoxigenic effect Effects 0.000 description 1
- 210000000981 epithelium Anatomy 0.000 description 1
- 239000000284 extract Substances 0.000 description 1
- 230000001605 fetal effect Effects 0.000 description 1
- 210000002950 fibroblast Anatomy 0.000 description 1
- 101150015947 fimH gene Proteins 0.000 description 1
- 102000034287 fluorescent proteins Human genes 0.000 description 1
- 108091006047 fluorescent proteins Proteins 0.000 description 1
- 238000007672 fourth generation sequencing Methods 0.000 description 1
- 230000008014 freezing Effects 0.000 description 1
- 238000007710 freezing Methods 0.000 description 1
- 230000004927 fusion Effects 0.000 description 1
- 101150036031 gD gene Proteins 0.000 description 1
- 101150020597 gG gene Proteins 0.000 description 1
- 230000002496 gastric effect Effects 0.000 description 1
- 230000002068 genetic effect Effects 0.000 description 1
- 244000037671 genetically modified crops Species 0.000 description 1
- 230000013595 glycosylation Effects 0.000 description 1
- 238000006206 glycosylation reaction Methods 0.000 description 1
- PCHJSUWPFVWCPO-UHFFFAOYSA-N gold Chemical compound [Au] PCHJSUWPFVWCPO-UHFFFAOYSA-N 0.000 description 1
- 239000010931 gold Substances 0.000 description 1
- 229910052737 gold Inorganic materials 0.000 description 1
- 210000002149 gonad Anatomy 0.000 description 1
- 101150013736 gyrB gene Proteins 0.000 description 1
- 229940047650 haemophilus influenzae Drugs 0.000 description 1
- 229940045808 haemophilus influenzae type b Drugs 0.000 description 1
- LNEPOXFFQSENCJ-UHFFFAOYSA-N haloperidol Chemical compound C1CC(O)(C=2C=CC(Cl)=CC=2)CCN1CCCC(=O)C1=CC=C(F)C=C1 LNEPOXFFQSENCJ-UHFFFAOYSA-N 0.000 description 1
- 230000036541 health Effects 0.000 description 1
- 210000002216 heart Anatomy 0.000 description 1
- 229910052739 hydrogen Inorganic materials 0.000 description 1
- 239000001257 hydrogen Substances 0.000 description 1
- 208000021319 infantile-onset periodic fever-panniculitis-dermatosis syndrome Diseases 0.000 description 1
- 208000037797 influenza A Diseases 0.000 description 1
- 208000037798 influenza B Diseases 0.000 description 1
- 239000004615 ingredient Substances 0.000 description 1
- 239000003112 inhibitor Substances 0.000 description 1
- 210000000936 intestine Anatomy 0.000 description 1
- 150000002500 ions Chemical class 0.000 description 1
- 229960003350 isoniazid Drugs 0.000 description 1
- QRXWMOHMRWLFEY-UHFFFAOYSA-N isoniazide Chemical compound NNC(=O)C1=CC=NC=C1 QRXWMOHMRWLFEY-UHFFFAOYSA-N 0.000 description 1
- 210000003734 kidney Anatomy 0.000 description 1
- 229940054346 lactobacillus helveticus Drugs 0.000 description 1
- 230000000670 limiting effect Effects 0.000 description 1
- 239000007788 liquid Substances 0.000 description 1
- 210000004185 liver Anatomy 0.000 description 1
- 244000144972 livestock Species 0.000 description 1
- 210000004072 lung Anatomy 0.000 description 1
- 210000002751 lymph Anatomy 0.000 description 1
- 210000003563 lymphoid tissue Anatomy 0.000 description 1
- 210000001161 mammalian embryo Anatomy 0.000 description 1
- 238000013507 mapping Methods 0.000 description 1
- 238000005259 measurement Methods 0.000 description 1
- 210000003716 mesoderm Anatomy 0.000 description 1
- 108020004999 messenger RNA Proteins 0.000 description 1
- 229910021645 metal ion Inorganic materials 0.000 description 1
- 229960003085 meticillin Drugs 0.000 description 1
- 239000002679 microRNA Substances 0.000 description 1
- 244000005700 microbiome Species 0.000 description 1
- 244000005706 microflora Species 0.000 description 1
- 239000008267 milk Substances 0.000 description 1
- 235000013336 milk Nutrition 0.000 description 1
- 210000004080 milk Anatomy 0.000 description 1
- 238000010369 molecular cloning Methods 0.000 description 1
- HYIMSNHJOBLJNT-UHFFFAOYSA-N nifedipine Chemical compound COC(=O)C1=C(C)NC(C)=C(C(=O)OC)C1C1=CC=CC=C1[N+]([O-])=O HYIMSNHJOBLJNT-UHFFFAOYSA-N 0.000 description 1
- 238000003499 nucleic acid array Methods 0.000 description 1
- 239000002751 oligonucleotide probe Substances 0.000 description 1
- 210000000056 organ Anatomy 0.000 description 1
- 239000005416 organic matter Substances 0.000 description 1
- VSZGPKBBMSAYNT-RRFJBIMHSA-N oseltamivir Chemical compound CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](N)C1 VSZGPKBBMSAYNT-RRFJBIMHSA-N 0.000 description 1
- 229960003752 oseltamivir Drugs 0.000 description 1
- 210000000496 pancreas Anatomy 0.000 description 1
- 101150073755 papX gene Proteins 0.000 description 1
- 230000003071 parasitic effect Effects 0.000 description 1
- 230000036961 partial effect Effects 0.000 description 1
- 239000008188 pellet Substances 0.000 description 1
- 230000002093 peripheral effect Effects 0.000 description 1
- 239000010452 phosphate Substances 0.000 description 1
- 210000002381 plasma Anatomy 0.000 description 1
- 210000004910 pleural fluid Anatomy 0.000 description 1
- 101150063938 ply gene Proteins 0.000 description 1
- 238000006116 polymerization reaction Methods 0.000 description 1
- 239000004323 potassium nitrate Substances 0.000 description 1
- 238000004321 preservation Methods 0.000 description 1
- 230000037452 priming Effects 0.000 description 1
- 239000006041 probiotic Substances 0.000 description 1
- 230000000529 probiotic effect Effects 0.000 description 1
- 235000018291 probiotics Nutrition 0.000 description 1
- 230000001915 proofreading effect Effects 0.000 description 1
- 238000003908 quality control method Methods 0.000 description 1
- 238000004445 quantitative analysis Methods 0.000 description 1
- 238000010791 quenching Methods 0.000 description 1
- 230000000171 quenching effect Effects 0.000 description 1
- 230000009257 reactivity Effects 0.000 description 1
- 230000001105 regulatory effect Effects 0.000 description 1
- 230000008439 repair process Effects 0.000 description 1
- 230000008672 reprogramming Effects 0.000 description 1
- 238000010839 reverse transcription Methods 0.000 description 1
- 238000012552 review Methods 0.000 description 1
- 125000002652 ribonucleotide group Chemical group 0.000 description 1
- 235000009566 rice Nutrition 0.000 description 1
- 229940049413 rifampicin and isoniazid Drugs 0.000 description 1
- 101150090202 rpoB gene Proteins 0.000 description 1
- 239000010979 ruby Substances 0.000 description 1
- 229910001750 ruby Inorganic materials 0.000 description 1
- 210000003296 saliva Anatomy 0.000 description 1
- 150000003839 salts Chemical class 0.000 description 1
- 238000005070 sampling Methods 0.000 description 1
- 238000007789 sealing Methods 0.000 description 1
- 238000010187 selection method Methods 0.000 description 1
- 210000000582 semen Anatomy 0.000 description 1
- 238000000926 separation method Methods 0.000 description 1
- 238000002864 sequence alignment Methods 0.000 description 1
- 210000002966 serum Anatomy 0.000 description 1
- 229940115939 shigella sonnei Drugs 0.000 description 1
- URWAJWIAIPFPJE-YFMIWBNJSA-N sisomycin Chemical compound O1C[C@@](O)(C)[C@H](NC)[C@@H](O)[C@H]1O[C@@H]1[C@@H](O)[C@H](O[C@@H]2[C@@H](CC=C(CN)O2)N)[C@@H](N)C[C@H]1N URWAJWIAIPFPJE-YFMIWBNJSA-N 0.000 description 1
- 210000002027 skeletal muscle Anatomy 0.000 description 1
- 210000003491 skin Anatomy 0.000 description 1
- 210000002460 smooth muscle Anatomy 0.000 description 1
- 229910052708 sodium Inorganic materials 0.000 description 1
- 239000008279 sol Substances 0.000 description 1
- 239000007787 solid Substances 0.000 description 1
- 238000011895 specific detection Methods 0.000 description 1
- 210000000952 spleen Anatomy 0.000 description 1
- 108010068698 spleen exonuclease Proteins 0.000 description 1
- 239000012536 storage buffer Substances 0.000 description 1
- JLKIGFTWXXRPMT-UHFFFAOYSA-N sulphamethoxazole Chemical compound O1C(C)=CC(NS(=O)(=O)C=2C=CC(N)=CC=2)=N1 JLKIGFTWXXRPMT-UHFFFAOYSA-N 0.000 description 1
- 239000013589 supplement Substances 0.000 description 1
- 230000009182 swimming Effects 0.000 description 1
- 210000001179 synovial fluid Anatomy 0.000 description 1
- 208000006379 syphilis Diseases 0.000 description 1
- 210000001138 tear Anatomy 0.000 description 1
- 210000001685 thyroid gland Anatomy 0.000 description 1
- 230000007704 transition Effects 0.000 description 1
- LENZDBCJOHFCAS-UHFFFAOYSA-N tris Chemical compound OCC(N)(CO)CO LENZDBCJOHFCAS-UHFFFAOYSA-N 0.000 description 1
- 238000011144 upstream manufacturing Methods 0.000 description 1
- 210000001635 urinary tract Anatomy 0.000 description 1
- 239000000304 virulence factor Substances 0.000 description 1
- 230000007923 virulence factor Effects 0.000 description 1
- 229940098232 yersinia enterocolitica Drugs 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
- C12Q1/701—Specific hybridization probes
- C12Q1/708—Specific hybridization probes for papilloma
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1034—Isolating an individual clone by screening libraries
- C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
- C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
- C12Q1/701—Specific hybridization probes
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- General Engineering & Computer Science (AREA)
- Analytical Chemistry (AREA)
- Genetics & Genomics (AREA)
- Immunology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Molecular Biology (AREA)
- General Health & Medical Sciences (AREA)
- Microbiology (AREA)
- Virology (AREA)
- Biomedical Technology (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Bioinformatics & Computational Biology (AREA)
- Crystallography & Structural Chemistry (AREA)
- Plant Pathology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Applications Claiming Priority (4)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US35401110P | 2010-06-11 | 2010-06-11 | |
| US37404110P | 2010-08-16 | 2010-08-16 | |
| US201161439167P | 2011-02-03 | 2011-02-03 | |
| PCT/US2011/040106 WO2011156795A2 (en) | 2010-06-11 | 2011-06-10 | Nucleic acids for multiplex organism detection and methods of use and making the same |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| SG186987A1 true SG186987A1 (en) | 2013-02-28 |
Family
ID=45098726
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| SG2013001573A SG186987A1 (en) | 2010-06-11 | 2011-06-10 | Nucleic acids for multiplex organism detection and methods of use and making the same |
Country Status (6)
| Country | Link |
|---|---|
| US (1) | US20130261196A1 (enExample) |
| EP (1) | EP2580354A4 (enExample) |
| JP (1) | JP2013531983A (enExample) |
| AU (1) | AU2011265205A1 (enExample) |
| SG (1) | SG186987A1 (enExample) |
| WO (1) | WO2011156795A2 (enExample) |
Families Citing this family (59)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US9562837B2 (en) | 2006-05-11 | 2017-02-07 | Raindance Technologies, Inc. | Systems for handling microfludic droplets |
| EP4047367A1 (en) | 2008-07-18 | 2022-08-24 | Bio-Rad Laboratories, Inc. | Method for detecting target analytes with droplet libraries |
| US12038438B2 (en) | 2008-07-18 | 2024-07-16 | Bio-Rad Laboratories, Inc. | Enzyme quantification |
| EP4484577A3 (en) | 2010-02-12 | 2025-03-26 | Bio-Rad Laboratories, Inc. | Digital analyte analysis |
| US10351905B2 (en) * | 2010-02-12 | 2019-07-16 | Bio-Rad Laboratories, Inc. | Digital analyte analysis |
| US9399797B2 (en) | 2010-02-12 | 2016-07-26 | Raindance Technologies, Inc. | Digital analyte analysis |
| WO2012112804A1 (en) | 2011-02-18 | 2012-08-23 | Raindance Technoligies, Inc. | Compositions and methods for molecular labeling |
| WO2013173795A1 (en) * | 2012-05-18 | 2013-11-21 | Pathogenica, Inc. | Realtime sequence based biosurveillance system |
| WO2013173774A2 (en) * | 2012-05-18 | 2013-11-21 | Pathogenica, Inc. | Molecular inversion probes |
| EP4414990A3 (en) | 2013-01-17 | 2024-11-06 | Personalis, Inc. | Methods and systems for genetic analysis |
| CA2901907C (en) * | 2013-02-20 | 2023-06-20 | Emory University | Methods of sequencing nucleic acids in mixtures and compositions related thereto |
| EP2971069B1 (en) | 2013-03-13 | 2018-10-17 | Illumina, Inc. | Methods and systems for aligning repetitive dna elements |
| WO2014151511A2 (en) * | 2013-03-15 | 2014-09-25 | Abbott Molecular Inc. | Systems and methods for detection of genomic copy number changes |
| US20150141257A1 (en) * | 2013-08-02 | 2015-05-21 | Roche Nimblegen, Inc. | Sequence capture method using specialized capture probes (heatseq) |
| US10508311B2 (en) | 2013-08-26 | 2019-12-17 | The Translational Genomics Research Institute | Single molecule-overlapping read analysis for minor variant mutation detection in pathogen samples |
| WO2015031689A1 (en) | 2013-08-30 | 2015-03-05 | Personalis, Inc. | Methods and systems for genomic analysis |
| WO2015071552A1 (en) * | 2013-11-18 | 2015-05-21 | Teknologian Tutkimuskeskus Vtt | Multi-unit probes with high specificity and a method of designing the same |
| CN106414775A (zh) | 2014-04-11 | 2017-02-15 | 宾夕法尼亚大学董事会 | 用于宏基因组生物标志检测的组合物和方法 |
| KR102535489B1 (ko) | 2014-06-13 | 2023-05-22 | 큐-리네아 에이비 | 미생물 검출 방법 및 특성 규명 방법 |
| EP2960818A1 (en) * | 2014-06-24 | 2015-12-30 | Institut Pasteur | Method, device, and computer program for assembling pieces of chromosomes from one or several organisms |
| US10125399B2 (en) | 2014-10-30 | 2018-11-13 | Personalis, Inc. | Methods for using mosaicism in nucleic acids sampled distal to their origin |
| TWI577803B (zh) * | 2015-01-15 | 2017-04-11 | 昕穎生醫技術股份有限公司 | 多重抗藥性結核病篩檢方法及套組 |
| GB201507026D0 (en) | 2015-04-24 | 2015-06-10 | Linea Ab Q | Medical sample transportation container |
| JP6858783B2 (ja) * | 2015-10-18 | 2021-04-14 | アフィメトリックス インコーポレイテッド | 一塩基多型及びインデルの複対立遺伝子遺伝子型決定 |
| EP3978627A1 (en) | 2016-03-25 | 2022-04-06 | Karius, Inc. | Methods using synthetic nucleic acid spike-ins |
| GB2554767A (en) | 2016-04-21 | 2018-04-11 | Q Linea Ab | Detecting and characterising a microorganism |
| US11299783B2 (en) | 2016-05-27 | 2022-04-12 | Personalis, Inc. | Methods and systems for genetic analysis |
| US10337051B2 (en) * | 2016-06-16 | 2019-07-02 | The Regents Of The University Of California | Methods and compositions for detecting a target RNA |
| MX2019003674A (es) | 2016-09-30 | 2021-01-08 | Univ California | Enzimas modificadoras de ácido nucleico guiadas por arn y métodos de uso de estas. |
| BR112019006388A2 (pt) | 2016-09-30 | 2019-06-25 | Univ California | enzimas modificadoras de ácido nucleico guiadas por rna e métodos de uso das mesmas |
| US10815525B2 (en) | 2016-12-22 | 2020-10-27 | 10X Genomics, Inc. | Methods and systems for processing polynucleotides |
| US10550429B2 (en) | 2016-12-22 | 2020-02-04 | 10X Genomics, Inc. | Methods and systems for processing polynucleotides |
| US11459603B2 (en) * | 2017-05-23 | 2022-10-04 | Rutgers, The State University Of New Jersey | Target mediated in situ signal amplification with dual interacting hairpin probes |
| WO2019028462A1 (en) | 2017-08-04 | 2019-02-07 | Billiontoone, Inc. | TARGET-ASSOCIATED MOLECULES FOR CHARACTERIZATION ASSOCIATED WITH BIOLOGICAL TARGETS |
| US11519024B2 (en) | 2017-08-04 | 2022-12-06 | Billiontoone, Inc. | Homologous genomic regions for characterization associated with biological targets |
| CN111094583A (zh) | 2017-08-04 | 2020-05-01 | 十亿至一公司 | 与生物靶相关的定量中利用靶相关分子的测序输出确定和分析 |
| WO2019089804A1 (en) | 2017-11-01 | 2019-05-09 | The Regents Of The University Of California | Casy compositions and methods of use |
| US11970719B2 (en) | 2017-11-01 | 2024-04-30 | The Regents Of The University Of California | Class 2 CRISPR/Cas compositions and methods of use |
| AU2018358051B2 (en) | 2017-11-01 | 2025-01-09 | The Regents Of The University Of California | CasZ compositions and methods of use |
| EP4650456A3 (en) | 2018-01-05 | 2026-01-21 | BillionToOne, Inc. | Quality control templates for ensuring validity of sequencing-based assays |
| SG11202007686VA (en) | 2018-02-12 | 2020-09-29 | 10X Genomics Inc | Methods characterizing multiple analytes from individual cells or cell populations |
| US11639928B2 (en) | 2018-02-22 | 2023-05-02 | 10X Genomics, Inc. | Methods and systems for characterizing analytes from individual cells or cell populations |
| WO2019169028A1 (en) | 2018-02-28 | 2019-09-06 | 10X Genomics, Inc. | Transcriptome sequencing through random ligation |
| US11959077B2 (en) | 2018-05-21 | 2024-04-16 | Battelle Memorial Institute | Methods and control compositions for sequencing |
| US10801064B2 (en) * | 2018-05-31 | 2020-10-13 | Personalis, Inc. | Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples |
| EP3830301B1 (en) | 2018-08-01 | 2024-05-22 | Mammoth Biosciences, Inc. | Programmable nuclease compositions and methods of use thereof |
| EP3833776A4 (en) | 2018-08-06 | 2022-04-27 | Billiontoone, Inc. | DILUTION MARKER FOR QUANTIFICATION OF BIOLOGICAL TARGETS |
| EP4700161A3 (en) | 2018-11-21 | 2026-03-11 | Karius, Inc. | Direct-to-library methods, systems, and compositions |
| US11441176B2 (en) | 2018-12-13 | 2022-09-13 | Battelle Memorial Institute | Methods and control compositions for a quantitative polymerase chain reaction |
| EP3931313A2 (en) | 2019-01-04 | 2022-01-05 | Mammoth Biosciences, Inc. | Programmable nuclease improvements and compositions and methods for nucleic acid amplification and detection |
| SG11202111242PA (en) | 2019-03-11 | 2021-11-29 | 10X Genomics Inc | Systems and methods for processing optically tagged beads |
| US20220389484A1 (en) * | 2019-06-06 | 2022-12-08 | Tata Consultancy Services Limited | System and method for combating infections due to pathogens belonging to phylum proteobacteria |
| CN111508561B (zh) * | 2019-07-04 | 2024-02-06 | 北京希望组生物科技有限公司 | 同源序列和同源序列中串联重复序列的检测方法、计算机可读介质和应用 |
| CN110592208B (zh) * | 2019-10-08 | 2022-05-03 | 北京诺禾致源科技股份有限公司 | 地中海贫血症三类亚型的捕获探针组合物及其应用方法和应用装置 |
| JP7470787B2 (ja) | 2019-11-05 | 2024-04-18 | パーソナリス，インコーポレイティド | 単一試料からの腫瘍純度の推定 |
| CN117015617B (zh) | 2021-02-23 | 2025-04-04 | 10X基因组学有限公司 | 基于探针的核酸和蛋白质分析 |
| EP4108783B1 (en) * | 2021-06-24 | 2024-02-21 | Miltenyi Biotec B.V. & Co. KG | Spatial sequencing with mictag |
| WO2023059654A1 (en) | 2021-10-05 | 2023-04-13 | Personalis, Inc. | Customized assays for personalized cancer monitoring |
| KR20250019610A (ko) | 2022-03-21 | 2025-02-10 | 빌리언투원, 인크. | 치료 모니터링을 위한 메틸화된 세포 유리 dna의 분자 계수 |
Family Cites Families (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20030134293A1 (en) * | 1999-11-16 | 2003-07-17 | Zhiping Liu | Method for rapid and accurate identification of microorganisms |
| DE60131903T2 (de) * | 2000-10-24 | 2008-11-27 | The Board of Trustees of the Leland S. Stanford Junior University, Palo Alto | Direkte multiplex charakterisierung von genomischer dna |
| EP1522853A4 (en) * | 2002-06-24 | 2005-10-19 | Canon Kk | DNA MICROARRAY WITH STANDARD PROBE AND KIT CONTAINING THE MICROARRAY |
| EP1756307A1 (en) * | 2004-05-20 | 2007-02-28 | Trillion Genomics Limited | Use of mass labelled probes to detect target nucleic acids using mass spectrometry |
| AU2007225238A1 (en) * | 2006-03-10 | 2007-09-20 | Wyeth | Microarray for monitoring gene expression in multiple strains of Streptococcus pneumoniae |
| US7897747B2 (en) * | 2006-05-25 | 2011-03-01 | The Board Of Trustees Of The Leland Stanford Junior University | Method to produce single stranded DNA of defined length and sequence and DNA probes produced thereby |
| EP2440251A4 (en) * | 2009-06-09 | 2013-01-16 | Defyrus Inc | INTERFERON ADMINISTRATION FOR PROPHYLAXIS AGAINST PATHOGEN INFECTION OR TREATMENT OF PATHOGEN INFECTION |
-
2011
- 2011-06-10 US US13/703,489 patent/US20130261196A1/en not_active Abandoned
- 2011-06-10 JP JP2013514408A patent/JP2013531983A/ja active Pending
- 2011-06-10 SG SG2013001573A patent/SG186987A1/en unknown
- 2011-06-10 WO PCT/US2011/040106 patent/WO2011156795A2/en not_active Ceased
- 2011-06-10 AU AU2011265205A patent/AU2011265205A1/en not_active Abandoned
- 2011-06-10 EP EP11793299.6A patent/EP2580354A4/en not_active Withdrawn
Also Published As
| Publication number | Publication date |
|---|---|
| WO2011156795A2 (en) | 2011-12-15 |
| EP2580354A4 (en) | 2013-10-30 |
| AU2011265205A1 (en) | 2013-01-31 |
| US20130261196A1 (en) | 2013-10-03 |
| JP2013531983A (ja) | 2013-08-15 |
| EP2580354A2 (en) | 2013-04-17 |
| WO2011156795A3 (en) | 2012-04-05 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| SG186987A1 (en) | Nucleic acids for multiplex organism detection and methods of use and making the same | |
| US12264357B2 (en) | Universal Sanger sequencing from next-gen sequencing amplicons | |
| CN108368542B (zh) | 用于基因组组装、单元型定相以及独立于靶标的核酸检测的方法 | |
| CN112752852A (zh) | 用于检测供体来源的细胞游离dna的方法 | |
| Pestana et al. | Early, rapid and sensitive veterinary molecular diagnostics-real time PCR applications | |
| US20150344973A1 (en) | Method and System for Detection of an Organism | |
| US20220251669A1 (en) | Compositions and methods for assessing microbial populations | |
| WO2013173774A2 (en) | Molecular inversion probes | |
| EP2788506A2 (en) | Method and system for detection of an organism | |
| JP2016520326A (ja) | マルチプレックス配列決定のための分子バーコード化 | |
| CN114269944A (zh) | 使用探针、探针分子以及包含探针的阵列组合检测基因组序列用于对生物体特异性检测 | |
| BRPI0517131B1 (pt) | Métodos para simplificar ácidos nucléicos microbiais por modificação química de citosinas | |
| JP2023519919A (ja) | 病原体を検出するためのアッセイ | |
| JP2023520590A (ja) | 病原体診断検査 | |
| US11866765B2 (en) | Composition for improving molecular barcoding efficiency and use thereof | |
| CN115916996A (zh) | 用于分析样品的系统和方法 | |
| US20260028669A1 (en) | Methods and compositions for nucleic acid analysis | |
| WO2013173795A1 (en) | Realtime sequence based biosurveillance system | |
| Commichaux et al. | Optimizing source tracking of Listeria monocytogenes with quasimetagenomics and integrated long and short read sequencing | |
| Yamana | Species-specific primer design | |
| US20220411861A1 (en) | A Multiplex Method of Preparing a Sequencing Library | |
| HK40091651A (zh) | 用於分析样品的系统和方法 | |
| TW202246525A (zh) | 基因體序列之改善之偵測及用於其之探針分子 | |
| Dwivedi et al. | Recent advances in molecular diagnostic approaches for microbial diseases | |
| CN121079433A (zh) | 用于减轻dna测序中索引跳跃的方法和组合物 |