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PMC:7143804 / 38489-43081 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
270 606-609 Gene denotes Rad Gene:6236
271 563-566 Gene denotes Rad Gene:6236
277 1223-1228 Chemical denotes water MESH:D014867
278 1324-1329 Chemical denotes water MESH:D014867
279 1525-1533 Chemical denotes EvaGreen
280 1826-1831 Chemical denotes water MESH:D014867
281 2170-2175 Chemical denotes water MESH:D014867
285 2349-2351 Chemical denotes Au MESH:D006046
286 2481-2486 Chemical denotes water MESH:D014867
287 2540-2545 Chemical denotes water MESH:D014867
290 2979-2981 Gene denotes μL Gene:4591
291 2992-2997 Chemical denotes water MESH:D014867
296 3861-3866 Chemical denotes water MESH:D014867
297 3903-3905 Chemical denotes Au MESH:D006046
298 4006-4011 Chemical denotes water MESH:D014867
299 4213-4220 Chemical denotes cyanine

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T58 5-8 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T59 156-158 Body_part denotes V2 http://purl.org/sig/ont/fma/fma13443|http://purl.org/sig/ont/fma/fma68615
T61 159-162 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T62 312-319 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T63 705-708 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T64 1070-1072 Body_part denotes AG http://purl.org/sig/ont/fma/fma61898
T65 1148-1150 Body_part denotes V2 http://purl.org/sig/ont/fma/fma13443|http://purl.org/sig/ont/fma/fma68615
T67 1151-1154 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T68 1506-1509 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T69 2090-2092 Body_part denotes A3 http://purl.org/sig/ont/fma/fma66599
T70 2096-2104 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T71 3488-3491 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T72 3660-3668 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T73 4176-4179 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T74 4266-4269 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T75 4332-4335 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 1054-1058 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T8 1449-1453 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T9 1568-1572 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T10 1793-1797 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T11 1937-1941 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T12 2135-2139 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T13 3631-3635 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T35 2989-2991 Disease denotes DI http://purl.obolibrary.org/obo/MONDO_0018849

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T258 280-282 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T259 320-328 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T260 344-345 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T261 376-377 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T262 404-410 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T263 544-545 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T264 791-792 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T265 879-881 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T266 1054-1058 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T267 1288-1290 http://purl.obolibrary.org/obo/UBERON_0003064 denotes im
T268 1383-1384 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T269 1449-1453 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T270 1568-1572 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T271 1587-1588 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T272 1746-1747 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T273 1793-1797 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T274 1815-1816 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T275 1937-1941 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T276 2090-2092 http://purl.obolibrary.org/obo/CLO_0001577 denotes A3
T277 2135-2139 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T278 2499-2503 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T279 2529-2530 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T280 2614-2615 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T281 2714-2715 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T282 2929-2934 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tubes
T283 3076-3077 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T284 3184-3185 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T285 3304-3307 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T286 3308-3309 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T287 3398-3404 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T288 3408-3409 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T289 3631-3635 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T290 3692-3698 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T291 4080-4086 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T292 4142-4143 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T293 4193-4194 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T294 4303-4304 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T295 4489-4490 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T238 5-8 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T239 80-83 Chemical denotes MDA http://purl.obolibrary.org/obo/CHEBI_566274
T240 159-162 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T241 207-210 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T242 312-319 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T243 418-421 Chemical denotes MDA http://purl.obolibrary.org/obo/CHEBI_566274
T244 705-708 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T245 1001-1004 Chemical denotes MDA http://purl.obolibrary.org/obo/CHEBI_566274
T246 1070-1072 Chemical denotes AG http://purl.obolibrary.org/obo/CHEBI_27569|http://purl.obolibrary.org/obo/CHEBI_40618|http://purl.obolibrary.org/obo/CHEBI_73757
T249 1151-1154 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T250 1199-1202 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T251 1223-1228 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T252 1262-1264 Chemical denotes RV http://purl.obolibrary.org/obo/CHEBI_73823
T253 1288-1290 Chemical denotes im http://purl.obolibrary.org/obo/CHEBI_30366
T254 1324-1329 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T255 1483-1490 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T256 1506-1509 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T257 1534-1537 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T258 1538-1546 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T259 1668-1671 Chemical denotes MDA http://purl.obolibrary.org/obo/CHEBI_566274
T260 1826-1831 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T261 2025-2033 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T262 2170-2175 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T263 2286-2289 Chemical denotes MDA http://purl.obolibrary.org/obo/CHEBI_566274
T264 2349-2351 Chemical denotes Au http://purl.obolibrary.org/obo/CHEBI_29287
T265 2481-2486 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T266 2540-2545 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T267 2949-2955 Chemical denotes quartz http://purl.obolibrary.org/obo/CHEBI_46727
T268 2992-2997 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T269 3028-3030 Chemical denotes MA http://purl.obolibrary.org/obo/CHEBI_474859|http://purl.obolibrary.org/obo/CHEBI_73610|http://purl.obolibrary.org/obo/CHEBI_90325
T272 3160-3167 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T273 3300-3303 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T274 3410-3417 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T275 3447-3453 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T276 3466-3472 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T277 3488-3491 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T278 3521-3528 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T279 3861-3866 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T280 3903-3905 Chemical denotes Au http://purl.obolibrary.org/obo/CHEBI_29287
T281 4006-4011 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T282 4176-4179 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T283 4234-4237 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T284 4266-4269 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T285 4278-4282 Chemical denotes dyes http://purl.obolibrary.org/obo/CHEBI_37958
T286 4332-4335 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T287 4344-4348 Chemical denotes dyes http://purl.obolibrary.org/obo/CHEBI_37958
T288 4374-4378 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T289 4484-4487 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T12 5-22 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA Amplification
T13 159-176 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T14 293-304 http://purl.obolibrary.org/obo/GO_0009056 denotes degradation
T15 705-722 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T16 1151-1168 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T298 0-4 Sentence denotes 3.5.
T299 5-22 Sentence denotes DNA Amplification
T300 23-211 Sentence denotes First, to determine the temperature window of operation, MDA reactions are performed at 25 °C and 30 °C using the Illustra GenomiPhi V2 DNA amplification kit and EvaGreen fluorescence dye.
T301 212-361 Sentence denotes From the literature, we know that this reaction does not work above 35 °C due to degradation of the protein activity in presence of a substrate [44].
T302 362-508 Sentence denotes In Figure 13, a graph of the fluorescence signal during MDA reactions at 25 °C and 30 °C, together with their non template control (NTC) is shown.
T303 509-884 Sentence denotes These reactions are carried out in a conventional Bio-Rad CFX96 Touch Real-Time PCR machine (Bio-Rad Laboratories, Inc., Hercules, CA, USA) and the results show that the chosen proof-of-principle DNA amplification reaction is temperature dependent to some extent, but that there is a wide range of temperatures at which the amplification can be performed, i.e., 25°C to 35°C.
T304 885-1000 Sentence denotes This makes the functioning of the integrated resistive heater less critical than the stability shown in Figure 11c.
T305 1001-1203 Sentence denotes MDA reactions are also performed inside an Eppendorf tube (Eppendorf AG, Hamburg, Germany) and inside the chip, again using the Illustra GenomiPhi V2 DNA amplification kit and EvaGreen fluorescence dye.
T306 1204-1318 Sentence denotes As heat supply the water bath of an IKA Rotary Evaporator RV 8V (IKA-Werke, Staufen im Breisgau, Germany) is used.
T307 1319-1422 Sentence denotes This water bath is according to its specification stable within a range of the set temperature ±0.1 °C.
T308 1423-1547 Sentence denotes The chip and an Eppendorf tube are loaded with the reaction mixture containing the DNA sample and the EvaGreen dye solution.
T309 1548-1681 Sentence denotes Here, the Eppendorf tube is serving as a control to show that the fabrication steps of the chips are not inhibiting the MDA reaction.
T310 1682-1772 Sentence denotes The inlet and outlet of the chip are sealed with the Microseal “B” PCR plate sealing foil.
T311 1773-1909 Sentence denotes The closed chip and tube are heated up in a separate water bath to 95 °C and kept at that temperature for 3 min to denaturate the dsDNA.
T312 1910-2044 Sentence denotes Subsequently, the chip and tube are cooled down by placing it in an ice bath for 5 min after which the rest of the reagents are added.
T313 2045-2107 Sentence denotes The complete mixtures are according to Table A3 in Appendix D.
T314 2108-2281 Sentence denotes After closing the chip and tube again, they are placed in the water bath of the rotary evaporater and left there for 90 min, after which the reaction is terminated at 65 °C.
T315 2282-2392 Sentence denotes The MDA is also performed inside the chip, but with the integrated Au resistive heater serving as heat source.
T316 2393-2437 Sentence denotes The set up shown schematically in Figure 12.
T317 2438-2504 Sentence denotes The same procedure is followed as with the water bath heated test.
T318 2505-2551 Sentence denotes Denaturation is done in a separate water bath.
T319 2552-2775 Sentence denotes The heater is driven by an input potential of 3.2 V to get to a temperature of 30 °C and at the end of the reaction, the system is heated up to 65 °C by applying a potential of 9.2 V in order to terminate the amplification.
T320 2776-2846 Sentence denotes In Figure 14 the logged temperature during the amplification is shown.
T321 2847-3037 Sentence denotes After the amplifications, the reaction mixtures are pipetted out of the chips and tubes and into 1 mL quartz cuvettes containing 55 μL MilliQ DI water (Merck Millipore, Burlington, MA, USA).
T322 3038-3155 Sentence denotes Fluorescence measurements are done in a Horiba Scientific FluoroMax+ spectrofluorometer to verify each amplification.
T323 3156-3331 Sentence denotes The mixture is excitated at a wavelength of 500 nm and the emission spectrum is measured at wavelengths from 510 nm to 550 nm (bounded EvaGreen dye has a peak at 525 nm [63]).
T324 3332-3492 Sentence denotes The measured spectra are normalized by subtracting the background signal of a mixture containing only the reaction buffer, the sample buffer, EvaGreen, and DNA.
T325 3493-3574 Sentence denotes No Enzyme was added to this mixture, therefore no amplification could take place.
T326 3575-3646 Sentence denotes See Figure 15 for the results obtained in the Eppendorf tube and chips.
T327 3647-3741 Sentence denotes Figure A4 in Appendix E shows the background signal which is subtracted from all measurements.
T328 3742-4017 Sentence denotes As can be seen in Figure 15, the spectra of the amplification performed inside the chip, and by applying heat with the water bath as well as with the integrated Au-resistive heater, show the same trend as the amplification performed in the Eppendorf and heated by water bath.
T329 4018-4087 Sentence denotes There is an order of magnitude difference in the fluorescence signal.
T330 4088-4180 Sentence denotes However, the fluorescence intensity cannot be used as a value to quantify the amount of DNA.
T331 4181-4321 Sentence denotes EvaGreen is a bis-intercalating cyanine fluorescence dye consisting of two monomeric DNA-binding dyes which are linked by a flexible spacer.
T332 4322-4464 Sentence denotes These two DNA-binding dyes bind each in between two base pairs, which make them simple and fast, but also nonuniform and non-specific [44,63].
T333 4465-4592 Sentence denotes However, with this dye, a simple yes-or-no answer can be obtained if the amplification took place, as can be seen in Figure 15.