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LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"303","span":{"begin":285,"end":293},"obj":"Gene"},{"id":"304","span":{"begin":98,"end":106},"obj":"Disease"},{"id":"305","span":{"begin":1241,"end":1258},"obj":"Disease"},{"id":"307","span":{"begin":1947,"end":1952},"obj":"Chemical"}],"attributes":[{"id":"A303","pred":"tao:has_database_id","subj":"303","obj":"Gene:164045"},{"id":"A304","pred":"tao:has_database_id","subj":"304","obj":"MESH:D015047"},{"id":"A305","pred":"tao:has_database_id","subj":"305","obj":"MESH:D015047"},{"id":"A307","pred":"tao:has_database_id","subj":"307","obj":"MESH:D014867"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"5. Outlook\nFuture steps, which will result in a device for early-stage detection of, for example, zoonoses, include studies on the optimization of this device for sequence specific DNA amplifications (e.g., primer design and reaction optimization), i.e., HDA or LAMP. HDA utilizes DNA helicase (an enzyme also used in vitro during DNA replication) to separate the dsDNA instead of thermal denaturation. After separation, ssDNA binding proteins hybridize on the ssDNA strands for stabilization, ensuring that the next primer will have time to bind to the ssDNA stripe and a DNA polymerase will extend the primers with the complementary bases. This method is a truly isothermal technique in which the separation of the dsDNA can be performed at the same temperature as the amplification reaction, i.e., 64 °C [9]. LAMP is more similar to MDA in the way it also uses heat to denature the dsDNA. After denaturation, a set of four primers (six can be used as well to achieve better selectivity) and a DNA polymerase is used at isothermal conditions (65 °C) to amplify the DNA [11]. When used in combination with reverse transcriptase, LAMP becomes a RNA amplification method, which could be used for RNA-containing viruses [11], like virus-based zoonoses diseases as the corona viruses [22]. Despite not being a truly isothermal technique, LAMP offers the possibility to use turbidity as detection method [76]. Such a detection method would simplify the required equipment even further as a decrease in transmitted light through the chip can be used as detection method.\nDifferent amplification techniques require different temperatures. Based on Table 1 one can conclude that a higher temperature would also give a larger temperature gradient within the system. This can be disadvantageous for amplification reactions, as optimal denaturation temperatures are in the range 92 °C to 94 °C [77]. The denaturation in this research was done in a separate water bath, so this temperature gradient was circumvented. However, when on-chip denaturation and/or another amplification technique will be used, a second step will be the optimization of the heater in order to create better temperature uniformity within the system. This can be done by using different heater geometries [26,37] or using double-sided heating [28].\nThe third step that has to be optimized in the sample collection and work-up procedure. One has to think of what kind of samples to collect in order to have the biggest chance of having the agent of the disease present in that sample (i.e., blood, mucus, saliva, etc.). Such crude samples contain full cells, with the DNA present within. There are different approaches to perform cell lysis in order to extract the DNA [78]. Various components of bodily fluids, and reagents and products of the lysis are well-known to inhibit the amplification reaction [79]. However, MDA [80] and HDA [9] could also be performed on crude samples.\nA fourth step in the near-future is the development of a first prototype with all hardware integrated in a single piece of equipment. Such a device in its pure essence will consist of a battery to power the heater and detection, a chip holder to firmly keep the chip in its place, a thermocouple for real-time monitoring of the temperature, and a LED light and a photodiode. The lamp and photodiode could both be used for fluorescence measurements and turbidity measurements."}

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T14","span":{"begin":2554,"end":2559},"obj":"Body_part"},{"id":"T15","span":{"begin":2561,"end":2566},"obj":"Body_part"},{"id":"T16","span":{"begin":2568,"end":2574},"obj":"Body_part"},{"id":"T17","span":{"begin":2760,"end":2773},"obj":"Body_part"}],"attributes":[{"id":"A14","pred":"uberon_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"A15","pred":"uberon_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/UBERON_0000912"},{"id":"A16","pred":"uberon_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/UBERON_0001836"},{"id":"A17","pred":"uberon_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/UBERON_0006314"}],"text":"5. Outlook\nFuture steps, which will result in a device for early-stage detection of, for example, zoonoses, include studies on the optimization of this device for sequence specific DNA amplifications (e.g., primer design and reaction optimization), i.e., HDA or LAMP. HDA utilizes DNA helicase (an enzyme also used in vitro during DNA replication) to separate the dsDNA instead of thermal denaturation. After separation, ssDNA binding proteins hybridize on the ssDNA strands for stabilization, ensuring that the next primer will have time to bind to the ssDNA stripe and a DNA polymerase will extend the primers with the complementary bases. This method is a truly isothermal technique in which the separation of the dsDNA can be performed at the same temperature as the amplification reaction, i.e., 64 °C [9]. LAMP is more similar to MDA in the way it also uses heat to denature the dsDNA. After denaturation, a set of four primers (six can be used as well to achieve better selectivity) and a DNA polymerase is used at isothermal conditions (65 °C) to amplify the DNA [11]. When used in combination with reverse transcriptase, LAMP becomes a RNA amplification method, which could be used for RNA-containing viruses [11], like virus-based zoonoses diseases as the corona viruses [22]. Despite not being a truly isothermal technique, LAMP offers the possibility to use turbidity as detection method [76]. Such a detection method would simplify the required equipment even further as a decrease in transmitted light through the chip can be used as detection method.\nDifferent amplification techniques require different temperatures. Based on Table 1 one can conclude that a higher temperature would also give a larger temperature gradient within the system. This can be disadvantageous for amplification reactions, as optimal denaturation temperatures are in the range 92 °C to 94 °C [77]. The denaturation in this research was done in a separate water bath, so this temperature gradient was circumvented. However, when on-chip denaturation and/or another amplification technique will be used, a second step will be the optimization of the heater in order to create better temperature uniformity within the system. This can be done by using different heater geometries [26,37] or using double-sided heating [28].\nThe third step that has to be optimized in the sample collection and work-up procedure. One has to think of what kind of samples to collect in order to have the biggest chance of having the agent of the disease present in that sample (i.e., blood, mucus, saliva, etc.). Such crude samples contain full cells, with the DNA present within. There are different approaches to perform cell lysis in order to extract the DNA [78]. Various components of bodily fluids, and reagents and products of the lysis are well-known to inhibit the amplification reaction [79]. However, MDA [80] and HDA [9] could also be performed on crude samples.\nA fourth step in the near-future is the development of a first prototype with all hardware integrated in a single piece of equipment. Such a device in its pure essence will consist of a battery to power the heater and detection, a chip holder to firmly keep the chip in its place, a thermocouple for real-time monitoring of the temperature, and a LED light and a photodiode. The lamp and photodiode could both be used for fluorescence measurements and turbidity measurements."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T36","span":{"begin":98,"end":106},"obj":"Disease"},{"id":"T37","span":{"begin":1241,"end":1249},"obj":"Disease"}],"attributes":[{"id":"A36","pred":"mondo_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/MONDO_0025481"},{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0025481"}],"text":"5. Outlook\nFuture steps, which will result in a device for early-stage detection of, for example, zoonoses, include studies on the optimization of this device for sequence specific DNA amplifications (e.g., primer design and reaction optimization), i.e., HDA or LAMP. HDA utilizes DNA helicase (an enzyme also used in vitro during DNA replication) to separate the dsDNA instead of thermal denaturation. After separation, ssDNA binding proteins hybridize on the ssDNA strands for stabilization, ensuring that the next primer will have time to bind to the ssDNA stripe and a DNA polymerase will extend the primers with the complementary bases. This method is a truly isothermal technique in which the separation of the dsDNA can be performed at the same temperature as the amplification reaction, i.e., 64 °C [9]. LAMP is more similar to MDA in the way it also uses heat to denature the dsDNA. After denaturation, a set of four primers (six can be used as well to achieve better selectivity) and a DNA polymerase is used at isothermal conditions (65 °C) to amplify the DNA [11]. When used in combination with reverse transcriptase, LAMP becomes a RNA amplification method, which could be used for RNA-containing viruses [11], like virus-based zoonoses diseases as the corona viruses [22]. Despite not being a truly isothermal technique, LAMP offers the possibility to use turbidity as detection method [76]. Such a detection method would simplify the required equipment even further as a decrease in transmitted light through the chip can be used as detection method.\nDifferent amplification techniques require different temperatures. Based on Table 1 one can conclude that a higher temperature would also give a larger temperature gradient within the system. This can be disadvantageous for amplification reactions, as optimal denaturation temperatures are in the range 92 °C to 94 °C [77]. The denaturation in this research was done in a separate water bath, so this temperature gradient was circumvented. However, when on-chip denaturation and/or another amplification technique will be used, a second step will be the optimization of the heater in order to create better temperature uniformity within the system. This can be done by using different heater geometries [26,37] or using double-sided heating [28].\nThe third step that has to be optimized in the sample collection and work-up procedure. One has to think of what kind of samples to collect in order to have the biggest chance of having the agent of the disease present in that sample (i.e., blood, mucus, saliva, etc.). Such crude samples contain full cells, with the DNA present within. There are different approaches to perform cell lysis in order to extract the DNA [78]. Various components of bodily fluids, and reagents and products of the lysis are well-known to inhibit the amplification reaction [79]. However, MDA [80] and HDA [9] could also be performed on crude samples.\nA fourth step in the near-future is the development of a first prototype with all hardware integrated in a single piece of equipment. Such a device in its pure essence will consist of a battery to power the heater and detection, a chip holder to firmly keep the chip in its place, a thermocouple for real-time monitoring of the temperature, and a LED light and a photodiode. The lamp and photodiode could both be used for fluorescence measurements and turbidity measurements."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T20","span":{"begin":181,"end":199},"obj":"http://purl.obolibrary.org/obo/GO_0006277"},{"id":"T21","span":{"begin":331,"end":346},"obj":"http://purl.obolibrary.org/obo/GO_0006260"},{"id":"T22","span":{"begin":1115,"end":1128},"obj":"http://purl.obolibrary.org/obo/GO_0003968"},{"id":"T23","span":{"begin":1115,"end":1128},"obj":"http://purl.obolibrary.org/obo/GO_0003899"},{"id":"T24","span":{"begin":2698,"end":2703},"obj":"http://purl.obolibrary.org/obo/GO_0019835"},{"id":"T25","span":{"begin":2808,"end":2813},"obj":"http://purl.obolibrary.org/obo/GO_0019835"}],"text":"5. Outlook\nFuture steps, which will result in a device for early-stage detection of, for example, zoonoses, include studies on the optimization of this device for sequence specific DNA amplifications (e.g., primer design and reaction optimization), i.e., HDA or LAMP. HDA utilizes DNA helicase (an enzyme also used in vitro during DNA replication) to separate the dsDNA instead of thermal denaturation. After separation, ssDNA binding proteins hybridize on the ssDNA strands for stabilization, ensuring that the next primer will have time to bind to the ssDNA stripe and a DNA polymerase will extend the primers with the complementary bases. This method is a truly isothermal technique in which the separation of the dsDNA can be performed at the same temperature as the amplification reaction, i.e., 64 °C [9]. LAMP is more similar to MDA in the way it also uses heat to denature the dsDNA. After denaturation, a set of four primers (six can be used as well to achieve better selectivity) and a DNA polymerase is used at isothermal conditions (65 °C) to amplify the DNA [11]. When used in combination with reverse transcriptase, LAMP becomes a RNA amplification method, which could be used for RNA-containing viruses [11], like virus-based zoonoses diseases as the corona viruses [22]. Despite not being a truly isothermal technique, LAMP offers the possibility to use turbidity as detection method [76]. Such a detection method would simplify the required equipment even further as a decrease in transmitted light through the chip can be used as detection method.\nDifferent amplification techniques require different temperatures. Based on Table 1 one can conclude that a higher temperature would also give a larger temperature gradient within the system. This can be disadvantageous for amplification reactions, as optimal denaturation temperatures are in the range 92 °C to 94 °C [77]. The denaturation in this research was done in a separate water bath, so this temperature gradient was circumvented. However, when on-chip denaturation and/or another amplification technique will be used, a second step will be the optimization of the heater in order to create better temperature uniformity within the system. This can be done by using different heater geometries [26,37] or using double-sided heating [28].\nThe third step that has to be optimized in the sample collection and work-up procedure. One has to think of what kind of samples to collect in order to have the biggest chance of having the agent of the disease present in that sample (i.e., blood, mucus, saliva, etc.). Such crude samples contain full cells, with the DNA present within. There are different approaches to perform cell lysis in order to extract the DNA [78]. Various components of bodily fluids, and reagents and products of the lysis are well-known to inhibit the amplification reaction [79]. However, MDA [80] and HDA [9] could also be performed on crude samples.\nA fourth step in the near-future is the development of a first prototype with all hardware integrated in a single piece of equipment. Such a device in its pure essence will consist of a battery to power the heater and detection, a chip holder to firmly keep the chip in its place, a thermocouple for real-time monitoring of the temperature, and a LED light and a photodiode. The lamp and photodiode could both be used for fluorescence measurements and turbidity measurements."}

LitCovid-sentences

2_test

{"project":"2_test","denotations":[{"id":"32106462-15247927-69893327","span":{"begin":808,"end":809},"obj":"15247927"},{"id":"32106462-21157218-69893328","span":{"begin":1072,"end":1074},"obj":"21157218"},{"id":"32106462-21157218-69893329","span":{"begin":1219,"end":1221},"obj":"21157218"},{"id":"32106462-21479543-69893330","span":{"begin":1282,"end":1284},"obj":"21479543"},{"id":"32106462-11708792-69893331","span":{"begin":1401,"end":1403},"obj":"11708792"},{"id":"32106462-2003928-69893332","span":{"begin":1885,"end":1887},"obj":"2003928"},{"id":"32106462-9327537-69893333","span":{"begin":2868,"end":2870},"obj":"9327537"},{"id":"32106462-11959976-69893334","span":{"begin":2887,"end":2889},"obj":"11959976"},{"id":"32106462-15247927-69893335","span":{"begin":2900,"end":2901},"obj":"15247927"}],"text":"5. Outlook\nFuture steps, which will result in a device for early-stage detection of, for example, zoonoses, include studies on the optimization of this device for sequence specific DNA amplifications (e.g., primer design and reaction optimization), i.e., HDA or LAMP. HDA utilizes DNA helicase (an enzyme also used in vitro during DNA replication) to separate the dsDNA instead of thermal denaturation. After separation, ssDNA binding proteins hybridize on the ssDNA strands for stabilization, ensuring that the next primer will have time to bind to the ssDNA stripe and a DNA polymerase will extend the primers with the complementary bases. This method is a truly isothermal technique in which the separation of the dsDNA can be performed at the same temperature as the amplification reaction, i.e., 64 °C [9]. LAMP is more similar to MDA in the way it also uses heat to denature the dsDNA. After denaturation, a set of four primers (six can be used as well to achieve better selectivity) and a DNA polymerase is used at isothermal conditions (65 °C) to amplify the DNA [11]. When used in combination with reverse transcriptase, LAMP becomes a RNA amplification method, which could be used for RNA-containing viruses [11], like virus-based zoonoses diseases as the corona viruses [22]. Despite not being a truly isothermal technique, LAMP offers the possibility to use turbidity as detection method [76]. Such a detection method would simplify the required equipment even further as a decrease in transmitted light through the chip can be used as detection method.\nDifferent amplification techniques require different temperatures. Based on Table 1 one can conclude that a higher temperature would also give a larger temperature gradient within the system. This can be disadvantageous for amplification reactions, as optimal denaturation temperatures are in the range 92 °C to 94 °C [77]. The denaturation in this research was done in a separate water bath, so this temperature gradient was circumvented. However, when on-chip denaturation and/or another amplification technique will be used, a second step will be the optimization of the heater in order to create better temperature uniformity within the system. This can be done by using different heater geometries [26,37] or using double-sided heating [28].\nThe third step that has to be optimized in the sample collection and work-up procedure. One has to think of what kind of samples to collect in order to have the biggest chance of having the agent of the disease present in that sample (i.e., blood, mucus, saliva, etc.). Such crude samples contain full cells, with the DNA present within. There are different approaches to perform cell lysis in order to extract the DNA [78]. Various components of bodily fluids, and reagents and products of the lysis are well-known to inhibit the amplification reaction [79]. However, MDA [80] and HDA [9] could also be performed on crude samples.\nA fourth step in the near-future is the development of a first prototype with all hardware integrated in a single piece of equipment. Such a device in its pure essence will consist of a battery to power the heater and detection, a chip holder to firmly keep the chip in its place, a thermocouple for real-time monitoring of the temperature, and a LED light and a photodiode. The lamp and photodiode could both be used for fluorescence measurements and turbidity measurements."}

PMC:7143804 / 45442-48862 JSONTXT

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PMC:7143804 / 45442-48862 JSON TXT