Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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INTRODUCTION
1
1
[ "b1", "b2", "b7", "b8", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "b21", "b22", "b23" ]
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
How regulation of an eukaryotic-like system could occur using bacterial-like regulators remains an intriguing question, mainly from an evolutionary point of view.
[ "1", "2", "7", "8", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23" ]
162
11,200
0
false
How regulation of an eukaryotic-like system could occur using bacterial-like regulators remains an intriguing question, mainly from an evolutionary point of view.
[]
How regulation of an eukaryotic-like system could occur using bacterial-like regulators remains an intriguing question, mainly from an evolutionary point of view.
true
true
true
true
true
1,791
0
INTRODUCTION
1
1
[ "b1", "b2", "b7", "b8", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "b21", "b22", "b23" ]
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
Some of these regulators have been studied in cell-free transcription systems.
[ "1", "2", "7", "8", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23" ]
78
11,201
0
false
Some of these regulators have been studied in cell-free transcription systems.
[]
Some of these regulators have been studied in cell-free transcription systems.
true
true
true
true
true
1,791
0
INTRODUCTION
1
16
[ "b1", "b2", "b7", "b8", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "b21", "b22", "b23" ]
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
Except the transcription activators Ptr2 from Methanocaldococcus jannaschii (16), and the homologous Lrp protein Mth from Methanothermococcus thermolithotrophicus (17), these were exclusively repressors: MDR1-repressor of the ABC-transporter-gene from Archaeoglobus fulgidus (18), LrpA from Pyrococcus furiosus (19,20), ...
[ "1", "2", "7", "8", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23" ]
463
11,202
1
false
Except the transcription activators Ptr2 from Methanocaldococcus jannaschii, and the homologous Lrp protein Mth from Methanothermococcus thermolithotrophicus, these were exclusively repressors: MDR1-repressor of the ABC-transporter-gene from Archaeoglobus fulgidus, LrpA from Pyrococcus furiosus, the negatively autoregu...
[ "16", "17", "18", "19,20", "21,22", "23" ]
Except the transcription activators Ptr2 from Methanocaldococcus jannaschii, and the homologous Lrp protein Mth from Methanothermococcus thermolithotrophicus, these were exclusively repressors: MDR1-repressor of the ABC-transporter-gene from Archaeoglobus fulgidus, LrpA from Pyrococcus furiosus, the negatively autoregu...
true
true
true
true
true
1,791
0
INTRODUCTION
1
1
[ "b1", "b2", "b7", "b8", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "b21", "b22", "b23" ]
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
However, the physiological functions of most of these regulators are still unclear.
[ "1", "2", "7", "8", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23" ]
83
11,203
0
false
However, the physiological functions of most of these regulators are still unclear.
[]
However, the physiological functions of most of these regulators are still unclear.
true
true
true
true
true
1,791
0
INTRODUCTION
1
1
[ "b1", "b2", "b7", "b8", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "b21", "b22", "b23" ]
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
It would appear that a majority of trans- and cis-acting regulatory transcription factors of the Archaea still remain unknown.
[ "1", "2", "7", "8", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23" ]
126
11,204
0
false
It would appear that a majority of trans- and cis-acting regulatory transcription factors of the Archaea still remain unknown.
[]
It would appear that a majority of trans- and cis-acting regulatory transcription factors of the Archaea still remain unknown.
true
true
true
true
true
1,791
1
INTRODUCTION
1
24
[ "b24" ]
16,973,899
pmid-15516589
In a situation in which efficient genetic tools are not yet available, one possibility to study transcription regulation in hypethermophilic archaea is offered by diverse crenarchaeal virus–host systems.
[ "24" ]
203
11,205
0
false
In a situation in which efficient genetic tools are not yet available, one possibility to study transcription regulation in hypethermophilic archaea is offered by diverse crenarchaeal virus–host systems.
[]
In a situation in which efficient genetic tools are not yet available, one possibility to study transcription regulation in hypethermophilic archaea is offered by diverse crenarchaeal virus–host systems.
true
true
true
true
true
1,792
1
INTRODUCTION
1
24
[ "b24" ]
16,973,899
pmid-15516589
Although studies on transcription of the Sulfolobus virus SSV1, crucial for the identification of archaeal promoter sequences, were carried out about two decades ago, detailed analysis of transcription of viruses of hyperthermophilic crenarchaea over the replication cycle was performed only recently.
[ "24" ]
301
11,206
0
false
Although studies on transcription of the Sulfolobus virus SSV1, crucial for the identification of archaeal promoter sequences, were carried out about two decades ago, detailed analysis of transcription of viruses of hyperthermophilic crenarchaea over the replication cycle was performed only recently.
[]
Although studies on transcription of the Sulfolobus virus SSV1, crucial for the identification of archaeal promoter sequences, were carried out about two decades ago, detailed analysis of transcription of viruses of hyperthermophilic crenarchaea over the replication cycle was performed only recently.
true
true
true
true
true
1,792
1
INTRODUCTION
1
24
[ "b24" ]
16,973,899
pmid-15516589
In vivo transcription studies on the rudiviruses SIRV1 and SIRV2 infecting the hyperthermophilic crenarchaeon Sulfolobus islandicus demonstrated a rather simple and barely chronological pattern of transcription, with a few cases of temporal regulation (24).
[ "24" ]
257
11,207
1
false
In vivo transcription studies on the rudiviruses SIRV1 and SIRV2 infecting the hyperthermophilic crenarchaeon Sulfolobus islandicus demonstrated a rather simple and barely chronological pattern of transcription, with a few cases of temporal regulation.
[ "24" ]
In vivo transcription studies on the rudiviruses SIRV1 and SIRV2 infecting the hyperthermophilic crenarchaeon Sulfolobus islandicus demonstrated a rather simple and barely chronological pattern of transcription, with a few cases of temporal regulation.
true
true
true
true
true
1,792
1
INTRODUCTION
1
24
[ "b24" ]
16,973,899
pmid-15516589
SIRV promoters, similar to the host promoters, contain a TATA-box and a TFB responsive element.
[ "24" ]
95
11,208
0
false
SIRV promoters, similar to the host promoters, contain a TATA-box and a TFB responsive element.
[]
SIRV promoters, similar to the host promoters, contain a TATA-box and a TFB responsive element.
true
true
true
true
true
1,792
1
INTRODUCTION
1
24
[ "b24" ]
16,973,899
pmid-15516589
However, most of them contain an additional virus-specific consensus element.
[ "24" ]
77
11,209
0
false
However, most of them contain an additional virus-specific consensus element.
[]
However, most of them contain an additional virus-specific consensus element.
true
true
true
true
true
1,792
1
INTRODUCTION
1
24
[ "b24" ]
16,973,899
pmid-15516589
These observations suggested a major role for the host transcription machinery in the transcription of viral genomes, as well as possible involvement of virus-specific transcription factors.
[ "24" ]
190
11,210
0
false
These observations suggested a major role for the host transcription machinery in the transcription of viral genomes, as well as possible involvement of virus-specific transcription factors.
[]
These observations suggested a major role for the host transcription machinery in the transcription of viral genomes, as well as possible involvement of virus-specific transcription factors.
true
true
true
true
true
1,792
2
INTRODUCTION
0
null
null
16,973,899
pmid-2671937
Here, we report on the isolation and characterization of a host-encoded transcription regulator Sta1 involved in the activation of transcription from promoters of the crenarchaeal virus SIRV1.
null
192
11,211
0
false
null
null
Here, we report on the isolation and characterization of a host-encoded transcription regulator Sta1 involved in the activation of transcription from promoters of the crenarchaeal virus SIRV1.
true
true
true
true
true
1,793
0
DISCUSSION
0
null
null
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
In order to isolate proteins involved in transcription of genes of the Sulfolobus virus SIRV1, DNA affinity purification experiments were conducted.
null
148
11,212
0
false
null
null
In order to isolate proteins involved in transcription of genes of the Sulfolobus virus SIRV1, DNA affinity purification experiments were conducted.
true
true
true
true
true
1,794
0
DISCUSSION
0
null
null
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
With the help of three different viral promoters immobilized on magnetic beads, we isolated a 14 kDa DNA-binding protein from crude extracts of host cells.
null
155
11,213
0
false
null
null
With the help of three different viral promoters immobilized on magnetic beads, we isolated a 14 kDa DNA-binding protein from crude extracts of host cells.
true
true
true
true
true
1,794
0
DISCUSSION
0
null
null
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
All three promoters bound to the same protein, which turned out to be encoded on the chromosome of the Sulfolobus host.
null
119
11,214
0
false
null
null
All three promoters bound to the same protein, which turned out to be encoded on the chromosome of the Sulfolobus host.
true
true
true
true
true
1,794
0
DISCUSSION
0
null
null
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
When we used crude extracts from virus-infected host cells in the purification experiments, the same protein was bound to all three promoters.
null
142
11,215
0
false
null
null
When we used crude extracts from virus-infected host cells in the purification experiments, the same protein was bound to all three promoters.
true
true
true
true
true
1,794
0
DISCUSSION
0
null
null
16,973,899
pmid-11282478|pmid-7597027|pmid-380989|pmid-10400604|pmid-9184236|pmid-10556324|pmid-12675791|pmid-12692306|pmid-16230629|pmid-10635322|pmid-10973967|pmid-11809882|pmid-10900210|pmid-10049378|pmid-12381724
The protein was identified as the product of the S.islandicus homolog of the gene SSO0048 from S.solfataricus, and was named Sta1.
null
130
11,216
0
false
null
null
The protein was identified as the product of the S.islandicus homolog of the gene SSO0048 from S.solfataricus, and was named Sta1.
true
true
true
true
true
1,794
1
DISCUSSION
0
null
null
16,973,899
pmid-15516589
Analysis of Sta1, either purified from host cell extracts or recombinant, showed an activating effect on transcription from two viral promoters in in vitro transcription experiments.
null
182
11,217
0
false
null
null
Analysis of Sta1, either purified from host cell extracts or recombinant, showed an activating effect on transcription from two viral promoters in in vitro transcription experiments.
true
true
true
true
true
1,795
2
DISCUSSION
1
25
[ "b25" ]
16,973,899
pmid-2671937
Sta1 is the first archaeal transcription regulator isolated by pull-down assays (25) with archaeal promoters directly from cells.
[ "25" ]
129
11,218
1
false
Sta1 is the first archaeal transcription regulator isolated by pull-down assays with archaeal promoters directly from cells.
[ "25" ]
Sta1 is the first archaeal transcription regulator isolated by pull-down assays with archaeal promoters directly from cells.
true
true
true
true
true
1,796
2
DISCUSSION
1
25
[ "b25" ]
16,973,899
pmid-2671937
All other archaeal transcription regulators have been identified by in silico analysis.
[ "25" ]
87
11,219
0
false
All other archaeal transcription regulators have been identified by in silico analysis.
[]
All other archaeal transcription regulators have been identified by in silico analysis.
true
true
true
true
true
1,796
2
DISCUSSION
1
25
[ "b25" ]
16,973,899
pmid-2671937
Our results open possibilities for the identification of unknown proteins involved in the regulation of archaeal gene expression.
[ "25" ]
129
11,220
0
false
Our results open possibilities for the identification of unknown proteins involved in the regulation of archaeal gene expression.
[]
Our results open possibilities for the identification of unknown proteins involved in the regulation of archaeal gene expression.
true
true
true
true
true
1,796
3
DISCUSSION
0
null
null
16,973,899
null
Binding sites for Sta1 were determined by DNase I footprinting.
null
63
11,221
0
false
null
null
Binding sites for Sta1 were determined by DNase I footprinting.
true
true
true
true
true
1,797
3
DISCUSSION
0
null
null
16,973,899
null
Two distinct protected regions of ∼20 bp could be clearly identified.
null
69
11,222
0
false
null
null
Two distinct protected regions of ∼20 bp could be clearly identified.
true
true
true
true
true
1,797
3
DISCUSSION
0
null
null
16,973,899
null
One of them was located in the core promoter region and the other was ∼30 nt upstream of it.
null
92
11,223
0
false
null
null
One of them was located in the core promoter region and the other was ∼30 nt upstream of it.
true
true
true
true
true
1,797
3
DISCUSSION
0
null
null
16,973,899
null
The analysis of the protected sequences allowed us to identify the imperfect 16 bp inverted repeat which is also present in the promoter region of the SIRV1 gene 56 (Figure 7).
null
176
11,224
0
false
null
null
The analysis of the protected sequences allowed us to identify the imperfect 16 bp inverted repeat which is also present in the promoter region of the SIRV1 gene 56 (Figure 7).
true
true
true
true
true
1,797
3
DISCUSSION
0
null
null
16,973,899
null
The alignment of the identified and putative Sta1-binding sites let us to design the consensus site as ATNT-N8-A/TNAT (Figure 7).
null
129
11,225
0
false
null
null
The alignment of the identified and putative Sta1-binding sites let us to design the consensus site as ATNT-N8-A/TNAT (Figure 7).
true
true
true
true
true
1,797
3
DISCUSSION
0
null
null
16,973,899
null
Location of a binding site in immediate proximity of the TATA-box and the BRE element suggested that the activating effect of Sta1 could be associated with the TBP and/or TFB, for example, by enhancing their recruitment or by stabilization of their binding.
null
257
11,226
0
false
null
null
Location of a binding site in immediate proximity of the TATA-box and the BRE element suggested that the activating effect of Sta1 could be associated with the TBP and/or TFB, for example, by enhancing their recruitment or by stabilization of their binding.
true
true
true
true
true
1,797
3
DISCUSSION
0
null
null
16,973,899
null
To confirm the possibility of a TBP/TFB-dependent effect, we performed in vitro transcription experiments under suboptimal concentrations of TBP and TFB.
null
153
11,227
0
false
null
null
To confirm the possibility of a TBP/TFB-dependent effect, we performed in vitro transcription experiments under suboptimal concentrations of TBP and TFB.
true
true
true
true
true
1,797
3
DISCUSSION
0
null
null
16,973,899
null
The results demonstrated that in the presence of low amounts of one of the two factors, either TBP or TFB, Sta1 is necessary for transcription initiation from the assayed viral promoter, especially in the case of low amounts of TBP.
null
232
11,228
0
false
null
null
The results demonstrated that in the presence of low amounts of one of the two factors, either TBP or TFB, Sta1 is necessary for transcription initiation from the assayed viral promoter, especially in the case of low amounts of TBP.
true
true
true
true
true
1,797
4
DISCUSSION
1
16
[ "b16", "b17", "b16", "b17" ]
16,973,899
pmid-12692306|pmid-16230629|pmid-12692306|pmid-16230629
In general, mechanisms of transcription activation in archaea are poorly understood.
[ "16", "17", "16", "17" ]
84
11,229
0
false
In general, mechanisms of transcription activation in archaea are poorly understood.
[]
In general, mechanisms of transcription activation in archaea are poorly understood.
true
true
true
true
true
1,798
4
DISCUSSION
1
16
[ "b16", "b17", "b16", "b17" ]
16,973,899
pmid-12692306|pmid-16230629|pmid-12692306|pmid-16230629
Sta1 is the first transcription activator from the Crenarchaeota for which an activating effect has been directly demonstrated in in vitro studies.
[ "16", "17", "16", "17" ]
147
11,230
0
false
Sta1 is the first transcription activator from the Crenarchaeota for which an activating effect has been directly demonstrated in in vitro studies.
[]
Sta1 is the first transcription activator from the Crenarchaeota for which an activating effect has been directly demonstrated in in vitro studies.
true
true
true
true
true
1,798
4
DISCUSSION
1
16
[ "b16", "b17", "b16", "b17" ]
16,973,899
pmid-12692306|pmid-16230629|pmid-12692306|pmid-16230629
The current knowledge on the molecular basis of transcription activation in the entire archaeal domain of life is limited to results gleaned from analysis of the recently described factor Ptr2 from M.janaschii and its Lrp ortholog from M.thermolithotrophicus (16,17).
[ "16", "17", "16", "17" ]
267
11,231
0
false
The current knowledge on the molecular basis of transcription activation in the entire archaeal domain of life is limited to results gleaned from analysis of the recently described factor Ptr2 from M.janaschii and its Lrp ortholog from M.thermolithotrophicus.
[ "16,17" ]
The current knowledge on the molecular basis of transcription activation in the entire archaeal domain of life is limited to results gleaned from analysis of the recently described factor Ptr2 from M.janaschii and its Lrp ortholog from M.thermolithotrophicus.
true
true
true
true
true
1,798
4
DISCUSSION
1
16
[ "b16", "b17", "b16", "b17" ]
16,973,899
pmid-12692306|pmid-16230629|pmid-12692306|pmid-16230629
Activation by Ptr2 is generated by recruitment of the TATA-binding protein to the promoter, and conveys its stimulatory effect, in contrast to Sta1, from two upstream-located binding sites (16,17).
[ "16", "17", "16", "17" ]
197
11,232
0
false
Activation by Ptr2 is generated by recruitment of the TATA-binding protein to the promoter, and conveys its stimulatory effect, in contrast to Sta1, from two upstream-located binding sites.
[ "16,17" ]
Activation by Ptr2 is generated by recruitment of the TATA-binding protein to the promoter, and conveys its stimulatory effect, in contrast to Sta1, from two upstream-located binding sites.
true
true
true
true
true
1,798
4
DISCUSSION
1
16
[ "b16", "b17", "b16", "b17" ]
16,973,899
pmid-12692306|pmid-16230629|pmid-12692306|pmid-16230629
Significantly, Sta1 is only distantly related to Ptr2 and appears to operate by distinct mechanisms from Ptr2, facilitating transcription at limiting TBP and TFB, suggesting that it belongs to a novel class of archaeal transcriptional activators.
[ "16", "17", "16", "17" ]
246
11,233
0
false
Significantly, Sta1 is only distantly related to Ptr2 and appears to operate by distinct mechanisms from Ptr2, facilitating transcription at limiting TBP and TFB, suggesting that it belongs to a novel class of archaeal transcriptional activators.
[]
Significantly, Sta1 is only distantly related to Ptr2 and appears to operate by distinct mechanisms from Ptr2, facilitating transcription at limiting TBP and TFB, suggesting that it belongs to a novel class of archaeal transcriptional activators.
true
true
true
true
true
1,798
5
DISCUSSION
1
39
[ "b39" ]
16,973,899
pmid-15215404
Genomic analysis implies that Sta1 could represent a group of archaeal-specific transcription regulators.
[ "39" ]
105
11,234
0
false
Genomic analysis implies that Sta1 could represent a group of archaeal-specific transcription regulators.
[]
Genomic analysis implies that Sta1 could represent a group of archaeal-specific transcription regulators.
true
true
true
true
true
1,799
5
DISCUSSION
1
39
[ "b39" ]
16,973,899
pmid-15215404
Conserved domains search (39) identified an archaea-specific domain in Sta1, annotated as predicted transcription regulator (CDD 12 688).
[ "39" ]
137
11,235
1
false
Conserved domains search identified an archaea-specific domain in Sta1, annotated as predicted transcription regulator (CDD 12 688).
[ "39" ]
Conserved domains search identified an archaea-specific domain in Sta1, annotated as predicted transcription regulator (CDD 12 688).
true
true
true
true
true
1,799
5
DISCUSSION
1
39
[ "b39" ]
16,973,899
pmid-15215404
Clear homologs of Sta1, containing 120–130 amino acids, are present on all three sequenced genomes of Sulfolobus species, at least in five copies in each of them, based on an E-value threshold of 0.01.
[ "39" ]
201
11,236
0
false
Clear homologs of Sta1, containing 120–130 amino acids, are present on all three sequenced genomes of Sulfolobus species, at least in five copies in each of them, based on an E-value threshold of 0.01.
[]
Clear homologs of Sta1, containing 120–130 amino acids, are present on all three sequenced genomes of Sulfolobus species, at least in five copies in each of them, based on an E-value threshold of 0.01.
true
true
true
true
true
1,799
5
DISCUSSION
1
39
[ "b39" ]
16,973,899
pmid-15215404
However, given the small size of the protein, additional homologs may be present but not identified as significant.
[ "39" ]
115
11,237
0
false
However, given the small size of the protein, additional homologs may be present but not identified as significant.
[]
However, given the small size of the protein, additional homologs may be present but not identified as significant.
true
true
true
true
true
1,799
5
DISCUSSION
1
39
[ "b39" ]
16,973,899
pmid-15215404
Applying the same threshold, Sta1 homologs of 120–130 amino acids were also identified in many other archaeal genomes.
[ "39" ]
118
11,238
0
false
Applying the same threshold, Sta1 homologs of 120–130 amino acids were also identified in many other archaeal genomes.
[]
Applying the same threshold, Sta1 homologs of 120–130 amino acids were also identified in many other archaeal genomes.
true
true
true
true
true
1,799
5
DISCUSSION
1
39
[ "b39" ]
16,973,899
pmid-15215404
In contrast, BLAST searches against bacterial proteins reveal only a weak similarity to proteins of the MarR family.
[ "39" ]
116
11,239
0
false
In contrast, BLAST searches against bacterial proteins reveal only a weak similarity to proteins of the MarR family.
[]
In contrast, BLAST searches against bacterial proteins reveal only a weak similarity to proteins of the MarR family.
true
true
true
true
true
1,799
5
DISCUSSION
1
39
[ "b39" ]
16,973,899
pmid-15215404
No evident homologs of Sta1 were found in eukaryotes.
[ "39" ]
53
11,240
0
false
No evident homologs of Sta1 were found in eukaryotes.
[]
No evident homologs of Sta1 were found in eukaryotes.
true
true
true
true
true
1,799
6
DISCUSSION
1
37
[ "b37", "b15", "b19", "b22", "b40", "b41", "b38", "b38", "b42" ]
16,973,899
pmid-11427726|pmid-12675791|pmid-10973967|pmid-10049378|pmid-11230123|pmid-8377180|pmid-12471609|pmid-12471609|pmid-11473263
The protein encoded by gene SSO0048 was initially annotated as a putative transcription regulator with a similarity to the S.solfataricus transcriptional regulator Lrs14 (37) of the Lrp family.
[ "37", "15", "19", "22", "40", "41", "38", "38", "42" ]
193
11,241
1
false
The protein encoded by gene SSO0048 was initially annotated as a putative transcription regulator with a similarity to the S.solfataricus transcriptional regulator Lrs14 of the Lrp family.
[ "37" ]
The protein encoded by gene SSO0048 was initially annotated as a putative transcription regulator with a similarity to the S.solfataricus transcriptional regulator Lrs14 of the Lrp family.
true
true
true
true
true
1,800
6
DISCUSSION
1
37
[ "b37", "b15", "b19", "b22", "b40", "b41", "b38", "b38", "b42" ]
16,973,899
pmid-11427726|pmid-12675791|pmid-10973967|pmid-10049378|pmid-11230123|pmid-8377180|pmid-12471609|pmid-12471609|pmid-11473263
However, we showed here using NMR and homology modeling that Sta1, in contrast to the classical regulators of the Lrp family that display a HTH module (15,19,22,40), comprises a wHTH motif with an antiparallel β-sheet, which is absent in Lrp-like proteins.
[ "37", "15", "19", "22", "40", "41", "38", "38", "42" ]
256
11,242
0
false
However, we showed here using NMR and homology modeling that Sta1, in contrast to the classical regulators of the Lrp family that display a HTH module, comprises a wHTH motif with an antiparallel β-sheet, which is absent in Lrp-like proteins.
[ "15,19,22,40" ]
However, we showed here using NMR and homology modeling that Sta1, in contrast to the classical regulators of the Lrp family that display a HTH module, comprises a wHTH motif with an antiparallel β-sheet, which is absent in Lrp-like proteins.
true
true
true
true
true
1,800
6
DISCUSSION
1
41
[ "b37", "b15", "b19", "b22", "b40", "b41", "b38", "b38", "b42" ]
16,973,899
pmid-11427726|pmid-12675791|pmid-10973967|pmid-10049378|pmid-11230123|pmid-8377180|pmid-12471609|pmid-12471609|pmid-11473263
Our results, together with a BLAST search and a DALI (41) search of homologous protein structures, indicated that Sta1 contained a wHTH domain similar to that of Mj233 (38) and multiple antibiotic resistance proteins such as MarR, which is implicated in stress response (38,42).
[ "37", "15", "19", "22", "40", "41", "38", "38", "42" ]
278
11,243
1
false
Our results, together with a BLAST search and a DALI search of homologous protein structures, indicated that Sta1 contained a wHTH domain similar to that of Mj233 and multiple antibiotic resistance proteins such as MarR, which is implicated in stress response.
[ "41", "38", "38,42" ]
Our results, together with a BLAST search and a DALI search of homologous protein structures, indicated that Sta1 contained a wHTH domain similar to that of Mj233 and multiple antibiotic resistance proteins such as MarR, which is implicated in stress response.
true
true
true
true
true
1,800
6
DISCUSSION
1
37
[ "b37", "b15", "b19", "b22", "b40", "b41", "b38", "b38", "b42" ]
16,973,899
pmid-11427726|pmid-12675791|pmid-10973967|pmid-10049378|pmid-11230123|pmid-8377180|pmid-12471609|pmid-12471609|pmid-11473263
The electrostatic potential of the model of the wHTH region of Sta1 suggested that helix H1 may be involved in hydrophobic interactions within the protein, and that the region of the molecule containing the loop between strands B1 and B2 (wing), rich in positively charged residues, the β-sheet as well as the so-called ...
[ "37", "15", "19", "22", "40", "41", "38", "38", "42" ]
407
11,244
0
false
The electrostatic potential of the model of the wHTH region of Sta1 suggested that helix H1 may be involved in hydrophobic interactions within the protein, and that the region of the molecule containing the loop between strands B1 and B2 (wing), rich in positively charged residues, the β-sheet as well as the so-called ...
[]
The electrostatic potential of the model of the wHTH region of Sta1 suggested that helix H1 may be involved in hydrophobic interactions within the protein, and that the region of the molecule containing the loop between strands B1 and B2 (wing), rich in positively charged residues, the β-sheet as well as the so-called ...
true
true
true
true
true
1,800
7
DISCUSSION
1
43
[ "b43", "b44", "b45", "b46", "b47" ]
16,973,899
pmid-11546759|pmid-7935407|pmid-1656080|pmid-2155400|NA
A strategy of the archaeal virus to implicate a host transcription regulator to promote transcription of viral genes resembles eukaryal virus–host relationships and is in line with pronounced similarities in transcription machineries of archaea and eukarya.
[ "43", "44", "45", "46", "47" ]
257
11,245
0
false
A strategy of the archaeal virus to implicate a host transcription regulator to promote transcription of viral genes resembles eukaryal virus–host relationships and is in line with pronounced similarities in transcription machineries of archaea and eukarya.
[]
A strategy of the archaeal virus to implicate a host transcription regulator to promote transcription of viral genes resembles eukaryal virus–host relationships and is in line with pronounced similarities in transcription machineries of archaea and eukarya.
true
true
true
true
true
1,801
7
DISCUSSION
1
43
[ "b43", "b44", "b45", "b46", "b47" ]
16,973,899
pmid-11546759|pmid-7935407|pmid-1656080|pmid-2155400|NA
Numerous cases of such regulations are known in eukaryal virus–host systems.
[ "43", "44", "45", "46", "47" ]
76
11,246
0
false
Numerous cases of such regulations are known in eukaryal virus–host systems.
[]
Numerous cases of such regulations are known in eukaryal virus–host systems.
true
true
true
true
true
1,801
7
DISCUSSION
1
43
[ "b43", "b44", "b45", "b46", "b47" ]
16,973,899
pmid-11546759|pmid-7935407|pmid-1656080|pmid-2155400|NA
Some examples include requirement of the host-encoded ribonucleoproteins A2/B1 and RBM3 in transcription activation of the vaccinia virus late genes (43); exploitation of the cellular transcription factor USF by herpes viruses for the regulation of their promoters (44); a presence of binding motifs for ubiquitous cellu...
[ "43", "44", "45", "46", "47" ]
660
11,247
1
false
Some examples include requirement of the host-encoded ribonucleoproteins A2/B1 and RBM3 in transcription activation of the vaccinia virus late genes ; exploitation of the cellular transcription factor USF by herpes viruses for the regulation of their promoters ; a presence of binding motifs for ubiquitous cellular tran...
[ "43", "44", "45,46", "47" ]
Some examples include requirement of the host-encoded ribonucleoproteins A2/B1 and RBM3 in transcription activation of the vaccinia virus late genes ; exploitation of the cellular transcription factor USF by herpes viruses for the regulation of their promoters ; a presence of binding motifs for ubiquitous cellular tran...
true
true
true
true
true
1,801
8
DISCUSSION
0
null
null
16,973,899
null
Known examples of recruitment by viruses of essential cellular regulators of different nature for the modulation of gene expression determine a considerable interest in the identification of cellular targets of Sta1.
null
216
11,248
0
false
null
null
Known examples of recruitment by viruses of essential cellular regulators of different nature for the modulation of gene expression determine a considerable interest in the identification of cellular targets of Sta1.
true
true
true
true
true
1,802
8
DISCUSSION
0
null
null
16,973,899
null
In this light, studies of gene regulation in archaeal viruses, in addition to contributing to the knowledge on diversity and evolution of molecular mechanisms of gene regulation, may provide a tool for identifying key regulators of cellular events.
null
248
11,249
0
false
null
null
In this light, studies of gene regulation in archaeal viruses, in addition to contributing to the knowledge on diversity and evolution of molecular mechanisms of gene regulation, may provide a tool for identifying key regulators of cellular events.
true
true
true
true
true
1,802
0
INTRODUCTION
1
1
[ "b1", "b6", "b7", "b18", "b19", "b23" ]
17,012,278
pmid-9131619|pmid-15844621|pmid-7519769|pmid-14980623|pmid-7574500|pmid-10872462
Functional DNA molecules, such as DNA aptamers and DNAzymes with functions similar to antibodies and enzymes (1–6) could be useful as research tools for molecular biology and as indicators of specific substances for the analysis of clinical and food samples.
[ "1", "6", "7", "18", "19", "23" ]
258
11,250
0
false
Functional DNA molecules, such as DNA aptamers and DNAzymes with functions similar to antibodies and enzymes could be useful as research tools for molecular biology and as indicators of specific substances for the analysis of clinical and food samples.
[ "1–6" ]
Functional DNA molecules, such as DNA aptamers and DNAzymes with functions similar to antibodies and enzymes could be useful as research tools for molecular biology and as indicators of specific substances for the analysis of clinical and food samples.
true
true
true
true
true
1,803
0
INTRODUCTION
1
1
[ "b1", "b6", "b7", "b18", "b19", "b23" ]
17,012,278
pmid-9131619|pmid-15844621|pmid-7519769|pmid-14980623|pmid-7574500|pmid-10872462
Recent progress has been made at introducing additional functionalities into these DNA molecules to diversify their function and improve their activity (7–18).
[ "1", "6", "7", "18", "19", "23" ]
159
11,251
0
false
Recent progress has been made at introducing additional functionalities into these DNA molecules to diversify their function and improve their activity.
[ "7–18" ]
Recent progress has been made at introducing additional functionalities into these DNA molecules to diversify their function and improve their activity.
true
true
true
true
true
1,803
0
INTRODUCTION
1
1
[ "b1", "b6", "b7", "b18", "b19", "b23" ]
17,012,278
pmid-9131619|pmid-15844621|pmid-7519769|pmid-14980623|pmid-7574500|pmid-10872462
Such functionally modified DNAs can be produced by in vitro selection or SELEX (systematic evolution of ligands by exponential enrichment) techniques involving screening of the sequences with desired activity from large pools of random sequences and amplification of the selected pools by PCR (19–23).
[ "1", "6", "7", "18", "19", "23" ]
301
11,252
0
false
Such functionally modified DNAs can be produced by in vitro selection or SELEX (systematic evolution of ligands by exponential enrichment) techniques involving screening of the sequences with desired activity from large pools of random sequences and amplification of the selected pools by PCR.
[ "19–23" ]
Such functionally modified DNAs can be produced by in vitro selection or SELEX (systematic evolution of ligands by exponential enrichment) techniques involving screening of the sequences with desired activity from large pools of random sequences and amplification of the selected pools by PCR.
true
true
true
true
true
1,803
1
INTRODUCTION
1
24
[ "b24", "b36", "b37", "b44", "b45", "b52" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
Modified DNAs can be efficiently prepared from modified 2′-deoxynucleoside triphosphates in the absence of the corresponding natural substrates by symmetric PCR, which is capable of direct exponential amplification of DNA (24–36).
[ "24", "36", "37", "44", "45", "52" ]
230
11,253
0
false
Modified DNAs can be efficiently prepared from modified 2′-deoxynucleoside triphosphates in the absence of the corresponding natural substrates by symmetric PCR, which is capable of direct exponential amplification of DNA.
[ "24–36" ]
Modified DNAs can be efficiently prepared from modified 2′-deoxynucleoside triphosphates in the absence of the corresponding natural substrates by symmetric PCR, which is capable of direct exponential amplification of DNA.
true
true
true
true
true
1,804
1
INTRODUCTION
1
24
[ "b24", "b36", "b37", "b44", "b45", "b52" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
Although, the production of modified DNAs is limited by the substrate specificity of the DNA polymerases, there are many examples of the enzymatic preparation of modified DNAs by primer extension or one-primer PCR from modified 2′-deoxynucleoside triphosphates or by symmetric PCR under coexistence of the corresponding ...
[ "24", "36", "37", "44", "45", "52" ]
347
11,254
0
false
Although, the production of modified DNAs is limited by the substrate specificity of the DNA polymerases, there are many examples of the enzymatic preparation of modified DNAs by primer extension or one-primer PCR from modified 2′-deoxynucleoside triphosphates or by symmetric PCR under coexistence of the corresponding ...
[ "37–44" ]
Although, the production of modified DNAs is limited by the substrate specificity of the DNA polymerases, there are many examples of the enzymatic preparation of modified DNAs by primer extension or one-primer PCR from modified 2′-deoxynucleoside triphosphates or by symmetric PCR under coexistence of the corresponding ...
true
true
true
true
true
1,804
1
INTRODUCTION
1
24
[ "b24", "b36", "b37", "b44", "b45", "b52" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
Symmetric PCR is the most convenient method for preparing modified DNAs that can be subjected to in vitro selection.
[ "24", "36", "37", "44", "45", "52" ]
116
11,255
0
false
Symmetric PCR is the most convenient method for preparing modified DNAs that can be subjected to in vitro selection.
[]
Symmetric PCR is the most convenient method for preparing modified DNAs that can be subjected to in vitro selection.
true
true
true
true
true
1,804
1
INTRODUCTION
1
24
[ "b24", "b36", "b37", "b44", "b45", "b52" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
Thus, in the current study, we synthesized a variety of 2′-deoxynucleoside triphosphates to systematically analyze how the chemical structures of modified bases affect the synthesis of modified DNAs by symmetric PCR.
[ "24", "36", "37", "44", "45", "52" ]
216
11,256
0
false
Thus, in the current study, we synthesized a variety of 2′-deoxynucleoside triphosphates to systematically analyze how the chemical structures of modified bases affect the synthesis of modified DNAs by symmetric PCR.
[]
Thus, in the current study, we synthesized a variety of 2′-deoxynucleoside triphosphates to systematically analyze how the chemical structures of modified bases affect the synthesis of modified DNAs by symmetric PCR.
true
true
true
true
true
1,804
1
INTRODUCTION
1
24
[ "b24", "b36", "b37", "b44", "b45", "b52" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
We also examined the influence of the type of DNA polymerase on the production of modified DNAs.
[ "24", "36", "37", "44", "45", "52" ]
96
11,257
0
false
We also examined the influence of the type of DNA polymerase on the production of modified DNAs.
[]
We also examined the influence of the type of DNA polymerase on the production of modified DNAs.
true
true
true
true
true
1,804
1
INTRODUCTION
1
24
[ "b24", "b36", "b37", "b44", "b45", "b52" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
Finally, to identify the critical step in the synthesis of modified DNA, we measured single nucleotide insertion under single turnover conditions (45–52) by using primers containing modified dUs at their 3′ ends and templates containing modified dUs adjacent to the elongation site.
[ "24", "36", "37", "44", "45", "52" ]
282
11,258
0
false
Finally, to identify the critical step in the synthesis of modified DNA, we measured single nucleotide insertion under single turnover conditions by using primers containing modified dUs at their 3′ ends and templates containing modified dUs adjacent to the elongation site.
[ "45–52" ]
Finally, to identify the critical step in the synthesis of modified DNA, we measured single nucleotide insertion under single turnover conditions by using primers containing modified dUs at their 3′ ends and templates containing modified dUs adjacent to the elongation site.
true
true
true
true
true
1,804
0
DISCUSSION
0
null
null
17,012,278
pmid-9131619|pmid-15844621|pmid-7519769|pmid-14980623|pmid-7574500|pmid-10872462
The efficiency of a PCR depends on a variety of parameters including temperature (denature, annealing and extension), reaction time and the number of reaction cycles.
null
166
11,259
0
false
null
null
The efficiency of a PCR depends on a variety of parameters including temperature (denature, annealing and extension), reaction time and the number of reaction cycles.
true
true
true
true
true
1,805
0
DISCUSSION
0
null
null
17,012,278
pmid-9131619|pmid-15844621|pmid-7519769|pmid-14980623|pmid-7574500|pmid-10872462
The PCR assays were performed under conditions optimized for the positive control using the natural 4 nt triphosphates.
null
119
11,260
0
false
null
null
The PCR assays were performed under conditions optimized for the positive control using the natural 4 nt triphosphates.
true
true
true
true
true
1,805
0
DISCUSSION
0
null
null
17,012,278
pmid-9131619|pmid-15844621|pmid-7519769|pmid-14980623|pmid-7574500|pmid-10872462
Therefore, some analogs that did not act as PCR substrates under these assay conditions could provide the corresponding PCR products if the parameters were separately optimized.
null
177
11,261
0
false
null
null
Therefore, some analogs that did not act as PCR substrates under these assay conditions could provide the corresponding PCR products if the parameters were separately optimized.
true
true
true
true
true
1,805
0
DISCUSSION
0
null
null
17,012,278
pmid-9131619|pmid-15844621|pmid-7519769|pmid-14980623|pmid-7574500|pmid-10872462
The amount of PCR product depends on the substrate and enzyme concentration as well as the sequences and length of the amplifying region; however, comparison of the yields obtained by PCR using modified and natural analogs under the same conditions should supply useful information on the efficiency of the modified anal...
null
342
11,262
0
false
null
null
The amount of PCR product depends on the substrate and enzyme concentration as well as the sequences and length of the amplifying region; however, comparison of the yields obtained by PCR using modified and natural analogs under the same conditions should supply useful information on the efficiency of the modified anal...
true
true
true
true
true
1,805
1
DISCUSSION
1
28
[ "b28", "b29", "b25", "b28", "b29", "b55", "b58", "b24", "b59", "b60" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
Our current finding that family B DNA polymerases accept a wider range of modified nucleoside triphosphates as PCR substrates than family A DNA polymerases agrees with previous reports (28,29).
[ "28", "29", "25", "28", "29", "55", "58", "24", "59", "60" ]
193
11,263
0
false
Our current finding that family B DNA polymerases accept a wider range of modified nucleoside triphosphates as PCR substrates than family A DNA polymerases agrees with previous reports.
[ "28,29" ]
Our current finding that family B DNA polymerases accept a wider range of modified nucleoside triphosphates as PCR substrates than family A DNA polymerases agrees with previous reports.
true
true
true
true
true
1,806
1
DISCUSSION
1
28
[ "b28", "b29", "b25", "b28", "b29", "b55", "b58", "b24", "b59", "b60" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
As shown in Figure 4A and B, family A DNA polymerases do not prefer substituents involving 2-oxoethyl linker arm, such as (2-aminoethylamino)-2-oxoethyl (A2), (4-aminobutylamino)-2-oxoethyl (A4), (6-aminohexylamino)-2-oxoethyl (A6), (6-guanidinohexylamino)-2-oxoethyl (G6) and 2-methoxy-2-oxoethyl (ME) as PCR substrates...
[ "28", "29", "25", "28", "29", "55", "58", "24", "59", "60" ]
408
11,264
0
false
As shown in Figure 4A and B, family A DNA polymerases do not prefer substituents involving 2-oxoethyl linker arm, such as (2-aminoethylamino)-2-oxoethyl (A2), (4-aminobutylamino)-2-oxoethyl (A4), (6-aminohexylamino)-2-oxoethyl (A6), (6-guanidinohexylamino)-2-oxoethyl (G6) and 2-methoxy-2-oxoethyl (ME) as PCR substrates...
[ "25,28,29" ]
As shown in Figure 4A and B, family A DNA polymerases do not prefer substituents involving 2-oxoethyl linker arm, such as -2-oxoethyl, (4-aminobutylamino)-2-oxoethyl (A4), (6-aminohexylamino)-2-oxoethyl (A6), (6-guanidinohexylamino)-2-oxoethyl (G6) and 2-methoxy-2-oxoethyl (ME) as PCR substrates as well as analogs with...
true
true
true
true
true
1,806
1
DISCUSSION
1
24
[ "b28", "b29", "b25", "b28", "b29", "b55", "b58", "b24", "b59", "b60" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
These results together with rigidity of the linker arm suggest that the difference in PCR efficiency between family A and B polymerases reflects the palm shape of the DNA polymerase complex bound to a DNA duplex (55–58); it is predicted that family A DNA polymerases cannot accommodate a flexible modified group close to...
[ "28", "29", "25", "28", "29", "55", "58", "24", "59", "60" ]
617
11,265
1
false
These results together with rigidity of the linker arm suggest that the difference in PCR efficiency between family A and B polymerases reflects the palm shape of the DNA polymerase complex bound to a DNA duplex ; it is predicted that family A DNA polymerases cannot accommodate a flexible modified group close to the nu...
[ "55–58", "24" ]
These results together with rigidity of the linker arm suggest that the difference in PCR efficiency between family A and B polymerases reflects the palm shape of the DNA polymerase complex bound to a DNA duplex ; it is predicted that family A DNA polymerases cannot accommodate a flexible modified group close to the nu...
true
true
true
true
true
1,806
1
DISCUSSION
1
28
[ "b28", "b29", "b25", "b28", "b29", "b55", "b58", "b24", "b59", "b60" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
This prediction, however, does not agree with the fact that the relative yields of the PCR products varied depending on whether the substitution was on dU or dC.
[ "28", "29", "25", "28", "29", "55", "58", "24", "59", "60" ]
161
11,266
0
false
This prediction, however, does not agree with the fact that the relative yields of the PCR products varied depending on whether the substitution was on dU or dC.
[]
This prediction, however, does not agree with the fact that the relative yields of the PCR products varied depending on whether the substitution was on dU or dC.
true
true
true
true
true
1,806
1
DISCUSSION
1
28
[ "b28", "b29", "b25", "b28", "b29", "b55", "b58", "b24", "b59", "b60" ]
17,012,278
NA|pmid-16359870|pmid-8774915|pmid-12736314|pmid-8485987|pmid-16411765|pmid-12202771|pmid-14552769|pmid-11266559|pmid-12202771|pmid-14552769|pmid-8717047|pmid-16311403|NA|pmid-9358149|pmid-12590605
This difference may instead be due to other effects, such as changes in the pKa at the N4 position of the cytosine base or differences in the contribution of the C5 substituent to base-stacking interactions (59,60).
[ "28", "29", "25", "28", "29", "55", "58", "24", "59", "60" ]
215
11,267
0
false
This difference may instead be due to other effects, such as changes in the pKa at the N4 position of the cytosine base or differences in the contribution of the C5 substituent to base-stacking interactions.
[ "59,60" ]
This difference may instead be due to other effects, such as changes in the pKa at the N4 position of the cytosine base or differences in the contribution of the C5 substituent to base-stacking interactions.
true
true
true
true
true
1,806
2
DISCUSSION
1
30
[ "b30" ]
17,012,278
pmid-12851926
The presence of a charge near the nucleobase decreased the yield of the PCR products.
[ "30" ]
85
11,268
0
false
The presence of a charge near the nucleobase decreased the yield of the PCR products.
[]
The presence of a charge near the nucleobase decreased the yield of the PCR products.
true
true
true
true
true
1,807
2
DISCUSSION
1
30
[ "b30" ]
17,012,278
pmid-12851926
Our previous study showed that the analog TME, which has no charge on the modified group, acts as a good substrate for PCR catalyzed by KOD Dash, whereas 5-(2-hydroxy-2-oxoethyl)-dUTP, which has a negative charge on the modified group, does not (30).
[ "30" ]
250
11,269
1
false
Our previous study showed that the analog TME, which has no charge on the modified group, acts as a good substrate for PCR catalyzed by KOD Dash, whereas 5-(2-hydroxy-2-oxoethyl)-dUTP, which has a negative charge on the modified group, does not.
[ "30" ]
Our previous study showed that the analog TME, which has no charge on the modified group, acts as a good substrate for PCR catalyzed by KOD Dash, whereas 5-(2-hydroxy-2-oxoethyl)-dUTP, which has a negative charge on the modified group, does not.
true
true
true
true
true
1,807
2
DISCUSSION
1
30
[ "b30" ]
17,012,278
pmid-12851926
Therefore, the amount of PCR products is decreased by either a negative or positive charge on the modified group.
[ "30" ]
113
11,270
0
false
Therefore, the amount of PCR products is decreased by either a negative or positive charge on the modified group.
[]
Therefore, the amount of PCR products is decreased by either a negative or positive charge on the modified group.
true
true
true
true
true
1,807
2
DISCUSSION
1
30
[ "b30" ]
17,012,278
pmid-12851926
Basic amino acid residues are found in the P/T binding region of the polymerases, and, thus, the mode of interaction between the enzyme and P/T may be important for the extension reaction.
[ "30" ]
188
11,271
0
false
Basic amino acid residues are found in the P/T binding region of the polymerases, and, thus, the mode of interaction between the enzyme and P/T may be important for the extension reaction.
[]
Basic amino acid residues are found in the P/T binding region of the polymerases, and, thus, the mode of interaction between the enzyme and P/T may be important for the extension reaction.
true
true
true
true
true
1,807
2
DISCUSSION
1
30
[ "b30" ]
17,012,278
pmid-12851926
The values of kcat and koff should be experimentally determined by running start experiments using two kinds of P/Ts containing modified groups with positive or negative charges, and the kinetic data should be compared to know which step of the reaction is more negatively affected by the presence of the modified group ...
[ "30" ]
327
11,272
0
false
The values of kcat and koff should be experimentally determined by running start experiments using two kinds of P/Ts containing modified groups with positive or negative charges, and the kinetic data should be compared to know which step of the reaction is more negatively affected by the presence of the modified group ...
[]
The values of kcat and koff should be experimentally determined by running start experiments using two kinds of P/Ts containing modified groups with positive or negative charges, and the kinetic data should be compared to know which step of the reaction is more negatively affected by the presence of the modified group ...
true
true
true
true
true
1,807
2
DISCUSSION
1
30
[ "b30" ]
17,012,278
pmid-12851926
Differences in the chemical structure of the modified nucleotide will alter the kcat and koff value in different ways.
[ "30" ]
118
11,273
0
false
Differences in the chemical structure of the modified nucleotide will alter the kcat and koff value in different ways.
[]
Differences in the chemical structure of the modified nucleotide will alter the kcat and koff value in different ways.
true
true
true
true
true
1,807
3
DISCUSSION
1
61
[ "b61" ]
17,012,278
pmid-15107492
Because the P/T forms a helix and the polymerase recognizes the base pair duplexes, how modified groups located on the upstream portion of the primer and on the downstream portion of the template affect the polymerase reaction should also be closely examined (61).
[ "61" ]
264
11,274
1
false
Because the P/T forms a helix and the polymerase recognizes the base pair duplexes, how modified groups located on the upstream portion of the primer and on the downstream portion of the template affect the polymerase reaction should also be closely examined.
[ "61" ]
Because the P/T forms a helix and the polymerase recognizes the base pair duplexes, how modified groups located on the upstream portion of the primer and on the downstream portion of the template affect the polymerase reaction should also be closely examined.
true
true
true
true
true
1,808
3
DISCUSSION
1
61
[ "b61" ]
17,012,278
pmid-15107492
The present standing-start experiments clearly revealed, however, that the modified group has a greater affect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template.
[ "61" ]
217
11,275
0
false
The present standing-start experiments clearly revealed, however, that the modified group has a greater affect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template.
[]
The present standing-start experiments clearly revealed, however, that the modified group has a greater affect on the polymerase reaction when it is adjacent to the elongation terminus than when it is on the template.
true
true
true
true
true
1,808
3
DISCUSSION
1
61
[ "b61" ]
17,012,278
pmid-15107492
These tendencies were also observed in similar experiments using KOD(exo-)
[ "61" ]
74
11,276
0
false
These tendencies were also observed in similar experiments using KOD(exo-)
[]
These tendencies were also observed in similar experiments using KOD(exo-)
true
true
false
true
false
1,808
3
DISCUSSION
1
61
[ "b61" ]
17,012,278
pmid-15107492
DNA polymerase (Figure 5 and see Supplementary Table 1).
[ "61" ]
56
11,277
0
false
DNA polymerase (Figure 5 and see Supplementary Table 1).
[]
DNA polymerase.
true
true
true
true
true
1,808
4
DISCUSSION
1
62
[ "b62", "b30" ]
17,012,278
NA|pmid-12851926
Recent studies have focused on the use of enzymatic methods for fluorescently labeling or functionalizing DNA molecules because they are more convenient than chemical methods.
[ "62", "30" ]
175
11,278
0
false
Recent studies have focused on the use of enzymatic methods for fluorescently labeling or functionalizing DNA molecules because they are more convenient than chemical methods.
[]
Recent studies have focused on the use of enzymatic methods for fluorescently labeling or functionalizing DNA molecules because they are more convenient than chemical methods.
true
true
true
true
true
1,809
4
DISCUSSION
1
62
[ "b62", "b30" ]
17,012,278
NA|pmid-12851926
Useful modifications of DNA molecules include conferring membrane permeability by incorporation of TG6 (62) in the polymerase reaction or by postsynthetic modification of modified DNAs prepared by PCR using TME (30).
[ "62", "30" ]
216
11,279
1
false
Useful modifications of DNA molecules include conferring membrane permeability by incorporation of TG6 in the polymerase reaction or by postsynthetic modification of modified DNAs prepared by PCR using TME.
[ "62", "30" ]
Useful modifications of DNA molecules include conferring membrane permeability by incorporation of TG6 in the polymerase reaction or by postsynthetic modification of modified DNAs prepared by PCR using TME.
true
true
true
true
true
1,809
4
DISCUSSION
1
62
[ "b62", "b30" ]
17,012,278
NA|pmid-12851926
Furthermore, TAF and CAF, which were much better as substrates in the PCR than the conventional substrates TAL and CAL, could be useful for preparing modified DNAs with a high density of functional groups if the trifluoroacetyl protecting group is removed and the DNA is then subjected to postsynthetic modification.
[ "62", "30" ]
316
11,280
0
false
Furthermore, TAF and CAF, which were much better as substrates in the PCR than the conventional substrates TAL and CAL, could be useful for preparing modified DNAs with a high density of functional groups if the trifluoroacetyl protecting group is removed and the DNA is then subjected to postsynthetic modification.
[]
Furthermore, TAF and CAF, which were much better as substrates in the PCR than the conventional substrates TAL and CAL, could be useful for preparing modified DNAs with a high density of functional groups if the trifluoroacetyl protecting group is removed and the DNA is then subjected to postsynthetic modification.
true
true
true
true
true
1,809
4
DISCUSSION
1
62
[ "b62", "b30" ]
17,012,278
NA|pmid-12851926
The kinetic study indicated that the existence of the modified group after incorporation into DNA greatly affected the enzymatic reaction rate.
[ "62", "30" ]
143
11,281
0
false
The kinetic study indicated that the existence of the modified group after incorporation into DNA greatly affected the enzymatic reaction rate.
[]
The kinetic study indicated that the existence of the modified group after incorporation into DNA greatly affected the enzymatic reaction rate.
true
true
true
true
true
1,809
4
DISCUSSION
1
62
[ "b62", "b30" ]
17,012,278
NA|pmid-12851926
Therefore, it is not surprising that generation of PCR products was suppressed depending on the amplifying sequences.
[ "62", "30" ]
117
11,282
0
false
Therefore, it is not surprising that generation of PCR products was suppressed depending on the amplifying sequences.
[]
Therefore, it is not surprising that generation of PCR products was suppressed depending on the amplifying sequences.
true
true
true
true
true
1,809
4
DISCUSSION
1
62
[ "b62", "b30" ]
17,012,278
NA|pmid-12851926
For screening of functional molecules by in vitro selection of modified DNA libraries, any bias except for the intended selection pressures is unfavorable.
[ "62", "30" ]
155
11,283
0
false
For screening of functional molecules by in vitro selection of modified DNA libraries, any bias except for the intended selection pressures is unfavorable.
[]
For screening of functional molecules by in vitro selection of modified DNA libraries, any bias except for the intended selection pressures is unfavorable.
true
true
true
true
true
1,809
4
DISCUSSION
1
62
[ "b62", "b30" ]
17,012,278
NA|pmid-12851926
Therefore, determining which combination of enzyme and substrate provides modified DNA in high yields and with low sequence dependency will be necessary for constructing a selection system that reduces unsuitable biases.
[ "62", "30" ]
220
11,284
0
false
Therefore, determining which combination of enzyme and substrate provides modified DNA in high yields and with low sequence dependency will be necessary for constructing a selection system that reduces unsuitable biases.
[]
Therefore, determining which combination of enzyme and substrate provides modified DNA in high yields and with low sequence dependency will be necessary for constructing a selection system that reduces unsuitable biases.
true
true
true
true
true
1,809
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,098,930
NA|NA|NA
The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera Cryptosporidium, Plasmodium and Toxoplasma.
[ "1", "2", "3" ]
188
11,285
0
false
The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera Cryptosporidium, Plasmodium and Toxoplasma.
[]
The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic species of the genera Cryptosporidium, Plasmodium and Toxoplasma.
true
true
true
true
true
1,810
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,098,930
NA|NA|NA
Multiple species of Plasmodium are capable of causing malaria in humans, a leading cause of morbidity and mortality in developing countries (1).
[ "1", "2", "3" ]
144
11,286
1
false
Multiple species of Plasmodium are capable of causing malaria in humans, a leading cause of morbidity and mortality in developing countries.
[ "1" ]
Multiple species of Plasmodium are capable of causing malaria in humans, a leading cause of morbidity and mortality in developing countries.
true
true
true
true
true
1,810
0
INTRODUCTION
1
2
[ "b1", "b2", "b3" ]
17,098,930
NA|NA|NA
Cryptosporidium causes a severe and chronic diarrheal disease that may be life threatening in immunocompromised patients (2).
[ "1", "2", "3" ]
125
11,287
1
false
Cryptosporidium causes a severe and chronic diarrheal disease that may be life threatening in immunocompromised patients.
[ "2" ]
Cryptosporidium causes a severe and chronic diarrheal disease that may be life threatening in immunocompromised patients.
true
true
true
true
true
1,810
0
INTRODUCTION
1
3
[ "b1", "b2", "b3" ]
17,098,930
NA|NA|NA
Toxoplasma gondii infections, although typically asymptomatic in healthy individuals, may lead to congenital birth defects and encephalitis in HIV/AIDS patients (3).
[ "1", "2", "3" ]
165
11,288
1
false
Toxoplasma gondii infections, although typically asymptomatic in healthy individuals, may lead to congenital birth defects and encephalitis in HIV/AIDS patients.
[ "3" ]
Toxoplasma gondii infections, although typically asymptomatic in healthy individuals, may lead to congenital birth defects and encephalitis in HIV/AIDS patients.
true
true
true
true
true
1,810
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,098,930
NA|NA|NA
Human infections with T.gondii may be acquired from food or soil contamination and infections with Cryptosporidium parvum from soil and water contamination.
[ "1", "2", "3" ]
156
11,289
0
false
Human infections with T.gondii may be acquired from food or soil contamination and infections with Cryptosporidium parvum from soil and water contamination.
[]
Human infections with T.gondii may be acquired from food or soil contamination and infections with Cryptosporidium parvum from soil and water contamination.
true
true
true
true
true
1,810
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,098,930
NA|NA|NA
Due to the potential threat to public health from intentional dispersal into the population, T.gondii and C.parvum are listed as Category B Biodefense Pathogens by the National Institutes of Health.
[ "1", "2", "3" ]
198
11,290
0
false
Due to the potential threat to public health from intentional dispersal into the population, T.gondii and C.parvum are listed as Category B Biodefense Pathogens by the National Institutes of Health.
[]
Due to the potential threat to public health from intentional dispersal into the population, T.gondii and C.parvum are listed as Category B Biodefense Pathogens by the National Institutes of Health.
true
true
true
true
true
1,810
1
INTRODUCTION
1
4
[ "b4", "b5", "b6" ]
17,098,930
pmid-16381902|pmid-12519984|pmid-12519989
The research communities for Cryptosporidium, Plasmodium and Toxoplasma have benefited from the bioinformatics resources provided by the distinct online genome databases CryptoDB (4), PlasmoDB (5) and ToxoDB (6), respectively (See supplementary material).
[ "4", "5", "6" ]
255
11,291
1
false
The research communities for Cryptosporidium, Plasmodium and Toxoplasma have benefited from the bioinformatics resources provided by the distinct online genome databases CryptoDB, PlasmoDB and ToxoDB, respectively (See supplementary material).
[ "4", "5", "6" ]
The research communities for Cryptosporidium, Plasmodium and Toxoplasma have benefited from the bioinformatics resources provided by the distinct online genome databases CryptoDB, PlasmoDB and ToxoDB, respectively (See supplementary material).
true
true
true
true
true
1,811
1
INTRODUCTION
1
4
[ "b4", "b5", "b6" ]
17,098,930
pmid-16381902|pmid-12519984|pmid-12519989
Because of the phylogenetic relationship of these human pathogens, (all are included in the phylum Apicomplexa, along with the prominent animal pathogens, Babesia, Theileria and Eimeria) comparative genomic and proteomic studies across these species is critical for expediting discovery of therapeutic targets, increasin...
[ "4", "5", "6" ]
428
11,292
0
false
Because of the phylogenetic relationship of these human pathogens, (all are included in the phylum Apicomplexa, along with the prominent animal pathogens, Babesia, Theileria and Eimeria) comparative genomic and proteomic studies across these species is critical for expediting discovery of therapeutic targets, increasin...
[]
Because of the phylogenetic relationship of these human pathogens, (all are included in the phylum Apicomplexa, along with the prominent animal pathogens, Babesia, Theileria and Eimeria) comparative genomic and proteomic studies across these species is critical for expediting discovery of therapeutic targets, increasin...
true
true
true
true
true
1,811
1
INTRODUCTION
1
4
[ "b4", "b5", "b6" ]
17,098,930
pmid-16381902|pmid-12519984|pmid-12519989
However, the researcher's ability to perform comparative studies utilizing multiple data sources has been tempered by the difficulty of managing and collating the data from the existing disparate resource databases.
[ "4", "5", "6" ]
215
11,293
0
false
However, the researcher's ability to perform comparative studies utilizing multiple data sources has been tempered by the difficulty of managing and collating the data from the existing disparate resource databases.
[]
However, the researcher's ability to perform comparative studies utilizing multiple data sources has been tempered by the difficulty of managing and collating the data from the existing disparate resource databases.
true
true
true
true
true
1,811
1
INTRODUCTION
1
4
[ "b4", "b5", "b6" ]
17,098,930
pmid-16381902|pmid-12519984|pmid-12519989
Here we describe the online apicomplexan Bioinformatics Resource Center (BRC), ApiDB (), which has been established to provide researchers centralized, integrated access to experimental and computational data, as well as tools to facilitate comparative research.
[ "4", "5", "6" ]
262
11,294
0
false
Here we describe the online apicomplexan Bioinformatics Resource Center (BRC), ApiDB (), which has been established to provide researchers centralized, integrated access to experimental and computational data, as well as tools to facilitate comparative research.
[]
Here we describe the online apicomplexan Bioinformatics Resource Center (BRC), ApiDB (), which has been established to provide researchers centralized, integrated access to experimental and computational data, as well as tools to facilitate comparative research.
true
true
true
true
true
1,811
2
INTRODUCTION
1
7
[ "b7" ]
17,098,930
pmid-12728276
ApiDB integrates the existing CryptoDB, ToxoDB and PlasmoDB component resources.
[ "7" ]
80
11,295
0
false
ApiDB integrates the existing CryptoDB, ToxoDB and PlasmoDB component resources.
[]
ApiDB integrates the existing CryptoDB, ToxoDB and PlasmoDB component resources.
true
true
true
true
true
1,812
2
INTRODUCTION
1
7
[ "b7" ]
17,098,930
pmid-12728276
Database integration is accomplished via a combination of federation and link integration technologies (7).
[ "7" ]
107
11,296
1
false
Database integration is accomplished via a combination of federation and link integration technologies.
[ "7" ]
Database integration is accomplished via a combination of federation and link integration technologies.
true
true
true
true
true
1,812
2
INTRODUCTION
1
7
[ "b7" ]
17,098,930
pmid-12728276
Link integration allows researchers to begin their query with one data source and then follow hypertext links to related information in other data sources.
[ "7" ]
155
11,297
0
false
Link integration allows researchers to begin their query with one data source and then follow hypertext links to related information in other data sources.
[]
Link integration allows researchers to begin their query with one data source and then follow hypertext links to related information in other data sources.
true
true
true
true
true
1,812
2
INTRODUCTION
1
7
[ "b7" ]
17,098,930
pmid-12728276
Database federation is achieved by decomposing distributed queries into component queries and executing these queries in the source databases, delivering the results into a uniform format.
[ "7" ]
188
11,298
0
false
Database federation is achieved by decomposing distributed queries into component queries and executing these queries in the source databases, delivering the results into a uniform format.
[]
Database federation is achieved by decomposing distributed queries into component queries and executing these queries in the source databases, delivering the results into a uniform format.
true
true
true
true
true
1,812
2
INTRODUCTION
1
7
[ "b7" ]
17,098,930
pmid-12728276
It leaves the information in its source databases but builds an environment around the databases that makes them all seem part of one large system.
[ "7" ]
147
11,299
0
false
It leaves the information in its source databases but builds an environment around the databases that makes them all seem part of one large system.
[]
It leaves the information in its source databases but builds an environment around the databases that makes them all seem part of one large system.
true
true
true
true
true
1,812