Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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INTRODUCTION
1
1
[ "b1", "b7", "b5", "b8" ]
16,855,284
pmid-1032904|pmid-15334112|pmid-12975310|pmid-15042091
More recently, with the increasing application of novel RNA silencing techniques, adenoviruses have been shown to be a powerful approach to facilitating the expression of short-interfering RNA (5,8).
[ "1", "7", "5", "8" ]
199
2,900
0
false
More recently, with the increasing application of novel RNA silencing techniques, adenoviruses have been shown to be a powerful approach to facilitating the expression of short-interfering RNA.
[ "5,8" ]
More recently, with the increasing application of novel RNA silencing techniques, adenoviruses have been shown to be a powerful approach to facilitating the expression of short-interfering RNA.
true
true
true
true
true
490
1
INTRODUCTION
1
9
[ "b9", "b13", "b14", "b17", "b14", "b16", "b13" ]
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
Over the years, many approaches have been developed for the generation of recombinant adenoviruses, which can be divided into two basic categories; direct plasmid construction of recombinant adenoviral genome (9–13) or indirect construction (14–17).
[ "9", "13", "14", "17", "14", "16", "13" ]
249
2,901
0
false
Over the years, many approaches have been developed for the generation of recombinant adenoviruses, which can be divided into two basic categories; direct plasmid construction of recombinant adenoviral genome or indirect construction.
[ "9–13", "14–17" ]
Over the years, many approaches have been developed for the generation of recombinant adenoviruses, which can be divided into two basic categories; direct plasmid construction of recombinant adenoviral genome or indirect construction.
true
true
true
true
true
491
1
INTRODUCTION
1
9
[ "b9", "b13", "b14", "b17", "b14", "b16", "b13" ]
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
The former involves the ligation of the adenoviral genome with the DNA fragments of interest, and the latter involves homologous recombination in mammalian cells or in Escherichia coli.
[ "9", "13", "14", "17", "14", "16", "13" ]
185
2,902
0
false
The former involves the ligation of the adenoviral genome with the DNA fragments of interest, and the latter involves homologous recombination in mammalian cells or in Escherichia coli.
[]
The former involves the ligation of the adenoviral genome with the DNA fragments of interest, and the latter involves homologous recombination in mammalian cells or in Escherichia coli.
true
true
true
true
true
491
1
INTRODUCTION
1
9
[ "b9", "b13", "b14", "b17", "b14", "b16", "b13" ]
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
The direct methods are handicapped by the limitation of choices of suitable restriction sites and the difficulty in the manipulation of the large adenoviral vector.
[ "9", "13", "14", "17", "14", "16", "13" ]
164
2,903
0
false
The direct methods are handicapped by the limitation of choices of suitable restriction sites and the difficulty in the manipulation of the large adenoviral vector.
[]
The direct methods are handicapped by the limitation of choices of suitable restriction sites and the difficulty in the manipulation of the large adenoviral vector.
true
true
true
true
true
491
1
INTRODUCTION
1
9
[ "b9", "b13", "b14", "b17", "b14", "b16", "b13" ]
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
On the other hand, the indirect methods utilize two plasmids coding for the homologous recombinant regions; one is a shuttle plasmid containing an expression cassette, and the other is the large plasmid containing the majority of the adenoviral genome.
[ "9", "13", "14", "17", "14", "16", "13" ]
252
2,904
0
false
On the other hand, the indirect methods utilize two plasmids coding for the homologous recombinant regions; one is a shuttle plasmid containing an expression cassette, and the other is the large plasmid containing the majority of the adenoviral genome.
[]
On the other hand, the indirect methods utilize two plasmids coding for the homologous recombinant regions; one is a shuttle plasmid containing an expression cassette, and the other is the large plasmid containing the majority of the adenoviral genome.
true
true
true
true
true
491
1
INTRODUCTION
1
9
[ "b9", "b13", "b14", "b17", "b14", "b16", "b13" ]
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
For example, the construction of the recombinant adenovirus through Cre-lox has been described in studies with mammalian cells and E.coli (14,16).
[ "9", "13", "14", "17", "14", "16", "13" ]
146
2,905
0
false
For example, the construction of the recombinant adenovirus through Cre-lox has been described in studies with mammalian cells and E.coli.
[ "14,16" ]
For example, the construction of the recombinant adenovirus through Cre-lox has been described in studies with mammalian cells and E.coli.
true
true
true
true
true
491
1
INTRODUCTION
1
9
[ "b9", "b13", "b14", "b17", "b14", "b16", "b13" ]
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
The major advantage of indirect construction is the elimination of repeated rounds of plaque purification.
[ "9", "13", "14", "17", "14", "16", "13" ]
106
2,906
0
false
The major advantage of indirect construction is the elimination of repeated rounds of plaque purification.
[]
The major advantage of indirect construction is the elimination of repeated rounds of plaque purification.
true
true
true
true
true
491
1
INTRODUCTION
1
9
[ "b9", "b13", "b14", "b17", "b14", "b16", "b13" ]
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
Although both of these methods work, the generation of recombinant adenoviruses is still limited by several factors, including the low efficiency and difficulty in the screening of homologous recombination, the need for time-consuming plaque purification, and the frequent contamination by wild-type adenoviruses.
[ "9", "13", "14", "17", "14", "16", "13" ]
313
2,907
0
false
Although both of these methods work, the generation of recombinant adenoviruses is still limited by several factors, including the low efficiency and difficulty in the screening of homologous recombination, the need for time-consuming plaque purification, and the frequent contamination by wild-type adenoviruses.
[]
Although both of these methods work, the generation of recombinant adenoviruses is still limited by several factors, including the low efficiency and difficulty in the screening of homologous recombination, the need for time-consuming plaque purification, and the frequent contamination by wild-type adenoviruses.
true
true
true
true
true
491
1
INTRODUCTION
1
13
[ "b9", "b13", "b14", "b17", "b14", "b16", "b13" ]
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
Given that there are probably 25 000 genes present in human cells, these traditional methods do not meet the increasing reqiurements for the post-genome research on gene expression and regulation as well as the development of novel gene therapy approaches especially for the high-throughput generation of viruses require...
[ "9", "13", "14", "17", "14", "16", "13" ]
348
2,908
1
false
Given that there are probably 25 000 genes present in human cells, these traditional methods do not meet the increasing reqiurements for the post-genome research on gene expression and regulation as well as the development of novel gene therapy approaches especially for the high-throughput generation of viruses require...
[ "13" ]
Given that there are probably 25 000 genes present in human cells, these traditional methods do not meet the increasing reqiurements for the post-genome research on gene expression and regulation as well as the development of novel gene therapy approaches especially for the high-throughput generation of viruses require...
true
true
true
true
true
491
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
Considering the aforementioned drawbacks, we have now developed a robust and scalable system to generate recombinant adenoviruses based on a previously reported in vivo cloning system called mating-assisted genetically integrated cloning (MAGIC) (18).
[ "18", "18", "18", "18", "18" ]
251
2,909
1
false
Considering the aforementioned drawbacks, we have now developed a robust and scalable system to generate recombinant adenoviruses based on a previously reported in vivo cloning system called mating-assisted genetically integrated cloning (MAGIC).
[ "18" ]
Considering the aforementioned drawbacks, we have now developed a robust and scalable system to generate recombinant adenoviruses based on a previously reported in vivo cloning system called mating-assisted genetically integrated cloning (MAGIC).
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
The newly developed MAGIC procedure utilizes bacterial mating to catalyze the transfer of a DNA fragment between a donor vector in one bacterial strain and a recipient plasmid in a separate bacterial strain (18).
[ "18", "18", "18", "18", "18" ]
212
2,910
1
false
The newly developed MAGIC procedure utilizes bacterial mating to catalyze the transfer of a DNA fragment between a donor vector in one bacterial strain and a recipient plasmid in a separate bacterial strain.
[ "18" ]
The newly developed MAGIC procedure utilizes bacterial mating to catalyze the transfer of a DNA fragment between a donor vector in one bacterial strain and a recipient plasmid in a separate bacterial strain.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
Then the recombination between these plasmids can be forced by inducing I-SceI to site-specific cleavage and the red and gam recombinase to homologous recombination.
[ "18", "18", "18", "18", "18" ]
165
2,911
0
false
Then the recombination between these plasmids can be forced by inducing I-SceI to site-specific cleavage and the red and gam recombinase to homologous recombination.
[]
Then the recombination between these plasmids can be forced by inducing I-SceI to site-specific cleavage and the red and gam recombinase to homologous recombination.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
The donor strain contains the F factor (F′) transfer system, a low-copy plasmid containing a transfer operon (tra) and a cis-acting origin of transfer (oriT).
[ "18", "18", "18", "18", "18" ]
158
2,912
0
false
The donor strain contains the F factor (F′) transfer system, a low-copy plasmid containing a transfer operon (tra) and a cis-acting origin of transfer (oriT).
[]
The donor strain contains the F factor (F′) transfer system, a low-copy plasmid containing a transfer operon (tra) and a cis-acting origin of transfer (oriT).
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
When the oriT is ligated into the donor plasmid, the modified F′ is able to efficiently mobilize the donor plasmid, but not itself (18).
[ "18", "18", "18", "18", "18" ]
136
2,913
1
false
When the oriT is ligated into the donor plasmid, the modified F′ is able to efficiently mobilize the donor plasmid, but not itself.
[ "18" ]
When the oriT is ligated into the donor plasmid, the modified F′ is able to efficiently mobilize the donor plasmid, but not itself.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
A donor plasmid must also have a conditional origin of replication from R6K, oriγ, which is required for the trans-activation of factor π encoded by the gene pir1 or its relaxed copy-number control allele, pir1-116.
[ "18", "18", "18", "18", "18" ]
215
2,914
0
false
A donor plasmid must also have a conditional origin of replication from R6K, oriγ, which is required for the trans-activation of factor π encoded by the gene pir1 or its relaxed copy-number control allele, pir1-116.
[]
A donor plasmid must also have a conditional origin of replication from R6K, oriγ, which is required for the trans-activation of factor π encoded by the gene pir1 or its relaxed copy-number control allele, pir1-116.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
Only the donor strain DH10β can express pir1-116, so the donor plasmid will replicate only in DH10β, but not in the recipient strain BUN21 that does not have pir1-116 (18).
[ "18", "18", "18", "18", "18" ]
172
2,915
1
false
Only the donor strain DH10β can express pir1-116, so the donor plasmid will replicate only in DH10β, but not in the recipient strain BUN21 that does not have pir1-116.
[ "18" ]
Only the donor strain DH10β can express pir1-116, so the donor plasmid will replicate only in DH10β, but not in the recipient strain BUN21 that does not have pir1-116.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
After the bacteria are mixed, the presence of arabinose will induce the homing endonuclease I-SceI to lyse the fragment of interest from the donor plasmid, and cut down the stuff fragment from the recipient plasmid.
[ "18", "18", "18", "18", "18" ]
215
2,916
0
false
After the bacteria are mixed, the presence of arabinose will induce the homing endonuclease I-SceI to lyse the fragment of interest from the donor plasmid, and cut down the stuff fragment from the recipient plasmid.
[]
After the bacteria are mixed, the presence of arabinose will induce the homing endonuclease I-SceI to lyse the fragment of interest from the donor plasmid, and cut down the stuff fragment from the recipient plasmid.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
In addition, the plasmid pML300 contained in BUN21 will be induced to express the red recombinase gene in the presence of rhamnose.
[ "18", "18", "18", "18", "18" ]
131
2,917
0
false
In addition, the plasmid pML300 contained in BUN21 will be induced to express the red recombinase gene in the presence of rhamnose.
[]
In addition, the plasmid pML300 contained in BUN21 will be induced to express the red recombinase gene in the presence of rhamnose.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
The cleavage of both the donor fragment and the recipient plasmid greatly enhances recombination events (18).
[ "18", "18", "18", "18", "18" ]
109
2,918
1
false
The cleavage of both the donor fragment and the recipient plasmid greatly enhances recombination events.
[ "18" ]
The cleavage of both the donor fragment and the recipient plasmid greatly enhances recombination events.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
The plasmid pML300 contains a temperature-sensitive mutant derivative of the pSC102 origin of replication and will not replicate when bacteria are grown at 42°C.
[ "18", "18", "18", "18", "18" ]
161
2,919
0
false
The plasmid pML300 contains a temperature-sensitive mutant derivative of the pSC102 origin of replication and will not replicate when bacteria are grown at 42°C.
[]
The plasmid pML300 contains a temperature-sensitive mutant derivative of the pSC102 origin of replication and will not replicate when bacteria are grown at 42°C.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
In the present study, we cultured the bacteria at 42°C in order to eliminate the plasmid pML300.
[ "18", "18", "18", "18", "18" ]
96
2,920
0
false
In the present study, we cultured the bacteria at 42°C in order to eliminate the plasmid pML300.
[]
In the present study, we cultured the bacteria at 42°C in order to eliminate the plasmid pML300.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
In brief, the MAGIC procedure only requires the simple mixing of bacterial strains, which would significantly save time, effort and expense.
[ "18", "18", "18", "18", "18" ]
140
2,921
0
false
In brief, the MAGIC procedure only requires the simple mixing of bacterial strains, which would significantly save time, effort and expense.
[]
In brief, the MAGIC procedure only requires the simple mixing of bacterial strains, which would significantly save time, effort and expense.
true
true
true
true
true
492
2
INTRODUCTION
1
18
[ "b18", "b18", "b18", "b18", "b18" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
Therefore, this method may have implications in high-throughput recombinant DNA production for functional genomics studies, including the generation of recombinant adenoviruses.
[ "18", "18", "18", "18", "18" ]
177
2,922
0
false
Therefore, this method may have implications in high-throughput recombinant DNA production for functional genomics studies, including the generation of recombinant adenoviruses.
[]
Therefore, this method may have implications in high-throughput recombinant DNA production for functional genomics studies, including the generation of recombinant adenoviruses.
true
true
true
true
true
492
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
Herein we report a novel approach to the generation of recombinant adenovirus based on the MAGIC procedure (18).
[ "18", "8", "18" ]
112
2,923
1
false
Herein we report a novel approach to the generation of recombinant adenovirus based on the MAGIC procedure.
[ "18" ]
Herein we report a novel approach to the generation of recombinant adenovirus based on the MAGIC procedure.
true
true
true
true
true
493
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
This method utilizes site-specific and intensive recombination with random 50 bp regions of homology under red and gam recombinase, integrating the fragment of interest into the full-length adenovirus genome.
[ "18", "8", "18" ]
208
2,924
0
false
This method utilizes site-specific and intensive recombination with random 50 bp regions of homology under red and gam recombinase, integrating the fragment of interest into the full-length adenovirus genome.
[]
This method utilizes site-specific and intensive recombination with random 50 bp regions of homology under red and gam recombinase, integrating the fragment of interest into the full-length adenovirus genome.
true
true
true
true
true
493
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
It is rapid (taking only 12–14 days to generate a recombinant adenovirus) and is free of parental virus contamination.
[ "18", "8", "18" ]
118
2,925
0
false
It is rapid (taking only 12–14 days to generate a recombinant adenovirus) and is free of parental virus contamination.
[]
It is rapid and is free of parental virus contamination.
true
true
true
true
true
493
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
We have constructed a novel donor vector pRTRA, in which the fragment of interest is flanked by two different 50 bp homology regions, H1 and H2, which in turn are flanked with two separate I-SceI sites.
[ "18", "8", "18" ]
202
2,926
0
false
We have constructed a novel donor vector pRTRA, in which the fragment of interest is flanked by two different 50 bp homology regions, H1 and H2, which in turn are flanked with two separate I-SceI sites.
[]
We have constructed a novel donor vector pRTRA, in which the fragment of interest is flanked by two different 50 bp homology regions, H1 and H2, which in turn are flanked with two separate I-SceI sites.
true
true
true
true
true
493
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
The novel recipient vector pAd-pheS also contains two I-SceI-linked H1 and H2 sites (8,18).
[ "18", "8", "18" ]
91
2,927
0
false
The novel recipient vector pAd-pheS also contains two I-SceI-linked H1 and H2 sites.
[ "8,18" ]
The novel recipient vector pAd-pheS also contains two I-SceI-linked H1 and H2 sites.
true
true
true
true
true
493
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
The recombination events are efficiently regulated by a series of intensive elements: an intron-encoding rare endonuclease I-SceI is induced by the sugar arabinose; and the red and gam recombinase is induced by the sugar rhamnose.
[ "18", "8", "18" ]
230
2,928
0
false
The recombination events are efficiently regulated by a series of intensive elements: an intron-encoding rare endonuclease I-SceI is induced by the sugar arabinose; and the red and gam recombinase is induced by the sugar rhamnose.
[]
The recombination events are efficiently regulated by a series of intensive elements: an intron-encoding rare endonuclease I-SceI is induced by the sugar arabinose; and the red and gam recombinase is induced by the sugar rhamnose.
true
true
true
true
true
493
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
Once the DNA fragment of interest in the donor vector and the stuff fragment in the recipient vector are both cut down by I-SceI, the recombination events mediated by the red and gam recombinase are stimulated.
[ "18", "8", "18" ]
210
2,929
0
false
Once the DNA fragment of interest in the donor vector and the stuff fragment in the recipient vector are both cut down by I-SceI, the recombination events mediated by the red and gam recombinase are stimulated.
[]
Once the DNA fragment of interest in the donor vector and the stuff fragment in the recipient vector are both cut down by I-SceI, the recombination events mediated by the red and gam recombinase are stimulated.
true
true
true
true
true
493
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
The efficiency of transfer of the DNA fragment of interest from pRTRA to pAd-pheS was shown to be very high; the positive recombination efficiency can be as high as 100%.
[ "18", "8", "18" ]
170
2,930
0
false
The efficiency of transfer of the DNA fragment of interest from pRTRA to pAd-pheS was shown to be very high; the positive recombination efficiency can be as high as 100%.
[]
The efficiency of transfer of the DNA fragment of interest from pRTRA to pAd-pheS was shown to be very high; the positive recombination efficiency can be as high as 100%.
true
true
true
true
true
493
3
INTRODUCTION
1
18
[ "b18", "b8", "b18" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
This novel method can be used for the high-throughput creation of recombinant adenoviruses, which may be suitable for constructing an adenoviral cDNA expression library as demonstrated in the present study.
[ "18", "8", "18" ]
206
2,931
0
false
This novel method can be used for the high-throughput creation of recombinant adenoviruses, which may be suitable for constructing an adenoviral cDNA expression library as demonstrated in the present study.
[]
This novel method can be used for the high-throughput creation of recombinant adenoviruses, which may be suitable for constructing an adenoviral cDNA expression library as demonstrated in the present study.
true
true
true
true
true
493
0
DISCUSSION
0
null
null
16,855,284
pmid-1032904|pmid-15334112|pmid-12975310|pmid-15042091
Following the completion of the Human Genome Project and the significant progress made in identifying disease-causing genes, an increasing need arises for the development of high-throughput adenovirus production for various researches and development projects.
null
260
2,932
0
false
null
null
Following the completion of the Human Genome Project and the significant progress made in identifying disease-causing genes, an increasing need arises for the development of high-throughput adenovirus production for various researches and development projects.
true
true
true
true
true
494
0
DISCUSSION
0
null
null
16,855,284
pmid-1032904|pmid-15334112|pmid-12975310|pmid-15042091
Traditional methods of constructing recombinant adenoviruses cannot meet these ever-growing needs.
null
98
2,933
0
false
null
null
Traditional methods of constructing recombinant adenoviruses cannot meet these ever-growing needs.
true
true
true
true
true
494
0
DISCUSSION
0
null
null
16,855,284
pmid-1032904|pmid-15334112|pmid-12975310|pmid-15042091
More recently, the site-specific recombination of an expression cassette into the adenovirus genome to generate recombinant adenoviruses in E.coli has become popular.
null
166
2,934
0
false
null
null
More recently, the site-specific recombination of an expression cassette into the adenovirus genome to generate recombinant adenoviruses in E.coli has become popular.
true
true
true
true
true
494
0
DISCUSSION
0
null
null
16,855,284
pmid-1032904|pmid-15334112|pmid-12975310|pmid-15042091
This method is rapid since it eliminates the numerous manipulations of sub cloning in vitro and multiple rounds of plaque purification.
null
135
2,935
0
false
null
null
This method is rapid since it eliminates the numerous manipulations of sub cloning in vitro and multiple rounds of plaque purification.
true
true
true
true
true
494
1
DISCUSSION
0
null
null
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
In this study, we described a novel, simple and efficient method for the construction of recombinant adenovirus.
null
112
2,936
0
false
null
null
In this study, we described a novel, simple and efficient method for the construction of recombinant adenovirus.
true
true
true
true
true
495
1
DISCUSSION
0
null
null
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
As illustrated in Figure 3, the novel strategy developed involves three major steps.
null
84
2,937
0
false
null
null
As illustrated in Figure 3, the novel strategy developed involves three major steps.
true
true
true
true
true
495
1
DISCUSSION
0
null
null
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
First, the gene of interest is cloned into a donor vector pRTRA.
null
64
2,938
0
false
null
null
First, the gene of interest is cloned into a donor vector pRTRA.
true
true
true
true
true
495
1
DISCUSSION
0
null
null
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
Second, the donor and the recipient bacteria are mixed for mating, and the recombinants are selected by using kanamycin, ampicillin and Cl-Phe.
null
143
2,939
0
false
null
null
Second, the donor and the recipient bacteria are mixed for mating, and the recombinants are selected by using kanamycin, ampicillin and Cl-Phe.
true
true
true
true
true
495
1
DISCUSSION
0
null
null
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
Multiple restriction digestion analysis is performed for further identification.
null
80
2,940
0
false
null
null
Multiple restriction digestion analysis is performed for further identification.
true
true
true
true
true
495
1
DISCUSSION
0
null
null
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
Third, the recombinant adenoviral plasmid is cleaved with PacI to expose its inverted terminal repeats and then transfected into a packaging cell line (e.g.
null
156
2,941
0
false
null
null
Third, the recombinant adenoviral plasmid is cleaved with PacI to expose its inverted terminal repeats and then transfected into a packaging cell line (e.g.
true
true
true
true
true
495
1
DISCUSSION
0
null
null
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
HEK 293 cells).
null
15
2,942
0
false
null
null
HEK 293 cells).
true
true
true
true
true
495
1
DISCUSSION
0
null
null
16,855,284
pmid-10871752|pmid-14645922|pmid-9032314|pmid-8676512|pmid-9032314|pmid-15879348|pmid-14645922
The positive selection by antibiotics, the negative selection by Cl-Phe and the ability to bypass further identification steps make the screening of recombinants simple and efficient.
null
183
2,943
0
false
null
null
The positive selection by antibiotics, the negative selection by Cl-Phe and the ability to bypass further identification steps make the screening of recombinants simple and efficient.
true
true
true
true
true
495
2
DISCUSSION
1
18
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
To our knowledge, the method described herein is the first successful example to apply MAGIC to the construction of recombinant adenoviruses.
[ "18", "21", "22" ]
141
2,944
0
false
To our knowledge, the method described herein is the first successful example to apply MAGIC to the construction of recombinant adenoviruses.
[]
To our knowledge, the method described herein is the first successful example to apply MAGIC to the construction of recombinant adenoviruses.
true
true
true
true
true
496
2
DISCUSSION
1
18
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
For adenoviral vector construction, this method has several advantages over other conventional methods.
[ "18", "21", "22" ]
103
2,945
0
false
For adenoviral vector construction, this method has several advantages over other conventional methods.
[]
For adenoviral vector construction, this method has several advantages over other conventional methods.
true
true
true
true
true
496
2
DISCUSSION
1
18
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
First, a small size plasmid (3.5 kb) is used, obviating the manipulation of the large adenoviral genome.
[ "18", "21", "22" ]
104
2,946
0
false
First, a small size plasmid (3.5 kb) is used, obviating the manipulation of the large adenoviral genome.
[]
First, a small size plasmid (3.5 kb) is used, obviating the manipulation of the large adenoviral genome.
true
true
true
true
true
496
2
DISCUSSION
1
18
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
Second, the recombination events depend on a λ red and gam recombinase-mediated cassette exchange in E.coli, eliminating multiple repeated rounds of plaque purification.
[ "18", "21", "22" ]
169
2,947
0
false
Second, the recombination events depend on a λ red and gam recombinase-mediated cassette exchange in E.coli, eliminating multiple repeated rounds of plaque purification.
[]
Second, the recombination events depend on a λ red and gam recombinase-mediated cassette exchange in E.coli, eliminating multiple repeated rounds of plaque purification.
true
true
true
true
true
496
2
DISCUSSION
1
18
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
Third, the efficiency of the recombination can reach 100% since the red and gam recombination system is highly efficient and the recombinants are selected by both arabinose and Cl-Phe (18,21).
[ "18", "21", "22" ]
192
2,948
0
false
Third, the efficiency of the recombination can reach 100% since the red and gam recombination system is highly efficient and the recombinants are selected by both arabinose and Cl-Phe.
[ "18,21" ]
Third, the efficiency of the recombination can reach 100% since the red and gam recombination system is highly efficient and the recombinants are selected by both arabinose and Cl-Phe.
true
true
true
true
true
496
2
DISCUSSION
1
18
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
This efficiency was further demonstrated in constructing an adenoviral cDNA expression library.
[ "18", "21", "22" ]
95
2,949
0
false
This efficiency was further demonstrated in constructing an adenoviral cDNA expression library.
[]
This efficiency was further demonstrated in constructing an adenoviral cDNA expression library.
true
true
true
true
true
496
2
DISCUSSION
1
22
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
Fourth, the system has potential for the modification of any adenoviral sequences (22).
[ "18", "21", "22" ]
87
2,950
1
false
Fourth, the system has potential for the modification of any adenoviral sequences.
[ "22" ]
Fourth, the system has potential for the modification of any adenoviral sequences.
true
true
true
true
true
496
2
DISCUSSION
1
18
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
Therefore, the approach described here is a highly efficient, less time-consuming and labor-intensive method for constructing recombinant adenoviruses.
[ "18", "21", "22" ]
151
2,951
0
false
Therefore, the approach described here is a highly efficient, less time-consuming and labor-intensive method for constructing recombinant adenoviruses.
[]
Therefore, the approach described here is a highly efficient, less time-consuming and labor-intensive method for constructing recombinant adenoviruses.
true
true
true
true
true
496
2
DISCUSSION
1
18
[ "b18", "b21", "b22" ]
16,855,284
pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-15731760|pmid-11753384|pmid-15610612
In addition, we speculate that the method can also be useful in the construction of other viruses.
[ "18", "21", "22" ]
98
2,952
0
false
In addition, we speculate that the method can also be useful in the construction of other viruses.
[]
In addition, we speculate that the method can also be useful in the construction of other viruses.
true
true
true
true
true
496
3
DISCUSSION
1
15
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
Many standard recombinant adenoviral vector systems have been established, including Adeasy™ and adenoviral vector system based on Cre-lox (15,17).
[ "15", "17", "15", "15", "16" ]
147
2,953
0
false
Many standard recombinant adenoviral vector systems have been established, including Adeasy™ and adenoviral vector system based on Cre-lox.
[ "15,17" ]
Many standard recombinant adenoviral vector systems have been established, including Adeasy™ and adenoviral vector system based on Cre-lox.
true
true
true
true
true
497
3
DISCUSSION
1
15
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
Compared with the original system (the Adeasy™ adenoviral vector system) (15), we have improved the design and the implementation of vector systems in three ways.
[ "15", "17", "15", "15", "16" ]
162
2,954
1
false
Compared with the original system (the Adeasy™ adenoviral vector system), we have improved the design and the implementation of vector systems in three ways.
[ "15" ]
Compared with the original system (the Adeasy™ adenoviral vector system), we have improved the design and the implementation of vector systems in three ways.
true
true
true
true
true
497
3
DISCUSSION
1
15
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
First, in the Adeasy system, the recombinant adenoviral plasmid cannot be effectively amplified in the recombinant strain BJ5183, so it is necessary to transform the recombinant plasmid to a recA, endA strain, (such as DH10B, XL-Gold).
[ "15", "17", "15", "15", "16" ]
235
2,955
0
false
First, in the Adeasy system, the recombinant adenoviral plasmid cannot be effectively amplified in the recombinant strain BJ5183, so it is necessary to transform the recombinant plasmid to a recA, endA strain, (such as DH10B, XL-Gold).
[]
First, in the Adeasy system, the recombinant adenoviral plasmid cannot be effectively amplified in the recombinant strain BJ5183, so it is necessary to transform the recombinant plasmid to a recA, endA strain,.
true
true
true
true
true
497
3
DISCUSSION
1
15
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
In contrast, for the MAGIC system, the desired recombinant adenoviral plasmid can be achieved in the recipient strain with greater yields.
[ "15", "17", "15", "15", "16" ]
138
2,956
0
false
In contrast, for the MAGIC system, the desired recombinant adenoviral plasmid can be achieved in the recipient strain with greater yields.
[]
In contrast, for the MAGIC system, the desired recombinant adenoviral plasmid can be achieved in the recipient strain with greater yields.
true
true
true
true
true
497
3
DISCUSSION
1
15
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
Second, in the Adeasy system, the pShuttle plasmid carries a foreign gene, rendering the treatment with PmeI and alkaline phosphatase necessary, which is not needed in the MAGIC procedure.
[ "15", "17", "15", "15", "16" ]
188
2,957
0
false
Second, in the Adeasy system, the pShuttle plasmid carries a foreign gene, rendering the treatment with PmeI and alkaline phosphatase necessary, which is not needed in the MAGIC procedure.
[]
Second, in the Adeasy system, the pShuttle plasmid carries a foreign gene, rendering the treatment with PmeI and alkaline phosphatase necessary, which is not needed in the MAGIC procedure.
true
true
true
true
true
497
3
DISCUSSION
1
15
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
Third, the MAGIC method is much more efficient than the Adeasy system, and it can save 2–3 days in constructing recombinant Adenoviruses.
[ "15", "17", "15", "15", "16" ]
137
2,958
0
false
Third, the MAGIC method is much more efficient than the Adeasy system, and it can save 2–3 days in constructing recombinant Adenoviruses.
[]
Third, the MAGIC method is much more efficient than the Adeasy system, and it can save 2–3 days in constructing recombinant Adenoviruses.
true
true
true
true
true
497
3
DISCUSSION
1
15
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
The high efficiency is attributable to that the combination via the Red system is 500–1000 times more efficient than the BJ5183 platform (15), that inducing I-SceI also results in a 20-fold enrichment for recombinants, and that an additional 25-fold enrichment can be achieved by pheS.
[ "15", "17", "15", "15", "16" ]
285
2,959
1
false
The high efficiency is attributable to that the combination via the Red system is 500–1000 times more efficient than the BJ5183 platform, that inducing I-SceI also results in a 20-fold enrichment for recombinants, and that an additional 25-fold enrichment can be achieved by pheS.
[ "15" ]
The high efficiency is attributable to that the combination via the Red system is 500–1000 times more efficient than the BJ5183 platform, that inducing I-SceI also results in a 20-fold enrichment for recombinants, and that an additional 25-fold enrichment can be achieved by pheS.
true
true
true
true
true
497
3
DISCUSSION
1
16
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
More recently, a new method called recombinase-mediated cassette exchange based on Cre-lox recombination in mammalian cells has been reported, which needs several repeated rounds of vector purification and suffers from frequent contamination of the replication-competent adenoviruses (16).
[ "15", "17", "15", "15", "16" ]
289
2,960
1
false
More recently, a new method called recombinase-mediated cassette exchange based on Cre-lox recombination in mammalian cells has been reported, which needs several repeated rounds of vector purification and suffers from frequent contamination of the replication-competent adenoviruses.
[ "16" ]
More recently, a new method called recombinase-mediated cassette exchange based on Cre-lox recombination in mammalian cells has been reported, which needs several repeated rounds of vector purification and suffers from frequent contamination of the replication-competent adenoviruses.
true
true
true
true
true
497
3
DISCUSSION
1
15
[ "b15", "b17", "b15", "b15", "b16" ]
16,855,284
pmid-15731760|pmid-15042091|pmid-15731760|pmid-9482916|pmid-8676512|pmid-9482916|pmid-9482916|pmid-15879348
Although the rest of this method is rapid and simple, the laborious manipulation of vector purification will remarkably limit the applications of this elegant system.
[ "15", "17", "15", "15", "16" ]
166
2,961
0
false
Although the rest of this method is rapid and simple, the laborious manipulation of vector purification will remarkably limit the applications of this elegant system.
[]
Although the rest of this method is rapid and simple, the laborious manipulation of vector purification will remarkably limit the applications of this elegant system.
true
true
true
true
true
497
4
DISCUSSION
1
21
[ "b21", "b22" ]
16,855,284
pmid-11753384|pmid-15610612
In conclusion, we have described a robust approach for the construction of recombinant adenoviruses based on MAGIC and the Adeasy™ adenoviral vector system, and it yields the desired recombinant adenoviral genome 100% of the time with high yields.
[ "21", "22" ]
247
2,962
0
false
In conclusion, we have described a robust approach for the construction of recombinant adenoviruses based on MAGIC and the Adeasy™ adenoviral vector system, and it yields the desired recombinant adenoviral genome 100% of the time with high yields.
[]
In conclusion, we have described a robust approach for the construction of recombinant adenoviruses based on MAGIC and the Adeasy™ adenoviral vector system, and it yields the desired recombinant adenoviral genome 100% of the time with high yields.
true
true
true
true
true
498
4
DISCUSSION
1
21
[ "b21", "b22" ]
16,855,284
pmid-11753384|pmid-15610612
The resulting plasmid containing the recombinant adenoviral genome is truly clonal, obviating the need for screening and several repeated rounds of plaque purification.
[ "21", "22" ]
168
2,963
0
false
The resulting plasmid containing the recombinant adenoviral genome is truly clonal, obviating the need for screening and several repeated rounds of plaque purification.
[]
The resulting plasmid containing the recombinant adenoviral genome is truly clonal, obviating the need for screening and several repeated rounds of plaque purification.
true
true
true
true
true
498
4
DISCUSSION
1
21
[ "b21", "b22" ]
16,855,284
pmid-11753384|pmid-15610612
Using this improved system based on MAGIC, a set of hundreds or even thousands of recombinant adenoviral plasmids could be obtained by mating with a large set of donor bacteria.
[ "21", "22" ]
177
2,964
0
false
Using this improved system based on MAGIC, a set of hundreds or even thousands of recombinant adenoviral plasmids could be obtained by mating with a large set of donor bacteria.
[]
Using this improved system based on MAGIC, a set of hundreds or even thousands of recombinant adenoviral plasmids could be obtained by mating with a large set of donor bacteria.
true
true
true
true
true
498
4
DISCUSSION
1
21
[ "b21", "b22" ]
16,855,284
pmid-11753384|pmid-15610612
Therefore, the method is compatible with high-throughput applications including the construction of cDNA expression library.
[ "21", "22" ]
124
2,965
0
false
Therefore, the method is compatible with high-throughput applications including the construction of cDNA expression library.
[]
Therefore, the method is compatible with high-throughput applications including the construction of cDNA expression library.
true
true
true
true
true
498
4
DISCUSSION
1
21
[ "b21", "b22" ]
16,855,284
pmid-11753384|pmid-15610612
Unlike conventional in vitro methods that use restriction enzymes or site-specific recombinases, recombinant adenoviral DNA assembled by MAGIC achieves a seamless transfer of genetic elements through homologous recombination in vivo without the need for DNA preparation and in vitro manipulation.
[ "21", "22" ]
296
2,966
0
false
Unlike conventional in vitro methods that use restriction enzymes or site-specific recombinases, recombinant adenoviral DNA assembled by MAGIC achieves a seamless transfer of genetic elements through homologous recombination in vivo without the need for DNA preparation and in vitro manipulation.
[]
Unlike conventional in vitro methods that use restriction enzymes or site-specific recombinases, recombinant adenoviral DNA assembled by MAGIC achieves a seamless transfer of genetic elements through homologous recombination in vivo without the need for DNA preparation and in vitro manipulation.
true
true
true
true
true
498
4
DISCUSSION
1
21
[ "b21", "b22" ]
16,855,284
pmid-11753384|pmid-15610612
Moreover, the highly efficient λ Red system will be of great use for the knockout or modification of other adenoviral sequences (21,22).
[ "21", "22" ]
136
2,967
0
false
Moreover, the highly efficient λ Red system will be of great use for the knockout or modification of other adenoviral sequences.
[ "21,22" ]
Moreover, the highly efficient λ Red system will be of great use for the knockout or modification of other adenoviral sequences.
true
true
true
true
true
498
4
DISCUSSION
1
21
[ "b21", "b22" ]
16,855,284
pmid-11753384|pmid-15610612
This robust, scalable and highly efficient method of constructing recombinant adenoviruses will be of great use in genomics and proteomics researches.
[ "21", "22" ]
150
2,968
0
false
This robust, scalable and highly efficient method of constructing recombinant adenoviruses will be of great use in genomics and proteomics researches.
[]
This robust, scalable and highly efficient method of constructing recombinant adenoviruses will be of great use in genomics and proteomics researches.
true
true
true
true
true
498
0
INTRODUCTION
1
1
[ "B1" ]
17,332,015
pmid-11357144
Cancer cells have large and small abnormalities in their genetic material: additional or missing chromosomes, mutated genes and other types of alterations.
[ "1" ]
155
2,969
0
false
Cancer cells have large and small abnormalities in their genetic material: additional or missing chromosomes, mutated genes and other types of alterations.
[]
Cancer cells have large and small abnormalities in their genetic material: additional or missing chromosomes, mutated genes and other types of alterations.
true
true
true
true
true
499
0
INTRODUCTION
1
1
[ "B1" ]
17,332,015
pmid-11357144
The lost of genome stability pathways is associated with genetic deterioration of cancer cells and is one of the most important aspects of carcinogenesis.
[ "1" ]
154
2,970
0
false
The lost of genome stability pathways is associated with genetic deterioration of cancer cells and is one of the most important aspects of carcinogenesis.
[]
The lost of genome stability pathways is associated with genetic deterioration of cancer cells and is one of the most important aspects of carcinogenesis.
true
true
true
true
true
499
0
INTRODUCTION
1
1
[ "B1" ]
17,332,015
pmid-11357144
In fact, mutations in mismatch repair (MMR), nucleotide-excision repair (NER), base-excision repair (BER) and recombinational repair genes have been causally implicated in the acquisition of a genome instability phenotype (1).
[ "1" ]
226
2,971
1
false
In fact, mutations in mismatch repair (MMR), nucleotide-excision repair (NER), base-excision repair (BER) and recombinational repair genes have been causally implicated in the acquisition of a genome instability phenotype.
[ "1" ]
In fact, mutations in mismatch repair (MMR), nucleotide-excision repair (NER), base-excision repair (BER) and recombinational repair genes have been causally implicated in the acquisition of a genome instability phenotype.
true
true
true
true
true
499
1
INTRODUCTION
1
2
[ "B2" ]
17,332,015
pmid-14993899
Genome instability in solid tumors originates from either somatic mutations (observed in the majority of sporadic cancers) or germline mutations (associated to rare hereditary cancer syndromes).
[ "2" ]
194
2,972
0
false
Genome instability in solid tumors originates from either somatic mutations (observed in the majority of sporadic cancers) or germline mutations (associated to rare hereditary cancer syndromes).
[]
Genome instability in solid tumors originates from either somatic mutations (observed in the majority of sporadic cancers) or germline mutations (associated to rare hereditary cancer syndromes).
true
true
true
true
true
500
1
INTRODUCTION
1
2
[ "B2" ]
17,332,015
pmid-14993899
Considering the list of repair genes presented in Cancer Gene Census (2), germline mutations can be observed in NER, BER and MMR, while somatic mutations are described only in recombinational repair (homologous recombination and non-homologous end joining).
[ "2" ]
257
2,973
1
false
Considering the list of repair genes presented in Cancer Gene Census, germline mutations can be observed in NER, BER and MMR, while somatic mutations are described only in recombinational repair (homologous recombination and non-homologous end joining).
[ "2" ]
Considering the list of repair genes presented in Cancer Gene Census, germline mutations can be observed in NER, BER and MMR, while somatic mutations are described only in recombinational repair (homologous recombination and non-homologous end joining).
true
true
true
true
true
500
1
INTRODUCTION
1
2
[ "B2" ]
17,332,015
pmid-14993899
On the other hand, mutations in apoptotic genes are recurrently observed in both types of solid tumors as listed in the census.
[ "2" ]
127
2,974
0
false
On the other hand, mutations in apoptotic genes are recurrently observed in both types of solid tumors as listed in the census.
[]
On the other hand, mutations in apoptotic genes are recurrently observed in both types of solid tumors as listed in the census.
true
true
true
true
true
500
2
INTRODUCTION
1
3
[ "B3", "B4", "B2" ]
17,332,015
pmid-15286780|pmid-16359931|pmid-14993899
The genotype signature of the malfunctioning of these stability gene networks is 2-fold: aneuploidy (e.g.
[ "3", "4", "2" ]
105
2,975
0
false
The genotype signature of the malfunctioning of these stability gene networks is 2-fold: aneuploidy (e.g.
[]
The genotype signature of the malfunctioning of these stability gene networks is 2-fold: aneuploidy (e.g.
true
true
true
true
true
501
2
INTRODUCTION
1
3
[ "B3", "B4", "B2" ]
17,332,015
pmid-15286780|pmid-16359931|pmid-14993899
translocations, gain or loss of entire or large parts of chromosomes) and/or random point mutations (e.g.
[ "3", "4", "2" ]
105
2,976
0
false
translocations, gain or loss of entire or large parts of chromosomes) and/or random point mutations (e.g.
[]
translocations, gain or loss of entire or large parts of chromosomes) and/or random point mutations (e.g.
false
true
true
true
false
501
2
INTRODUCTION
1
3
[ "B3", "B4", "B2" ]
17,332,015
pmid-15286780|pmid-16359931|pmid-14993899
nucleotide changes randomly distributed throughout the genome) (3).
[ "3", "4", "2" ]
67
2,977
1
false
nucleotide changes randomly distributed throughout the genome).
[ "3" ]
nucleotide changes randomly distributed throughout the genome).
false
true
true
true
false
501
2
INTRODUCTION
1
4
[ "B3", "B4", "B2" ]
17,332,015
pmid-15286780|pmid-16359931|pmid-14993899
The omnipresence of random point mutations in sporadic solid tumors (4) and the recurrent absence of mutations in nucleotide repair genes (2) suggest a functional deficiency in these stability pathways without structural alterations in the related DNA sequence.
[ "3", "4", "2" ]
261
2,978
1
false
The omnipresence of random point mutations in sporadic solid tumors and the recurrent absence of mutations in nucleotide repair genes suggest a functional deficiency in these stability pathways without structural alterations in the related DNA sequence.
[ "4", "2" ]
The omnipresence of random point mutations in sporadic solid tumors and the recurrent absence of mutations in nucleotide repair genes suggest a functional deficiency in these stability pathways without structural alterations in the related DNA sequence.
true
true
true
true
true
501
3
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8", "B9", "B10" ]
17,332,015
pmid-12142522|pmid-17109012|pmid-16373963|pmid-12951588|pmid-12552134|pmid-16959974
There are different views explaining how a cell loses genome stability and acquires a cancerous phenotype (5,6).
[ "5", "6", "7", "8", "9", "10" ]
112
2,979
0
false
There are different views explaining how a cell loses genome stability and acquires a cancerous phenotype.
[ "5,6" ]
There are different views explaining how a cell loses genome stability and acquires a cancerous phenotype.
true
true
true
true
true
502
3
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8", "B9", "B10" ]
17,332,015
pmid-12142522|pmid-17109012|pmid-16373963|pmid-12951588|pmid-12552134|pmid-16959974
In one proposed scenario, large chromosomal changes are required for triggering the onset of cancer, such as varying the number of whole chromosomes or cutting and/or pasting their fragments among different chromosomes.
[ "5", "6", "7", "8", "9", "10" ]
219
2,980
0
false
In one proposed scenario, large chromosomal changes are required for triggering the onset of cancer, such as varying the number of whole chromosomes or cutting and/or pasting their fragments among different chromosomes.
[]
In one proposed scenario, large chromosomal changes are required for triggering the onset of cancer, such as varying the number of whole chromosomes or cutting and/or pasting their fragments among different chromosomes.
true
true
true
true
true
502
3
INTRODUCTION
1
7
[ "B5", "B6", "B7", "B8", "B9", "B10" ]
17,332,015
pmid-12142522|pmid-17109012|pmid-16373963|pmid-12951588|pmid-12552134|pmid-16959974
Then either the expression of unbalanced gene dosage (7) and/or alterations in mitotic check points (8) can, under adequate conditions, give place to a cancer.
[ "5", "6", "7", "8", "9", "10" ]
159
2,981
1
false
Then either the expression of unbalanced gene dosage and/or alterations in mitotic check points can, under adequate conditions, give place to a cancer.
[ "7", "8" ]
Then either the expression of unbalanced gene dosage and/or alterations in mitotic check points can, under adequate conditions, give place to a cancer.
true
true
true
true
true
502
3
INTRODUCTION
1
9
[ "B5", "B6", "B7", "B8", "B9", "B10" ]
17,332,015
pmid-12142522|pmid-17109012|pmid-16373963|pmid-12951588|pmid-12552134|pmid-16959974
An alternative idea proposes that cancer cells have a ‘mutator phenotype’ that favors the acquisition of point mutations, which eventually affect tumor suppressors or oncogenes yielding to cancer (9).
[ "5", "6", "7", "8", "9", "10" ]
200
2,982
1
false
An alternative idea proposes that cancer cells have a ‘mutator phenotype’ that favors the acquisition of point mutations, which eventually affect tumor suppressors or oncogenes yielding to cancer.
[ "9" ]
An alternative idea proposes that cancer cells have a ‘mutator phenotype’ that favors the acquisition of point mutations, which eventually affect tumor suppressors or oncogenes yielding to cancer.
true
true
true
true
true
502
3
INTRODUCTION
1
10
[ "B5", "B6", "B7", "B8", "B9", "B10" ]
17,332,015
pmid-12142522|pmid-17109012|pmid-16373963|pmid-12951588|pmid-12552134|pmid-16959974
Supporting this idea, a list of mutated genes found in human colorectal and breast cancer covering several gene functions shows that point mutations are the most common alterations found throughout the genome of cancer cells (over 87%) (10).
[ "5", "6", "7", "8", "9", "10" ]
241
2,983
1
false
Supporting this idea, a list of mutated genes found in human colorectal and breast cancer covering several gene functions shows that point mutations are the most common alterations found throughout the genome of cancer cells.
[ "over 87%", "10" ]
Supporting this idea, a list of mutated genes found in human colorectal and breast cancer covering several gene functions shows that point mutations are the most common alterations found throughout the genome of cancer cells.
true
true
true
true
true
502
4
INTRODUCTION
1
11
[ "B11", "B12" ]
17,332,015
pmid-12119410|pmid-12519941
The two scenarios are qualitatively possible, since both offer explanations to the typical chromosome configurations and nucleotide alterations of a cancer cell.
[ "11", "12" ]
161
2,984
0
false
The two scenarios are qualitatively possible, since both offer explanations to the typical chromosome configurations and nucleotide alterations of a cancer cell.
[]
The two scenarios are qualitatively possible, since both offer explanations to the typical chromosome configurations and nucleotide alterations of a cancer cell.
true
true
true
true
true
503
4
INTRODUCTION
1
11
[ "B11", "B12" ]
17,332,015
pmid-12119410|pmid-12519941
In order to discriminate between different scenarios, studies of chromosome and gene structures should be complemented by quantitative analysis of gene expression of cancer cells.
[ "11", "12" ]
179
2,985
0
false
In order to discriminate between different scenarios, studies of chromosome and gene structures should be complemented by quantitative analysis of gene expression of cancer cells.
[]
In order to discriminate between different scenarios, studies of chromosome and gene structures should be complemented by quantitative analysis of gene expression of cancer cells.
true
true
true
true
true
503
4
INTRODUCTION
1
11
[ "B11", "B12" ]
17,332,015
pmid-12119410|pmid-12519941
As a contribution in this direction, we present here a pioneer, comprehensive statistical analysis of 10 gene expression pathways in normal and cancer cells using serial analysis of gene expression (SAGE) data from the public gene expression resource (SAGE Genie) (11) available at Cancer Genome Anatomy Project (CGAP) (...
[ "11", "12" ]
324
2,986
1
false
As a contribution in this direction, we present here a pioneer, comprehensive statistical analysis of 10 gene expression pathways in normal and cancer cells using serial analysis of gene expression (SAGE) data from the public gene expression resource (SAGE Genie) available at Cancer Genome Anatomy Project (CGAP).
[ "11", "12" ]
As a contribution in this direction, we present here a pioneer, comprehensive statistical analysis of 10 gene expression pathways in normal and cancer cells using serial analysis of gene expression (SAGE) data from the public gene expression resource (SAGE Genie) available at Cancer Genome Anatomy Project (CGAP).
true
true
true
true
true
503
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,740,739
pmid-16478693|pmid-16296791|pmid-15538359|pmid-15990405|pmid-12771197
One of the key problems facing the development of siRNA and other small molecule therapeutics is delivery, both systemic and to specific cell or tissue types (1,2).
[ "1", "2", "3", "4", "5" ]
164
2,987
0
false
One of the key problems facing the development of siRNA and other small molecule therapeutics is delivery, both systemic and to specific cell or tissue types.
[ "1,2" ]
One of the key problems facing the development of siRNA and other small molecule therapeutics is delivery, both systemic and to specific cell or tissue types.
true
true
true
true
true
504
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,740,739
pmid-16478693|pmid-16296791|pmid-15538359|pmid-15990405|pmid-12771197
A variety of small molecules, lipids, peptides and proteins have previously been examined as potential delivery vehicles and vectors for nucleic acids.
[ "1", "2", "3", "4", "5" ]
151
2,988
0
false
A variety of small molecules, lipids, peptides and proteins have previously been examined as potential delivery vehicles and vectors for nucleic acids.
[]
A variety of small molecules, lipids, peptides and proteins have previously been examined as potential delivery vehicles and vectors for nucleic acids.
true
true
true
true
true
504
0
INTRODUCTION
1
3
[ "b1", "b2", "b3", "b4", "b5" ]
16,740,739
pmid-16478693|pmid-16296791|pmid-15538359|pmid-15990405|pmid-12771197
For example, the non-specific uptake of cholesterol labeled siRNAs has been demonstrated to be effective for delivery to cells grown in culture as well to liver, heart, kidney and lung tissue in mice (3).
[ "1", "2", "3", "4", "5" ]
204
2,989
1
false
For example, the non-specific uptake of cholesterol labeled siRNAs has been demonstrated to be effective for delivery to cells grown in culture as well to liver, heart, kidney and lung tissue in mice.
[ "3" ]
For example, the non-specific uptake of cholesterol labeled siRNAs has been demonstrated to be effective for delivery to cells grown in culture as well to liver, heart, kidney and lung tissue in mice.
true
true
true
true
true
504
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,740,739
pmid-16478693|pmid-16296791|pmid-15538359|pmid-15990405|pmid-12771197
Similarly, a portion of the HIV-1 gp41 protein fused to a nuclear localization sequence has been demonstrated to be an effective means for the general delivery of siRNAs in tissue culture (4,5).
[ "1", "2", "3", "4", "5" ]
194
2,990
0
false
Similarly, a portion of the HIV-1 gp41 protein fused to a nuclear localization sequence has been demonstrated to be an effective means for the general delivery of siRNAs in tissue culture.
[ "4,5" ]
Similarly, a portion of the HIV-1 gp41 protein fused to a nuclear localization sequence has been demonstrated to be an effective means for the general delivery of siRNAs in tissue culture.
true
true
true
true
true
504
1
INTRODUCTION
1
6
[ "b6", "b7", "b8" ]
16,740,739
pmid-15520458|pmid-16204072|pmid-15908939|pmid-12782573|pmid-10626807|pmid-11166685|pmid-16199376|pmid-14996706|pmid-10647616|pmid-11344318
Peptides have also been utilized for the cell-specific delivery of siRNAs.
[ "6", "7", "8" ]
74
2,991
0
false
Peptides have also been utilized for the cell-specific delivery of siRNAs.
[]
Peptides have also been utilized for the cell-specific delivery of siRNAs.
true
true
true
true
true
505
1
INTRODUCTION
1
6
[ "b6", "b7", "b8" ]
16,740,739
pmid-15520458|pmid-16204072|pmid-15908939|pmid-12782573|pmid-10626807|pmid-11166685|pmid-16199376|pmid-14996706|pmid-10647616|pmid-11344318
For example, Shchiffelers et al.
[ "6", "7", "8" ]
32
2,992
0
false
For example, Shchiffelers et al.
[]
For example, Shchiffelers et al.
true
true
true
true
true
505
1
INTRODUCTION
1
6
[ "b6", "b7", "b8" ]
16,740,739
pmid-15520458|pmid-16204072|pmid-15908939|pmid-12782573|pmid-10626807|pmid-11166685|pmid-16199376|pmid-14996706|pmid-10647616|pmid-11344318
utilized PEGylated polyethyleneimine and an integrin-binding RGD peptide to direct siRNA uptake to tumor neovalsulature (6).
[ "6", "7", "8" ]
124
2,993
1
false
utilized PEGylated polyethyleneimine and an integrin-binding RGD peptide to direct siRNA uptake to tumor neovalsulature.
[ "6" ]
utilized PEGylated polyethyleneimine and an integrin-binding RGD peptide to direct siRNA uptake to tumor neovalsulature.
false
true
true
true
false
505
1
INTRODUCTION
1
6
[ "b6", "b7", "b8" ]
16,740,739
pmid-15520458|pmid-16204072|pmid-15908939|pmid-12782573|pmid-10626807|pmid-11166685|pmid-16199376|pmid-14996706|pmid-10647616|pmid-11344318
In addition to small peptides, larger, protein-based targeting moieties have also been utilized.
[ "6", "7", "8" ]
96
2,994
0
false
In addition to small peptides, larger, protein-based targeting moieties have also been utilized.
[]
In addition to small peptides, larger, protein-based targeting moieties have also been utilized.
true
true
true
true
true
505
1
INTRODUCTION
1
7
[ "b6", "b7", "b8" ]
16,740,739
pmid-15520458|pmid-16204072|pmid-15908939|pmid-12782573|pmid-10626807|pmid-11166685|pmid-16199376|pmid-14996706|pmid-10647616|pmid-11344318
For example, the iron-binding protein transferrin has been used to target colloids composed of siRNA and cyclodextrin-containg polycations to transferrin receptor-expressing tumor cells (7).
[ "6", "7", "8" ]
190
2,995
1
false
For example, the iron-binding protein transferrin has been used to target colloids composed of siRNA and cyclodextrin-containg polycations to transferrin receptor-expressing tumor cells.
[ "7" ]
For example, the iron-binding protein transferrin has been used to target colloids composed of siRNA and cyclodextrin-containg polycations to transferrin receptor-expressing tumor cells.
true
true
true
true
true
505
1
INTRODUCTION
1
6
[ "b6", "b7", "b8" ]
16,740,739
pmid-15520458|pmid-16204072|pmid-15908939|pmid-12782573|pmid-10626807|pmid-11166685|pmid-16199376|pmid-14996706|pmid-10647616|pmid-11344318
More recently, the tissue-specific delivery of siRNAs has been achieved using fusions between protamine and antibodies.
[ "6", "7", "8" ]
119
2,996
0
false
More recently, the tissue-specific delivery of siRNAs has been achieved using fusions between protamine and antibodies.
[]
More recently, the tissue-specific delivery of siRNAs has been achieved using fusions between protamine and antibodies.
true
true
true
true
true
505
1
INTRODUCTION
1
6
[ "b6", "b7", "b8" ]
16,740,739
pmid-15520458|pmid-16204072|pmid-15908939|pmid-12782573|pmid-10626807|pmid-11166685|pmid-16199376|pmid-14996706|pmid-10647616|pmid-11344318
In this system, siRNAs were bound by the basic protamine and then targeted to tumor cells via antibodies.
[ "6", "7", "8" ]
105
2,997
0
false
In this system, siRNAs were bound by the basic protamine and then targeted to tumor cells via antibodies.
[]
In this system, siRNAs were bound by the basic protamine and then targeted to tumor cells via antibodies.
true
true
true
true
true
505
1
INTRODUCTION
1
8
[ "b6", "b7", "b8" ]
16,740,739
pmid-15520458|pmid-16204072|pmid-15908939|pmid-12782573|pmid-10626807|pmid-11166685|pmid-16199376|pmid-14996706|pmid-10647616|pmid-11344318
In one example, by using a fusion to an anti-ERbB2-specific single chain antibody, siRNAs could be targeted to tumor cells expressing the epidermal growth factor receptor ERbB2 (8).
[ "6", "7", "8" ]
181
2,998
1
false
In one example, by using a fusion to an anti-ERbB2-specific single chain antibody, siRNAs could be targeted to tumor cells expressing the epidermal growth factor receptor ERbB2.
[ "8" ]
In one example, by using a fusion to an anti-ERbB2-specific single chain antibody, siRNAs could be targeted to tumor cells expressing the epidermal growth factor receptor ERbB2.
true
true
true
true
true
505
2
INTRODUCTION
1
9
[ "b9", "b10", "b13", "b14" ]
16,740,739
pmid-11032850|pmid-11279054|pmid-9501188|pmid-15520166
Selected nucleic acid binding species (aptamers) are frequently viewed as non-protein based alternatives to antibodies and are thus also potential targeting agents for the delivery of siRNA cargoes (9).
[ "9", "10", "13", "14" ]
202
2,999
1
false
Selected nucleic acid binding species (aptamers) are frequently viewed as non-protein based alternatives to antibodies and are thus also potential targeting agents for the delivery of siRNA cargoes.
[ "9" ]
Selected nucleic acid binding species (aptamers) are frequently viewed as non-protein based alternatives to antibodies and are thus also potential targeting agents for the delivery of siRNA cargoes.
true
true
true
true
true
506