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Deoxyribonucleases, Type II Site-Specific (4):
Recent article
Deoxyribonucleases, Type II Site-Specific
Abstract
We have examined the interatomic distances between metal ions and proposed key catalytic residues in the binding sites of seventeen type II restriction endonucleases whose crystal structures are documented in literature. The summary and critical evaluation of structural assignments and predictions m...
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PMID: 20888795
PDF is available here.
PDF is available here.
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Biochemical Genetics (48)9-10 2010
Abstract
AvaII and NcoI polymorphisms in the low-density lipoprotein receptor (LDL-R) gene are reported to alter cholesterol levels. Although found to be highly polymorphic worldwide, these mutations have not been validated in any Indian population. This case-control association study was conducted in an end...
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PMID: 20628808
PDF is available here.
PDF is available here.
Acta Diabetologica (47)3 2010
Abstract
Associations between the TAQIB and I405V polymorphisms and obesity risk were studied for a single locus as well as in combination. A total of 934 obese subjects and 924 normal controls were included in the study. TAQIB was associated with high-density lipoprotein (HDL) levels (P < 0.001), while I405...
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PMID: 19360375
PDF is available here.
PDF is available here.
Abstract
We were able to differentiate all Borrelia species and their subtypes within particular species. RT-PCR based on Tm determination identified unique strains within the species Borreliaafzelii (Tm 66.11 degrees C), B. burgdorferi sensu stricto (Tm 68.18 degrees C), Borreliaspielmanii (Tm 59.45 degrees...
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PMID: 20451566
PDF is available here.
PDF is available here.
Abstract
The drug-metabolizing enzyme CYP2E1 is of great interest in environmental medicine because of its involvement in the bioactivation of multiple procarcinogens.
This study is aimed at determining the frequency of genetic polymorphisms of the three restriction fragment length polymorphisms: PstI and Rs...
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PMID: 20406102
PDF is available here.
PDF is available here.
Abstract
We observed that the most redundant sequences of 349 clones in a human CGI library were all generated from the human mitochondrial genome. Further analysis indicated that there was a 5,845-bp DNA transfer from mtDNA to chromosome 1, and all the clones should be the products of a 510-bp MseI fragment...
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PMID: 20691393
PDF is available here.
PDF is available here.
Abstract
The different cleavage patterns of pYBamy59 plasmid isolated from E. coli DH5alpha and B. longum MG1 by the cell extract of B. longum MG1 suggested that the main reason for low transformation efficiency was related to the restriction modification (R-M) system. To confirm correlation between R-M syst...
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PMID: 20622503
PDF is available here.
PDF is available here.
Journal of Parasitology (96)3 2010
Abstract
We originally published a physical map of this chromosome and, now, using the sequence data from 46 chromosome-specific probes, have produced a sequence map of the 2 Mb chromosome. Comparison of the probe sequences with the Giardia genome database (http://GiardiaDB.org) has identified 4 scaffolds (C...
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PMID: 20557214
PDF is available here.
PDF is available here.
Meat Science (85)2 2010
Abstract
We investigated the effect of homogentisate 1, 2 dioxygenase (HGD) gene on meat quality and carcass traits in 287 Chinese red cattle. The PCR-SSCP method was used to identify polymorphism of the HGD gene in the exon 1 and intron 1. Two polymorphisms were detected in intron 1 and two restriction site...
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PMID: 20374897
PDF is available here.
PDF is available here.
Abstract
The results from this study do not indicate that the TaqIB variation at the CETP gene locus is a significant predictor for assessing the risk of developing coronary restenosis following PTCA and stenting. This result was not affected when considering any one of the additionally studied factors....
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PMID: 19815603
PDF is available here.
PDF is available here.
Methods in Molecular Biology (639)639 2010
Abstract
We describe in detail the SSH procedure and explain the subtle changes that have been incorporated to make this technique adaptable for identifying stress-responsive genes in plants....
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PMID: 20387045
PDF is available here.
PDF is available here.
Abstract
It was possible to create a database of molecular profiles, which are being used in the Laboratory for comparing and identifying strains isolated from clinical cases....
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PMID: 20464147
PDF is available here.
PDF is available here.
Abstract
I enzymes that cut DNA randomly, but in terms of gene organization and protein assembly, most Type IIB restriction-modification systems have more in common with Type I than with other Type II systems. Our current knowledge of the Type IIB systems is reviewed in the present paper....
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PMID: 20298193
PDF is available here.
PDF is available here.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics (27)2 2010
Abstract
I endonuclease, can be used to introduce targeted double-stranded breaks (DSBs). ZFN-mediated cleavage leads to mutations when double-stranded breaks are repaired by homologous recombination (HR) or nonhomologous end joining (NHEJ). In recent years, ZFNs are widely used in the fields of genetic rese...
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PMID: 20376797
PDF is available here.
PDF is available here.
Abstract
In this study, a method was developed to measure replication rates of rolling-circle replicon-based plasmids in eukaryotic cells. This method is based on the discriminative quantitation of MboI-resistant, non-replicated input plasmids and DpnI-resistant, replicated plasmids. To do so, porcine circov...
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PMID: 20026194
PDF is available here.
PDF is available here.
Abstract
We employed Cfr9I PFGE on 100 German and 5 Dutch ST398 isolates and compared their PFGE profiles, protein A gene variable repeat regions (spa types), and types of the staphylococcal cassette chromosome mec (SCCmec). The isolates (from healthy carrier pigs, clinical samples from pigs, dust from farms...
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PMID: 20023093
PDF is available here.
PDF is available here.
Genetika (Moskva) (46)1 2010
Abstract
The study on polymorphism within the STAT5A gene (transition C6853T) was conducted using the PCR-RFLP method and AvaI restrictase. The study covered a herd of 723 cows of the Polish Red-and-White variety of Holstein Friesian breed, kept for dairy purposes in the Opole region, Poland. Two alleles (C...
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PMID: 20198884
PDF is available here.
PDF is available here.
Abstract
We investigated whether there was an association of VDR: g.59979G>T or c.1025-49G>T (ApaIG>T) and g.60058T>C or c.1056T>C (TaqIT>C) polymorphisms in the 3' untranslated region of VDR with T2DM in a Turkish population. We collected blood samples from 241 individuals (72 patients with T2DM and 169 hea...
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PMID: 19186074
PDF is available here.
PDF is available here.
Abstract
We revealed the direct junction of the monomers, which are longer than 100 bp length and belong to distinct families of tandem repeats from plant genomes....
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PMID: 20198853
PDF is available here.
PDF is available here.
Abstract
FokI polymorphism in VDR gene may be associated with the susceptibility to spinal TB in Chinese Han population. Furthermore, the ff genotype may be the susceptible genotype of spinal TB.
2010 IMSS. Published by Elsevier Inc. All rights reserved....
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PMID: 20430254
PDF is available here.
PDF is available here.
Abstract
We hypothesized a positive correlation of DRD2 polymorphisms in the combined type of ADHD patients without co-morbidity.
Our research sample included 586 unrelated boys of the Czech origin aged between 6 and 13 years. The ADHD group consisted of 269 boys and the control group consisted of 317 boys....
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PMID: 20150882
PDF is available here.
PDF is available here.
Abstract
We investigated the XbaIG > T and HaeIIIT > C polymorphisms in six different Brazilian populations: 102 individuals from Salvador population (Northern Brazil), 56 European descendants from Joinville (South Brazil), 85 Indians from Tiryió tribe (North Brazil) and 127 samples from Southern Brazil: 44...
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PMID: 19347605
PDF is available here.
PDF is available here.
Abstract
We found that in the presence of Xmn1 polymorphic site on both chromosomes (+/+) the level of Hb F tended to be increased compared to the absence of Xmn1 (-/-). The present investigation has studied the frequency of Xmn1 polymorphic site in beta-thalassemia major patients from Western Iran and has r...
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PMID: 19444645
PDF is available here.
PDF is available here.
Abstract
We previously reported that a single DNA double-strand break (DSB) near a telomere in mouse embryonic stem cells can result in chromosome instability. We have observed this same type of instability as a result of spontaneous telomere loss in human tumor cell lines, suggesting that a deficiency in th...
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PMID: 19540174
PDF is available here.
PDF is available here.
Abstract
POU1F1 is a positive regulator for prolactin (PRL) whose metabolites may directly or indirectly affect some aspects of the hair growth cycle, therefore, POU1F1 gene is an important candidate gene for cashmere traits selection through marker-assisted selection (MAS). Hence, in this study, the PCR-RFL...
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PMID: 18654839
PDF is available here.
PDF is available here.
Abstract
The distribution of VDR TaqI genotypes and alleles between the two groups was significantly different (P = 0.019 and P = 0.039, respectively). The TT genotype and T allele seemed to increase the susceptibility of severe CP (odds ratio, 2.75; 95% confidence interval [CI]: 1.17 to 6.47; odds ratio, 2....
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PMID: 19335080
PDF is available here.
PDF is available here.
EMBO Journal (28)8 2009
Abstract
We show that the replication checkpoint suppresses the formation of Rad52 foci in an Mrc1-dependent manner and prevents homologous recombination (HR) at chromosome breaks induced by the HO endonuclease. This repression operates at least in part by impeding resection of DNA ends, which is essential t...
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PMID: 19322196
PDF is available here.
PDF is available here.
Abstract
We reported that p57 produced by Renibacterium salmoninarum Strain 684 contains a mutation that disrupts monoclonal antibody (MAb) 4C11 binding. In the present study, we examined MAb binding to a panel of 23 additional R. salmoninarum isolates obtained from diverse geographic locations to examine th...
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PMID: 19326793
PDF is available here.
PDF is available here.
Abstract
We show that SIRT6 forms a macromolecular complex with the DNA double-strand break (DSB) repair factor DNA-PK (DNA-dependent protein kinase) and promotes DNA DSB repair. In response to DSBs, SIRT6 associates dynamically with chromatin and is necessary for an acute decrease in global cellular acetyla...
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PMID: 20157594
PDF is available here.
PDF is available here.
Abstract
We show that SIRT6 forms a macromolecular complex with the DNA double-strand break (DSB) repair factor DNA-PK (DNA-dependent protein kinase) and promotes DNA DSB repair. In response to DSBs, SIRT6 associates dynamically with chromatin and is necessary for an acute decrease in global cellular acetyla...
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PMID: 20157594
PDF is available here.
PDF is available here.
Abstract
Three streptomycete strains (Streptomnyces sp. 14, Streptomnzyces sp. 34, Streptomyces sp. 48)--producers of isoschisomers of restrictase Asull (Ssp34, Ssp48, Ssp14) were studied for the presence of synthesis of those site-specific endonucleases after long-term storage. Mycelium of streptomycete cul...
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PMID: 19663326
PDF is available here.
PDF is available here.
Abstract
We provide an optimized protocol for I-SceI meganuclease-mediated transgenesis in zebrafish. This simple protocol provides a reliable method to transiently test tissue-specific reporter expression of meganuclease constructs in injected embryos (F0). Furthermore, it substantially facilitates the gene...
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PMID: 19378101
PDF is available here.
PDF is available here.
Oncology (Basel) (76)3 2009
Abstract
Our data did not demonstrate any significant difference in the prevalence of the p53 Arg72Pro genotype between patients and controls, providing evidence that this polymorphism is only weakly associated with the risk of endometrial cancer and prognostic factors in Caucasian women.
Copyright 2009 S. K...
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PMID: 19209008
PDF is available here.
PDF is available here.
Abstract
Our goal was to evaluate usefulness of these endonucleases and two other rarely used (SfiI and SmaI) ones for the differentiation of Y enterocoilitica clinical isolates by PFGE. Reference strains used in this study belong to the major agents of human yersiniosis in Poland, the bioserotype 4/O3 (n=5)...
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PMID: 19780491
PDF is available here.
PDF is available here.
Language and Speech (52)Pt 4 2009
Abstract
We examined three types of monosyllabic late positive CCVC words: (a) existing words [see text], (b) wellformed novel words [see text] and component (c) illformed novel words [see text] as instances of Obligatory Contour Principle non-word (OCP) violations. Wellformed and illformed novel words evoke...
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PMID: 20121040
PDF is available here.
PDF is available here.
Abstract
We have shown previously that the endonucleolytic activity of MmeI is strongly dependent on the presence of S-adenosyl-l-methionine (J. Nakonieczna, J. W. Zmijewski, B. Banecki, and A. J. Podhajska, Mol. Biotechnol. 37:127-135, 2007), which puts MmeI in subtype IIG. The same cofactor is used by MmeI...
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PMID: 18997032
PDF is available here.
PDF is available here.
Chromosome Research (17)8 2009
Abstract
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromo...
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PMID: 19842052
PDF is available here.
PDF is available here.
Chromosome Research (17)8 2009
Abstract
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromo...
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PMID: 19842052
PDF is available here.
PDF is available here.
Chromosome Research (17)8 2009
Abstract
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromo...
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PMID: 19842052
PDF is available here.
PDF is available here.
Chromosome Research (17)8 2009
Abstract
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromo...
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PMID: 19842052
PDF is available here.
PDF is available here.
Chromosome Research (17)8 2009
Abstract
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromo...
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PMID: 19842052
PDF is available here.
PDF is available here.
Chromosome Research (17)8 2009
Abstract
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromo...
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PMID: 19842052
PDF is available here.
PDF is available here.
Chromosome Research (17)8 2009
Abstract
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromo...
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PMID: 19842052
PDF is available here.
PDF is available here.
Chromosome Research (17)8 2009
Abstract
The genome of the gut protozoan parasite Giardia duodenalis (assemblage A) has been sequenced and compiled as contigs and scaffolds (GiardiaDB- http://GiardiaDB.org ), but specific chromosome location of all scaffolds is unknown. To determine which scaffolds belong to the 3-Mb chromo...
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PMID: 19842052
PDF is available here.
PDF is available here.
FEMS Microbiology Letters (290)2 2009
Abstract
We identify Marth_orf138 as a candidate marI gene. Marth_orf138 was cloned in Escherichia coli and its TGA codons converted to TGG. DNA isolated from E. coli cells expressing the modified Marth_orf138 gene was degraded by the AluI nuclease, indicating that Marth_orf138 does not code for MarI. Howeve...
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PMID: 19054074
PDF is available here.
PDF is available here.
Hemoglobin (33)6 2009
Abstract
We report a novel polymorphism upstream of the beta-globin gene characterized by RsaI digestion. Sequencing of a fragment containing this area showed a nucleotide change (T>C) at position -223 upstream of the beta-globin gene. This change could interfere with precise interpretation of the RsaI diges...
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PMID: 19958186
PDF is available here.
PDF is available here.
Abstract
A method for the amplified analysis of a gene sequence by a Fok I/DNA machine is described. A tailored nucleic acid that includes a recognition sequence for the analyzed gene and a hybridized sequence of the gene itself acting as the "fuel" substrate of the "machine". Upon recognition of the gene by...
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PMID: 19049271
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)3 2008
Abstract
The SfiI restriction endonuclease is a tetramer in which two subunits form a dimeric unit that contains one DNA binding cleft and the other two subunits contain a second cleft on the opposite side of the protein. Full activity requires both clefts to be filled with its recognition sequence: SfiI has...
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PMID: 18848951
PDF is available here.
PDF is available here.
Journal of General Virology (89)Pt 12 2008
Abstract
We have demonstrated that HYVV is unable to trans-replicate other satellites. To investigate the basis of trans-replication compatibility, deletion mutagenesis of AYVV DNA-beta has been used to localize the origin of replication to approximately 360 nt, encompassing the ubiquitous nonanucleotide/ste...
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PMID: 19008407
PDF is available here.
PDF is available here.
Journal of Bacteriology (190)24 2008
Abstract
We tested the capacity of the mutant enzymes to function in vivo as the counterpart of a restriction endonuclease, which can cleave either site. The viability of Escherichia coli cells carrying recombinant plasmids with the mutant methyltransferase genes and expressing the GGNCC-specific Sau96I rest...
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PMID: 18849437
PDF is available here.
PDF is available here.
Abstract
This study provides the first evidence of an association between polymorphisms in the COL1A2 gene with dental fluorosis in high fluoride exposed populations. Future studies are needed to confirm the association....
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PMID: 18284430
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)21 2008
Abstract
We report a previously uncharacterized H. pylori type II R-M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC sites, which are rare in the H. pylori chromosome but numerous in ribosomal RNA genes. As predicted, this type II R-M system showed attributes of a selfish element. Deletio...
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PMID: 18978016
PDF is available here.
PDF is available here.
Restriction landmark genomic scanning: analysis of CpG islands in genomes by 2D gel electrophoresis.
Abstract
Restriction landmark genomic scanning (RLGS) is a method that provides a quantitative genetic and epigenetic (cytosine methylation) assessment of thousands of CpG islands in a single gel without prior knowledge of gene sequence. The method is based on two-dimensional separation of radiolabeled genom...
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PMID: 18987812
PDF is available here.
PDF is available here.
Medical Mycology (46)7 2008
Abstract
We previously showed the insertion at the RB2 region might initiate chromosome translocation in strain STN22u2 of C. albicans. To ask whether the insertion of a URA cassette into the RB2 but not into RPS and HOK causes chromosome translocation in C. albicans strains, we transformed three URA cassett...
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PMID: 18608900
PDF is available here.
PDF is available here.
Abstract
We investigated (i) main associations between CRC, vitamin D and calcium dietary intake and 4 VDR single nucleotide polymorphisms (rs10735810, rs1544410, rs11568820, rs7975232) and (ii) interaction associations between the VDR variants, vitamin D and calcium intakes. Inverse and dose-dependent assoc...
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PMID: 18709640
PDF is available here.
PDF is available here.
Journal of Molecular Biology (383)1 2008
Abstract
Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca(2+), Mg(2+), and Mn(2+)) are presented. While previous structures were produced from soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new structures are der...
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PMID: 18762194
PDF is available here.
PDF is available here.
Abstract
The Bispectral Index (BIS) is one of the most frequently used electroencephalogram-derived depth of anaesthesia monitors. Previous studies in children have suggested BIS performs well in older children, however these studies have used earlier versions of the BIS device. The aim of this study was to...
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PMID: 19115649
PDF is available here.
PDF is available here.
Abstract
The isolation of high quality DNA is essential for many molecular biology applications including polymerase chain reaction (PCR) and endonuclease restriction digestion based techniques. An easy and inexpensive protocol has been developed for extracting genomic DNA from seven species of algae viz. Lo...
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PMID: 19297990
PDF is available here.
PDF is available here.
Abstract
We show physically interact. Real-time imaging and chromatin immunoprecipitation confirmed stable recruitment of damaged DNA to nuclear pores. Relocation required the Nup84 complex and Mec1/Tel1 kinases. Spontaneous gene conversion can be enhanced in a Slx8- and Nup84-dependent manner by tethering d...
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PMID: 18948542
PDF is available here.
PDF is available here.
Abstract
We tested whether striatal activation in response to food intake is related to current and future increases in body mass and whether these relations are moderated by the presence of the A1 allele of the TaqIA restriction fragment length polymorphism, which is associated with dopamine D2 receptor (DR...
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PMID: 18927395
PDF is available here.
PDF is available here.