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Results for “targeted integration”

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PubMed2000

The TECO theory and lawful dependency in successive episodic memory tests.

A large number of experiments in successive tests of episodic memory have focused on an experimental paradigm called recognition failure of recallable words. In this paradigm, a cued recall test follows a recognition test. Large amounts of data have revealed a lawful moderate dependence between recognition and cued recall. TECO (Sikström, 1996b), a general connectionist theory of memory, has been applied for the phenomenon of recognition failure. This paper makes a strong claim that all possible pairwise combinations of successive tests between recognition, cued recognition, cued recall, and free recall follow a lawful relationship. The quantitative degree of the dependency predicted between these tests can be summarized in one function. Four experiments were conducted to test this claim. In line with the predictions, the results show that all pairwise combinations of these tests fit reasonably well with the proposed function. The TECO theory suggests theoretical insights into how recognition and recall may be divided into a recollection component, a familiarity component, and a cue-target integration component.

Adolescent↗

PubMed1999

Mre11 is essential for the maintenance of chromosomal DNA in vertebrate cells.

Yeast Mre11 functions with Rad50 and Xrs2 in a complex that has pivotal roles in homologous recombination (HR) and non-homologous end-joining (NHEJ) DNA double-strand break (DSB) repair pathways. Vertebrate Mre11 is essential. Conditionally, MRE11 null chicken DT40 cells accumulate chromosome breaks and die upon Mre11 repression, showing frequent centrosome amplification. Mre11 deficiency also causes increased radiosensitivity and strongly reduced targeted integration frequencies. Mre11 is, therefore, crucial for HR and essential in mitosis through its role in chromosome maintenance by recombinational repair. Surprisingly perhaps, given the role of Mre11 in yeast NHEJ, disruption of NHEJ by deletion of KU70 greatly exacerbates the effects of MRE11 deficiency, revealing a significant Mre11-independent component of metazoan NHEJ.

Animals↗

PubMed2001

Identification of a polymorphic mucin-like gene expressed in the midgut of the mosquito, Aedes aegypti, using an integrated bulked segregant and differential display analysis.

The identification of putative differentially expressed genes within genome regions containing QTL determining susceptibility of the mosquito, Aedes aegypti, to the malarial parasite, Plasmodium gallinaceum, was investigated using an integrated, targeted approach based on bulked segregant and differential display analysis. A mosquito F2 population was obtained from pairwise matings between the parasite-susceptible RED strain and the resistant MOYO-R substrain. DNA from female carcasses was used to genotype individuals at RFLP markers of known chromosomal position around the major QTL (pgs 1). Midguts, dissected 48 hr after an infected blood meal, were used to prepare two RNA bulks, each representing one of the parental genotypes at the QTL interval. The RNA bulks were compared by differential display PCR. A mucin-like protein gene (AeIMUC1) was isolated and characterized. The gene maps within the pgs 1 QTL interval and is expressed in the adult female midgut. AeIMUC1 RNA abundance decreased with time after blood meal ingestion. No differential expression was observed between the two mosquito strains but three different alleles with inter- and intrastrain allelic polymorphisms including indels and SNPs were characterized. The AeIMUC1 gene chromosome location and allelic polymorphisms raise the possibility that the protein might be involved in parasite-mosquito interactions.

Aedes↗

PubMed1985

Aging and delay effects on recognition of words and designs.

Based on a model of inter- and intraitem processes in recognition, this study examined age differences in word recognition (emphasizing interitem elaborative rehearsal) and in design recognition (emphasizing intraitem perceptual processes) over delays of 2, 20, and 200 min. Because repeated exposures should increase intraitem integration, targets were repeated from first to second test halves. Young and old adults showed equivalent accuracy in design recognition and equivalent increases from first to second test halves; the predicted lack of intraitem age differences was supported. Young adults, however, were more accurate than old adults in word recognition, supporting the prediction of age differences in interitem processing. The decline across delays was different for words and designs but was parallel for both age groups. Young and old adults also had equivalent decision criteria and decision speeds.

Adult↗

PubMed1995

A transcribed human sequence related to the mouse HC1 and the human papillomavirus type 18 E5 genes is located at chromosome 7p13-14.

The papillomavirus E5 genes play an important role in the induction of proliferation of infected cells, and these HPV genomic regions are affected by the events leading to integration of genital HPVs. Two HPV18 E5-related, transcribed mouse sequences, HC1 and Q300, have recently been described. We searched for human equivalents to these sequences, and isolated a clone with a 9.6 kb insert (633b) from a laryngeal carcinoma DNA library, that strongly cross-hybridised with both the HPV18 E5 and HC1 sequences. Restriction and Southern blot analysis showed that 633b is a single copy sequence without rearrangements and viral sequences. The E5-related region is transcribed, producing a 1.9 kb RNA band detected in the poly(A)+ RNA from different cell lines tested. Sequence alignments showed a close similarity to the HC1 and HPV18 E5 sequences, as well as to Q300 and different viral and human growth factors, allowing to fit a putative phylogenetic tree. The corresponding human gene was named PE5L. It was mapped to the short arm of chromosome 7, at 7p13-14 as determined by in situ hybridisation. A genomic region with similarities to HPV E5 sequences may constitute an HPV-DNA integration target, which is often located near chromosomal breakpoints, oncogenes, etc. We conclude that PE5L belongs to an E5-like family of cellular sequences, and that it may constitute a target for HPV recombination.

Animals↗

PubMed1989

Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements.

The DNA sequences were determined at the boundaries of the integrated copy of the archaebacterial genetic element SSV1. A 44 bp sequence present as a single copy on the 15.5 kb circular SSV1 DNA flanked the integrated copy as a direct DNA sequence repeat, suggesting that SSV1 integration occurred by recombination between this 44 bp SSV1 sequence and an identical sequence on the bacterial chromosome. At the left attachment site, a region encompassing the 44 bp attachment core sequence and the 31 nucleotides upstream of it displayed all characteristics expected for an arginine tRNA gene. An analysis of published attachment site sequences of other systems revealed that tRNA genes also constitute the bacterial attachment site in the case of three temperate phages and two transmissible plasmids in eubacteria, indicating a widespread occurrence of tRNA genes as integration target sites. This finding may be important for the understanding of mechanisms and evolution of site-specific recombination.

Archaea↗

PubMed2002

A Physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) model for the organophosphate insecticide chlorpyrifos in rats and humans.

A PBPK/PD model was developed for the organophosphate insecticide chlorpyrifos (CPF) (O,O-diethyl-O-[3,5,6-trichloro-2-pyridyl]-phosphorothioate), and the major metabolites CPF-oxon and 3,5,6-trichloro-2-pyridinol (TCP) in rats and humans. This model integrates target tissue dosimetry and dynamic response (i.e., esterase inhibition) describing uptake, metabolism, and disposition of CPF, CPF-oxon, and TCP and the associated cholinesterase (ChE) inhibition kinetics in blood and tissues following acute and chronic oral and dermal exposure. To facilitate model development, single oral-dose pharmacokinetic studies were conducted in rats (0.5-100 mg/kg) and humans (0.5-2 mg/kg), and the kinetics of CPF, CPF-oxon, and TCP were determined, as well as the extent of blood (plasma/RBC) and brain (rats only) ChE inhibition. In blood, the concentration of analytes followed the order TCP >> CPF >> CPF-oxon; in humans CPF-oxon was not quantifiable. Simulations were compared against experimental data and previously published studies in rats and humans. The model was utilized to quantitatively compare dosimetry and dynamic response between rats and humans over a range of CPF doses. The time course of CPF and TCP in both species was linear over the dose range evaluated, and the model reasonably simulated the dose-dependent inhibition of plasma ChE, RBC acetylcholinesterase (AChE), and brain (rat only) AChE. Model simulations suggest that rats exhibit greater metabolism of CPF to CPF-oxon than humans do, and that the depletion of nontarget B-esterase is associated with a nonlinear, dose-dependent increase in CPF-oxon blood and brain concentration. This CPF PBPK/PD model quantitatively estimates target tissue dosimetry and AChE inhibition and is a strong framework for further organophosphate (OP) model development and for refining a biologically based risk assessment for exposure to CPF under a variety of scenarios.

Acetylcholinesterase↗

PubMed2005

A minor catalase/peroxidase from Burkholderia cenocepacia is required for normal aconitase activity.

The opportunistic bacterium Burkholderia cenocepacia C5424 contains two catalase/peroxidase genes, katA and katB. To investigate the functions of these genes, katA and katB mutants were generated by targeted integration of suicide plasmids into the katA and katB genes. The catalase/peroxidase activity of the katA mutant was not affected as compared with that of the parental strain, while no catalase/peroxidase activity was detected in the katB mutant. However, the katA mutant displayed reduced resistance to hydrogen peroxide under iron limitation, while the katB mutant showed hypersensitivity to hydrogen peroxide, and reduced growth under all conditions tested. The katA mutant displayed reduced growth only in the presence of carbon sources that are metabolized through the tricarboxylic acid (TCA) cycle, as the growth defect was abrogated in cultures supplemented with glucose or glycerol. This phenotype was also correlated with a marked reduction in aconitase activity. In contrast, aconitase activity was not reduced in the katB mutant and parental strains. The authors conclude that the KatA protein is a specialized catalase/peroxidase that has a novel function by contributing to maintain the normal activity of the TCA cycle, while KatB is a classical catalase/peroxidase that plays a global role in cellular protection against oxidative stress.

Aconitate Hydratase↗

PubMed2005

ATG deserts define a novel core promoter subclass.

The MHC class I gene, PD1, has neither functional TATAA nor Initiator (Inr) elements in its core promoter and initiates transcription at multiple, dispersed sites over an extended region in vitro. Here, we define a novel core promoter feature that supports regulated transcription through selective transcription start site (TSS) usage. We demonstrate that TSS selection is actively regulated and context dependent. Basal and activated transcriptions initiate from largely nonoverlapping TSS regions. Transcripts derived from multiple TSS encode a single protein, due to the absence of any ATG triplets within approximately 430 bp upstream of the major transcription start site. Thus, the PD1 core promoter is embedded within an "ATG desert". Remarkably, extending this analysis genome-wide, we find that ATG deserts define a novel promoter subclass. They occur nonrandomly, are significantly associated with non-TATAA promoters that use multiple TSS, independent of the presence of CpG islands (CGI). We speculate that ATG deserts may provide a core promoter platform upon which complex upstream regulatory signals can be integrated, targeting multiple TSS whose products encode a single protein.

Animals↗

PubMed2004

A gene encoding, prespore-cell-inducing factor in Dictyostelium discoideum.

Two factors that exist in conditioned medium (CM) of Dictyostelium discoideum induce amoebae to differentiate into prespore cells when they are incubated at a very low cell density in submerged monolayer culture. Previously, we purified one of them, a glycoprotein factor with an apparent molecular mass of 106 kDa, and we named it psi factor (psi, prespore-inducing factor). Based on the partial amino acid sequence of the purified psi factor, we have isolated the corresponding cDNA clone, which is expressed maximally at the loose mound stage. The cDNA encodes a novel protein and the predicted molecular mass of the mature secreted protein is 60 kDa. Knockout mutant strains of the psi factor gene, psiA(-), were created by targeted integration. Although these mutant strains appear to develop normally, CM from these mutants showed reduced prespore-cell-inducing activity. Rescuing the mutant strains by expression of psi factor under control of a constitutive promoter causes overproduction of psi factor protein and CM from such cells showed a 20-fold higher level of prespore-cell-inducing activity than that from wild-type cells. Further, CM from parental cells induced prespore cell division, while that from psiA null strains showed no cell division inducing activity. Our results indicate that psi factor protein is a novel type of growth factor that does not belong to any of the families of growth factor so far identified in animals.

Amino Acid Sequence↗

PubMed2001

Ura-status-dependent adhesion of Candida albicans mutants.

Gene disruptions in the diploid opportunistic human fungal pathogen Candida albicans are usually created using multiple rounds of targeted integration called the 'ura-blaster' method. Resulting heterozygous and homozygous null mutants can be auxotrophic (Ura(-)) or prototrophic (Ura(+)) for uracil biosynthesis. Here we demonstrate that the Ura-status of otherwise isogenic mutants affected the adhesion of C. albicans. Moreover the effect of Ura-status on adhesion was also dependent on the null mutant background, the nature of the underlying surface and the carbon source for growth. Therefore the Ura-status is not neutral in determining adhesive properties of C. albicans mutants that are generated via the ura-blaster protocol.

Candida albicans↗

PubMed2025

CsMYB219 and CsMYB196 influence epigallocatechin gallate biosynthesis in tea plant (Camellia sinensis) by regulating CsSCPL1A gene expression.

Epigallocatechin gallate (EGCG) is the most abundant and biologically active catechin in tea leaves and has been widely utilized in the development of functional foods. EGCG is catalyzed by serine carboxypeptidase-like 1A (CsSCPL1A) acyltransferases in tea plants. Although CsSCPL family genes are regulated by several transcription factors (TFs), systematic studies on their regulation by MYB TFs are lacking. This study integrates targeted metabolomics, transcriptomics, DNA-protein, and protein-protein interaction analyses to elucidate the transcriptional regulation of EGCG biosynthesis-related genes CsSCPL4 and CsSCPL5-1 by R2R3-MYB TFs. CsMYB219 and CsMYB196 can specifically bind to CsSCPL4 and CsSCPL5-1 promoters and activate their expression. CsMYB196 also interacted with CsTT8a and CsTTG1 to activate the transcription activity of CsSCPL4 and CsSCPL5-1 promoters by forming a MYB/bHLH/WD40 (MBW) complex. Promoter truncation assays delineated MYB-responsive cis-elements in CsSCPL4 (-613 to -1 bp with enhancers at -1967 to -1622) and CsSCPL5-1 (-503 to -296 bp). Silencing of CsMYB219 and CsMYB196 by virus-induced gene silencing (VIGS) assay significantly reduced the expression levels of CsSCPL4 and CsSCPL5-1 and EGCG content in tea leaves. Transient overexpression of CsMYB219 and CsMYB196 in tea leaves upregulated CsSCPL4 and CsSCPL5-1 expression and elevated EGCG content. These findings enhance our understanding of the regulatory network underlying EGCG biosynthesis in tea plants and provide a solid foundation for future genetic improvement of tea plant cultivars.

Catechin↗

PubMed2006

Study of a prototype high quantum efficiency thick scintillation crystal video-electronic portal imaging device.

Image quality in portal imaging suffers significantly from the loss in contrast and spatial resolution that results from the excessive Compton scatter associated with megavoltage x rays. In addition, portal image quality is further reduced due to the poor quantum efficiency (QE) of current electronic portal imaging devices (EPIDs). Commercial video-camera-based EPIDs or VEPIDs that utilize a thin phosphor screen in conjunction with a metal buildup plate to convert the incident x rays to light suffer from reduced light production due to low QE (<2% for Eastman Kodak Lanex Fast-B). Flat-panel EPIDs that utilize the same luminescent screen along with an a-Si:H photodiode array provide improved image quality compared to VEPIDs, but they are expensive and can be susceptible to radiation damage to the peripheral electronics. In this article, we present a prototype VEPID system for high quality portal imaging at sub-monitor-unit (subMU) exposures based on a thick scintillation crystal (TSC) that acts as a high QE luminescent screen. The prototype TSC system utilizes a 12 mm thick transparent CsI(Tl) (thallium-activated cesium iodide) scintillator for QE=0.24, resulting in significantly higher light production compared to commercial phosphor screens. The 25 X 25 cm2 CsI(Tl) screen is coupled to a high spatial and contrast resolution Video-Optics plumbicon-tube camera system (1240 X 1024 pixels, 250 microm pixel width at isocenter, 12-bit ADC). As a proof-of-principle prototype, the TSC system with user-controlled camera target integration was adapted for use in an existing clinical gantry (Siemens BEAMVIEW(PLUS)) with the capability for online intratreatment fluoroscopy. Measurements of modulation transfer function (MTF) were conducted to characterize the TSC spatial resolution. The measured MTF along with measurements of the TSC noise power spectrum (NPS) were used to determine the system detective quantum efficiency (DQE). A theoretical expression of DQE(0) was developed to be used as a predictive model to propose improvements in the optics associated with the light detection. The prototype TSC provides DQE(0)=0.02 with its current imaging geometry, which is an order of magnitude greater than that for commercial VEPID systems and comparable to flat-panel imaging systems. Following optimization in the imaging geometry and the use of a high-end, cooled charge-coupled-device (CCD) camera system, the performance of the TSC is expected to improve even further. Based on our theoretical model, the expected DQE(0)=0.12 for the TSC system with the proposed improvements, which exceeds the performance of current flat-panel EPIDs. The prototype TSC provides high quality imaging even at subMU exposures (typical imaging dose is 0.2 MU per image), which offers the potential for daily patient localization imaging without increasing the weekly dose to the patient. Currently, the TSC is capable of limited frame-rate fluoroscopy for intratreatment visualization of patient motion at approximately 3 frames/second, since the achievable frame rate is significantly reduced by the limitations of the camera-control processor. With optimized processor control, the TSC is expected to be capable of intratreatment imaging exceeding 10 frames/second to monitor patient motion.

Equipment Design↗

PubMed1996

Expression of a Plasmodium gene introduced into subtelomeric regions of Plasmodium berghei chromosomes.

Targeted integration of exogenous DNA into the genome of malaria parasites will allow their phenotype to be modulated by means of gene disruption or the stable expression of foreign and mutated genes. Described here is the site-specific integration through reciprocal exchange, and subsequent expression, of a selectable marker gene into the genome of the pathogenic, bloodstage forms of the rodent malaria parasite Plasmodium berghei. Stable integration of a single copy of the marker gene (retained for more than 70 generations in the absence of drug pressure) into a nontranscribed subtelomeric repeat array of different chromosomes was observed. Expression of the gene within the subtelomeres indicated that the previously recorded absence of transcription in these regions could be due to a corresponding absence of genes rather than active silencing mechanisms.

Animals↗

PubMed1998

A gene system for glucitol transport and metabolism in Clostridium beijerinckii NCIMB 8052.

The gutD gene of Clostridium beijerinckii NCIMB 8052 encoding glucitol 6-phosphate dehydrogenase was cloned on a 5.7-kbp chromosomal DNA fragment by complementing an Escherichia coli gutD mutant strain and selecting for growth on glucitol. Five open reading frames (ORFs) in the order gutA1 gutA2 orfX gutB gutD were identified in a 4.0-kbp region of the cloned DNA. The deduced products of four of these ORFs were homologous to components of the glucitol phosphotransferase system (PTS) and glucitol 6-phosphate dehydrogenase from E. coli, while the remaining ORF (orfX) encoded an enzyme which had similarities to members of a family of transaldolases. A strain in which gutD was inactivated by targeted integration lacked glucitol 6-phosphate dehydrogenase activity. The gutA1 and gutA2 genes encoded two polypeptides forming enzyme IIBC of the glucitol PTS comprising three domains in the order CBC. Domain IIA of the glucitol PTS was encoded by gutB. Glucitol phosphorylation assays in which soluble and membrane fractions of cells grown on glucose (which did not synthesize the glucitol PTS) or cells grown on glucitol were used confirmed that there is a separate, soluble, glucitol-specific PTS component, which is the product of the gutB gene. The gut genes were regulated at the level of transcription and were induced in the presence of glucitol. Cells grown in the presence of glucose and glucitol utilized glucose preferentially. Following depletion of glucose, the glucitol PTS and glucitol 6-phosphate dehydrogenase were synthesized, and glucitol was removed from the culture medium. RNA analysis showed that the gut genes were not expressed until glucose was depleted.

Amino Acid Sequence↗

PubMed1994

Biologically active Rep proteins of adeno-associated virus type 2 produced as fusion proteins in Escherichia coli.

Four Rep proteins are encoded by the human parvovirus adeno-associated virus type 2 (AAV). The two largest proteins, Rep68 and Rep78, have been shown in vitro to perform several activities related to AAV DNA replication. The Rep78 and Rep68 proteins are likely to be involved in the targeted integration of the AAV DNA into human chromosome 19, and the full characterization of these proteins is important for exploiting this phenomenon for the use of AAV as a vector for gene therapy. To obtain sufficient quantities for facilitating the characterization of the biochemical properties of the Rep proteins, the AAV rep open reading frame was cloned and expressed in Escherichia coli as a fusion protein with maltose-binding protein (MBP). Recombinant MBP-Rep68 and MBP-Rep78 proteins displayed the following activities reported for wild-type Rep proteins when assayed in vitro: (i) binding to the AAV inverted terminal repeat (ITR), (ii) helicase activity, (iii) site-specific (terminal resolution site) endonuclease activity, (iv) binding to a sequence within the integration locus for AAV DNA on human chromosome 19, and (v) stimulation of radiolabeling of DNA containing the AAV ITR in a cell extract. These five activities have been described for wild-type Rep produced from mammalian cell extracts. Furthermore, we recharacterized the sequence requirements for Rep binding to the ITR and found that only the A and A' regions are necessary, not the hairpin form of the ITR.

ATP-Binding Cassette Transporters↗

PubMed2000

An adeno-associated virus (AAV) initiator protein, Rep78, catalyzes the cleavage and ligation of single-stranded AAV ori DNA.

The Rep78 protein of adeno-associated virus (AAV) contains amino acid sequence motifs common to rolling-circle replication (RCR) initiator proteins. In this report, we describe RCR initiator-like activities of Rep78. We demonstrate that a maltose-binding protein (MBP)-Rep78 fusion protein can catalyze the cleavage and ligation of single-stranded DNA substrates derived from the AAV origin of replication. Rep-mediated single-stranded DNA cleavage was strictly dependent on the presence of certain divalent cations (e.g., Mn(2+) or Mg(2+)) but did not require the presence of a nucleoside triphosphate cofactor. Electrophoretic mobility shift assays demonstrated that binding of single-stranded DNA by MBP-Rep78 was influenced by the length of the substrate as well as the presence of potential single-stranded cis-acting sequence elements. Site-directed mutagenesis was used to examine the role of specific tyrosine residues within a conserved RCR motif (motif 3) of Rep78. Replacement of Tyr-156 with phenylalanine abolished the ability of MBP-Rep78 to mediate the cleavage and ligation of single-stranded DNA substrates but not the ability to stably bind single-stranded DNA. The cleaving-joining activity of Rep78 is consistent with the mechanism of replicative intermediate dimer resolution proposed for the autonomous parvoviruses and may have implications for targeted integration of recombinant AAV vectors.

Base Sequence↗

PubMed1999

The essential functions of human Rad51 are independent of ATP hydrolysis.

Genetic recombination and the repair of double-strand DNA breaks in Saccharomyces cerevisiae require Rad51, a homologue of the Escherichia coli RecA protein. In vitro, Rad51 binds DNA to form an extended nucleoprotein filament and catalyzes the ATP-dependent exchange of DNA between molecules with homologous sequences. Vertebrate Rad51 is essential for cell proliferation. Using site-directed mutagenesis of highly conserved residues of human Rad51 (hRad51) and gene targeting of the RAD51 locus in chicken DT40 cells, we examined the importance of Rad51's highly conserved ATP-binding domain. Mutant hRad51 incapable of ATP hydrolysis (hRad51K-133R) binds DNA less efficiently than the wild type but catalyzes strand exchange between homologous DNAs. hRad51 does not need to hydrolyze ATP to allow vertebrate cell proliferation, form nuclear foci, or repair radiation-induced DNA damage. However, cells expressing hRad51K-133R show greatly reduced targeted integration frequencies. These findings show that ATP hydrolysis is involved in DNA binding by hRad51 and suggest that the extent of DNA complexed with hRad51 in nucleoprotein influences the efficiency of recombination.

Adenosine Triphosphate↗