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At least 847 records · Page 47Linked to original sources
PubMed2004

Vaccination with a DNA vaccine encoding herpes simplex virus type 1 VP22 linked to antigen generates long-term antigen-specific CD8-positive memory T cells and protective immunity.

Intradermal vaccination with DNA encoding herpes simplex virus type 1 (HSV-1) VP22 linked to antigen leads to spread of antigen within the epithelium and results in enhanced antigen-specific CD8+ T cell immune responses in vaccinated mice. In this study, we characterized the number of antigen-expressing dendritic cells (DCs) in the draining lymph nodes of vaccinated mice and determined whether the linkage of VP22 to antigen would influence the ability of antigen-expressing DCs to activate antigen-specific CD8+ T cells in vivo. Vaccination with DNA encoding HSV-1 VP22 linked to human papillomavirus type 16 E7 antigen generated more antigen-expressing DCs in the draining lymph nodes of vaccinated mice than E7 alone. In addition, the linkage of VP22 to E7 improved the MHC class I presentation of E7 in transfected DCs and led to enhanced activation of E7-specific CD8+ T cells. We also observed that vaccination with DNA encoding VP22 linked to E7 generated more E7-specific CD8+ memory T cells, and enhanced long-term protective antitumor immunity against an E7-expressing tumor in vaccinated mice compared with vaccination with DNA encoding E7 alone. Thus, administration of DNA encoding VP22 linked to antigen represents a plausible approach for the development of protective DNA vaccines.

Animals↗
PubMed1998

Targeted delivery of DNA encoding cytotoxic proteins through high-affinity fibroblast growth factor receptors.

Nonviral DNA delivery strategies for gene therapy have generally been limited by a lack of specificity and efficacy. However, ligand-mediated endocytosis can specifically deliver DNA in vitro to cells bearing the appropriate cognate receptors. Similarly, in order to circumvent problems related to efficacy, DNA must encode proteins with high intrinsic activities. We show here that the ligand basic fibroblast growth factor (FGF2) can target FGF receptor-bearing cells with DNA encoding therapeutic proteins. Delivery of genes encoding saporin, a highly potent ribosomal inactivating protein, or the conditionally cytotoxic herpes simplex virus thymidine kinase, a protein that can kill cells by activating the prodrug ganciclovir, is demonstrated. The saporin gene was codon optimized for mammalian expression and demonstrated to express functional protein in a cell-free assay. FGF2-mediated delivery of saporin DNA or thymidine kinase DNA followed by ganciclovir treatment resulted in a 60 and 75% decrease in cell number, respectively. Specificity of gene delivery was demonstrated in competition assays with free FGF2 or with recombinant soluble FGF receptor. Alternatively, when histone H1, a ligand that binds to cell surface heparan sulfate proteoglycans ("low-affinity" FGF receptors), was used to deliver DNA encoding thymidine kinase, no ganciclovir sensitivity was observed. These findings establish the feasibility of using ligands such as FGF2 to specifically deliver genes encoding molecular chemotherapeutic agents to cells.

Amino Acid Sequence↗
PubMed2002

Brain activity underlying encoding and retrieval of source memory.

Neural activity elicited during the encoding and retrieval of source information was investigated with event-related functional magnetic resonance imaging (efMRI). During encoding, 17 subjects performed a natural/artificial judgement on pictures of common objects which were presented randomly in one of the four quadrants of the display. At retrieval, old pictures were mixed with new ones and subjects judged whether each picture was new or old and, if old, indicated in which quadrant it was presented at encoding. During encoding, study items that were later recognized and assigned a correct source judgement elicited greater activity than recognized items given incorrect judgements in a variety of regions, including right lateral occipital and left prefrontal cortex. At retrieval, regions showing greater activity for recognized items given correct versus incorrect source judgements included the right hippocampal formation and the left prefrontal cortex. These findings indicate a role for these regions in the encoding and retrieval of episodic information beyond that required for simple item recognition.

Adult↗
PubMed2006

Fragments of a larger whole: retrieval cues constrain observed neural correlates of memory encoding.

Laying down a new memory involves activity in a number of brain regions. Here, it is shown that the particular regions associated with successful encoding depend on the way in which memory is probed. Event-related functional magnetic resonance imaging signals were acquired while subjects performed an incidental encoding task on a series of visually presented words denoting objects. A recognition memory test using the Remember/Know procedure to separate responses based on recollection and familiarity followed 1 day later. Critically, half of the studied objects were cued with a corresponding spoken word, and half with a corresponding picture. Regardless of cue, activity in prefrontal and hippocampal regions predicted subsequent recollection of a word. Type of retrieval cue modulated activity in prefrontal, temporal, and parietal cortices. Words subsequently recognized on the basis of a sense of familiarity were at study also associated with differential activity in a number of brain regions, some of which were probe dependent. Thus, observed neural correlates of successful encoding are constrained by type of retrieval cue, and are only fragments of all encoding-related neural activity. Regions exhibiting cue-specific effects may be sites that support memory through the degree of overlap between the processes engaged during encoding and those engaged during retrieval.

Adult↗
PubMed1989

The maltose permease encoded by the MAL61 gene of Saccharomyces cerevisiae exhibits both sequence and structural homology to other sugar transporters.

The MAL61 gene of Saccharomyces cerevisiae encodes maltose permease, a protein required for the transport of maltose across the plasma membrane. Here we report the nucleotide sequence of the cloned MAL61 gene. A single 1842 bp open reading frame is present within this region encoding the 614 residue putative MAL61 protein. Hydropathy analysis suggests that the secondary structure consists of two blocks of six transmembrane domains separated by an approximately 71 residue intracellular region. The N-terminal and C-terminal domains of 100 and 67 residues in length, respectively, also appear to be intracellular. Significant sequence and structural homology is seen between the MAL61 protein and the Saccharomyces high-affinity glucose transporter encoded by the SNF3 gene, the Kluyveromyces lactis lactose permease encoded by the LAC12 gene, the human HepG2 glucose transporter and the Escherichia coli xylose and arabinose transporters encoded by the xylE and araE genes, indicating that all are members of a family of sugar transporters and are related either functionally or evolutionarily. A mechanism for glucose-induced inactivation of maltose transport activity is discussed.

Amino Acid Sequence↗
PubMed1998

The isolation and characterization of nrc-1 and nrc-2, two genes encoding protein kinases that control growth and development in Neurospora crassa.

Using an insertional mutagenesis approach, a series of Neurospora crassa mutants affected in the ability to control entry into the conidiation developmental program were isolated. One such mutant, GTH16-T4, was found to lack normal vegetative hyphae and to undergo constitutive conidiation. The affected gene has been named nrc-1, for nonrepressible conidiation gene #1. The nrc-1 gene was cloned from the mutant genomic DNA by plasmid rescue, and was found to encode a protein closely related to the protein products of the Saccharomyces cerevisiae STE11 and Schizosaccharomyces pombe byr2 genes. Both of these genes encode MAPKK kinases that are necessary for sexual development in these organisms. We conclude the nrc-1 gene encodes a MAPKK kinase that functions to repress the onset of conidiation in N. crassa. A second mutant, GTH16-T17, was found to lack normal vegetative hyphae and to constitutively enter, but not complete, the conidiation program. The affected locus is referred to as nrc-2 (nonrepressible conidiation gene #2). The nrc-2 gene was cloned and found to encode a serine-threonine protein kinase. The kinase is closely related to the predicted protein products of the S. pombe kad5, and the S. cerevisiae YNRO47w and KIN82 genes, three genes that have been identified in genome sequencing projects. The N. crassa nrc-2 gene is the first member of this group of kinases for which a phenotype has been defined. We conclude a functional nrc-2-encoded serine/threonine kinase is required to repress entry into the conidiation program.

Amino Acid Sequence↗
PubMed1996

A 1.8 kb alternative transcript from the human epidermal growth factor receptor gene encodes a truncated form of the receptor.

The epidermal growth factor receptor (EGFR) is encoded by the c-erbB1 proto-oncogene and plays an important role in the control of cell growth and differentiation. To study the potential growth regulatory role of soluble EGF receptors, we have isolated cDNA clones encoding a truncated, secreted form of the human EGFR. The 5' sequence of this cDNA is identical to the EGFR transcript encoding the full-length receptor through exon 10. The unique 3' sequence encodes two additional amino acid residues before encountering an in-frame stop codon, a poly(A) addition site and a poly(A)+ tail. Sequence comparison with genomic DNA sequences demonstrates that this alternative transcript arises by read-through of a splice donor site. As a result, this transcript encodes a portion of the extracellular ligand-binding domain, but lacks the transmembrane domain and the intracellular tyrosine kinase catalytic domain present in the EGFR. Conditioned medium from transfected fibroblast cells contains a 60 kDa protein that is specifically immunoprecipitated by an EGFR monoclonal antibody. These findings demonstrate that alternative processing of the human EGFR transcript produces a secreted product composed of only the extracellular ligand-binding domain.

Alternative Splicing↗
PubMed2000

A family of developmentally excised DNA elements in Tetrahymena is under selective pressure to maintain an open reading frame encoding an integrase-like protein.

Tlr1 is a member of a family of approximately 20-30 DNA elements that undergo developmentally regulated excision during formation of the macronucleus in the ciliated protozoan TETRAHYMENA: Analysis of sequence internal to the right boundary of Tlr1 revealed the presence of a 2 kb open reading frame (ORF) encoding a deduced protein with similarity to retrotransposon integrases. The ORFs of five unique clones were sequenced. The ORFs have 98% sequence conservation and align without frameshifts, although one has an additional trinucleotide at codon 561. Nucleotide changes among the five clones are highly non-random with respect to the position in the codon and 93% of the nucleotide changes among the five clones encode identical or similar amino acids, suggesting that the ORF has evolved under selective pressure to preserve a functional protein. Nineteen T/C transitions in T/CAA and T/CAG codons suggest selection has occurred in the context of the TETRAHYMENA: genome, where TAA and TAG encode Gln. Similarities between the ORF and those encoding retrotransposon integrases suggest that the Tlr family of elements may encode a polynucleotide transferase. Possible roles for the protein in transposition of the elements within the micronuclear genome and/or their developmentally regulated excision from the macronucleus are discussed.

Amino Acid Sequence↗
PubMed2003

Putative proteins related to group II intron reverse transcriptase/maturases are encoded by nuclear genes in higher plants.

The Arabidopsis thaliana nuclear genome sequence revealed several open reading frames encoding proteins related to group II intron-encoded reverse transcriptase/maturases. Here, we show via sequence alignments that at least four such open reading frames are conserved in the nuclear genomes of A.thaliana and Oryza sativa (rice) and that they encode putative proteins belonging to two different classes (nMat-1 and nMat-2), neither of which is associated with a group II intron RNA structure. The two nMat-1 proteins have reverse transcriptase, maturase and DNA endonuclease domains characteristic of canonical group II intron-encoded proteins, while the two nMat-2 proteins have reverse transcriptase and maturase domains linked to a novel C-terminal domain. Although some nMat proteins have mutations expected to inactivate intron mobility functions, all could potentially retain the RNA splicing function. These nuclear maturase-like proteins may be imported into organelles to function in group II intron splicing and/or they may have assumed other cellular functions. Nuclear-encoded maturases could regulate organellar gene expression and may reflect a step in the evolution of mobile group II introns into spliceosomal introns.

Amino Acid Sequence↗
PubMed2000

Ancestral exonic organization of FUT8, the gene encoding the alpha6-fucosyltransferase, reveals successive peptide domains which suggest a particular three-dimensional core structure for the alpha6-fucosyltransferase family.

Based on PCR strategies and expression studies, we define the genomic organization of the FUT8b gene. This gene encodes the only known mammalian enzyme transferring fucose in an alpha1-->6 linkage on the asparagine-branched GlcNAc residue of the chitobiose unit of complex N:-glycans. The intron/exon organization of the bovine coding sequence determines five successive functional domains. The first exon encodes a domain homologous to cytoskeleton proteins, the second presents a proline-rich region including a motif XPXPPYXP similar to the peptide ligand of the SH3-domain proteins, the third encodes a gyrase-like domain (an enzyme which can bind nucleotides), and the fourth encodes a peptide sequence homologous to the catalytic domain of proteins transferring sugars. Finally, the last exon encodes a domain homologous to the SH3 conserved motif of the SH2-SH3 protein family. This organization suggests that intramolecular interactions might give a tulip-shaped scaffolding, including the catalytic pocket of the enzyme in the Golgi lumen. Deduced from the published sequence of chromosome 14 (AL109847), the human gene organization of FUT8 seems to be similar to that of bovine FUT8b, although the exon partition is more pronounced (bovine exons 1 and 2 correspond to human exons 1-6). The mosaicism and phylogenetic positions of the alpha6-fucosyltransferase genes are compared with those of other fucosyltransferase genes.

Amino Acid Sequence↗
PubMed1991

Enhanced expression of oncogene-encoded mRNA in a rat model of colon cancer.

We have studied the expression of oncogene-encoded mRNAs in a rat model of colon cancer. In this model, rats are intrarectally administered several low doses of the direct-acting carcinogen, N-methyl-N-nitrosourea (MNU). Tumors, predominantly adenomas, develop 5-7 months following administration of the carcinogen, and many of these progress to carcinomas. Upon assaying the steady-state levels of oncogene-encoded transcripts in normal rat colon, we found that fos and N-myc are highly expressed; H-ras, K-ras, myc, myb, and neu messages are present at lower levels; and N-ras, abl, and raf mRNAs are absent. When we compared transcript levels in rat tumors to those in normal colons from the same animal, we observed a 2-4 fold increase in both myc- and H-ras-encoded mRNAs and a 2-7 fold increase in myb message, but no change in expression of any of the 7 other genes. To test whether this increased expression is related to tumor production or is simply a result of the more rapid cellular turnover observed in tumor tissue, the level of oncogene-encoded transcripts was assayed in colonic mucosae of rats given two treatments known to enhance cell turnover and DNA synthesis in the colon. Neither acute application of MNU nor a diet containing 1% cholic acid caused any change in the level of oncogene-encoded mRNAs in rat colons, thus suggesting that the increased abundance of myc, myb, and H-ras messages in tumors is associated with tumor formation. The enhancement of expression of these genes in adenomas, as well as in carcinomas, further suggests that these alterations occur relatively early during the tumorigenic process.

Adenoma↗
PubMed1998

Material-specific lateralization of prefrontal activation during episodic encoding and retrieval.

Although numerous neuroimaging studies have examined the functional neuroanatomy supporting episodic memory for verbal material, there have been few investigations of non-verbal episodic encoding and retrieval. We used fMRI to directly compare prefrontal activation elicited by verbal and non-verbal material during encoding and during retrieval. Regardless of the mnemonic operation (encoding/retrieval), inferior prefrontal activation lateralized based on material type. Verbal encoding and retrieval resulted in greater left inferior prefrontal activation, whereas non-verbal encoding and retrieval resulted in greater right inferior prefrontal activation. The similarity between inferior prefrontal activity during encoding and during retrieval indicates that these mnemonic operations depend on shared processes mediated by inferior prefrontal regions.

Acoustic Stimulation↗
PubMed2001

Neural correlates of verbal memory encoding during semantic and structural processing tasks.

Eighteen participants were imaged using fMRI to explore whether brain regions predicting successful verbal memory encoding during semantic decisions would continue to predict encoding during structural (non-semantic) decisions. Consistent with prior studies, left inferior frontal and fusiform regions were more active during semantic than structural decisions, and activity was greater for remembered than forgotten words during semantic decisions. Critically, structural decisions yielded significantly greater activity for remembered than forgotten words in these regions providing evidence that a common frontal-temporal network supports verbal memory encoding irrespective of orienting task. Further analysis revealed activity associated with successful encoding in the right precentral gyrus, suggesting other regions may also play a role in verbal encoding during non-semantic processing.

Adult↗
PubMed2004

Incidental and intentional encoding in young and elderly adults.

Event-related potentials (ERPs) were recorded in young and elderly adults during the performance of an incidental encoding task (subjects were unexpectedly given a recognition test) followed by an intentional task (subjects expected the recognition test). Both tasks consisted of an encoding stage in which subjects classified words (natural/artificial) and a recognition stage in which they indicated whether the words were old (presented during the encoding stage) or new. In both groups and tasks, the ERPs, during encoding, differed as a function of subsequent recognition: the old words correctly recognized generated greater amplitude potentials than the incorrect ones. The memory processes expressed by these ERPs are preserved in elderly adults, independently of whether the information is incidentally or intentionally encoded.

Adult↗
PubMed2005

Spatial encoding in mountain chickadees: features overshadow geometry.

Encoding the global geometric shape of an enclosed environment is a principal means of orientation in human and non-human animals. Animals spontaneously encode the geometry of an enclosure even when featural information is available. Although features can be used, they typically do not overshadow geometry. However, all previously tested organisms have been reared in human-made environments with salient geometrical cues. Here, we show that wild-caught mountain chickadees (Poecile gambeli) do not spontaneously encode the geometry of an enclosure when salient features are present near the goal. However, chickadees trained without salient features encode geometric information, but this encoding is overshadowed by features.

Animals↗
PubMed1999

When encoding yields remembering: insights from event-related neuroimaging.

To understand human memory, it is important to determine why some experiences are remembered whereas others are forgotten. Until recently, insights into the neural bases of human memory encoding, the processes by which information is transformed into an enduring memory trace, have primarily been derived from neuropsychological studies of humans with select brain lesions. The advent of functional neuroimaging methods, such as positron emission tomography (PET) and functional magnetic resonance imaging (fMRI), has provided a new opportunity to gain additional understanding of how the brain supports memory formation. Importantly, the recent development of event-related fMRI methods now allows for examination of trial-by-trial differences in neural activity during encoding and of the consequences of these differences for later remembering. In this review, we consider the contributions of PET and fMRI studies to the understanding of memory encoding, placing a particular emphasis on recent event-related fMRI studies of the Dm effect: that is, differences in neural activity during encoding that are related to differences in subsequent memory. We then turn our attention to the rich literature on the Dm effect that has emerged from studies using event-related potentials (ERPs). It is hoped that the integration of findings from ERP studies, which offer higher temporal resolution, with those from event-related fMRI studies, which offer higher spatial resolution, will shed new light on when and why encoding yields subsequent remembering.

Brain↗
PubMed1990

The protein kinase encoded in the short unique region of pseudorabies virus: description of the gene and identification of its product in virions and in infected cells.

We have cloned and determined the nucleotide sequence of a gene, pk, that lies immediately upstream from the gene encoding glycoprotein X in the short unique region of the alphaherpesvirus, pseudorabies virus (PRV). The gene has the potential to encode a protein of 334 amino acids, and is related to gene US3 of herpes simplex virus type 1 (HSV-1), which has been shown to encode a protein kinase. The predicted amino acid sequence encoded by the PRV pk gene is homologous to the corresponding sequence encoded by the HSV-1 US3 gene in the C-terminal catalytic domain, but diverges markedly in the N-terminal domain. As with HSV-1, the mRNA for the pk gene appears to be 3' coterminal with that for the glycoprotein downstream. An antiserum was raised against a protein generated from the fusion of part of the PRV pk catalytic domain with Escherichia coli beta-galactosidase. This specifically reacted with a previously described physically homogeneous protein kinase, PRV-PK, isolated from hamster fibroblasts lytically infected with PRV. Although the majority of the PRV-PK is found in the cytoplasm, some was also detected in purified PRV virions by using the same antibody; a similar distribution was found for the HSV-1 protein kinase, using an antiserum raised against the corresponding HSV-1 fusion protein. When presented with heatinactivated virions, purified PRV-PK (in common with certain cellular protein kinases also present in the virion) was able to phosphorylate in vitro the major virion phosphoprotein phosphorylated in vivo.

Amino Acid Sequence↗
PubMed2000

Functional analysis of proteins encoded by banana bunchy top virus DNA-4 to -6.

Green fluorescent protein (GFP)-tagging was used to determine the intracellular localization pattern of the proteins encoded by banana bunchy top virus (BBTV) DNA-3, -4 and -6. The protein encoded by BBTV DNA-4, which possesses a hydrophobic N terminus, was found to localize exclusively to the cell periphery while the proteins encoded by BBTV DNA-3 and -6 were found in both the nucleus and the cytoplasm. Co-expression of the DNA-4 protein and the proteins encoded by BBTV DNA-3 and -6 revealed that the DNA-4 protein was able to re-locate the DNA-6 protein, but not the DNA-3 protein, to the cell periphery. The 29 amino acid N-terminal hydrophobic region of the DNA-4 gene product appeared to be essential for specific localization of this protein since deletion of this region abolished its ability to localize to the cell periphery. These results indicate that BBTV may utilize a system analogous to that of the begomoviruses with the BBTV DNA-6 protein acting as a nuclear shuttle protein (NSP) while the DNA-4 protein transports the NSP-DNA complexes to the cell periphery for intercellular transport. The protein encoded by BBTV DNA-5 was found to contain an LXCXE motif and yeast two-hybrid analysis revealed that the DNA-5 protein has retinoblastoma (Rb)-binding activity. This activity was dependent on an intact LXCXE motif since specific mutations to either the C or E residue completely abolished Rb-binding activity. These results indicate that the gene product of BBTV DNA-5 is an Rb-binding-like protein and may play an important role in host-cell cycle manipulation.

Amino Acid Motifs↗