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At least 1,099 records · Page 61Linked to original sources
PubMed1998

Virtual frequency encoding: achieving symmetry in k-space.

Chemical shift artifacts and other off-resonance spatial shifts in 2DFT MRI arise from the linear time dependence in the k-space data in the readout direction. Introduction of a view-dependent time shift of the readout window adds a time dependence to the phase-encoding direction and results in a virtual frequency-encoding direction that is a linear combination of the phase-encode and readout axes. By this method, the readout and phase-encode directions can be made identical in their sensitivity to off-resonance effects and can be arbitrarily swapped with no change in chemical shift or inhomogeneity effects, improving previously reported methods that swap these axes for signal averaging or reduction of motion artifacts.

Artifacts↗
PubMed2025

Approaches to Study Proteins Encoded by Essential Genes.

Although the phenotypes and functions of nonessential proteins can be studied by deletion of their coding sequences (both gene copies in diploid organisms), essential genes cannot be deleted unless loss of the encoded protein can be bypassed. Bypass is often achieved by supplementation with the product of the enzyme. However, supplementation cannot bypass loss of essential genes such as those encoding enzymes of DNA or RNA synthesis. To study proteins encoded by essential genes that cannot be bypassed, the mutations must be conditional in nature. The mutant cells must be able to grow under a permissive condition, but fail to grow under a different condition, the nonpermissive condition. Several methods have been developed to obtain conditional mutations in essential genes. Mutations that result in proteins abnormally sensitive to high temperatures are called temperature-sensitive (Ts) mutants and are a widely used type of conditional mutation. An alternative to Ts mutants is the "degron" system to target proteins for destruction by cellular proteases. Approaches to conditionally control the functions of proteins encoded by essential genes, plus the advantages and disadvantages of these and other approaches, will be considered.

Genes, Essential↗
PubMed2005

SKG1, a suppressor gene of synthetic lethality of kex2Deltagas1Delta mutations, encodes a novel membrane protein that affects cell wall composition.

The fungal GAS1-related genes encode GPI-anchored beta-1,3-glucanosyltransferase, and their loss causes a defect in the assembly of the cell wall. The KEX2 gene encodes a processing protease in the late Golgi compartment and its loss also results in defects in the cell wall. Simultaneous mutations of these genes are lethal in Saccharomyces cerevisiae. To understand the basis of this synthetic lethality, we screened for multicopy suppressors and identified 13 SKG (suppressor of kex2 gas1 synthetic lethality) genes. SKG1 encodes a transmembrane protein that localizes on the inner surface of the plasma membrane at the bud and in the daughter cell. The multicopy SKG1 increases the sensitivity of cells to zymolyase, and the skg1Delta null mutation increases resistance to it. This zymolyase susceptibility corresponds to an increase of alkali-soluble beta-1,3-glucan and a decrease of chitin in the cell wall. Thus SKG1 encodes a novel protein that affects the cell wall polymer composition in the growing region of the cell.

Amino Acid Sequence↗
PubMed1994

RPL44 and RPL44', encoding acidic ribosomal phosphoproteins YP2 alpha(L44) and YP1 beta(L44'), are adjacent to rig and STF1 on Saccharomyces cerevisiae chromosomes XV and IV respectively.

The RPL44' gene from Saccharomyces cerevisiae encoding the ribosomal protein YP1 beta(L44') has been found to be linked to the STF1 gene, encoding a stabilizing factor of the F1F0-ATPase inhibitor protein from mitochondria. Evidence of this linkage comes from results obtained from Northern hybridization using a DNA probe that contains a complementary region to the 5' end of the mRNA of RPL44'. Similarly, a data bank search has shown that RPL44, encoding ribosomal protein YP2 alpha (L44) is linked to the rig gene that encodes ribosomal protein S21.

Chromosome Mapping↗
PubMed1997

Saccharomyces cerevisiae expresses two genes encoding isozymes of 5-aminoimidazole-4-carboxamide ribonucleotide transformylase.

We have isolated and cloned two Saccharomyces cerevisiae genes which encode isozymes of 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase, the ninth step of the de novo purine biosynthesis pathway. This reaction involves the formylation of AICAR using 10-formyltetrahydrofolate as the formyl donor. ADE16 is located on chromosome XII and encodes an open reading frame of 591 amino acids. ADE17 is located on chromosome XIII and encodes an open reading frame of 592 amino acids. The deduced amino acid sequences of the two genes are 84% identical to each other and are 60-63% identical to the chicken and human bifunctional AICAR transformylase/IMP cyclohydrolase amino acid sequences. Disruption of the two chromosomal yeast genes resulted in adenine auxotrophy, while the expression of either gene alone was sufficient to support growth without adenine. In vitro assays of AICAR transformylase activity demonstrated the lack of IMP production in the double disruptant strain. S. cerevisiae is the only organism known thus far to possess isozymes of this protein. Because it is likely that the proteins encoded by ADE16 and ADE17 also contain IMP cyclohydrolase activity, these two genes complete the set of clones and mutants for the entire de novo purine biosynthesis pathway in yeast.

Acyltransferases↗
PubMed1999

Saccharomyces cerevisiae expresses two genes encoding isozymes of methylenetetrahydrofolate reductase.

The identification, expression, and assay of two Saccharomyces cerevisiae genes encoding methylenetetrahydrofolate reductases (MTHFR) is described. MTHFR catalyzes the reduction of 5, 10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, used to methylate homocysteine in methionine synthesis. The MET12 gene is located on chromosome XVI and encodes a protein of 657 amino acids. The MET13 gene is located on chromosome VII and encodes a protein of 599 amino acids. The deduced amino acid sequences of these two genes are 34% identical to each other and 32-37% identical to the human MTHFR. A phenotype for the single disruption of MET12 was not observed, however, single disruption of MET13 resulted in methionine auxotrophy. Double disruption of both MET12 and MET13 also resulted in methionine auxotrophy. Growth of the methionine auxotrophs was supported by both methionine and S-adenosylmethionine. Transcripts of both MET12 and MET13 were detected in total RNA from wild type cells grown in the presence or absence of methionine. The methionine requirement of the met12 met13 double disruptant was complemented by plasmid-borne MET13, but not MET12 even when a multicopy plasmid was used. Furthermore, overexpression of the human MTHFR in the met12 met13 double disruptant complemented the methionine auxotrophy of this strain. In contrast, overexpression of the Escherichia coli metF gene did not complement the methionine requirement of met12 met13 cells. Assays for MTHFR in crude extracts and expression of the yeast proteins in Escherichia coli verified that both MET12 and MET13 encode functional MTHFR isozymes.

Amino Acid Sequence↗
PubMed1993

Characterization of a rat airway cDNA encoding a mucin-like protein.

The purpose of this study was to isolate airway mucin cDNAs for use in studies of mucin biosynthesis in rat models of human airway disease. To this end, we screened a rat airway cDNA library with the human intestinal mucin cDNA SMUC 41 and obtained 7 positive clones. Preliminary characterization of each of these led us to focus on the clone expressing the 390 bp cDNA RAM 7s. Evidence indicating that RAM 7s encodes part of a rat airway mucin gene is that RAM 7s: (a) hybridizes in plaque lifts to SMUC 41, (b) hybridizes in Northern blots to large, polydisperse transcripts, (c) has a sequence encoding threonine-rich tandem repeats and (d) shows appropriate tissue-specific expression of cognate mRNA. The repetitive peptide encoded by RAM 7s includes five copies of the consensus sequence TTTTIITI. Because this sequence is different from those reported for two cDNAs previously isolated from rat intestinal libraries, we tentatively conclude that RAM 7s encodes part of a previously unidentified rat mucin gene.

Amino Acid Sequence↗
PubMed1995

Melanotropin and corticotropin are encoded on two distinct genes in the lamprey, the earliest evolved extant vertebrate.

In the lamprey, which is a member of the oldest extant class of vertebrates, the agnathans, melanotropins (MSH) and corticotropin (ACTH) were found to be encoded on two distinct genes. In all other vertebrates, a single precursor gene, proopiomelanocortin (POMC), encodes MSH and ACTH, as well as beta-endorphin (END). Two different cDNAs were cloned from a lamprey pituitary lambda gt11 cDNA library using antisera against lamprey MSH-B and ACTH(1-16). One cDNA encoded MSH-B, MSH-A and beta-END, while the other cDNA encoded nasohypophysial factor (NHF), ACTH and a different beta-END, but not MSH-A and MSH-B. Northern blot analysis demonstrated that in the adult lamprey pituitary, genes for MSH and ACTH are expressed in the pars intermedia (PI) and pars distalis (PD), respectively.

Adrenocorticotropic Hormone↗
PubMed1998

Genetic structure of the bphG gene encoding 2-hydroxymuconic semialdehyde dehydrogenase of Achromobacter xylosoxidans KF701.

2-Hydroxymuconic semialdehyde dehydrogenase catalyzes the conversion of 2-hydroxymuconic semialdehyde (HMS) to an enol form of 4-oxalocrotonate which is a step in the catechol meta-cleavage pathway. A bphG gene encoding HMS dehydrogenase of A. xylosoxidans KF701, a soil bacterium degrading biphenyl, was identified at between catechol 2,3-dioxygenase gene and HMS hydrolase gene, and its sequence was analyzed. An open reading frame (ORF) corresponding to bphG gene was consisted of 1461 nucleotides with ATG initiation codon and TGA termination codon. The ORF exhibited 66% of G + C content, and a putative ribosome-binding sequence, AGAGA, was identified at about 10 nucleotides upstream initiation codon of the bphG gene. The bphG gene can encode a polypeptide of molecular weight 52 kDa containing 486 amino acid residues. A deduced amino acid sequence of HMS dehydrogenase encoded in bphG gene from A. xylosoxidans KF701 exhibited the highest 94% homology with that of corresponding enzyme encoded in xylG from P. putida mt-2, 63% to 90% homology with those of other reported HMS dehydrogenases, and 29% to 42% homology with those of betaine aldehyde dehydrogenase, 5-carboxy-HMS dehydrogenase, aldehyde dehydrogenase, indole-3-acetaldehyde dehydrogenase, succinic semialdehyde dehydrogenase, methylmalonate semialdehyde dehydrogenase, and succinylglutamate 5-semialdehyde dehydrogenase. From an alignment of amino acid sequence of HMS dehydrogenase from A xylosoxidans KF701 with other reported dehydrogenases, putative cofactor NAD(+)-binding regions and catalytic residues were identified.

Alcaligenes↗
PubMed2000

The nuclear-encoded SDH2-RPS14 precursor is proteolytically processed between SDH2 and RPS14 to generate maize mitochondrial RPS14.

In maize, the functional gene encoding mitochondrial ribosomal protein S14 (rps14) has been translocated to the nucleus where it became integrated between both exons of a gene encoding the iron-sulfur subunit of succinate dehydrogenase (sdh2). Two transcripts are generated from this locus by alternative splicing. One transcript encodes a precursor for a functional SDH2 protein, while the second transcript encodes a chimeric SDH2(t)-RPS14 precursor protein. In this paper we show that the same mitochondrial targeting presequence is able to direct the import of both precursors into isolated mitochondria and is removed during import. This processing event generates a 28 kDa protein from the SDH2 precursor, which corresponds to the iron-sulfur subunit of respiratory complex II present in maize mitochondria. In addition to cleavage of the presequence, the chimeric precursor undergoes proteolytical processing between SDH2 and RPS14. This processing generates RPS14, which is found assembled into mitochondrial ribosomes, and a truncated SDH2 protein which is degraded. Therefore, our results support a role of the SDH2 domain in the chimeric precursor only in providing a mitochondrial targeting function for RPS14.

Amino Acid Sequence↗
PubMed2001

Peptides encoded by exon 6 of VEGF inhibit endothelial cell biological responses and angiogenesis induced by VEGF.

VEGF induces pathological angiogenesis and is an important target for the development of novel antiangiogenic molecules. In this study, we tested synthetic peptides based on the sequence of VEGF(189) for their ability to inhibit VEGF receptor binding and biological responses. We identified 12-amino acid peptides derived from exon 6 that inhibited VEGF binding to HUVECs, VEGF-stimulated ERK activation, and prostacyclin production. These peptides inhibited VEGF-induced mitogenesis, migration, and VEGF-dependent survival of endothelial cells, but caused no increase in apoptosis in the absence of VEGF. Exon 6-encoded peptides also caused a marked inhibition of VEGF-induced angiogenesis in vitro. Studies of effects of peptides on cross-linking of VEGF to its receptors and on binding of VEGF to porcine aortic endothelial cells expressing either KDR or neuropilin-1 showed that exon 6-encoded peptides effectively blocked the interaction of VEGF with both receptors. Exon 6-derived peptides caused release of bFGF from endothelial cells but inhibited bFGF-dependent ERK activation, cell proliferation and angiogenesis. Our findings indicate that VEGF exon 6-encoded peptides inhibit VEGF-induced angiogenesis, at least in part through inhibition of VEGF binding to KDR. In addition, exon 6-encoded peptides are also effective inhibitors of bFGF-mediated angiogenesis.

Angiogenesis Inhibitors↗
PubMed2001

A transmembrane trap method for efficient cloning of genes encoding proteins possessing transmembrane domain.

To facilitate searching for genes encoding cell membrane proteins, we developed a method for isolating cDNAs that contain sequences for hydrophobic transmembrane runs. This cloning strategy, termed the "transmembrane (TM) trap method," utilizes a vector that directs the cell surface expression of mouse CD4 fusion protein when an insert encoding hydrophobic transmembrane sequences is cloned in-frame with correct orientation. We applied this novel method to isolation of cytokine receptor cDNAs. Our strategy enabled efficient isolation of relatively rare species encoding receptors such as IL-2Rgamma, IL-3Rbeta, IL-4Ralpha, IL-5Ralpha, and IL-6Ralpha. This method also could be used to isolate cDNAs for intracellular molecules with a transmembrane region, e.g., bcl-2. These results indicate that the TM trap method provides an efficient cloning strategy for identification of various families of genes encoding proteins with one or more transmembrane regions.

Animals↗
PubMed1999

Dendritic encoding: an alternative to temporal synaptic coding of conscious experience.

In this commentary, arguments are made for a dendritic code being preferable to a temporal synaptic code as a model of conscious experience. A temporal firing pattern is a product of an ongoing neural computation; hence, it is based on a neural algorithm and an algorithm may not provide the most suitable model for conscious experience. Reiteration of a temporal firing code as suggested in a preceding article (Helekar, 1999) does not necessarily improve the situation. The alternative model presented here is that certain synaptic activity patterns, possibly those possessing universal features as suggested by Helekar, can become encoded in the dendritic structure. Following dendritic encoding, quantum phenomena in those specific dendrite sets could illuminate the static image of that encoded synaptic activity. It is the activation of the static image that would be equivalent to conscious experience; thus, conscious awareness would not be directly affiliated with synaptic activity. This dendrite encoding model may go farther than other models to explain the gestalt nature of consciousness, insofar as quantum entanglement could produce an interconnectedness between specific sets of dendrites-an interconnectedness that need not be based on neural computation or neural connections.

Consciousness↗
PubMed1997

The region encoded by the alternatively spliced exon IIIA in mesenchymal fibronectin appears essential for chondrogenesis at the level of cellular condensation.

Fibronectin in the extracellular matrix of tissues acts as a substrate for cell adhesion and migration during development. Heterogeneity in the structure of fibronectin is largely due to the alternative splicing of at least three exons (IIIB, IIIA, and V) during processing of a single primary transcript. Fibronectin mRNA alternative splicing patterns change from B+A+V+ to B+A-V+ during chondrogenesis. In this report, immunohistochemical analysis demonstrates that while fibronectin protein containing the region encoded by exon IIIB is present throughout the limb at all stages of development, fibronectin protein containing the region encoded by exon IIIA disappears from cartilaginous regions just after condensation in vivo and in high-density mesenchymal micromass cultures in vitro. Treatment of mesenchymal micromass cultures prior to condensation with an antibody specific for the region encoded by exon IIIA disrupts the formation of cellular condensations and inhibits subsequent chondrogenesis in a dose- and time-dependent manner. Furthermore, microinjection of the exon IIIA antibody into embryonic chick limb primordia in vivo results in malformations characterized by smaller limbs and loss of limb skeletal elements. These results strongly suggest that the presence of the region encoded by exon IIIA in mesenchymal fibronectin is necessary for the condensation event that occurs during chondrogenesis.

Alternative Splicing↗
PubMed2001

Sequence and expression of a cDNA encoding both pituitary adenylate cyclase activating polypeptide and growth hormone-releasing hormone-like peptide in channel catfish (Ictalurus punctatus).

In nonmammalian vertebrates, pituitary adenylate cyclase activating polypeptide (PACAP) and a putative growth hormone-releasing hormone (GHRH-like peptide) are encoded by a single mRNA transcript. Both PACAP and GHRH have been implicated in the control of fish growth. Although the gene encoding PACAP and GHRH-like peptide (GHRHLP) has been cloned in other fishes, characterization of this gene in the commercially important channel catfish (Ictalurus punctatus) has not been previously reported. In this study, the GHRHLP/PACAP cDNA was cloned from channel catfish hypothalamic tissue and a brain cDNA library. Two cDNA variants of the GHRHLP/PACAP precursor gene were identified as a result of alternative splicing, a long form encoding both PACAP and GHRHLP and a short form encoding only PACAP. Both the long and the short forms of the GHRHLP/PACAP precursor cDNA were identified in channel catfish brain, pituitary, fat, gastrointestinal tract, ovary, testes, and muscle by RT-PCR detection. This study is the first to demonstrate mRNA expression of this gene in fat or skeletal muscle of fish. By characterizing the GHRHLP/PACAP gene and its distribution in channel catfish, we have developed essential tools to investigate the roles of these peptides in the regulation of catfish growth.

Alternative Splicing↗
PubMed1994

Structure and chromosomal localization of the gene (BDKRB2) encoding human bradykinin B2 receptor.

The bradykinin B2 receptor (BDKRB2) has high affinity for the intact kinins, which mediate a wide spectrum of biological effects, including pain, inflammation, vasodilation, and smooth muscle contraction and relaxation. In the present study, we have cloned and sequenced the gene encoding human bradykinin B2 receptor from a human genomic library. The B2 receptor gene contains three exons separated by two introns. The first and second exons are noncoding, while the third exon contains the full-length coding region, which encodes a protein of 364 amino acids forming 7 transmembrane domains. The human B2 gene shares high sequence identity with rat and mouse B2 receptor genes and significant similarity with the gene encoding the angiotensin II type I receptor in the nucleotide sequence and exon-intron arrangement. In the 5' flanking region, a consensus TATA box and several putative transcription factor-binding sites have been identified. Genomic Southern blot analysis showed that the B2 receptor is encoded by a single-copy gene that was localized to chromosome 14q32 by in situ hybridization. In a Southern blot analysis following reverse transcription and polymerase chain reaction, the human B2 receptor was found to be expressed in most human tissues.

Amino Acid Sequence↗
PubMed1995

Cloning and chromosomal mapping of three novel genes, GPR9, GPR10, and GPR14, encoding receptors related to interleukin 8, neuropeptide Y, and somatostatin receptors.

We employed the polymerase chain reaction and genomic DNA library screening to clone novel human genes, GPR9 and GPR10, and a rat gene, GPR14. GPR9, GPR10, and GPR14 each encode G protein-coupled receptors. GPR10 and GPR14 are intronless within their coding regions, while GPR9 contains at least one intron. The receptor encoded by GPR9 shares the highest identity with human IL-8 receptor type B (38% overall and 53% in the transmembrane regions), followed by IL-8 receptor type A (36% overall and 51% in the transmembrane domains). GPR10 encodes a receptor that shares highest identity with the neuropeptide Y receptor (31% overall and 46% in the transmembrane domains). The receptor encoded by GPR14 shares highest identity with the somatostatin receptor SSTR 4 (27% overall and 41% in the transmembrane domains). Fluorescence in situ hybridization analysis localized GPR9 to chromosome 8p11.2-p12 and GPR10 to chromosome 10q25.3-q26.

Amino Acid Sequence↗
PubMed1996

A novel transcript encoded within the 10-kb first intron of the human p53 tumor suppressor gene (D17S2179E) is induced during differentiation of myeloid leukemia cells.

Two promoters were previously shown to map to the 5'-end of the human p53 gene. p53p1 was located upstream of the first exon and is responsible for transcription of the major p53 mRNA species. p53p2 is a stronger promoter than p53p1 and was located within the 10, 738-bp first intron, approximately 1000 bp downstream of exon 1. mRNA transcripts that initiated from p53p2 were previously identified in HL-60 cells by primer extension analysis and were observed to increase in abundance during differentiation of HL-60 cells to granulocytes. By screening a cDNA library with a probe derived from sequences downstream of the p53p2 start site, we have cloned and characterized a cDNA that represents a mRNA that appears to have been initiated from the p53p2 promoter. We have designated the gene encoding this transcript Hp53int1 (the GDB designation is D17S2179E). The cDNA is 1125 bp and is polyadenylated downstream from a consensus poly(A) addition site. The entire 1125 bp is derived from intron 1 of the p53 gene, with no introns having been removed. The cDNA contains no major open reading frame although reading frame +1 contains a relatively low abundance of stop codons compared to the other two reading frames and could possibly encode a protein of 119 amino acids. Analysis of the +1 reading frame shows a region of high homology to a portion of the DNA-binding domain of NF-kappaB. These results indicate that a novel polyadenylated transcript is encoded by the first intron of the human p53 gene. Hp53int1 may be a pseudogene for a gene that may have encoded a DNA-binding protein. Alternatively, the transcript may have a function, since RNA transcripts of this gene are present in a number of human cells and their levels are induced during terminal differentiation of myeloid leukemia cells such as HL-60 and U937.

Amino Acid Sequence↗