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At least 1,639 records · Page 91Linked to original sources
PubMed1994

Structure, chromosomal localization, and expression of 12 genes of the MAGE family.

We reported previously that human gene MAGE-1 directs the expression of a tumor antigen recognized on a melanoma by autologous cytolytic T lymphocytes. Probing cosmid libraries with a MAGE-1 sequence, we identified 11 closely related genes. The analysis of hamster-human somatic cell hybrids indicated that the 12 MAGE genes are located in the q terminal region of chromosome X. Like MAGE-1, the 11 additional MAGE genes have their entire coding sequence located in the last exon, which shows 64%-85% identity with that of MAGE-1. The coding sequences of the MAGE genes predict the same main structural features for all MAGE proteins. In contrast, the promoters and first exons of the 12 MAGE genes show considerable variability, suggesting that the existence of this gene family enables the same function to be expressed under different transcriptional controls. The expression of each MAGE gene was evaluated by reverse transcription and polymerase chain reaction amplification. Six genes of the MAGE family including MAGE-1 were found to be expressed at a high level in a number of tumors of various histological types. None was expressed in a large panel of healthy tissues, with the exception of testis and placenta.

Amino Acid Sequence↗
PubMed1994

Simulation of three-dimensional pulsatile flow through an asymmetric stenosis.

The main objective of this work was to use desktop workstations to evaluate the computer code HEMO as a tool for predicting coronary blood flows. The flows are usually characterised by complex vortical structures and transitional effects, and as such present challenging computational problems. As the results of the computations shown in the paper demonstrate, we can predict realistic pulsatile flows in constricted tubes using the Sun Sparcstation 1+ in a matter of hours. The results shown in the paper have also demonstrated that the computer simulations can be very useful as a complementary tool for experimental investigations.

Arterial Occlusive Diseases↗
PubMed1992

Variants of human L1 cell adhesion molecule arise through alternate splicing of RNA.

The L1 cell adhesion molecule was initially identified and characterized in mouse as a cell-surface glycoprotein that mediates neuron-neuron and neuron-Schwann cell adhesion. We have characterized L1 in humans using cDNA structural and mRNA expression analyses. We present the entire coding sequence for human L1, which predicts a 1253-amino acid protein displaying a signal sequence, transmembrane segment, RGD sequence, and potential glycosylation and phosphorylation sites. Nucleotide and deduced amino acid sequence identities between human and mouse L1 are 85% and 87%, respectively. In contrast, the amino acid identity between human L1 and the L1-related molecule chicken Ng-CAM is only 45%. Using Northern blot analyses, a single L1 transcript of 5.5 kb is detected in human fetal brain and in neuroblastoma (IMR-32) and retinoblastoma (Y-79) cell lines. L1 is also expressed in the rhabdomyosarcoma cell lines RD and A-204, which display several muscle characteristics. Two forms of L1, which differ by the presence or absence of a 12-bp cytoplasmic segment, are expressed in both human and mouse. This segment is encoded by a single exon that can be alternately spliced to give rise to the two forms, which appear to be expressed in tissue-specific patterns.

Amino Acid Sequence↗
PubMed2026

Hybrid genome assembly of Penicillium oxalicum UV4 delineates cryptic secondary metabolite pathways and robust lignocellulolytic potential.

Penicillium oxalicum is a saprophytic fungus well-known for its hydrolytic potential; however, little is known about its metabolic flexibility and secondary metabolite biosynthesis, especially in isolates from underrepresented areas. In this study, we sequenced the genomic DNA of Penicillium oxalicum UV4 using Illumina and Oxford Nanopore platforms, generating a high-quality hybrid genome assembly of 30.28 Mb. The genome features 7,944 predicted genes (7,747 protein-coding sequences and 197 tRNAs) and demonstrates high completeness (99.0% BUSCO). Genomic analysis revealed 40 Biosynthetic Gene Clusters (BGCs), including distant orthologs of the Alternaria phytotoxin ACT-toxin II and the mycotoxin alternariol, as well as a putative clavaric acid-like biosynthetic cluster. Further investigation revealed an expanded CAZyme repertoire comprising 150 secreted proteins, featuring an AA16 lytic polysaccharide monooxygenase and putative multi-domain architectures, such as a pectin methylesterase-polygalacturonase fusion. This comprehensive genomic profiling highlights the dynamic metabolic capacity of P. oxalicum UV4, establishing it as a highly promising candidate for bio-refining studies and the discovery of cryptic bioactive metabolites.

Penicillium↗
PubMed2007

Time and decision making: differential contribution of the posterior insular cortex and the striatum during a delay discounting task.

Delay discounting refers to the fact that an immediate reward is valued more than the same reward if it occurs some time in the future. To examine the neural substrates underlying this process, we studied 13 healthy volunteers who repeatedly had to decide between an immediate and parametrically varied delayed hypothetical reward using a delay discounting task during event-related functional magnetic resonance imaging. Subject's preference judgments resulted in different discounting slopes for shorter (<1 year) and for longer (> or =1 year) delays. Neural activation associated with the shorter delays relative to the longer delays was associated with increased activation in the head of the left caudate nucleus and putamen. When individuals selected the delayed relative to the immediate reward, a strong activation was found in bilateral posterior insular cortex. Several brain areas including the left caudate nucleus showed a correlation between the behaviorally determined discounting and brain activation for the contrast of intervals with delays <1 and > or =1 year. These results suggest that (1) the posterior insula, which is a critical component of the decision-making neural network, is involved in delaying gratification and (2) the degree of neural activation in the striatum, which plays a fundamental role in reward prediction and in time estimation, may code for the time delay.

Adolescent↗
PubMed2001

Motor learning enhances perceptual judgment: a case for action-perception transfer.

Transfer from perception to action is well documented, for instance in the form of observational learning. Transfer from action to perception, on the other hand, has not been researched. Such action-perception transfer (APT) is compatible with several learning theories and has been predicted within the framework of common coding of perceptual and motor events (Prinz, 1992, 1997). Our first experiment aimed at an empirical evaluation of APT and involved motor practice of timed two-cycle arm movements on verbal command without visual feedback. In a transfer test, visual judgments of similar patterns had to be made. In addition, transfer from the visual to the motor task was studied. In Experiment 2 we separated kinesthetic aspects of motor practice from preparatory and efferent contributions to APT. The experiments provide evidence that transfer between perception and action is bi-directional. Transfer from perception to action and, more importantly, from action to perception was found. Furthermore, APT was equally pronounced for participants who had actively practiced movements during training and for passive participants who had received merely kinesthetic feedback about the movement. This kinesthetic-visual transfer is likely to be achieved via visuomotor-kinesthetic matching or via timekeeping mechanisms that are involved in both motor and visual performance.

Adult↗
PubMed2004

Molecular characterization of a Brugia malayi transglutaminase.

Prior studies have demonstrated that transglutaminase (TGase) from the human filarial parasite Brugia malayi is critical for the growth and development of the larval stages. In this report, we describe the cloning and partial characterization of a cDNA encoding the B. malayi TGase (BmTGase). Using RT-PCR and RACE-PCR, the cDNA was amplified from adult worm mRNA. BmTGase is 1,881 bp long and codes for a protein with a predicted molecular mass of 54 kDa. Amino acid sequence analysis of BmTGase revealed significant homology to the protein disulfide isomerase (PDI), particularly, to the PDI-related protein ERp60, a PDI isoform found in the lumen of endoplasmic reticulum. The activity of recombinant B. malayi TGase enzyme (rBmTG) was found to be calcium-dependent and could be inhibited by EDTA. ELISA studies showed that approximately 88% of 48 sera from healthy Indian patients living in a bancroftian filariasis endemic area were reactive with rBmTG. In contrast, only 33% of sera from patients with clinical filariasis were reactive to rBmTG. Non-endemic sera were uniformly non-reactive. Additional studies are needed to elucidate the role, if any, of B. malayi TGase in protective immunity to filariasis.

Amino Acid Sequence↗
PubMed2003

Interrelations between the efficiency of translation start sites and other sequence features of yeast mRNAs.

The translation start site (TSS) plays an important role in the control of the translational efficiency and cytoplasmic stability of eukaryotic mRNAs. The efficiency of TSS recognition is known to be influenced by sequence context, and mRNAs with "weak" TSSs are relatively abundant. We analyzed a sample of 4113 yeast genes in a search for features that might serve to compensate for the inefficient recognition of "weak" TSSs by initiating ribosomes. The first feature found to correlate with variations in TSS strength is differences in the stability of secondary structure upstream and downstream of the start AUG codon. The second feature concerns the characteristics of AUG triplets found at the beginning of the coding sequence, i.e., downstream of the predicted TSS. In particular, the proximal downstream AUG lies in frame with the CDS significantly more often if the TSS itself is located in a "weak" context. The accuracy of TSS annotation, the possibility of polypeptide heterogeneity due to the use of alternative downstream AUGs, and the influence of related features of mRNA sequences are discussed.

5' Untranslated Regions↗
PubMed2002

Nonsense-mediated RNA decay in the TSC1 gene suggests a useful tool pre- and post-positional cloning.

Many mRNAs carrying mutations that are predicted to encode a truncated protein are subject to a mechanism known as nonsense-mediated mRNA decay (NMD), which results in reduced levels of mutant transcript. Tuberous sclerosis (TSC), an autosomal dominant neurocutaneous disorder with mutations in either of two genes, TSC1 or TSC2, requires comprehensive screening of both genes for molecular diagnosis. Virtually all TSC1 mutations are predicted to truncate the protein product. Coding and newly identified 3' untranslated region polymorphisms in TSC1 were used to develop a transcript imbalance assay to investigate TSC1 transcript levels in patients. This approach allowed the correct identification of six out of seven TSC1 patients tested blind from a panel of TSC1 and TSC2 patients, with no false positives. The extent of NMD in TSC1 was found to correlate with each individual mutation regardless of intra-familial variation in clinical features and with no strong evidence for positional bias. NMD in TSC1 was more pronounced in cultured cells than in RNA prepared directly from peripheral lymphocytes (in which novel splicing of exon 5 was observed). The advent of a dense SNP map of transcribed regions of the genome may allow a similar transcript imbalance assay in the assessment of candidate genes for diseases whose causes are still unknown.

3' Untranslated Regions↗
PubMed2005

Acculturation, income, education, safety belt use, and fatal motor vehicle crashes in California.

This paper investigates the role that acculturation, income, and education play in safety belt nonuse among Californian drivers involved in fatal Motor Vehicle Crashes (MVCs). To achieve this goal, measures of acculturation, income, and education were stochastically incorporated into the Fatality Analysis Reporting System (FARS). Using the 1990 California Tobacco Survey and U.S. Census data, we estimated the combination of zip-code-based measures that most accurately predicts an individual, language-based acculturation index for Hispanics and Asians. Logistic regression was used to investigate the role of these variables in safety belt nonuse in fatal MVCs. We found that acculturation has a positive direct effect on safety belt use among Hispanics. We hypothesize that this positive direct effect is caused by Hispanic immigrants learning the benefits of wearing safety belts. However, our study also suggests an indirect negative effect of acculturation on safety belt use through drinking and driving. Prevention programs aimed at increasing the safety of Hispanic drivers not only need to take acculturation differences into account, but also need to be comprehensive in their message, simultaneously targeting both seat belt nonuse and drinking-and-driving problems.

Accidents, Traffic↗
PubMed1994

Isolation and characterization of a gene for a ryanodine receptor/calcium release channel in Drosophila melanogaster.

The nucleotide sequence of a 25.7 kilobase Drosophila melanogaster genomic DNA segment containing a gene for a ryanodine receptor/calcium release channel homologue has been determined. Computer analysis and partial cDNA cloning revealed 26 exons comprising the protein-coding sequence in this gene. The predicted protein is homologous in amino acid sequence and shares characteristic structural features with the mammalian ryanodine receptors. In blot hybridization analysis, a approximately 16 kilobase RNA species was identified abundantly in a 6-12 h embryo as the transcript from this gene. In situ hybridization to polytene chromosomes indicated that this gene locates at band position 44F on the second chromosome.

Amino Acid Sequence↗
PubMed1991

Identifying potential tRNA genes in genomic DNA sequences.

We have developed an algorithm that automatically and reproducibly identifies potential tRNA genes in genomic DNA sequences, and we present a general strategy for testing the sensitivity of such algorithms. This algorithm is useful for the flagging and characterization of long genomic sequences that have not been experimentally analyzed for identification of functional regions, and for the scanning of nucleotide sequence databases for errors in the sequences and the functional assignments associated with them. In an exhaustive scan of the GenBank database, 97.5% of the 744 known tRNA genes were correctly identified (true-positives), and 42 previously unidentified sequences were predicted to be tRNAs. A detailed analysis of these latter predictions reveals that 16 of the 42 are very similar to known tRNA genes, and we predict that they do, in fact, code for tRNA, yielding a false-positive rate for the algorithm of 0.003%. The new algorithm and testing strategy are a considerable improvement over any previously described strategies for recognizing tRNA genes, and they allow detections of genes (including introns) embedded in long genomic sequences.

Algorithms↗
PubMed1989

Nucleotide sequence and mode of transmission of the wild mouse ecotropic virus, HoMuLV.

HoMuLV is an NB-tropic wild mouse leukemia virus (MuLV) with ecotropic host range which induces lymphoma, erythroleukemia, and myelogenous leukemia in NIH Swiss mice. Although HoMuLV uses the same cell surface receptor as other ecotropic MuLVs, hybridization studies suggested that the HoMuLV envelope glycoprotein differs from that of other ecotropic MuLVs. We have now molecularly cloned HoMuLV and sequenced its LTR, gag, and env regions. HoMuLV differs markedly from other MuLVs in the LTR U3 region, in the SU protein of env, and in p12gag. U3 contains a single copy of a sequence analogous to the direct repeat found in other LTRs, and this region includes several previously defined protein binding sites. The predicted amino acid sequence for the coding regions of env and gag reveal that p12 and the SU protein show less than 59 and 65% sequence identity, respectively, with those of other MuLVs. A 0.6-kb segment of the 5' region of the HoMuLV env was used as a hybridization probe to examine inbred and wild mouse genomic DNAs for proviral sequences. HoMuLV env sequences were not present in the germline of any of the inbred strains or wild mice examined including the Mus hortulanus mice which harbored infectious virus. Therefore, HoMuLV represents an evolutionarily related, but distinct, subgroup of ecotropic MuLV which is not genetically transmitted in its natural host.

Amino Acid Sequence↗
PubMed1984

The Drosophila ras oncogenes: structure and nucleotide sequence.

Three Drosophila genes homologous to the Ha-ras probe were isolated and mapped to positions 85D, 64B, and 62B on chromosome 3. Two of these genes (termed Dras 1 and Dras 2) were sequenced. In the case of Dras 1, which contains multiple introns, a cDNA clone was isolated and sequenced. In the case of Dras2, the nucleotide sequence fo the genomic clone was determined. Each gene codes for a protein with a predicted molecular weight of 21.6 kd. Alignment of the amino acid sequence of Dras 1 with the vertebrate Ha-ras protein shows that at the amino terminus and central portion (residues 1-121 and 137-164) the two proteins are remarkably similar, and have an overall homology of 75%. The Dras 2 gene lacks significant homology to the vertebrate counterpart at the extreme amino terminus and is homologous only between positions 28-120 and 139-161 (overall homology of 50%). This result suggests that the N terminus of p21 forms a distinct regulatory or functional domain. At the carboxy terminus, the major region of variability among the vertebrate ras proteins, the two Drosophila sequences also display considerable variability. However, both appear to be more similar to exon 4B of the Ki-ras gene.

Amino Acid Sequence↗
PubMed1986

Evidence for trans splicing in trypanosomes.

The 5' ends of trypanosome mRNAs consist of an identical sequence of 35 nucleotides. This "mini-exon" sequence is derived from the 5' end of a 137 nucleotide RNA (medRNA). The remainder of each mRNA is derived from a protein-coding exon that is not linked to the mini-exon. We propose that medRNA is spliced in trans to de-novo-initiated transcripts of protein-coding genes. This trans splicing model predicts that the downstream portion of medRNA will be part of a branched structure and then be released as a free product (minRNA). We demonstrate that significant levels of minRNA exist in trypanosome RNA. Furthermore, minRNA can be released from high molecular weight RNA by a HeLa cell S100 "debranching" extract. We conclude that trans splicing is the physiological process by which mature mRNA molecules are synthesized in trypanosomes.

Animals↗
PubMed1996

Identification of two prolactin cDNA sequences from a goldfish pituitary cDNA library.

We have identified two different cDNA clones encoding for goldfish prolactin (gfPRL) from a pituitary cDNA library. The coding regions of these clones are predicted to encode for an identical amino acid (aa) sequence with four silent mutations. The 3'-untranslated regions (UTRs) of these clones show only 72% nucleotide (nt) sequence identity. The two genes each encoding gfPRL might have derived from recent gene duplication before the divergence of goldfish from other Cypriniforms. Genomic Southern blot analysis of goldfish DNA also demonstrated that there is a small family of two genes for prolactin in the genome of goldfish.

Amino Acid Sequence↗
PubMed1992

Nucleotide sequence comparison of the M1 genome segment of reovirus type 1 Lang and type 3 Dearing.

The mammalian reoviruses possess a genome composed of 10 double stranded RNA segments. The serotype 1 strain Lang M1 segment was sequenced and compared to the published type 3 sequence. Both segments were 2304 base-pairs long coding for the mu 2 protein predicted to be 736 amino acids long. The sequences were highly conserved with 97.2% conservation of nucleotide sequence and 98.6% conservation of amino acid sequence. The M1 segments of serotypes 1 and 3 have recently diverged as indicated by the distribution of variation with respect to codon positions. The conservation of amino acid sequence indicated that the mu 2 protein has a relatively high functional density.

Amino Acid Sequence↗
PubMed1983

Plasmid-encoded hygromycin B resistance: the sequence of hygromycin B phosphotransferase gene and its expression in Escherichia coli and Saccharomyces cerevisiae.

The plasmid-borne gene hph coding for hygromycin B phosphotransferase (HPH) in Escherichia coli has been identified and its nucleotide sequence determined. The hph gene is 1026 nucleotides long, coding for a protein with a predicted Mr of 39 000. The hph gene was placed in a shuttle plasmid vector, downstream from the promoter region of the cyc 1 gene of Saccharomyces cerevisiae, and an hph construction containing a single AUG in the 5' noncoding region allowed direct selection following transformation in yeast and in E. coli. Thus the hph gene can be used in cloning vectors for both pro- and eukaryotes.

Anti-Bacterial Agents↗