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At least 991 records · Page 55Linked to original sources
PubMed1991

Amplification and molecular cloning of the IMP dehydrogenase gene of Leishmania donovani.

A mutant (MPA100) strain of Leishmania donovania was generated from a wild type (D1700) population by virtue of its ability to survive the selective pressure of gradually increasing concentrations of mycophenolic acid (MPA), an inhibitor of IMP dehydrogenase (IMPDH) activity. Comparative growth experiments revealed that the MPA100 strain was 100-fold more resistant to MPA toxicity and cross-resistant to ribavarin, another inhibitor of IMPDH. A direct comparison of IMPDH levels in D1700 and MPA100 cells showed that the latter expressed at least 20-fold higher enzyme activity. In order to evaluate the mechanism by which MPA100 cells overexpressed IMPDH, the leishmanial gene encoding IMPDH was isolated from a genomic library in EMBL3 by cross-hybridization to a mouse IMPDH cDNA, and a 2.3-kilobase EcoRV-PstI fragment was subcloned into a Bluescript vector and sequenced. The EcoRV-PstI fragment contained an open reading frame of 514 amino acids that encompassed the entire leishmanial IMPDH coding sequence. The predicted amino acid sequence showed a 52.5% identity with that of the corresponding human IMPDH. The codon usage of the leishmanial IMPDH gene reflected a strong bias toward codons containing either G or C in the wobble position. The EcoRV-PstI fragment hybridized to a 3.0-kilobase mRNA that was expressed at 10-20-fold greater levels in the MPA100 cells. Using the EcoRV-PstI fragment as a probe, the increased amount of IMPDH activity and IMPDH mRNA in the MPA100 cells could be attributed to an approximately 10-20-fold amplification of the leishmanial IMPDH gene.

Amino Acid Sequence↗
PubMed1992

COQ2 is a candidate for the structural gene encoding para-hydroxybenzoate:polyprenyltransferase.

Coenzyme Q functions as a lipid-soluble electron carrier in eukaryotes. In Saccharomyces cerevisiae, the enzymes responsible for the assembly of the polyisoprenoid side chain and subsequent transfer to para-hydroxybenzoate (PHB) are encoded by the nuclear genes COQ1 and COQ2, respectively. Yeast mutants defective in coenzyme Q biosynthesis are respiratory defective and provide a useful tool to study this non-sterol branch of the isoprenoid biosynthetic pathway. We isolated a 5.5-kilobase genomic DNA fragment that was able to functionally complement a coq2 strain. Additional complementation analyses located the COQ2 gene within a 2.1-kilobase HindIII-BglII restriction fragment. Sequence analyses revealed the presence of a 1,116-base pair open reading frame coding for a predicted protein of 372 amino acids and a molecular mass of 41,001 daltons. The amino acid sequence exhibits a typical amino-terminal mitochondrial leader sequence and six potential membrane-spanning domains. Primer extension and Northern analyses indicate the gene is transcriptionally active. Transformation of a coq2 strain with the 2.1-kilobase HindIII-BglII genomic restriction fragment on a multicopy plasmid restores PHB:polyprenyltransferase activity to wild-type levels. Disruption of the chromosomal COQ2 gene indicates the gene is not essential for viability, yet is required for PHB:polyprenyltransferase activity and respiratory function. In addition, the deduced amino acid sequence of PHB:polyprenyltransferase contains a putative allylic polyprenyl diphosphate-binding site. The presence of this aspartate-rich domain in a number of functionally distinct proteins which utilize polyprenyl diphosphate substrates is reported.

Alkyl and Aryl Transferases↗
PubMed1989

A 31 kilodalton beta-protein immunoreactive polypeptide in neuronal lipofuscin.

The beta-protein, a small fibrillar peptide which is the main constituent of the amyloid deposits in senile neuritic plaques and congophilic angiopathy derives by proteolytic cleavage from at least one of three large precursor proteins of 695 to 770 amino acids encoded by a gene on chromosome 21. In the brain the mRNA coding for these predicted proteins has been localized to neurons and non-neuronal cell types. Monoclonal antibodies raised to a synthetic peptide corresponding to residues 1 to 24 of the beta-protein do not only stain the amyloid deposits characteristic for Alzheimer neuropathology, but also neuronal lipofuscin. This material is immunoreactive in every brain area examined (cerebral and cerebellar cortices, basal ganglia, brainstem) and its reactivity is independent from the presence of Alzheimer's disease. At the ultrastructural level immunoreactivity is associated with the proteinaceous matrix part of lipofuscin which does not contain any fibrillar structures. Western blotting of a lipofuscin enriched fraction shows a beta-protein immunoreactive polypeptide migrating at approximately 31 kDa position on SDS-polyacrylamide gel electrophoresis. These results suggest that a large fragment of the amyloid precursor protein (approximately 280 residues) is associated with lipofuscin. Unlike in the microglial cell where the amyloid precursor is processed in a manner to release the beta-protein which forms amyloid fibers, one pathway of its physiological breakdown in the nerve cell seems to yield a large fragment which accumulates on a lipopigment characteristic for normal aging.

Aged↗
PubMedDate not supplied

Evaluation of the color coded Doppler ultrasound in detecting carotid bifurcation disease.

The color coded continuous wave doppler ultrasound was compared with angiography in 201 arteries, 83 with greater than 50% diameter stenosis and 118 with less than 50% stenosis. Overall accuracy in identifying hemodynamically significant (greater than 50% diameter stenosis) was 87% in the presence of peak velocities greater than 5000 Hz and a blue color coded image. Negative predictive value was 94.5%. False positives were mainly due to the presence of severe external carotid stenosis and increased flow due to contralateral carotid occlusion. Within the limitations of the test being an indirect method, it is a reliable screening method for detecting hemodynamically significant carotid artery disease.

Arterial Occlusive Diseases↗
PubMed1995

Developmental and regional expression pattern of a novel NMDA receptor-like subunit (NMDAR-L) in the rodent brain.

A novel NMDA receptor-like (NMDAR-L) cDNA was isolated that contained an open reading frame coding for a predicted polypeptide of 1115 amino acids that shares approximately 27% identity with NMDA receptor subunits. In situ hybridization experiments indicated that NMDAR-L mRNA was expressed in the developing rodent CNS. On postnatal day 1 (P1), NMDAR-L mRNA expression was pronounced in the entorhinal cortex, the subiculum and the thalamus, in layer V of the developing neocortex, in the superior and inferior colliculi, and various regions of the hindbrain, excluding the cerebellum. On P5, NMDAR-L mRNA was expressed in layer V of the neocortex, in the entorhinal cortex, in the subiculum, and in the thalamus. On P14, NMDAR-L mRNA was expressed in layers II-VI of the neocortex, in the entorhinal and piriform cortex, in the subiculum and CA1 field, and in the nucleus of the lateral olfactory tract. In the adult brain, NMDAR-L mRNA was detected predominately in the nucleus of the lateral olfactory tract. Injection of NMDAR-L cRNA into Xenopus oocytes did not lead to the expression of homomeric glutamate-activated channels. However, coinjection of the triple combination of NMDAR-L with NMDAR1 and NMDAR2B cRNAs led to a striking decrease in the current magnitude compared to currents obtained after coexpression of the double combination of NMDAR1 with NMDAR2B. While the function of NMDAR-L remains to be established, its developmental and regional expression pattern suggests that NMDAR-L may influence axonal outgrowth and synaptogenesis during brain development.

Aging↗
PubMed1994

Identification and characterization of metallothionein cDNA from mRNA transcripts induced by starvation in Atlantic cod (Gadus morhua).

A cDNA from metallothionein (MT) messenger RNA was identified in a library representing mRNA transcripts that are abundant in starving Atlantic cod larvae. The cod MT cDNA is closely related to MT mRNAs from other fish species and codes for a predicted 60 amino acid peptide. In adult cod liver MT mRNA is abundant and it is detected in cod eggs and larvae. Levels of MT mRNA were four times higher in three-week-old cod larvae starved for six days than in fed larvae, while starvation of four-week-old larvae for eight days resulted in a nearly seven-fold elevation in MT mRNA levels.

Amino Acid Sequence↗
PubMed1994

Novel human oncogene lbc detected by transfection with distinct homology regions to signal transduction products.

In order to isolate transforming genes involved in leukemias, DNA from a CML acute phase sample was transfected into NIH-3T3 cells and found to be tumorigenic in nude mice. Partial genomic cloning using human repeat sequence as probe followed by cDNA cloning of this oncogene, termed lbc, was undertaken. The lbc cDNA sequence shows no identity to known proteins and codes for a predicted hydrophilic protein product of 47 kD, which contains several consensus kinase phosphorylation sites. The N-terminus encodes a consensus E-F hand motif followed by a region of homology to the transforming human oncogene dbl associated with regulatory activity for the ras superfamily of small G proteins, while the C-terminus contains homology with pleckstrin and rac protein kinase in a region which overlaps with the recently defined PH (pleckstrin homology) domain. Lbc expression is restricted to human hematopoietic cells and skeletal muscle, lung and heart. Transfection of 3T3 cells with an expression vector encoding lbc cDNA results in focus formation, demonstrating its biological activity. These data indicate that the lbc oncogene encodes a novel product implicated in distinct cellular signal transduction functions.

3T3 Cells↗
PubMed1993

The PRE4 gene codes for a subunit of the yeast proteasome necessary for peptidylglutamyl-peptide-hydrolyzing activity. Mutations link the proteasome to stress- and ubiquitin-dependent proteolysis.

Proteinase yscE, the yeast proteasome, is a member of the nonlysosomal, high molecular mass (approximately 700 kDa) multifunctional proteinase complexes that are highly conserved from yeast to man. We have isolated mutants defective in one of the three proteolytic activities of the enzyme complex, i.e. in cleavage of peptide bonds after acidic amino acids. Using one of these mutants (pre4-1), we cloned the PRE4 gene and uncovered an open reading frame with 266 amino acids coding for a predicted protein of 29.4 kDa. The protein proved to be a subunit of proteinase yscE. The Pre4 amino acid sequence shows strong homology to the beta-subunit of the Xenopus laevis proteasome. Chromosomal deletion of the PRE4 gene is lethal. The pre4-1 mutant allele was cloned and sequenced. The mutant protein is shortened by 15 amino acids at the carboxyl terminus. Mutations (pre1-1, pre2-2) in the chymotrypsin-like activity of proteinase yscE uncovered the enzyme to be involved in ubiquitin-linked and stress-dependent proteolytic pathways. In contrast to these mutants, pre4-1 mutants did not exhibit any apparent stress-dependent phenotypes. However, pre1-1 pre4-1 double mutants showed enhanced canavanine sensitivity and increased accumulation of ubiquitin protein conjugates, as compared with pre1-1 single mutants.

Amino Acid Sequence↗
PubMed1993

Cloning and expression of a novel cyclic GMP-dependent protein kinase from mouse brain.

Synthetic oligonucleotides were used to amplify mouse brain cDNA sequences homologous to conserved regions of known cGMP-dependent protein kinases, and two classes of products were identified. The first class (CGKI) of amplification products contained approximately 1.0 kilobase (kb) of DNA sequence between the oligonucleotide primers, and this sequence showed a high degree of homology (90% identity) with the known bovine and human type I cDNA sequences for cGMP-dependent protein kinase. The second class (CGKII) of amplification products contained approximately 1.1 kb of DNA sequence between the oligonucleotide primers, and this sequence showed a much lower homology (65% identity) with the bovine and human type I cDNA sequences. Northern blot analysis showed that CGKI transcripts of 8.5 kb were abundant in brain and lung, whereas a 7-kb transcript could be detected in testis. CGKII transcripts of 6 kb were also abundant in brain and lung but could be detected at lower levels in kidney. The CGKII amplification product was used to screen a mouse brain cDNA library, and four overlapping cDNA clones were isolated which comprised the entire CGKII coding region. The predicted CGKII protein consists of 761 amino acids and has a molecular mass of 87 kDa. The CGKII protein shows highest homology to the catalytic (66% amino acid identity) and regulatory domains (45% identity) of bovine and human CGKI. Little homology is observed at the amino terminus or in the region linking the regulatory and catalytic domains. An expression vector for mouse CGKII was constructed and transfected into COS-1 cells where it directed the expression of a protein kinase which was activated by cGMP with an apparent K alpha of 300 nM cGMP.

Amino Acid Sequence↗
PubMed1996

Somatic and germline mutations of the BRCA2 gene in sporadic ovarian cancer.

The breast and ovarian cancer susceptibility gene BRCA2 has recently been isolated. A role for BRCA2 in sporadic breast and ovarian cancer has been suggested by loss of heterozygosity (LOH) studies which show frequent LOH in the BRCA2 region at chromosome 13q12. In addition, the observation of nonrandom loss of the wild-type chromosome in a breast/ovarian cancer family which shows linkage to BRCA2 suggests it may act as a tumor suppressor gene. To determine the extent of somatic alteration involving BRCA2 in sporadic ovarian cancer, 50 tumors were analyzed for mutations throughout the entire BRCA2 coding region. Mutations predicted to result in truncation of the BRCA2 protein were detected in four tumors. Analysis of germline DNA revealed two of these alterations to be of somatic origin. In addition, all four tumors exhibited loss of the second BRCA2 allele as predicted by Knudson's hypothesis for a tumor suppressor gene. These results suggest that, as is the case with BRCA1, somatic mutations of BRCA2 are infrequent in sporadic ovarian cancer, despite the relatively high frequency of LOH detected around the BRCA2 locus.

BRCA2 Protein↗
PubMed1997

The HRX proto-oncogene product is widely expressed in human tissues and localizes to nuclear structures.

Chromosomal rearrangement of the HRX (MLL, ALL-1, Htrx) gene situated at chromosome band 11q23 is one of the most frequent genetic changes in infant leukemias of myeloid and lymphoid lineage and in treatment-induced secondary leukemias. The HRX gene codes for a predicted 431-kD protein that shows significant homology to the Drosophila trithorax protein, an Hox epigenetic regulator. Typically, the region encoding the HRX gene is rearranged, mostly in reciprocal translocations with a number of partners, resulting in a range of fusion genes. However, this is not the only abnormality affecting HRX because partial duplication of the gene, as well as interstitial deletions, can occur. Despite extensive studies of HRX at the genetic level, the protein products of the HRX gene and their patterns of expression in normal and leukemic cells remain uncharacterized. In this study we analyzed the distribution and localization of HRX proteins in cell lines and human tissues, using both polyclonal and monoclonal antibodies. The specificity of these reagents was confirmed using cells transfected with the HRX-ENL fusion gene. Western blot analyses of protein extracts from cells carrying the t(11;19) and t(4;11) translocations showed HRX chimeric proteins whose migrations corresponded to the sizes predicted from analyses of translocation-induced fusion mRNAs expressed by the derivative 11 chromosomes. Immunocytochemical analysis showed a punctate distribution of wild-type and chimeric HRX proteins within cell nuclei, suggesting that HRX localizes to nuclear structures in cells with and without 11q23 translocations. Nuclear staining was found in the majority of tissues studied with the strongest reactivity in cerebral cortex, kidney, thyroid, and lymphoid tissues. Thus, HRX is widely expressed in most cell types including hematopoietic cells, a finding that precludes an immunocytochemical approach for diagnosis of leukemias bearing 11q23 structural abnormalities.

Animals↗
PubMed1997

RP1, a new member of the adenomatous polyposis coli-binding EB1-like gene family, is differentially expressed in activated T cells.

Cross-linking of the CD3 and CD28 molecules on T lymphocytes represents one of the most effective signals for T lymphocyte activation and triggering of their cytotoxic effector function. To identify genes that are expressed in T cells after stimulation, mRNA from T lymphocytes that had been activated by the simultaneous stimulation of the CD3 and CD28 trigger molecules was transcribed for a differential mRNA display analysis into cDNA and was compared with cDNA from CD28- or CD3-activated or resting lymphocytes. Differential expression was confirmed subsequently by Northern blot analysis. One of the cDNA fragments expressed specifically in CD3- and CD28-activated T cells was designated RP1. The predictive protein-coding region of RP1 had a significant homology to members of the recently found adenomatous polyposis coli (APC) protein-binding EB1 gene family, which codes for yet unknown protein(s). Bacterially expressed RP1 protein revealed specific binding to wild-type but not to mutated APC protein. The rapid up-regulation of RP1 mRNA in properly activated T cells suggests that this gene might belong to the immediate/early gene family, which controls the signal transduction cascade downstream of the TCR. As the expression level of the RP1 gene in activated T cells and a spectrum of tumor-derived cell lines correlates with the proliferative status of the cells, members of the EB1-like gene family may not only be involved in the tumorigenesis of colorectal cancers but may also play a role in the proliferative control of normal cells.

Adenomatous Polyposis Coli↗
PubMed1998

Full-length GBV-C/HGV genomes from nine Japanese isolates: characterization by comparative analyses.

The genomes of nine GBV-C/HGV isolates from Japanese chronic hepatitis patients were fully sequenced and characterized. They shared 85% nucleotide sequence homology with previously characterized isolates from the US and West Africa. Homology studies and phylogenetic analyses showed that the Japanese isolates formed a third group distinct from the established groups 1 and 2. The genetic distances between the three groups of GBV-C/HGV were very similar to the distances between the two classical swine fever virus (CSFV) serotypes, which suggested that they might belong to a separate GBV-C/HGV serotype. Plot similarity analysis comparing the three groups exposed relatively conserved terminal non-coding regions. Hairpin structures predicted in the Japanese isolates are probably involved in viral replication. The region coding E1-E2-NS-2 showed the least similarity (80%); in HCV the similarity here is only 50% due to its hypervariability. NS-3 and NS-5b that respectively encode the helicase/protease and RNA-dependent RNA polymerase, had a high degree of amino acid homology, suggesting a high degree of functional constraint in this region. The NS-5b nucleotide sequence was highly conserved perhaps because of constraints from RNA secondary structure and/or an open reading frame in the negative strand.

Base Sequence↗
PubMed2000

Coding neuroradiology reports for the Northern Manhattan Stroke Study: a comparison of natural language processing and manual review.

Automated systems using natural language processing may greatly speed chart review tasks for clinical research, but their accuracy in this setting is unknown. The objective of this study was to compare the accuracy of automated and manual coding in the data acquisition tasks of an ongoing clinical research study, the Northern Manhattan Stroke Study(NOMASS). We identified 471 neuroradiology reports of brain images used in the NOMASS study. Using both automated and manual coding, we completed a standardized NOMASS imaging form with the information contained in these reports. We then generated ROC curves for both manual and automated coding by comparing our results to the original NOMASS data, where study in investigators directly coded their interpretations of brain images. The areas under the ROC curves for both manual and automated coding were the main outcome measure. The overall predictive value of the automated system (ROC area 0.85, 95% CI 0.84-0.87) was not statistically different from the predictive value of the manual coding (ROC area 0.87, 95% CI 0.83-0.91). Measured in terms of accuracy, the automated system performed slightly worse than manual coding. The overall accuracy of the automated system was 84% (CI 83-85%). The overall accuracy of manual coding was 86% (CI 84-88%). The difference in accuracy between the two methods was small but statistically significant (P = 0.026). Errors in manual coding appeared to be due to differences between neurologists' and nueroradiologists' interpretation, different use of detailed anatomic terms, and lack of clinical information. Automated systems can use natural language processing to rapidly perform complex data acquisition tasks. Although there is a small decrease in the accuracy of the data as compared to traditional methods, automated systems may greatly expand the power of chart review in clinical research design and implementation.

Brain↗
PubMed1996

A theory of the visual motion coding in the primary visual cortex.

This paper demonstrates that much of visual motion coding in the primary visual cortex can be understood from a theory of efficient motion coding in a multiscale representation. The theory predicts that cortical cells can have a spectrum of directional indices, be tuned to different directions of motion, and have spatiotemporally separable or inseparable receptive fields (RF). The predictions also include the following correlations between motion coding and spatial, chromatic, and stereo codings: the preferred speed is greater when the cell receptive field size is larger, the color channel prefers lower speed than the luminance channel, and both the optimal speeds and the preferred directions of motion can be different for inputs from different eyes to the same neuron. These predictions agree with experimental observations. In addition, this theory makes predictions that have not been experimentally investigated systematically and provides a testing ground for an efficient multiscale coding framework. These predictions are as follows: (1) if nearby cortical cells of a given preferred orientation and scale prefer opposite directions of motion and have a quadrature RF phase relationship with each other, then they will have the same directional index, (2) a single neuron can have different optimal motion speeds for opposite motion directions of monocular stimuli, and (3) a neuron's ocular dominance may change with motion direction if the neuron prefers opposite directions for inputs from different eyes.

Color Perception↗
PubMed1993

Genomic organization and mapping of transcription and translation products of the NADL-2 strain of porcine parvovirus.

The NADL-2 strain of PPV was cloned into pUC19 and independent infectious clones were sequenced. This permitted a correction of published sequences and to predict a cruciform structure as an alternative to the 5'-hairpin of the "-" strand. This 5'-end structural covariance is shared with other parvoviruses of the same group and two alternative sequences ("flip" and "flop") were present in the region of the cruciform. Transcript and translation product mapping allowed the prediction of the location of the different expression signals. The 5'-startpoints of the transcripts were located at nucleotides 225 and 2035, respectively, and the polyadenylation site at nucleotides 4829-4833. This indicated that the TATA boxes at 196-TATA and 2004-AATA and the 4813-AATAAA polyadenylation sequence would be functional. Alternative splicing of capsid gene (VP) transcripts (either 2280-AG/GT or 2313-AG/GT spliced with 2386-AG/GA), to maintain or remove the first AUG (at 2287) in the ORF, yielded two 2.9-kb mRNAs containing a nested set of protein-coding sequences (VP-1 and VP-2 with predicted molecular mass 80.9 and 64.3 kDa, respectively). Three nonstructural (NS) protein gene transcripts were identified. The 4.7-kb transcript was not spliced in the NS gene and was predicted to code for a 75.5-kDa protein (NS-1; published value of phosphorylated form 84 kDa). The splicing sites of two different 3.3-kb NS transcripts were analyzed. These transcripts were predicted to code for the NS-2 protein (18.1 kDa). Of the two NS-2 transcripts, one had also the VP-intron removed downstream of the NS-2 coding sequences. A 2.9-kb transcript would code for an NS-3 protein (12.4 kDa) although such a protein has not been described before. A flow chart of the information from the viral DNA to the viral proteins is presented and several differences, both for the NS and the VP genes, with closely related parvoviruses are noted.

Amino Acid Sequence↗
PubMed1988

Bacillus sporulation gene spo0H codes for sigma 30 (sigma H).

The DNA sequences of the spo0H genes from Bacillus licheniformis and B. subtilis are described, and the predicted open reading frames code for proteins of 26,097 and 25,447 daltons, respectively. The two spo0H gene products are 91% identical to one another and about 25% identical to most of the procaryotic sigma factors. The predicted proteins have a conserved 14-amino-acid sequence at their amino terminal end, typical of sigma factors. Antibodies raised against the spo0H gene product of B. licheniformis specifically react with RNA polymerase sigma factor protein, sigma 30, purified from B. subtilis. We conclude that the spo0H genes of B. licheniformis and B. subtilis code for sigma 30, now known as sigma H.

Amino Acid Sequence↗
PubMed2006

YASSPP: better kernels and coding schemes lead to improvements in protein secondary structure prediction.

The accurate prediction of a protein's secondary structure plays an increasingly critical role in predicting its function and tertiary structure, as it is utilized by many of the current state-of-the-art methods for remote homology, fold recognition, and ab initio structure prediction. We developed a new secondary structure prediction algorithm called YASSPP, which uses a pair of cascaded models constructed from two sets of binary SVM-based models. YASSPP uses an input coding scheme that combines both position-specific and nonposition-specific information, utilizes a kernel function designed to capture the sequence conservation signals around the local window of each residue, and constructs a second-level model by incorporating both the three-state predictions produced by the first-level model and information about the original sequence. Experiments on three standard datasets (RS126, CB513, and EVA common subset 4) show that YASSPP is capable of producing the highest Q3 and SOV scores than that achieved by existing widely used schemes such as PSIPRED, SSPro 4.0, SAM-T99sec, as well as previously developed SVM-based schemes. On the EVA dataset it achieves a Q3 and SOV score of 79.34 and 78.65%, which are considerably higher than the best reported scores of 77.64 and 76.05%, respectively.

Algorithms↗