Comparison of vector space model methodologies to reconcile cross-species neuroanatomical concepts.

Generating informational thesauri that classify, cross-reference, and retrieve diverse and highly detailed neuroscientific information requires identifying related neuroanatomical terms and acronyms within and between species (Gorin et al., 2001) Manual construction of such informational thesauri is laborious, and we describe implementing and evaluating a neuroanatomical term and acronym reconciliation (NTAR) system to assist domain experts with this task. NTAR is composed of two modules. The neuroanatomical term extraction (NTE) module employs a hidden Markov model (HMM) in conjunction with lexical rules to extract neuroanatomical terms (NT) and acronyms (NA) from textual material. The output of the NTE is formatted into collections of term- or acronym-indexed documents composed of sentences and word phrases extracted from textual material. The second information retrieval (IR) module utilizes a vector space model (VSM) and includes a novel, automated relevance feedback algorithm. The IR module retrieves statistically related neuroanatomical terms and acronyms in response to queried neuroanatomical terms and acronyms. Neuroanatomical terms and acronyms retrieval obtained from term-based inquiries were compared with (1) term retrieval obtained by including automated relevance feedback and with (2) term retrieval using "document-to-document" comparisons (context-based VSM). The retrieval of synonymous and similar primate and macaque thalamic terms and acronyms in response to a query list of human thalamic terminology by these three IR approaches was compared against a previously published, manually constructed concordance table of homologous cross-species terms and acronyms. Term-based VSM with automated relevance feedback retrieved 70% and 80% of these primate and macaque terms and acronyms, respectively, listed in the concordance table. Automated feedback algorithm correctly identified 87% of the macaque terms and acronyms that were independently selected by a domain expert as being appropriate for manual relevance feedback. Context-based VSM correctly retrieved 97% and 98% of the primate and macaque terms and acronyms listed in the term homology table. These results indicate that the NTAR system could assist neuroscientists with thesauri creation for closely related, highly detailed neuroanatomical domains.

The cyclin-dependent kinase (CDK) inhibitor flavopiridol inhibits glycogen phosphorylase.

Flavopiridol has been shown to induce cell cycle arrest and apoptosis in various tumor cells in vitro and in vivo. Using immobilized flavopiridol, we identified glycogen phosphorylases (GP) from liver and brain as flavopiridol binding proteins from HeLa cell extract. Purified rabbit muscle GP also bound to the flavopiridol affinity column. GP is the rate-limiting enzyme in intracellular glycogen breakdown. Flavopiridol significantly inhibited the AMP-activated GP-b form of the purified rabbit muscle isoenzyme (IC50 of 1 microM at 0.8 mM AMP), but was less inhibitory to the active phosphorylated form of GP, GP-a (IC50 of 2.5 microM). The AMP-bound GP-a form was poorly inhibited by flavopiridol (40% at 10 microM). Increasing concentrations of the allosteric effector AMP resulted in a linear decrease in the GP-inhibitory activity of flavopiridol suggesting interference between flavopiridol and AMP. In contrast the GP inhibitor caffeine had no effect on the relative GP inhibition by flavopiridol, suggesting an additive effect of caffeine. Flavopiridol also inhibited the phosphorylase kinase-catalyzed phosphorylation of GP-b by inhibiting the kinase in vitro. Flavopiridol thus is able to interfere with both activating modifications of GP-b, AMP activation and phosphorylation. In A549 NSCLC cells flavopiridol treatment caused glycogen accumulation despite of an increase in GP activity, suggesting direct GP inhibition in vivo rather than inhibition of GP activation by phosphorylase kinase. These results suggest that the cyclin-dependent kinase inhibitor flavopiridol interferes with glycogen degradation, which may be responsible for flavopiridol's cytotoxicity and explain its resistance in some cell lines.

Terminology Query Language: a server interface for concept-oriented terminology systems.

Designers of medical computing applications increasingly require terminology support for their systems. Yet, terminology systems today lack standard methodologies for providing terminology support. This invariably means increased implementation time and expense for system developers who need to use terminologies in their applications. We introduce Terminology Query Language (TQL), a simple query language interface to server implementations of concept-oriented terminologies. TQL is a declarative, set-based query language built on a generic entity-relationship (E/R) schema. TQL defines a common query-based mechanism for accessing terminology information from one or more terminology servers over a network connection.

Stretch-activated ion channels contribute to membrane depolarization after eccentric contractions.

We tested the hypothesis that eccentric contractions activate mechanosensitive or stretch-activated ion channels (SAC) in skeletal muscles, producing increased cation conductance. Resting membrane potentials and contractile function were measured in rat tibialis anterior muscles after single or multiple exposures to a series of eccentric contractions. Each exposure produced a significant and prolonged (>24 h) membrane depolarization in exercised muscle fibers. The magnitude and duration of the depolarization were related to the number of contractions. Membrane depolarization was due primarily to an increase in Na(+) influx, because the estimated Na(+)-to-K(+) permeability ratio was increased in exercised muscles and resting membrane potentials could be partially repolarized by substituting an impermeant cation for extracellular Na(+) concentration. Neither the Na(+)/H(+) antiport inhibitor amiloride nor the fast Na(+) channel blocker TTX had a significant effect on the depolarization. In contrast, addition of either of two nonselective SAC inhibitors, streptomycin or Gd(3+), produced significant membrane repolarization. The results suggest that muscle fibers experience prolonged depolarization after eccentric contractions due, principally, to the activation of Na(+)-selective SAC.

Malignant gliomas display altered pH regulation by NHE1 compared with nontransformed astrocytes.

Malignant gliomas exhibit alkaline intracellular pH (pH(i)) and acidic extracellular pH (pH(e)) compared with nontransformed astrocytes, despite increased metabolic H(+) production. The acidic pH(e) limits the availability of HCO(-)(3), thereby reducing both passive and dynamic HCO(-)(3)-dependent buffering. This implies that gliomas are dependent upon dynamic HCO(-)(3)-independent H(+) buffering pathways such as the type 1 Na(+)/H(+) exchanger (NHE1). In this study, four rapidly proliferating gliomas exhibited significantly more alkaline steady-state pH(i) (pH(i) = 7.31-7.48) than normal astrocytes (pH(i) = 6.98), and increased rates of recovery from acidification, under nominally CO(2)/HCO(-)(3)-free conditions. Inhibition of NHE1 in the absence of CO(2)/HCO(-)(3) resulted in pronounced acidification of gliomas, whereas normal astrocytes were unaffected. When suspended in CO(2)/HCO(-)(3) medium astrocyte pH(i) increased, yet glioma pH(i) unexpectedly acidified, suggesting the presence of an HCO(-)(3)-dependent acid loading pathway. Nucleotide sequencing of NHE1 cDNA from the gliomas demonstrated that genetic alterations were not responsible for this altered NHE1 function. The data suggest that NHE1 activity is significantly elevated in gliomas and may provide a useful target for the development of tumor-selective therapies.

Cloning and expression of the Na+/H+ exchanger from Amphiuma RBCs: resemblance to mammalian NHE1.

The cDNA encoding the Na+/H+ exchanger (NHE) from Amphiuma erythrocytes was cloned, sequenced, and found to be highly homologous to the human NHE1 isoform (hNHE1), with 79% identity and 89% similarity at the amino acid level. Sequence comparisons with other NHEs indicate that the Amphiuma tridactylum NHE isoform 1 (atNHE1) is likely to be a phylogenetic progenitor of mammalian NHE1. The atNHE1 protein, when stably transfected into the NHE-deficient AP-1 cell line (37), demonstrates robust Na+-dependent proton transport that is sensitive to amiloride but not to the potent NHE1 inhibitor HOE-694. Interestingly, chimeric NHE proteins constructed by exchanging the amino and carboxy termini between atNHE1 and hNHE1 exhibited drug sensitivities similar to atNHE1. Based on kinetic, sequence, and functional similarities between atNHE1 and mammalian NHE1, we propose that the Amphiuma exchanger should prove to be a valuable model for studying the control of pH and volume regulation of mammalian NHE1. However, low sensitivity of atNHE1 to the NHE inhibitor HOE-694 in both native Amphiuma red blood cells (RBCs) and in transfected mammalian cells distinguishes this transporter from its mammalian homologue.

Role of E and CArG boxes in developmental regulation of muscle glycogen phosphorylase promoter during myogenesis.

Muscle glycogen phosphorylase (MGP) transcript and protein levels increase during skeletal muscle development in tandem with the products of other muscle genes responsible for glucose and glycogen metabolism. Previous studies demonstrated that a 269 bp region 5' to exon 1 of MGP is sufficient for developmental regulation in the C2C12 myogenic cell line (Froman et al., 1994). This genomic region (-209 to +60) contains four consensus E box motifs, a CArG-like sequence, and a GC-rich domain. Native MGP transcripts were not detected in pluripotent CH310T1/2 fibroblasts, but low levels of MGP mRNA were measured in CH310T1/2 cells that were stably transfected with MyoD. Three of the E box motifs in the MGP proximal promoter interacted with C2C12 nuclear proteins. However, cotransfection of the MGP promoter with myogenic regulatory factors, including MyoD and myogenin, produced less than 2-fold activation compared with 20-fold activation of the desmin promoter. Mutational analyses of the MGP promoter demonstrated that increased expression in C2C12 myotubes did not require any of the E box motifs or the CArG-like element. A small region (-76 to -68) upstream of GC-rich domain (-64 to -51) significantly reduced promoter activities in both myoblasts and myotubes. The functional studies suggest that MGP is developmentally regulated during myogenesis by alternative pathways that utilize unidentified regulatory elements or ancillary factors.

Prolonged recovery and reduced adaptation in aged rat muscle following eccentric exercise.

We tested the hypothesis that exposure to eccentric (lengthening) contractions results in greater damage and more prolonged recovery in aged rat muscle (32 months) than in adult muscle (6 months), and that the adaptation usually associated with a single exposure to eccentric exercise is reduced in the aged muscle. Experiments were performed using a new rat model for aging studies. Fisher 344/Brown Norway F1 Hybrid. An ankle flexor, the tibialis anterior (TA), was subjected to a series of 24 eccentric contractions in situ and contractile function was assessed 1, 2, 5 and 14 days following. Eccentric exercise produced a similar reduction in maximum specific twitch and tetanic tension in the aged and adult muscles at 1 and 2 days postexercise. Adult muscles recovered by 5 days, while aged TA remained significantly impaired. Aged TA was fully restored by 14 days. Exercise adaptation was tested by subjecting the TA to a second exercise 14 days following the first. Contractile function was determined 2 days following the second exercise. Adult TA maintained its pre-exercise specific force following the second exercise, while aged TA again showed a significant reduction. Thus, a single exposure to eccentric exercise produced complete adaptation in the adult TA, but not in the aged muscles.

Primate rod and cone photoreceptors may differ in glucose accessibility.

PURPOSE: Glucose is crucial for the function of retinal photoreceptors, other retinal neurons, and glial cells. Exogenous glucose can be extracted from the retinal and choroidal circulation, and endogenous glucose may be generated from breakdown of intracellular glycogen stores. Because glucose deprivation is a critical component of retinal ischemia, the authors sought to determine the sites of glucose entry into and generation within the retina. METHODS: The localization of the glucose transporter, GluT-1, and the brain and muscle isozymes of glycogen phosphorylase, GlyP, was studied by immunohistochemistry of adult human and monkey retinas. RESULTS: Brain glycogen phosphorylase (B-GlyP) immunoreactivity was found in cone, but not rod, photoreceptors. There was immunostaining of foveal and peripheral cones throughout the cytoplasm from the outer segment to the synaptic pedicle. Short wavelength ("blue") cones were positive for B-GlyP. Diffuse staining of the inner and outer plexiform and the nerve fiber layers did not resemble the distinct morphology of Müller cells. Immunoreactivity to muscle GlyP (M-GlyP) was confined to selected synaptic layers of the inner plexiform layer in monkey retina. Staining with antibody to GluT-1 demonstrated diffuse reactivity throughout the retina, including the blood-retinal barrier cells, retinal pigment epithelium, and vascular endothelium. Ultrastructural immunohistochemistry showed staining of rod and cone inner and outer segments. CONCLUSIONS: These immunohistochemical studies indicate that rod and cone photoreceptors have the biochemical capability to transport exogenous glucose from the circulation. Only cones appear capable of using endogenous glycogen stores. These findings imply that cones could be more resistant to acute reductions in circulating glucose during hypoglycemia. However, during hypoxic insult, glycogenolysis and anaerobic glycolysis could result in increased production of intracellular lactic acid, potentially predisposing the cone to acidotic damage.

Regulation of the rat muscle glycogen phosphorylase-encoding gene during muscle cell development.

The muscle isozyme of glycogen phosphorylase (MGP) catalyzes the hydrolysis hydrolysis of intracellular glycogen in mammalian tissues and is produced in skeletal muscle, brain and heart. The MGP gene is developmentally and neutrally regulated in skeletal muscle, but little is known about the gene's transcriptional regulation. We have isolated and characterized the 5' flanking region of rat MGP. Truncated portions of the MGP 5' flanking region were coupled to the bacterial cat reporter gene and used in transient transfection assays in the mouse muscle C2C12 cell line. The region between -211 and +62 contained the smallest regulatory domain capable of demonstrating developmentally regulated myogenic expression in C2C12 cells. This was in contrast with findings from another investigation that transfected this cell line with human MGP [Lockyer and McCracken, J. Biol. Chem. 266 (1991) 20262-20269]. A 172-nucleotide (nt) region between -839 and -666 functioned as a potent enhancer in C2C12 cells when coupled to its cognate promoter, but not when coupled to a simian virus 40 promoter. This rat MGP enhancer region is 78% identical to a comparable region of the human MGP 5' flanking region, but contains only one putative regulatory element that has been previously identified in other muscle genes. These data suggest that rat MGP transcription in C2C12 muscle cells is modulated by a potent enhancer that utilizes novel regulatory elements.

Characterization of the 5' flanking region of the gene encoding rat liver glycogen phosphorylase.

A genomic region encompassing 800 bp of the promoter-regulatory region and exon 1 of the gene (LGP) encoding rat liver glycogen phosphorylase has been isolated and characterized. Transcripts of the LGP gene initiate predominantly within an 8-bp region 48-bp upstream from the start codon. Additional transcripts were detected that initiate as far as 95 bp upstream from the start codon. To identify cis-acting sequences involved in regulating transcription, HepG2 cells were transfected with vectors containing serial deletions of the promoter-regulatory region of LGP ligated to the cat reporter gene. Two upstream regions were found to enhance transcription. One of these regions contains an alternating purine-pyrimidine sequence. LGP, which lacks a consensus TATA sequence, is like TATA-less and CAAT-less housekeeping genes in that it contains G + C-rich domains upstream from multiple transcription start points. Nuclear proteins from adult rat tissues bound in a tissue-specific fashion to one of these G + C-rich regions.

M4 and M9 antibodies in the overlap syndrome of primary biliary cirrhosis and chronic active hepatitis: epitopes or epiphenomena?

Before the identification of the major mitochondrial antigens of primary biliary cirrhosis as components of the 2-oxo-acid dehydrogenase enzyme family, mitochondrial autoantigens were believed to be extremely heterogeneous and were divided into nine subtypes termed M1 to M9. This classification was based on the data derived from the relatively nonspecific biochemical and immunological techniques that were available. After the cloning and definition of the major autoantigens, more than 95% of the sera of patients with primary biliary cirrhosis were found to react with components of the 2-oxo-dehydrogenase enzymes; these enzymes correspond to the old M2 classification. Two other "M" species, dubbed M4 and M9, have attracted significant attention because they have been postulated to be prognostic indicators and more recently have been tentatively identified respectively as sulfite oxidase (EC 1.8.3.1) and glycogen phosphorylase (EC 2.4.1.1). Indeed, patients with the "overlap syndrome" are reported to have antibodies to M4 and a poor prognosis, whereas patients with antibodies to M9 have a favorable prognosis. To address the significance and definition of M4 and M9, we performed in-depth studies of sera from 11 patients with the overlap syndrome, 75 patients with primary biliary cirrhosis, 19 chronic active hepatitis patients, 13 patients with primary sclerosing cholangitis, 10 patients with cholangiocarcinoma, 20 patients with systemic lupus erythematosus, 20 patients with alcoholic cirrhosis, 17 patients with scleroderma and 30 normal individuals, using techniques of ELISA, complement fixation, immunoblotting and enzyme inhibition. We report herein that we were unable to show any disease-specific reactivity toward the proposed M4 and M9 antigens.(ABSTRACT TRUNCATED AT 250 WORDS)

Coordinated expression of phosphorylase kinase subunits in regenerating skeletal muscle.

The developmental expression of the alpha, beta, and gamma subunits of skeletal muscle phosphorylase kinase has been examined in regenerating muscle. Rat extensor digitorum longus (EDL) muscles, treated with bupivacaine, promptly undergo a rapid degeneration of the muscle, followed by regeneration and recovery of essentially normal morphology and physiology by 3-4 weeks post-treatment (Hall-Craggs, E. C. B., and Seyan, H. S. (1975) Exp. Neurol. 46, 345-354). Phosphorylase kinase activity dropped to approximately 10% of control within 3 days of bupivacaine treatment and remained at this low level for several days but had attained at least 60% of normal levels by day 21. The pH 6.8/8.2 activity ratio was unusually high during the period of low activity, suggesting that the catalytic activity was not under normal regulation at this time. The subunit mRNAs were readily detected in control EDL but were undetectable at day 3 post-bupivacaine treatment. Very small amounts of message for all three subunits were evident by day 6 and began to approach normal levels by day 12-15. The mRNA for both the alpha and alpha' subunits of phosphorylase kinase exhibited a similar pattern of recovery, as did also the mRNA for phosphorylase. In contrast to both phosphorylase kinase and phosphorylase, actin mRNA exhibited a quite a different pattern, with a nearly full recovery of message levels by day 6 post-bupivacaine. These data indicate that synthesis of phosphorylase and the alpha, beta, and gamma subunits of phosphorylase kinase appears to be coordinately regulated at the level of message accumulation and that the expression of phosphorylase kinase activity is likely to be also regulated post-transcriptionally.

The gene encoding rat liver glycogen phosphorylase contains multiple polyadenylation signal sequences.

RNA blot analysis of rat liver and adipose tissues detected two glycogen phosphorylase (GP)-encoding transcripts. The polymerase chain reaction was used to characterize the 3'-noncoding region of the gene (L-GP) encoding liver-GP (L-GP) from the lean Zucker rat (Fa/Fa). Three distinct classes of colinear cDNA clones were identified by nucleotide (nt) sequence analysis, demonstrating that the L-GP gene contains at least three functional polyadenylation sites. The predominant L-GP transcript was generated by polyadenylation 130 nt 3' from the end of the coding region. A previously uncharacterized L-GP transcript is generated by polyadenylation at 346 nt 3' of the first polyadenylation site. Polyadenylation site selection does not appear to be regulated in a tissue-specific fashion. The relative steady-state L-GP mRNA levels in the different types of adipose tissues were comparable to, or exceeded transcript levels in liver.

Human astrocytoma U251 RNA and genomic brain glycogen phosphorylase sequences.

There are two versions of human brain glycogen phosphorylase (B-GP) cDNA in the literature that differ significantly in their C-terminal coding and 3' untranslated regions; one isolated from human fetal brain, and the other from human brain astrocytoma cell line U251. A 280 bp absence in the cDNA sequence isolated from human brain astrocytoma cell line U251 changes the predicted protein length from 842 aa (estimated from fetal brain cDNA) to 862 aa. RNA and genomic DNA were isolated from U251 cells and the 280 bp region of interest was amplified by the polymerase chain reaction (PCR). Sequence analysis of the amplified region has unexpectedly confirmed the presence of the 280 bp in U251 RNA and genomic DNA. Thus, the predicted protein length of 842 aa, as reported for fetal brain glycogen phosphorylase, is most likely the correct one.

Brain isozyme of glycogen phosphorylase: immunohistological localization within the central nervous system.

An antibody specific for the predicted carboxyterminal sequence of the human brain isozyme of glycogen phosphorylase (alpha-1,4-D-glucan:orthophosphate D-glucosyltransferase, EC 2.4.1.1) was generated to verify the carboxyterminal amino acid sequence of this protein. The isozyme-specific antibody was used to examine the localization of this protein in primate and non-primate brain. The highest levels of the brain isozyme in cerebrum and cerebellum were found in fibrous astrocytes, many with glial processes that appear to terminate upon blood vessels.

Human brain glycogen phosphorylase: characterization of fetal cDNA and genomic sequences.

Glycogen phosphorylase (alpha-1,4-glucan:orthophosphate D-glucosyltransferase, EC 2.4.1.1) is the rate-determining enzyme catalyzing glycogen degradation. Human brain has been demonstrated previously to express genes of both the liver and muscle isozymes of glycogen phosphorylase. In this report, a human fetal brain cDNA and genomic DNA corresponding to the brain isozyme of glycogen phosphorylase were isolated and characterized. Transcripts corresponding to this isozyme are present in human adult and fetal brain, and at low levels in other human fetal tissues. The predicted C-terminal sequence of the protein encoded by this cDNA and gene differ from that encoded by a phosphorylase cDNA isolated from a human astrocytoma cell line.