bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic, geographic, and linguistic distances in Europe.
Authors: Sokal R R
Published: May 2006

Genetic and taxonomic distances were computed for 3466 samples of human populations in Europe based on 97 allele frequencies and 10 cranial variables. Since the actual samples employed differed among the genetic systems studied, the genetic distances were computed separately for each system, as were matrices of geographic distances and of linguistic distances based on membership in the same language family or phylum. Significant matrix correlations between genetics and geography were found for the majority of systems; somewhat less frequent are significant correlations between genetics and language. The effects of the two factors can be separated by means of partial matrix correlations. These show significant values for both genetics and geography, language kept constant, and genetics and language, geography kept constant, with a tendency for the former to be higher. These findings demonstrate that speakers of different language families in Europe differ genetically and that this difference remains even after geographic differentiation is allowed for. The greater effect of geography than of language may be due to the several factors that bring about spatial differentiation in human populations.
Neoplastic transformation inactivates specific trans-acting factor(s) required for the expression of the thyroglobulin gene.
Authors: Avvedimento V E , Musti A , Fusco A , Bonapace M J , Di Lauro R
Published: May 2006

The expression of rat thyroglobulin gene is repressed following the transformation of rat thyroid cells with Kirsten murine sarcoma virus. The expression of a reporter gene fused to the thyroglobulin promoter is down-regulated in transformed thyroid cells in transient or in stable transfection assays. DNase and exonuclease III cleavage-protection analysis reveals that a promoter binding activity located at -60 base pairs from the transcription start site is substantially reduced in transformed thyroid cells. The repression in the transformed cells of the reporter gene joined to the thyroglobulin promoter can be reversed by fusion with normal differentiated thyroid cells. Fusion of transformed thyroid cells to liver cells does not reactivate the reporter under control of the thyroglobulin promoter.
Cloning and complete nucleotide sequence of a full-length cDNA encoding a catalytically functional tumor-associated aldehyde dehydrogenase.
Authors: Jones D E , Brennan M D , Hempel J , Lindahl R
Published: May 2006

To study the mechanism(s) controlling expression of the tumor-associated aldehyde dehydrogenase (tumor ALDH), which appears during rat hepatocarcinogenesis, cDNAs encoding this isozyme were cloned and identified with an antibody probe. Poly(A)-containing RNA from HTC rat hepatoma cells, which have been shown to possess high levels of tumor ALDH, was used as template to synthesize double-stranded cDNA. The cDNA was methylated to protect internal sites. Two different synthetic DNA linkers were added sequentially to the cDNA to insure correct orientation for expression from the lac promoter of pUC8. A library of 100,000 independent members carrying inserts greater than 1 kilobase was obtained. From this library, two apparently identical tumor ALDH clones, differing only in size, were identified with an indirect immunological probe. The larger of the cDNA clones identified, pTALDH, was chosen for further study. Interestingly, since tumor ALDH is a dimeric enzyme, pTALDH directs synthesis of a functional tumor ALDH in the bacterial cell. The cDNA sequence has been confirmed by comparison to the amino acid sequence of tumor ALDH purified from HTC cells.
Gene encoding the human beta-hexosaminidase beta chain: extensive homology of intron placement in the alpha- and beta-chain genes.
Authors: Proia R L
Published: May 2006

Lysosomal beta-hexosaminidase (EC 3.2.1.52) is composed of two structurally similar chains, alpha and beta, that are the products of different genes. Mutations in either gene causing beta-hexosaminidase deficiency result in the lysosomal storage disease GM2-gangliosidosis. To enable the investigation of the molecular lesions in this disorder and to study the evolutionary relationship between the alpha and beta chains, the beta-chain gene was isolated, and its organization was characterized. The beta-chain coding region is divided into 14 exons distributed over approximately 40 kilobases of DNA. Comparison with the alpha-chain gene revealed that 12 of the 13 introns interrupt the coding regions at homologous positions. This extensive sharing of intron placement demonstrates that the alpha and beta chains evolved by way of the duplication of a common ancestor.
Early cross-striation formation in twitching Xenopus myocytes in culture.
Authors: Kidokoro Y , Saito M
Published: May 2006

Spontaneous release of neurotransmitter has been demonstrated in various types of synapses. Its physiological significance, however, is still unknown. In nerve-muscle cultures of embryonic Xenopus laevis, we observed that acetylcholine, which is released spontaneously at the synaptic terminal, caused frequent twitches of muscle cells. These muscle cells developed cross-striations earlier than neighboring non-twitching cells. This effect of innervation was unaffected by tetrodotoxin but was blocked by alpha-bungarotoxin. Repeated iontophoretic application of acetylcholine or KCl to muscle cells caused twitches and also accelerated the formation of cross-striations. Thus twitching apparently promotes lateral alignment of myofibrils. It is also known that myosin synthesis is higher in twitching muscle cells. Therefore, successfully innervated twitching muscle cells may have an advantage for faster differentiation over neighboring non-twitching muscle cells. We suggest that spontaneously released transmitter may serve as a mediator for trophic interaction at forming synapses.
Nonsense mutations in the human beta-globin gene affect mRNA metabolism.
Authors: Baserga S J , Benz E J
Published: May 2006

A number of premature translation termination mutations (nonsense mutations) have been described in the human alpha- and beta-globin genes. Studies on mRNA isolated from patients with beta zero-thalassemia have shown that for both the beta-17 and the beta-39 mutations less than normal levels of beta-globin mRNA accumulate in peripheral blood cells. (The codon at which the mutation occurs designates the name of the mutation; there are 146 codons in human beta-globin mRNA.) In vitro studies using the cloned beta-39 gene have reproduced this effect in a heterologous transfection system and have suggested that the defect resides in intranuclear metabolism. We have asked if this phenomenon of decreased mRNA accumulation is a general property of nonsense mutations and if the effect depends on the location or the type of mutation. Toward this end, we have studied the effect of five nonsense mutations and two missense mutations on the expression of human beta-globin mRNA in a heterologous transfection system. In all cases studied, the presence of a translation termination codon correlates with a decrease in the steady-state level of mRNA. The data suggest that the metabolism of a mammalian mRNA is affected by the presence of a mutation that affects translation.
Assembly of functional proton-translocating ATPase complex in yeast mitochondria with cytoplasmically synthesized subunit 8, a polypeptide normally encoded within the organelle.
Authors: Nagley P , Farrell L B , Gearing D P , Nero D , Meltzer S , Devenish R J
Published: May 2006

A mitochondrial gene from Saccharomyces cerevisiae encoding a hydrophobic membrane protein, subunit 8 of the F0/F1-type mitochondrial ATPase complex, has been functionally replaced by an artificial nuclear gene specifying an imported version of this protein. The experiments reported here utilized a multicopy expression vector (pLF1) that replicates in the nucleus of yeast cells and that carries an inserted DNA segment, specifying a precursor protein (N9/Y8) consisting of subunit 8 fused to an N-terminal cleavable transit peptide (the leader sequence from Neurospora crassa ATPase subunit 9). The successful incorporation of the imported subunit 8 into functional ATPase complexes after transformation with pLF1 expressing N9/Y8 was indicated by the efficient genetic complementation of respiratory growth defects of aap1 mit- mutants, which lack endogenous subunit 8. The reconstitution of ATPase function was confirmed by biochemical assays of ATPase performance in mitochondria and by immunochemical analyses that demonstrated the assembly of the cytoplasmically synthesized subunit 8 into the ATPase complex. Reconstitution of ATPase function required the cytoplasmically synthesized subunit to have a transit peptide. The strategy for importation and reconstitution developed for subunit 8 leads to a systematic approach to the directed manipulation of mitochondrially encoded membrane-associated proteins that has general implications for exploring membrane biogenesis mechanistically and evolutionarily.
Antibodies to an alpha subunit of skeletal muscle calcium channels regulate parathyroid cell secretion.
Authors: Fitzpatrick L A , Chin H , Nirenberg M , Aurbach G D
Published: May 2006

We have shown previously that Ca2+-channel agonists, which open Ca2+ channels, inhibit parathyroid hormone (PTH) secretion from dispersed bovine parathyroid cells, whereas Ca2+-channel antagonists, which close Ca2+ channels, stimulate PTH release. We now have tested the effects of mouse antibodies specific for purified alpha subunits of rat skeletal muscle Ca2+-channel proteins on PTH secretion by bovine parathyroid cells in vitro. Mouse antisera (MC-2, MC-3, MC-4) blocked the secretion of PTH from parathyroid cells incubated with 0.5 mM Ca2+ ions. Affinity-purified MC-4 antibodies inhibited PTH release in a concentration-dependent manner. Incubation of parathyroid cells with pertussis toxin markedly reduced MC-4-dependent inhibition of PTH secretion. Parathyroid cell membrane proteins were fractionated by NaDodSO4/polyacrylamide gel electrophoresis under either reducing or nonreducing conditions and immunoblotted with MC-4 antiserum. Antibodies bound to one major band of protein with Mr approximately equal to 150,000. These results suggest that the antibodies bind to Ca2+-channel alpha subunits and act as agonists that open the channels and inhibit PTH release.
The yeast SNF3 gene encodes a glucose transporter homologous to the mammalian protein.
Authors: Celenza J L , Marshall-Carlson L , Carlson M
Published: May 2006

The SNF3 gene is required for high-affinity glucose transport in the yeast Saccharomyces cerevisiae and has also been implicated in control of gene expression by glucose repression. We report here the nucleotide sequence of the cloned SNF3 gene. The predicted amino acid sequence shows that SNF3 encodes a 97-kilodalton protein that is homologous to mammalian glucose transporters and has 12 putative membrane-spanning regions. We also show that a functional SNF3-lacZ gene-fusion product cofractionates with membrane proteins and is localized to the cell surface, as judged by indirect immunofluorescence microscopy. Expression of the fusion protein is regulated by glucose repression.
Mouse ornithine decarboxylase gene: cloning, structure, and expression.
Authors: Brabant M , McConlogue L , van Daalen Wetters T , Coffino P
Published: May 2006

We used molecular cloning to isolate a functional gene for mouse ornithine decarboxylase (OrnDCase; L-ornithine carboxy-lyase, EC 4.1.1.17) from a cell line in which that gene had been selectively amplified. The position of the 5' terminus of the mRNA was identified, and the coding sequence was shown to be preceded by a 312- or 313-nucleotide (nt) untranslated leader. The latter is highly G + C rich, particularly in its 5'-most portion. The leader can be anticipated to have extensive and stable secondary structure. The transcription unit of the gene is of relatively small size, approximately equal to 6.2 kilobases (kb) from the start site to the proximal site of polyadenylylation. Sequence analysis of DNA near the transcription start position demonstrated the presence of a "TATA" box, but no "CAAT" box. Functional properties of the cloned gene were tested by transfecting it into cultured cells. Expression of the putative full-length gene efficiently conferred ornithine decarboxylase activity on recipient mutant cells deficient in that activity. To assess the function and strength of the OrnDCase promoter region and to delimit its boundaries, we used a transient expression assay. Upstream of a bacterial chloramphenicol acetyltransferase gene was placed a portion of the OrnDCase gene, including the presumed promoter region, spanning a region from approximately equal to 3.0 kb 5' of the site of transcription initiation to the first 250 nt of the transcript. When expressed in mouse NIH 3T3 cells, this OrnDCase genomic element was comparable in strength to the Rous sarcoma virus long terminal repeat promoter. A similar construct, truncated so as to retain only 264 base pairs of the OrnDCase gene 5' to the site of transcription start, yielded undiminished levels of expression.
Localization of the human JUN protooncogene to chromosome region 1p31-32.
Authors: Haluska F G , Huebner K , Isobe M , Nishimura T , Croce C M , Vogt P K
Published: May 2006

The oncogene jun is the putative transforming gene of avian sarcoma virus 17; jun appears to be derived from a gene of the chicken genome and has homologues in several other vertebrate species. Recent genetic and immunological data indicate that jun codes for a protein that is closely related and probably identical to the transcription factor AP-1. We have isolated a genomic DNA clone encompassing the human cellular counterpart of the gene, JUN, and used this DNA to determine the chromosomal location of the gene. A panel of DNA preparations derived from rodent-human somatic cell hybrids with defined chromosome complements was first screened with the JUN probe. This Southern blot analysis indicated that JUN is situated on the short arm of chromosome 1. In situ hybridization then assigned JUN to chromosome region 1p31-32, a chromosomal region involved in both translocations and deletions of chromosomes seen in human malignancies.
The lethal myospheroid gene of Drosophila encodes a membrane protein homologous to vertebrate integrin beta subunits.
Authors: MacKrell A J , Blumberg B , Haynes S R , Fessler J H
Published: May 2006

A mutant of Drosophila melanogaster carrying the lethal(1) myospheroid mutation [l(1)mys] has a defective musculature and a phenotype that suggests a defect of basement membranes. The genomic region that is interrupted by an insertion in a mutant carrying l(1)mys was used to isolate cDNA clones, and their sequences are presented here. The cDNA sequence predicts a cysteine-rich integral membrane protein that displays 45% sequence identity to chicken integrin and the human fibronectin receptor beta subunit and much greater similarity over localized segments. These similarities extend to other vertebrate integrin beta subunits, and we conclude that the myospheroid protein is an integrin beta subunit of Drosophila. This implies evolutionary conservation of a group of transmembrane proteins that are receptors for extracellular matrix and, coupled with the myospheroid phenotype, indicates an important role for the interaction of cells with extracellular matrix during development.
Specific translational activation by nuclear gene products occurs in the 5' untranslated leader of a yeast mitochondrial mRNA.
Authors: Costanzo M C , Fox T D
Published: May 2006

Translation of the yeast mitochondrial mRNA encoding cytochrome c oxidase subunit III (coxIII) is specifically activated by the products of at least three nuclear genes, PET494, PET54, and PET122. To investigate whether the target site for translational activation is within the 5' untranslated leader of the coxIII mRNA, we asked whether translation of another mitochondrial protein, apo-cytochrome b, from a chimeric mRNA bearing the coxIII mRNA leader required PET494, PET54, or PET122. Mutations in any of these three genes abolished translation of cytochrome b from an mRNA bearing the 5' two-thirds of the coxIII mRNA 5' untranslated leader, showing that all three gene products are required for translation of the chimeric mRNA and must act within the 5' two-thirds of the coxIII mRNA leader. Our data suggest that in wild-type cells, the specific activation of coxIII translation by PET494, PET54, and PET122 occurs by the action of these three gene products at a site or sites in a region of the 5' untranslated leader at least 172 nucleotides upstream of the initiation codon.
rpt-1, an intracellular protein from helper/inducer T cells that regulates gene expression of interleukin 2 receptor and human immunodeficiency virus type 1.
Authors: Patarca R , Freeman G J , Schwartz J , Singh R P , Kong Q T , Murphy E , Anderson Y , Sheng F Y , Singh P , Johnson K A
Published: May 2006

The Rpt-1 (for regulatory protein, T-lymphocyte, 1) gene, selectively expressed by resting but not by activated CD4+ inducer T cells, encodes an intracellular protein (rpt-1, Mr 41,000) that down-regulates gene expression directed by the promoter region of the gene encoding interleukin 2 receptor alpha chain and by the long terminal repeat of human immunodeficiency virus type 1. The data reported here suggest that rpt-1 levels may be inversely correlated with activation of CD4+ T cells and human immunodeficiency virus replication leading to clinical symptoms of the acquired immunodeficiency syndrome.
A tissue-specific DNase I-hypersensitive site in a class II A alpha gene is under trans-regulatory control.
Authors: Liou H C , Polla B S , Aragnol D , Leserman L D , Griffith I J , Glimcher L H
Published: May 2006

Class II major histocompatibility complex molecules are integral membrane glycoproteins whose distribution is limited to certain tissues. To identify the molecular basis for such specificity, the chromatin configuration of the class II A alpha gene was examined in intact nuclei from various cell types. We show that there are three DNase I-hypersensitive sites in the A alpha gene. One of these sites, located near the promoter region, is specific to cells that normally express class II molecules at some stage of differentiation. Furthermore, this tissue-specific site appears to be under trans-regulatory control.
Homozygous and heterozygous deletions of the von Willebrand factor gene in patients and carriers of severe von Willebrand disease.
Authors: Ngo K Y , Glotz V T , Koziol J A , Lynch D C , Gitschier J , Ranieri P , Ciavarella N , Ruggeri Z M , Zimmerman T S
Published: May 2006

Severe von Willebrand disease is characterized by undetectable or trace quantities of von Willebrand factor in plasma and tissue stores. We have studied the genomic DNA of 10 affected individuals from six families with this disorder using probes from the 5' and 3' ends of the vWF cDNA and with a probe extending from the 5' end into the central region. Southern blots of restriction endonuclease digests and gene dosage analysis measurements carried out with quantitative slot blots of undigested genomic DNA separated these patients into three groups. The first group consisted of a family with complete homozygous deletions of the vWF gene in the four probands. Gene dosage analysis was consistent with heterozygous deletions in both of the asymptomatic parents and four asymptomatic siblings of this kindred (P less than 0.01). The second group was comprised of a family in which there was a complete heterozygous deletion of the vWF gene in the proband and one asymptomatic parent, suggesting that a different type of genetic abnormality was inherited from the other parent. Thus, the patient appeared to be doubly heterozygous for interacting genetic abnormalities affecting vWF expression. In the third group, no gene deletions could be detected. Alloantibodies developed only in the kindred with homozygous deletions. These techniques should prove useful in identifying carriers of severe von Willebrand disease and also in defining patients predictably at risk of developing alloantibodies to vWF.
Altered controls of proliferation in proximal small intestine of the senescent rat.
Authors: Holt P R , Yeh K Y , Kotler D P
Published: May 2006

The proximal small intestine responds to starvation by rapidly reducing crypt cell proliferation rate and villus cellularity and to resumption of food intake (refeeding) by abruptly increasing proliferation and the number of villus epithelial cells. We show that villus cellularity responds to starvation and refeeding similarly in young and aging animals. However, as compared to young animals, senescent rats showed increased basal DNA synthetic activity, starvation resulted in a smaller decrease in DNA labeling of crypt cells, and refeeding produced an abrupt broadening of the proliferative zone in older animals without concomitant increased numbers of villus cells. Such altered crypt proliferative responses resemble precancerous changes seen in the colon and the aberrant proliferation found in both small and large intestine after administration of the carcinogen dimethylhydrazine.
Identification of the binding subunit of the sigma-type opiate receptor by photoaffinity labeling with 1-(4-azido-2-methyl[6-3H]phenyl)-3-(2-methyl[4,6-3H]phenyl)guanidine.
Authors: Kavanaugh M P , Tester B C , Scherz M W , Keana J F , Weber E
Published: May 2006

The sigma-type opiate receptor is a distinct binding site in the brain that may mediate some of the psychotomimetic effects caused by benzomorphan opiates and phencyclidine in humans. We have developed a synthetic, highly selective ligand for this receptor, 1,3-di-o-tolylguanidine (DTG). To identify the binding protein(s) of the sigma receptor, we have now synthesized a radiolabeled azide derivative of DTG, 1-(4-azido-2-methyl[6-3H]phenyl)-3-(2-methyl[4,6-3H]phenyl)-guanidine ([3H]N3DTG). In guinea pig brain membrane binding assays conducted in the dark, [3H]N3DTG bound reversibly, selectively, and with high affinity (Kd = 10 nM) to sigma receptors. The drug specificity profile of reversible [3H]-N3DTG binding was identical to that of [3H]DTG and 3H-labeled (+)-3-(3-hydroxyphenyl)-N-(1-propyl)piperidine binding indicating that [3H]N3DTG is a selective sigma receptor ligand. Guinea pig brain membranes were photoaffinity-labeled with [3H]N3DTG. NaDodSO4/PAGE of detergent-solubilized membrane extract identified a single 29-kDa radioactive band. Sepharose Cl-6B gel chromatography of photolabeled brain membranes solubilized with the nondenaturing detergent sodium cholate showed a radioactive complex with a Stoke's radius of 4.6 nm (Mr, 150,000) that may represent the intact sigma receptor complex. NaDodSO4/PAGE of this complex showed that the radiolabeled material was a 29-kDa polypeptide that may be the binding subunit of the sigma receptor. The specific sigma receptor photoaffinity ligand described here should be a useful tool for purifying and characterizing the sigma receptor.
Developmental regulation of constitutive and inducible expression of hepatocyte-specific genes in the mouse.
Authors: Donner M E , Leonard C M , Gluecksohn-Waelsch S
Published: May 2006

Deletions in chromosome 7 of the mouse have been shown to cause failure of expression of certain liver-specific enzymes in newborn deletion homozygotes. Among these enzymes are L-tyrosine:2-oxoglutarate aminotransferase (EC 2.6.1.5) and phosphoenolpyruvate carboxykinase (GTP) [GTP:oxaloacetate carboxy-lase (transphosphorylating); EC 4.1.1.32]. The studies reported here show that in fetal stages constitutive expression of the relevant genes on the level of steady-state mRNA is identical in the livers of homozygous deletion mutants and normal littermates. Furthermore, prenatally these enzymes are expressed also in cell types other than hepatocytes. Thus, the putative trans-acting regulatory factors encoded in the deleted region of chromosome 7 of the mouse appear to be concerned specifically with the regulation of cell type-specific inducible expression of various hepatocyte-specific genes, whereas constitutive expression of the same genes is not affected.
An alternative approach to somatic cell gene therapy.
Authors: St Louis D , Verma I M
Published: May 2006

Mouse primary skin fibroblasts were infected with a recombinant retrovirus containing human factor IX cDNA. Bulk infected cells capable of synthesizing and secreting biologically active human factor IX protein were embedded in collagen, and the implant was grafted under the epidermis. Sera from the transplanted mice contain human factor IX protein for at least 10-12 days. Loss of immunoreactive human factor IX protein in the mouse serum is not due to graft rejection. Instead, the mouse serum contains anti-human factor IX antibodies, which react with the protein. We suggest that retroviral-infected primary skin fibroblasts offer an alternative approach to somatic cell gene therapy.
Antibodies that inhibit fusion of human immunodeficiency virus-infected cells bind a 24-amino acid sequence of the viral envelope, gp120.
Authors: Rusche J R , Javaherian K , McDanal C , Petro J , Lynn D L , Grimaila R , Langlois A , Gallo R C , Arthur L O , Fischinger P J
Published: May 2006

Antisera to recombinant human immunodeficiency virus (HIV) proteins containing the entire envelope, gp160, or the central portion of the envelope, PB1, can inhibit fusion of virally infected cells in culture. This fusion inhibition is HIV-variant specific--that is, anti-gp160-IIIB inhibits fusion of isolate HTLV-IIIB-infected cells but not of isolate HTLV-IIIRF-infected cells. Both anti-gp160 and anti-PB1 are completely blocked in fusion inhibition activity by the addition of PB1 protein. A 24-amino acid peptide (RP135, amino acids 307-330) completely blocks fusion inhibition activity of both antisera and also blocks the activity of serum from a chimpanzee infected with HTLV-IIIB. Thus, the principal epitope that elicits fusion-inhibiting antibodies is located in the central portion of gp120.
Simultaneous demonstrations of neuropeptide Y gene expression and peptide storage in single neurons of the human brain.
Authors: Chan-Palay V , Yasargil G , Hamid Q , Polak J M , Palay S L
Published: May 2006

A combination of in situ hybridization for neuropeptide Y mRNA that used a 32P-labeled complementary RNA probe and immunocytochemistry with polyclonal antibodies against neuropeptide Y were applied to human cortical brain samples to simultaneously localize neuropeptide Y and its mRNA. These two techniques allowed simultaneous identification of neuropeptide Y gene expression and peptide storage in single neurons of the human brain.
Remodeling of synaptic architecture during hippocampal "kindling".
Authors: Geinisman Y , Morrell F , deToledo-Morrell L
Published: May 2006

The "kindling" phenomenon is associated with long-lasting facilitation of synaptic transmission. A possible mechanism of such facilitation could involve changes in the number of synaptic contacts. However, previous attempts to demonstrate a synaptic morphological alteration that could account for the long-term effects of kindling had failed, possibly due to the unavailability, at the time, of unbiased methods for synapse quantitation. Using the unbiased stereological disector technique, we estimated the number of synapses per neuron in the middle molecular layer of the hippocampal dentate gyrus in rats kindled by electrical stimulation of the medial perforant path with implanted electrodes. Unkindled but stimulated (coulombic control) and unstimulated but implanted rats served as controls. Animals were coded and killed 4 weeks after reaching the kindling criterion of five generalized seizures. The most important results were obtained when axospinous synapses with continuous or discontinuous postsynaptic densities ("nonperforated" or "perforated" synapses) were differentially analyzed. Kindling resulted in a selective loss of nonperforated synaptic contacts in contrast to preservation of perforated ones. Furthermore, the ratio of perforated to nonperforated synapses was increased by 45% or 40% in kindled rats relative to unstimulated or coulombic controls, respectively. These findings suggest that synaptic efficacy may depend on a balance of the two synaptic types; selective elimination of nonperforated synapses may augment the potency of remaining synaptic contacts, a process reminiscent of synaptic remodeling during development.
Effect of Ca2+ on cross-bridge turnover kinetics in skinned single rabbit psoas fibers: implications for regulation of muscle contraction.
Authors: Brenner B
Published: May 2006

The effect of Ca2+ upon the rate constant of force redevelopment following a period of isotonic shortening with immediate restretch to the starting sarcomere length was studied in rabbit psoas fibers at 5 degrees C. Control experiments support the assumption that the rate constant of force redevelopment represents isometric cross-bridge turnover kinetics (fapp + gapp), where fapp and gapp are the rate constants characterizing the transitions from the non-force-generating states to the force-generating states and back to the non-force-generating states, respectively. Parallel measurements of the rate constant of force redevelopment and of force, stiffness, and fiber ATPase during isometric contraction allow the effect of Ca2+ upon fapp and gapp to be determined. Analysis reveals that Ca2+ has a marked effect upon fapp, while gapp remains approximately unchanged. Furthermore, in the range above 25-30% of maximum Ca2+ activation, regulation of force, stiffness, and ATPase is mediated through changes in fapp. Below this range, however, it cannot be ruled out that, in addition, cross-bridges are also switched in and out of the turnover process ("recruitment"). As a consequence of regulation through turnover kinetics, both Ca2+ sensitivity and the slope of force-pCa (-log[Ca2+]) relations are shown to be affected by the ratio fapp/gapp, which may represent an important mechanism of modulation of contractile function in addition to modulation through changes within the regulatory protein system.
Regulation of thromboxane receptor activation in human platelets.
Authors: Murray R , FitzGerald G A
Published: May 2006

Thromboxane A2 (TxA2) is a potent platelet agonist that serves as an amplifying signal after exposure of platelets to other stimulants, such as thrombin, in vitro. Exposure of platelets to the TxA2 receptor agonists U46619 and SQ 26,655 (1.4 microM) resulted in a 60-90% decrease in subsequent TxA2 receptor-stimulated aggregation, calcium release, and protein kinase C activation. The desensitization was rapid, with a half-time of 2-3 min. The sequence of events involved in TxA2 receptor desensitization involves initial uncoupling of the receptor from a guanine nucleotide binding (G) protein followed by eventual receptor down-regulation. Consistent with this hypothesis were (i) a 60-70% decrease in SQ 26,655-stimulated platelet GTPase activity, (ii) a shift to the right of the dose-response curve for U46619-stimulated release of calcium [EC50, 275 +/- 51 nM (control)] vs. 475 +/- 71 nM (desensitized); P less than 0.01], and (iii) a delayed loss of receptor sites. In summary, exposure of platelets to TxA2 receptor agonists results in rapid desensitization of the biochemical and functional responses to interaction with its receptor in human platelets. The kinetics of these events are consistent with the hypothesis that this icosanoid functions in the regulation as well as amplification of platelet activation in vivo.
Protein secondary structure prediction with a neural network.
Authors: Holley L H , Karplus M
Published: May 2006

A method is presented for protein secondary structure prediction based on a neural network. A training phase was used to teach the network to recognize the relation between secondary structure and amino acid sequences on a sample set of 48 proteins of known structure. On a separate test set of 14 proteins of known structure, the method achieved a maximum overall predictive accuracy of 63% for three states: helix, sheet, and coil. A numerical measure of helix and sheet tendency for each residue was obtained from the calculations. When predictions were filtered to include only the strongest 31% of predictions, the predictive accuracy rose to 79%.
Structure and heterogeneity of the oligosaccharides from the lipopolysaccharides of a pyocin-resistant Neisseria gonorrhoeae.
Authors: Gibson B W , Webb J W , Yamasaki R , Fisher S J , Burlingame A L , Mandrell R E , Schneider H , Griffiss J M
Published: May 2006

The compositions and partial structures of the oligosaccharides from the lipopolysaccharides (LPS) of a pyocin-resistant Neisseria gonorrhoeae (strain JW31R) have been determined by liquid secondary ion mass spectrometry (LSIMS), tandem mass spectrometry, and methylation analysis. Four major structures were identified with Mr 2123, 2000, 1961, and 1838, as well as seven species of lower abundance of Mr 1758-1272. The largest of the major oligosaccharides (Mr, 2122) consists of 3-deoxymanno-2-ketooctulosonic acid (KDO)-Hep2GalNAcGlcNAcGal4Glc2 (Hep, heptose) and phosphoethanolamine (PEA). The smaller oligosaccharides are truncated versions of this larger oligosaccharide. The oligosaccharides consist of a common triantennary structure containing KDO at the reducing terminus attached to a heptose disaccharide. A hexose (Hex)2-3 branch is attached to the heptose linked directly to KDO and a GalNAc-Hex3, GlcNAc, and PEA are separately attached to the second heptose. These oligosaccharides are the first structures to be determined for a gonococcal LPS and should further our understanding of the structural and antigenic diversity of these glycolipids.
Esperamicins, a class of potent antitumor antibiotics: mechanism of action.
Authors: Long B H , Golik J , Forenza S , Ward B , Rehfuss R , Dabrowiak J C , Catino J J , Musial S T , Brookshire K W , Doyle T W
Published: May 2006

The esperamicins represent a class of antitumor antibiotics characterized by an unusual chemical core structure and extremely potent cytotoxicity. The mechanism by which these drugs produce cytotoxicity was investigated and found to be related to the formation of single- and double-strand DNA breaks. Using five structurally related analogs, we defined a structure-activity relationship for cytotoxicity in various eukaryotic and DNA-repair-deficient prokaryotic cell lines, for DNA breakage in a human colon carcinoma cell line, and for DNA breakage in vitro in pBR322 DNA. Mild reducing agents such as dithiothreitol greatly increased the DNA breakage potency of these analogs in vitro. Results suggest that the pendant aromatic chromophore of esperamicin A1 may contribute to the uptake of the drug into cells but may also hinder double-strand DNA break formation. Little DNA breakage specificity was observed for the drug in a 139-base-pair fragment of pBR322 DNA. Evidence supports a previously proposed mechanism whereby esperamicins may produce the observed DNA breaks through reduction of the methyl trisulfide group to a thiolate anion followed by a Michael addition of the anion across the alpha,beta-unsaturated ketone. This addition may result in the saturation of the bridgehead double bond, thus allowing the two triple bonds to approach each other, causing cyclization of the diyn-ene to form a phenylene diradical. It is likely that this diradical is the active form of the drug responsible for single- and double-strand DNA breakage produced by this class of antitumor agents.
Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes.
Authors: Sheffield V C , Cox D R , Lerman L S , Myers R M
Published: May 2006

Denaturing gradient gel electrophoresis (DGGE) can be used to distinguish two DNA molecules that differ by as little as a single-base substitution. This method detects approximately 50% of all possible single-base changes in DNA fragments ranging from 50 to approximately 1000 base pairs. To increase the number of single-base changes that can be distinguished by DGGE, we used the polymerase chain reaction to attach a 40-base-pair G + C-rich sequence, designated a GC-clamp, to one end of amplified DNA fragments that encompass regions of the mouse and human beta-globin genes. We show that this GC-clamp allows the detection of mutations, including the hemoglobin sickle (HbS) and hemoglobin C (HbC) mutations within the human beta-globin gene, that were previously indistinguishable by DGGE. In addition to providing an easy way to attach a GC-clamp to genomic DNA fragments, the polymerase chain reaction technique greatly increases the sensitivity of DGGE. With this approach, DNA fragments derived from less than 5 ng of human genomic DNA can be detected by ethidium bromide staining of the gel, obviating the need for radioactive probes. These improvements extend the applicability of DGGE for the detection of polymorphisms and mutations in genomic and cloned DNA.
Human interleukin 7: molecular cloning and growth factor activity on human and murine B-lineage cells.
Authors: Goodwin R G , Lupton S , Schmierer A , Hjerrild K J , Jerzy R , Clevenger W , Gillis S , Cosman D , Namen A E
Published: May 2006

A cDNA encoding biologically active human interleukin 7 was isolated by hybridization with the homologous murine clone. Nucleotide sequence analysis indicated that this cDNA was capable of encoding a protein of 177 amino acids with a signal sequence of 25 amino acids and a calculated mass of 17.4 kDa for the mature protein. Recombinant human interleukin 7 stimulated the proliferation of murine pre-B cells and was active on cells harvested from human bone marrow that are enriched for B-lineage progenitor cells. Analysis of RNA by blot hybridization demonstrated the presence of two size classes of interleukin 7 mRNA in human splenic and thymic tissue.
Cloning and expression of the gene cluster encoding key proteins involved in acetyl-CoA synthesis in Clostridium thermoaceticum: CO dehydrogenase, the corrinoid/Fe-S protein, and methyltransferase.
Authors: Roberts D L , James-Hagstrom J E , Garvin D K , Gorst C M , Runquist J A , Baur J R , Haase F C , Ragsdale S W
Published: May 2006

Acetogenic bacteria fix CO or CO2 by a pathway of autotrophic growth called the acetyl-CoA (or Wood) pathway. Key enzymes in the pathway are a methyltransferase, a corrinoid/Fe-S protein, a disulfide reductase, and a carbon monoxide dehydrogenase. This manuscript describes the isolation of the genes that code for the methyltransferase, the two subunits of the corrinoid/Fe-S protein, and the two subunits of carbon monoxide dehydrogenase. These five genes were found to be clustered within an approximately 10-kilobase segment on the Clostridium thermoaceticum genome. The proteins were expressed at up to 5-10% of Escherichia coli cell protein, and isopropyl beta-D-thiogalactopyranoside had no effect on the levels of expression, implying that the C. thermoaceticum inserts contained transcriptional and translational signals that were recognized by E. coli. The methyltransferase is expressed in E. coli in a fully active dimeric form with a specific activity and heat stability similar to the enzyme expressed in C. thermoaceticum. However, both the corrinoid/Fe-S protein and carbon dioxide dehydrogenase, although expressed in high amounts and with identical subunit molecular weights in E. coli, are inactive and less heat stable than are the native enzymes from C. thermoaceticum.
Enzymatic cleavage of a bacterial genome at a 10-base-pair recognition site.
Authors: Weil M D , McClelland M
Published: May 2006

The circular genome of Staphylococcus aureus was cut into two fragments by a simple enzymatic method that cleaves a 10-base-pair site. The recognition sequence, A-T-C-G-mA decreases T-C-G-mA-T, was created by the combined use of the methylase M.Cla I (A-T-C-G-mA-T) and the restriction endonuclease Dpn I (G-mA decreases T-C). This technique is insensitive to CpG methylation and in human DNA is predicted to produce fragments that, on average, are greater than five million base pairs. The ability to create such long pieces of DNA should facilitate mapping of large, complex chromosomes.
Structure of human neutrophil elastase in complex with a peptide chloromethyl ketone inhibitor at 1.84-A resolution.
Authors: Navia M A , McKeever B M , Springer J P , Lin T Y , Williams H R , Fluder E M , Dorn C P , Hoogsteen K
Published: May 2006

Human neutrophil elastase (HNE) has been implicated as a major contributor to tissue destruction in various disease states, including emphysema. The structure of HNE, at neutral pH, in complex with methoxysuccinyl-Ala-Ala-Pro-Ala chloromethyl ketone (MSACK), has been solved and refined to an R factor of 16.4% at 1.84-A resolution. Results are consistent with the currently accepted mechanism of peptide chloromethyl ketone inhibition of serine proteases, in that MSACK cross-links the catalytic residues His-57 and Ser-195. The structure of the HNE-MSACK complex is compared with that of porcine pancreatic elastase in complex with L-647,957, a beta-lactam inhibitor of both elastases. The distribution of positively charged residues on HNE is highly asymmetric and may play a role in its specific association with the underlying negatively charged proteoglycan matrix of the neutrophil granules in which the enzyme is stored.
Regulation of the iron uptake system in Vibrio anguillarum: evidence for a cooperative effect between two transcriptional activators.
Authors: Salinas P C , Tolmasky M E , Crosa J H
Published: May 2006

We have identified a 110-kDa polypeptide that has a trans-acting regulatory activity on the expression of the pJM1 plasmid iron-uptake genes in Vibrio anguillarum. This protein is encoded by the angR gene and maps in a 3.6-kilobase-pair pJM1 DNA region located downstream of the iron transport genes. Full expression of this gene occurs under iron-limiting conditions and requires a 2.9-kilobase-pair upstream region in cis that maps within the coding region of the OM2 outer membrane protein, essential for the transport of iron into the cell cytosol. Determination of the siderophore anguibactin levels as well as analysis of specific transcripts for anguibactin biosynthetic genes demonstrated that AngR and another transcriptional activator, Taf, regulate in a synergistic fashion the level of anguibactin production by activation of transcription of the anguibactin biosynthetic genes under iron-limiting conditions.
Auxin-binding protein located in the endoplasmic reticulum of maize shoots: molecular cloning and complete primary structure.
Authors: Inohara N , Shimomura S , Fukui T , Futai M
Published: May 2006

We previously purified an auxin-binding protein (ABP) from the microsomal fraction of maize shoots (Zea mays L. cv. Golden Cross Bantam). In the present study cDNA clones derived from mRNAs encoding the ABP were isolated and sequenced. The nucleotide sequence of the 822-base-pair cDNA includes a 603-base-pair open reading frame. RNA blot hybridization analysis indicated a single mRNA species of approximately 1.0 kilobase. The predicted precursor of ABP is composed of 201 amino acid residues and has a molecular weight of 21,976. The NH2-terminal sequence of 38 residues is hydrophobic and may be a signal peptide for translocation of the ABP across the membrane of the endoplasmic reticulum. The mature ABP, composed of 163 residues with a molecular weight of 18,352, contains a potential N-glycosylation site (Asn-Thr-Thr), and the COOH-terminal tetrapeptide (Lys-Asp-Glu-Leu) may be a signal for retention of the ABP in the lumen of the endoplasmic reticulum.
Progression of human breast cancer cells from hormone-dependent to hormone-independent growth both in vitro and in vivo.
Authors: Clarke R , Brünner N , Katzenellenbogen B S , Thompson E W , Norman M J , Koppi C , Paik S , Lippman M E , Dickson R B
Published: May 2006

We have isolated a series of sublines of the hormone-dependent MCF-7 human breast cancer cell line after selection both in vivo and in vitro for growth in the presence of subphysiological concentrations of estrogens. These sublines represent a model system for study of the processes leading to hormonal autonomy. The cells form growing tumors in ovariectomized athymic nude mice in the absence of estrogen supplementation but retain some responsivity to estrogen as determined by stimulation of the rate of tumor growth in vivo and by induction of progesterone receptor. An ovarian-independent but hormone-responsive phenotype may occur early in the natural progression to hormone-independent and unresponsive growth in breast cancer. We observed no change in the affinity or decrease in the level of expression of estrogen receptors and progesterone receptors among the sublines and the parental cells. Epidermal growth factor receptors are not overexpressed in ovarian-independent cells. Thus, altered hormone receptor expression may be a late event in the acquisition of a hormone-independent and unresponsive phenotype. Sublines isolated by in vivo but not in vitro selection are more invasive than the parental cells both in vivo and across an artificial basement membrane in vitro. Thus, as yet unknown tumor-host interactions may be important in the development of an invasive phenotype. Furthermore, acquisition of the ovarian-independent and invasive phenotypes can occur independently.
Genomic sequencing reveals a 5-methylcytosine-free domain in active promoters and the spreading of preimposed methylation patterns.
Authors: Toth M , Lichtenberg U , Doerfler W
Published: May 2006

Previous work demonstrated an inverse correlation between methylation at the three 5'-CCGG-3' sequences in positions +24, +6, and -215 relative to the cap site of the late E2A promoter of adenovirus type 2 (Ad2) DNA and its activity. In the study presented here, we used the genomic sequencing method to detect 5-methyl-2'-deoxycytidine (m5dC) residues in 5'-CG-3' sequences other than the 5'-CCGG-3' (Hpa II) sites. The patterns of methylation in all 5'-CG-3' sequences over a region of about 180 base pairs required for gene activity in the late E2A promoter of integrated Ad2 DNA were determined in cell lines that carry this promoter in an active or inactive state. In cell lines HE1 and uc2, the late E2A promoter is active and all thirteen 5'-CG-3' sequences between positions +24 and -160 are unmethylated. In cell line HE2, the same promoter is permanently shut off and all 5'-CG-3' sequences are methylated in both strands. Thus, the inverse correlation is perfect in these cell lines over a region of about 180 base pairs in the late E2A promoter. The same promoter segment was analyzed in cell lines mc23 and mc40, in which a late E2A promoter-chloramphenicol acetyltransferase (CAT) gene construct had been genomically fixed after in vitro 5'-CCGG-3' methylation and subsequent transfection. In cell line mc23, the preimposed methylation pattern was stable and the CAT gene was inactive. Genomic sequencing confirmed the presence of m5dC in the 5'-CCGG-3' sequences and revealed the spreading of methylation to neighboring 5'-CG-3' sequences along the entire promoter. Some of these sites were hemimethylated. In cell line mc40, several of the 120 integrated copies became demethylated in positions +24 and +6, but the promoter was methylated in some of the copies upstream of position -50. Cell line mc40 expressed the CAT gene.