bluuebunny/crossref_metadata_2025 huggingface dataset:
B ring regulation of colchicine binding kinetics and fluorescence.
Authors: Bhattacharyya B , Howard R , Maity S N , Brossi A , Sharma P N , Wolff J
Published: May 2006

Several properties of the colchicine-tubulin interaction such as association rate, reversibility, and the promotion of drug fluorescence have been related to the B ring of colchicine. The B ring itself retards the binding rate, and substitution at C-7 leads to further binding rate decreases that appear to be related to both substituent bulk and the presence of a N-acyl group. Thus, the decreasing order of binding rates is 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone greater than deacetamidocolchicine greater than deacetylcolchicine greater than or equal to colcemid greater than colchicine greater than N-benzoyldeacetylcolchicine, etc. The apparent irreversibility of the binding seems more closely related to the presence of an N-acyl group rather than the bulk of the substituent at C-7. Substitution at C-7 also affects the tropolone fluorophore. Thus, amines (deacetylcholchicine, colcemid, or N-methylcolcemid) fluoresce poorly in the presence of tubulin, whereas substitution of the amino group with an acyl group enhances fluorescence. The presence of an N-acyl group at C-7 is essential for enhanced fluorescence. We conclude that, in addition to A- and the C-ring portion of the molecule, the B ring of colchicine is a third determinant recognized by the binding site on tubulin.
The active site structure of Na+/K+-transporting ATPase: location of the 5'-(p-fluorosulfonyl)benzoyladenosine binding site and soluble peptides released by trypsin.
Authors: Ohta T , Nagano K , Yoshida M
Published: May 2006

When the dog kidney Na+/K+-transporting ATPase (EC 3.6.1.37, formerly EC 3.6.1.3) was labeled with an ATP analogue, 5'-(p-fluorosulfonyl)benzoyladenosine (FSBA), there was a concomitant loss of ATPase activity. The presence of ATP protected the enzyme from both labeling and inactivation. The ATP-sensitive incorporation of FSBA is associated only with modification of the alpha subunit from which two labeled tryptic peptides were purified and sequenced. To establish any regions of the enzyme protruding from the membrane, the native Na+/K+-transporting ATPase from the electric ray, Torpedo californica, was treated with trypsin; and four peptides, which were released into the water phase, were purified and sequenced. A comparison of the peptide sequences with the deduced amino acid sequences of the DNA coding for the alpha subunit of T. californica and sheep kidney reveal the following. (i) FSBA-labeled peptides from the dog kidney enzyme are located in the central hydrophilic domain and show almost complete sequence homology with the same region in the alpha subunit from the electric ray and sheep kidney. Furthermore, the sequence homology of one of the two labeled peptides can be extended to the sarcoplasmic Ca2+-transporting ATPase and B subunit of Escherichia coli K+-transporting ATPase. (ii) Three trypsin-exposed peptides are found in the central hydrophilic domain, and one peptide is in the hydrophilic segment near the C terminus of the alpha subunit. (iii) The active center of Na+/K+-transporting ATPase is likely to be constructed from at least four different stretches in the primary sequence and, irrespective of the different specificity of cations, the various cation transport ATPases that form phosphorylated enzyme appear to have a common structure at the catalytic site for ATP hydrolysis.
Secretion of endogenous and exogenous proteins from polarized MDCK cell monolayers.
Authors: Gottlieb T A , Beaudry G , Rizzolo L , Colman A , Rindler M , Adesnik M , Sabatini D D
Published: May 2006

Confluent monolayers of MDCK (Madin-Darby canine kidney) cells provide a widely used system to study the biogenesis of epithelial cell polarity. We now report that these cells are also capable of the vectorial constitutive secretion of a major endogenous product, a glycoprotein of 81 kDa, which is released into the medium from the apical surface within 30 min of its synthesis. This release represents a bona fide exocytotic secretory process and is not the result of proteolytic cleavage of a plasma membrane-associated precursor since, in cells treated with chloroquine, a protein indistinguishable from the mature secretory product accumulated intracellularly. In contrast to the vectorial secretion of the endogenous product, a variety of exogenous exocrine and endocrine proteins synthesized in MDCK cells transfected with the corresponding genes were secreted from both the apical and basolateral surfaces. These included proteins such as rat growth hormone, chicken oviduct lysozyme, bovine gastric prochymosin, and rat salivary gland alpha 2u-globulin, which in their cells of origin are secreted via a regulated pathway, as well as the liver form of the alpha 2u-globulin and the immunoglobulin kappa chain, which are normally released constitutively. These results demonstrate the existence of secretory pathways that lead to both surfaces of MDCK cells and are accessible to the foreign secretory products. They are consistent with the operation of a sorting mechanism in which the polarized secretion of the endogenous product is effected through the recognition of signals that prevent its random distribution within the fluid phase in the cellular endomembrane system.
Two large glycosylated polypeptides found in myelinating oligodendrocytes but not in myelin.
Authors: Gulcher J R , Marton L S , Stefansson K
Published: May 2006

Previous work has shown that high molecular weight polypeptides sharing epitopes with myelin-associated glycoprotein are transiently expressed in developing human central nervous system. We describe here the isolation of two of these polypeptides (150 and 225 kDa), their biochemical characterization, and their immunochemical localization. They are both glycosylated and 15 kDa of the apparent molecular mass of both polypeptides is contributed by N-linked carbohydrate moiety(ies). Both have multimeric forms held together by disulfide bonds. Immunochemical and immunohistochemical studies failed to show these polypeptides in myelin. However, in developing human central nervous system, one or both of them are present in the perikaryal cytoplasm and processes of cells with morphology consistent with actively myelinating oligodendrocytes.
Cloning and sequence determination of a human rheumatoid factor light-chain gene.
Authors: Jirik F R , Sorge J , Fong S , Heitzmann J G , Curd J G , Chen P P , Goldfien R , Carson D A
Published: May 2006

The contribution of germ-line variable regions to autoantibody formation in humans is poorly understood. To study the gene structure of a human autoantibody, chronic lymphatic leukemia (CLL) cells from a patient with an IgM anti-IgG (rheumatoid factor, RF) paraprotein were utilized. The rearranged immunoglobulin gene encoding the kappa light chain for the RF was cloned, and the nucleic acid sequence of its variable region was determined. As demonstrated by Southern blot analysis using a kappa joining-region probe, the CLL cells, stable CLL-WIL2-729-HF2 RF-secreting hybridomas, and the cloned light-chain gene all had an identical restriction fragment containing the rearranged light-chain gene. The CLL RF light chains reacted weakly with an antipeptide antibody against a primary structure-dependent idiotype present on the light chains of the majority of IgM RF paraproteins. The nucleotide and predicted amino acid sequences of the CLL light-chain gene place it in the kappa III variable-region subgroup, and a comparison to known RF paraproteins reveals marked homology to the light-chain amino acid sequence of the IgM RF paraprotein Pom. Both Pom and the CLL light chain appear to identify a second kappa III gene or gene group that is able to encode RF paraprotein light chains.
Synthesis of infectious poliovirus RNA by purified T7 RNA polymerase.
Authors: van der Werf S , Bradley J , Wimmer E , Studier F W , Dunn J J
Published: May 2006

Plasmids containing the entire cDNA sequence of poliovirus type 1 (Mahoney strain) under control of a promoter for T7 RNA polymerase have been constructed. Purified T7 RNA polymerase efficiently transcribes the entire poliovirus cDNA in either direction to produce full-length poliovirus RNA [(+)RNA] or its complement [(-)RNA]. The (+)RNA produced initially had 60 nucleotides on the 5' side of the poliovirus RNA sequence, including a string of 18 consecutive guanine residues generated in the original cloning and an additional 626 nucleotides of pBR322 sequence beyond the poly(A) tract at the 3' end. Such RNA, while much more infectious than the plasmid DNA, is only about 0.1% as infectious as RNA isolated from the virus. Subsequently, a T7 promoter was placed only 2 base pairs ahead of the poliovirus sequence, so that T7 RNA polymerase synthesizes poliovirus RNA with only 2 additional guanine residues at the 5' end and no more than seven nucleotides past the poly(A) tract at the 3' end. Such RNA has much higher specific infectivity, about 5% that of RNA isolated from the virus. The ability to make infectious poliovirus RNA efficiently from cloned DNA makes it possible to apply techniques of in vitro mutagenesis to the analysis of poliovirus functions and the construction of novel and perhaps useful derivatives of poliovirus. A source of variant RNAs should also allow detailed study of the synthesis and processing of poliovirus proteins in vitro.
Cloning and expression of human lecithin-cholesterol acyltransferase cDNA.
Authors: McLean J , Fielding C , Drayna D , Dieplinger H , Baer B , Kohr W , Henzel W , Lawn R
Published: May 2006

cDNA and genomic cloning has been used to determine the mRNA and amino acid sequence of human plasma lecithin-cholesterol acyltransferase (LCATase; EC 2.3.1.43). The mature protein was found to contain 416 amino acid residues with a hydrophobic leader sequence of 24 amino acids. An unusual feature of the message is that the poly(A) signal AATAAA overlaps the COOH-terminal glutamic acid and stop codons, and the 3' untranslated region is only 23 bases. The protein itself is distinguished by a number of extended sequences of hydrophobic amino acids, one of which contains a hexapeptide identical with the interfacial binding segment of the active site of pancreatic lipase and is similar to the same site of lingual lipase. The cloned cDNA allows the expression of active LCATase by transfected tissue culture cells.
Structure and sequence of the human c-sis/platelet-derived growth factor 2 (SIS/PDGF2) transcriptional unit.
Authors: Rao C D , Igarashi H , Chiu I M , Robbins K C , Aaronson S A
Published: May 2006

The structure of the normal human c-sis/platelet-derived growth factor 2 (SIS/PDGF2) transcript was determined by a combination of cDNA cloning, nuclease S1 mapping, and primer extension. Nucleotide sequence analysis revealed that the 3373-nucleotide SIS/PDGF2 mRNA contained only a 723-base-pair (bp) coding sequence for the PDGF2 precursor polypeptide. The coding sequence was flanked by long 5' (1022 bp) and 3' (1625 bp) untranslated regions. The 5' noncoding region, as well as upstream flanking genomic sequences, contained clusters of specific short repeat sequences. A consensus transcriptional promoter sequence, TATAAA, was identified 24 bp upstream of the mRNA start site and an enhancer-like "TG element" was detected about 180 bp downstream from the site of polyadenylylation. These findings identify putative regulatory elements of the SIS/PDGF2 gene.
ATP-dependent acidification and tonoplast hyperpolarization in isolated vacuoles from green suspension cells of
Chenopodium rubrum
L
Authors: Bentrup F.-W. , Gogarten-Boekels M. , Hoffmann B. , Gogarten J. P. , Baumann C.
Published: May 2006

The tonoplast of isolated vacuoles from photoautotrophic suspension cells of
Chenopodium rubrum
L. was studied by means of the patch-clamp technique. In a symmetrical K
+
concentration of 46 mM, similar to
in vivo
conditions, the tonoplast displayed a membrane potential near zero and a linear current-voltage relationship with a mean slope of 1.0 S/m
2
. ATP at 2 mM hyperpolarized the tonoplast (vacuole positive) by 15-20 mV and, in a parallel experiment, acidified the vacuole (outside pH 7.0) to pH 5.0, as monitored by accumulation of acridine orange. Analysis of the voltage-clamp current indicates a 2-fold, ATP-dependent increase of the membrane capacitance, from 4 to 8 mF/m
2
, and an ATP-independent, unidentified ion channel having a mean opening time of about 5 msec and a conductivity of 0.5-1.0 pS.
Zero-order ultrasensitivity in the regulation of glycogen phosphorylase.
Authors: Meinke M H , Bishop J S , Edstrom R D
Published: May 2006

The activity of glycogen phosphorylase (1,4-alpha-D-glucan:orthophosphate alpha-D-glucosyltransferase, EC 2.4.1.1) is controlled by a cyclic phosphorylation-dephosphorylation process through the action of the interconverting enzymes, phosphorylase b kinase (ATP:phosphorylase-b phosphotransferase, EC 2.7.1.38) and phosphorylase a phosphatase (phosphorylase a phosphohydrolase, EC 3.1.3.17). In muscle tissue, the combined concentration of the activated (phospho-) form, phosphorylase a, and the nonactivated (dephospho-) form, phosphorylase b, is substantially greater than the Km of either of the interconverting enzymes for its phosphorylase substrate. It has been predicted that, under such a set of conditions, a sensitivity amplification will occur for phosphorylase regulation due to the zero-order ultrasensitivity effect [LaPorte, D. C. & Koshland, D. E., Jr. (1983) Nature (London) 305, 286-290]. The sensitivity amplification will enhance the responsiveness of the phosphorylase interconversion cycle to changes in the ratio of activities of the kinase to phosphatase. We have studied the cyclic interconversion process using purified muscle enzymes in steady-state reactions and found that there is an enhancement in the control sensitivity of the process due to the zero-order ultrasensitivity effect. The potential for the in vivo enhancement of sensitivity in glycogen degradation by this effect is discussed.
Exon/intron organization of the genes coding for the delta chains of the human and murine T-cell receptor/T3 complex.
Authors: van den Elsen P , Georgopoulos K , Shepley B A , Orkin S , Terhorst C
Published: May 2006

Genomic DNA clones containing the gene coding for the 20-kDa T3 glycoprotein of the T-cell receptor/T3 complex (T3-delta chain) of human and mouse were isolated and characterized. The human T3-delta gene is approximately equal to 4 kilobases (kb) long and contains five exons: a 151-base-pair (bp) exon containing the 5' untranslated and the coding sequences of the signal peptide, one exon of 219 bp, which contains most of the extracellular segment of the T3-delta chain, one 130-bp-long exon coding mainly for the transmembrane portion of the molecule, and two exons of 44 bp and 156 bp encoding the cytoplasmic domain and 3' untranslated region of the T3-delta chain, respectively. The murine T3-delta gene, which has a similar organization, contains 5 kb, because the first intron is approximately equal to 1 kb larger than in the human gene. Two major mRNA initiation sites within a small area approximately equal to 100 nucleotides 5' of the AUG codon were determined by S1 nuclease analysis and primer-extension studies. The remarkably high level of conservation of nucleotide sequences in this region suggests that this segment may be important for the regulation of T-cell-specific transcription of the T3-delta gene. The T3-delta gene does not contain the "TATA box" found in many eukaryotic promoters.
Isolation and characterization of human factor VIII: molecular forms in commercial factor VIII concentrate, cryoprecipitate, and plasma.
Authors: Andersson L O , Forsman N , Huang K , Larsen K , Lundin A , Pavlu B , Sandberg H , Sewerin K , Smart J
Published: May 2006

Human factor VIII has been isolated from a high purity factor VIII concentrate by immunoaffinity chromatography and HPLC on Mono Q gel. Two fractions of factor VIII were obtained with a specific activity of approximately equal to 7000 units/mg. The major fraction contained eight peptide chains of 200, 180, 160, 150, 135, 130, 115, and 105 kDa plus one doublet chain of 80 kDa. The minor fraction contained one peptide chain of 90 kDa plus the chain of 80 kDa. Both fractions were activated by thrombin to the same extent. Amino-terminal amino acid sequence analysis was performed on the 180-kDa, 130-kDa, and 90-kDa chains and showed an identical amino-terminal sequence in these chains. Each chain from 200 kDa to 90 kDa was linked to one 80-kDa chain by a metal-ion bridge(s). Studies on factor VIII in plasma and cryoprecipitate, prepared and gel filtered in the presence of protease inhibitors, showed that one 200-kDa plus one 80-kDa chain were the only or dominating chains in the materials and may represent native factor VIII. The results indicated that all chains from 180 kDa to 90 kDa are fragments of the 200-kDa chain. All of these more or less fragmented chains form active factor VIII complexes with the 80-kDa chain.
Acetylcholine raises excitability by inhibiting the fast transient potassium current in cultured hippocampal neurons.
Authors: Nakajima Y , Nakajima S , Leonard R J , Yamaguchi K
Published: May 2006

The effects of acetylcholine on cultured hippocampal neurons were investigated by using the whole-cell version of the patch-clamp technique. The CA1 region of the hippocampus was excised from brain slices of young rats (12-19 day old), incubated in a papain solution, and dissociated. Neurons were plated on a glial feeder layer. The experiments were conducted mostly on neurons cultured for 2-6 days. Upon depolarization under voltage clamp, these cells exhibited a fast transient outward current (A-current), which was inhibited by 4-aminopyridine (2.5 mM). Acetylcholine (0.1 microM) also inhibited this A-current, as did the muscarinic agonists bethanechol and muscarine. As expected from their inhibition of the A-current, acetylcholine and 4-aminopyridine both increased the amplitude of the action potential and prolonged its duration. We conclude that the inhibition of the A-current constitutes a mechanism by which acetylcholine exerts its excitatory influence on hippocampal neurons.
Reconstitution of chlorophyll a/b light-harvesting complexes: Xanthophyll-dependent assembly and energy transfer
Authors: Plumley F. Gerald , Schmidt Gregory W.
Published: May 2006

A method for
in vitro
reconstitution of the chlorophyll a/b light-harvesting complex from LiDodSO
4
/heat-denatured or acetone-extracted photosynthetic membranes has been developed. Characterization of the minimum components necessary for the functional organization of pigments in these membrane complexes reveals that xanthophylls are essential structural components.
Multiple nuclear proteins bind upstream sequences in the promotor region of a T-cell receptor beta-chain variable-region gene: evidence for tissue specificity.
Authors: Royer H D , Reinherz E L
Published: May 2006

DNA-nuclear protein binding interactions were examined in the promoter region of a representative T-cell receptor Ti beta-chain variable-region gene by means of electrophoretic mobility-shift and DNase I-protection analysis. Within 175 bases upstream of the transcription initiation site, four protected regions ("footprints") were identified on the coding strand, at nucleotides -46 to -68 (I), -72 to -92 (II), -113 to -134 (III), and -136 to -175 (IV). Nuclear proteins (0.6 M NaCl fraction from a heparin-Sepharose column chromatography of nuclear extracts) of a variety of cell types produced footprints I, III, and IV and a fifth footprint (beyond nucleotide -200). In contrast, footprint II was produced only by T-cell extracts, although nuclear extracts of a transformed B-lymphoblastoid line produced a partial footprint in this region. Furthermore, footprint analysis of the noncoding strand showed that a continuous region of protection corresponding to the entire region of footprints I and II was generated, along with a DNase I-hypersensitive site, by nuclear proteins derived from T cells but not other cell types. Footprint I has the sequence structure of many well-defined protein-DNA binding sites. Nucleotide sequences in the region of footprint II bore no homology to known sequences, whereas those in the areas of footprints III and IV were similar to motifs within immunoglobulin and other enhancers. These findings may have implications for the tissue specificity of human Ti beta-chain gene transcription.
Structure of apolipoprotein C-IIToronto, a nonfunctional human apolipoprotein.
Authors: Connelly P W , Maguire G F , Hofmann T , Little J A
Published: May 2006

We previously reported a family with apolipoprotein C-II (apoC-II) deficiency characterized by the presence of a mutant apoC-II, apoC-IIToronto. We now report the purification and primary structure of apoC-IIToronto. The sequence of apoC-IIToronto is identical to that of normal apoC-II from residues 1-68. It differs from residue 69, where Asp69-Gln70-Val71-Leu72-Ser73-Val74- Leu75-Lys76-Gly77-Glu78-Glu79 is replaced by Thr69-Lys70-Phe71-Phe72-Leu73-Cys74. This is consistent with the deletion of a nucleotide in the codon for either Thr68 or Asp69 and a translation reading frame shift.
Nucleotide and amino acid sequences of pulmonary surfactant protein SP 18 and evidence for cooperation between SP 18 and SP 28-36 in surfactant lipid adsorption.
Authors: Hawgood S , Benson B J , Schilling J , Damm D , Clements J A , White R T
Published: May 2006

Pulmonary surfactant is a lipid-rich material that promotes alveolar stability by lowering the surface tension at the air-fluid interface in the peripheral air spaces. The turnover of surfactant phospholipids in the alveolar space is fast, and several lines of evidence suggest there is rapid formation and replenishment of the phospholipid surface film during normal respiration. Specific proteins may regulate these dynamic surface properties. The predominant surfactant protein is a well-characterized, lipid-associated glycoprotein, SP 28-36 (28-36 kDa). A second group of very hydrophobic proteins has recently been shown to affect the surface activity of surfactant phospholipids. We have isolated this group of hydrophobic proteins, herein called SP 5-18 (5-18 kDa), from canine surfactant and have shown by NH2-terminal sequence analysis that at least two proteins, SP 5-8 and SP 18, are present in this group. We have derived the full amino acid sequence of SP 18 from the nucleotide sequence of the cDNAs identified with oligonucleotide probes that were based on the NH2-terminal amino acids of SP 18. The protein isolated from extracellular surfactant appears to be a fragment of a much larger precursor protein (40 kDa). The amino acid sequence of SP 18 is markedly hydrophobic and contains two possible bilayer-spanning domains. We have shown that SP 18 and the glycoprotein SP 28-36 have a cooperative, calcium-dependent action in promoting the formation of phospholipid surface films.
Cloning and DNA sequence of the mercuric- and organomercurial-resistance determinants of plasmid pDU1358.
Authors: Griffin H G , Foster T J , Silver S , Misra T K
Published: May 2006

The broad-spectrum mercurial-resistance plasmid pDU1358 was analyzed by cloning the resistance determinants and preparing a physical and genetic map of a 45-kilobase (kb) region of the plasmid that contains two separate mercurial-resistance operons that mapped about 20 kb apart. One encoded narrow-spectrum mercurial resistance to Hg2+ and a few organomercurials; the other specified broad-spectrum resistance to phenylmercury and additional organomercurials. Each determinant governed mercurial transport functions. Southern DNA X DNA hybridization experiments using gene-specific probes from the plasmid R100 mer operon indicated close homology with the R100 determinant. The 2153 base pairs of the promoter-distal part of the broad-spectrum Hg2+-resistance operon of pDU1358 were sequenced. This region included the 3'-terminal part of the merA gene, merD, unidentified reading frame URF1, and a part of URF2 homologous to previously sequenced determinants of plasmid R100. Between the merA and merD genes, an open reading frame encoding a 212 amino acid polypeptide was identified as the merB gene that determines the enzyme organomercurial lyase that cleaves the C--Hg bond of phenylmercury.
Aberrant splicing events that are induced by proviral integration: implications for myb oncogene activation.
Authors: Rosson D , Dugan D , Reddy E P
Published: May 2006

Activation of the mouse c-myb oncogene in Abelson virus-induced plasmacytoid lymphosarcomas was studied using cDNA cloning and nucleotide sequence analysis. The results presented here show that viral integration in the myb locus generates splicing errors at the 5' and 3' regions. Viral integration results in transcriptional initiation within the viral long terminal repeat and generation of a chimeric mRNA that lacks the first three coding exons. The alterations at the 3' end are caused by an aberrant splicing event in which additional splice-donor and -acceptor sequences within intronic sequences are used to splice an additional 363 nucleotides into the myb transcripts. The resulting insertion of 121 amino acids is in a region of the protein where other activated forms of the myb gene product have deletions. These results suggest that alterations in the 3' end of the myb gene play a crucial role in the activation of this gene.
Homology between the DNA-binding domain of the GCN4 regulatory protein of yeast and the carboxyl-terminal region of a protein coded for by the oncogene jun.
Authors: Vogt P K , Bos T J , Doolittle R F
Published: May 2006

The product of the recently described oncogene jun shows significant amino acid sequence homology with the GCN4 yeast transcriptional activator protein. The similarity is restricted to the 66 carboxyl-terminal amino acids, thought to be the DNA-binding domain of the GCN4 protein. In these alpha-helix-permissive regions of the jun and GCN4 products there is also a lesser but still significant amino acid resemblance to the fos protein and a marginal degree of similarity to myc proteins. The amino acid sequence homology between GCN4 and jun gene products suggests that the jun protein may bind to DNA in a sequence-specific way and exert a regulatory function.
Comparative anatomy of the human APRT gene and enzyme: nucleotide sequence divergence and conservation of a nonrandom CpG dinucleotide arrangement.
Authors: Broderick T P , Schaff D A , Bertino A M , Dush M K , Tischfield J A , Stambrook P J
Published: May 2006

The functional human adenine phosphoribosyltransferase (APRT) gene is less than 2.6 kilobases in length and contains five exons. The amino acid sequences of APRTs have been highly conserved throughout evolution. The human enzyme is 82%, 90%, and 40% identical to the mouse, hamster, and Escherichia coli enzymes, respectively. The promoter region of the human APRT gene, like that of several other "housekeeping" genes, lacks "TATA" and "CCAAT" boxes but contains five GC boxes that are potential binding sites for the Sp1 transcription factor. The distal three, however, are dispensable for gene expression. Comparison between human and mouse APRT gene nucleotide sequences reveals a high degree of homology within protein coding regions but an absence of significant homology in 5' flanking, 3' untranslated, and intron sequences, except for similarly positioned GC boxes in the promoter region and a 26-base-pair region in intron 3. This 26-base-pair sequence is 92% identical with a similarly positioned sequence in the mouse gene and is also found in intron 3 of the hamster gene, suggesting that its retention may be a consequence of stringent selection. The positions of all introns have been precisely retained in the human and both rodent genes, as has an unusual AG/GC donor splice site in intron 2. Particularly striking is the distribution of CpG dinucleotides within human and rodent APRT genes. Although the nucleotide sequences of intron 1 and the 5' flanking regions of human and mouse APRT genes have no substantial homology, they have a frequency of CpG dinucleotides that is much higher than expected and nonrandom considering the G + C content of the gene. Retention of an elevated CpG dinucleotide content, despite loss of sequence homology, suggests that there may be selection for CpG dinucleotides in these regions and that their maintenance may be important for APRT gene function.
Recognition of tau epitopes by anti-neurofilament antibodies that bind to Alzheimer neurofibrillary tangles.
Authors: Ksiezak-Reding H , Dickson D W , Davies P , Yen S H
Published: May 2006

Eleven anti-neurofilament (anti-NF) monoclonal antibodies were studied for their reactivity with heat-stable, microtubule-associated proteins and Alzheimer neurofibrillary tangles (ANT). On immunoblots of NF proteins, the antibodies recognized epitopes that were variably sensitive to Escherichia coli alkaline phosphatase. Eight of the antibodies showed reactivity with ANT and decreased binding to electroblotted NF after phosphatase treatment. The same eight antibodies reacted with tau proteins from bovine and rat brain, binding to tau proteins was also substantially reduced by phosphatase. Of the eight antibodies that bound to animal tau proteins, five also bound to tau proteins from normal human brain. All of the antibodies that bound to animal tau proteins stained ANT in frozen tissue sections. Brief treatment of tissue sections with trypsin in most cases enhanced antibody binding to ANT. All antibodies that lacked reactivity with tau proteins failed to bind ANT. Phosphatase treatment of Alzheimer tissue sections did not change the immunoreactivity of ANT and neurites in senile plaques with ANT-reactive, anti-NF antibodies, except for two antibodies that showed decreased binding to ANT. In contrast, axonal staining was decreased or eliminated by phosphatase treatment, similar to the response of electroblotted NF and tau proteins. These results suggest that staining of ANT by anti-NF antibodies may be due to cross-reaction of anti-NF with epitopes in tau proteins, the epitopes in axons, NF, and tau are sensitive to the effect of phosphatase, whereas the majority of those in ANT are not, and some of the epitopes in ANT that are shared with NF and tau proteins are not readily accessible to antibody binding.
Activation of a potassium current by rapid photochemically generated step increases of intracellular calcium in rat sympathetic neurons.
Authors: Gurney A M , Tsien R Y , Lester H A
Published: May 2006

Although Ca2+ is a well-established intracellular messenger, there are many questions concerning the kinetics and spatial localization of its effects. Such problems may now be approached with the photosensitive Ca2+ chelator nitr-5. The Ca2+ affinity of this molecule decreases by a factor of 40 after absorption of near-UV light; Ca2+ is liberated with a time constant of approximately equal to 300 microseconds. Nitr-5 or the related compounds nitr-2 and nitr-7, complexed with Ca2+, were introduced into rat sympathetic ganglion cells by dialysis from a patch pipette electrode operating in the whole-cell, voltage-clamp mode. Light flashes released Ca2+ and activated a K+ current. Flash-induced current relaxations followed a simple exponential time course with time constants as brief as 5 ms. Comparison of the kinetics among the chelators, which photolyze at different rates, suggests that release of Ca2+ from nitr-5 is too fast to limit the relaxation. Thus we confirm directly that Ca2+ can modulate membrane properties within a few milliseconds after entering a cell. A preliminary kinetic description of K+ current activation by Ca2+ in rat sympathetic neurons is presented; Ca2+ appears to bind to the channel with a rate constant of at least 2 X 10(7) M-1 X s-1.
Binding of transcription factors and creation of a large nucleoprotein complex on the human cytomegalovirus enhancer.
Authors: Ghazal P , Lubon H , Fleckenstein B , Hennighausen L
Published: May 2006

The effect of the human cytomegalovirus immediate early region 1 enhancer on transcription was studied in vitro with HeLa cell nuclear extract. Stimulation of in vitro transcription mediated by the enhancer element involves its recognition by specific trans-acting factors present in the nuclear extract. DNase I protection analysis was used to determine at the nucleotide level those enhancer sequences that interact with nuclear factors. At least nine sites of protein-DNA interaction were detected over approximately 400 base pairs of enhancer sequence. The regions of nuclease protection are associated with 21-, 19-, 18-, and 17-base-pair repeat elements as well as with a unique sequence, creating a large nucleoprotein complex. The relationship between the protein binding and the activity of the immediate early region 1 enhancer is discussed.
Identification of the receptor for erythropoietin by cross-linking to Friend virus-infected erythroid cells.
Authors: Sawyer S T , Krantz S B , Luna J
Published: May 2006

Erythropoietin (Epo) is a glycoprotein hormone that regulates erythroid development and interacts with surface receptors on developing erythroid cells. In this laboratory, a cell system with a relatively pure population of erythroid cells that respond to Epo has been developed. Immature erythroid cells are obtained from the spleens of mice infected with the anemia strain of Friend virus. The binding of 125I-labeled Epo (125I-Epo) to plasma membranes from these cells was studied in this investigation. 125I-Epo binding reached equilibrium within 20 min at 37 degrees C. Twenty percent of the receptors bound 125I-Epo with a Kd of 0.08 X 10(-9) M, while the remaining receptors bound the hormone with a Kd of 0.6 X 10(-9) M. In this study, a receptor for Epo was identified by cross-linking 125I-Epo to the receptor in intact cells and plasma membrane preparations using disuccinimidyl suberate. Polyacrylamide gel electrophoresis revealed two labeled bands of 100 and 85 kDa. The 85-kDa band was more heavily labeled (65%) than the 100-kDa band. Both bands were equally decreased when increasing amounts of unlabeled Epo were included in the binding mixture, indicating a specific interaction of 125I-Epo with the receptor.
Regulation of the host range of human papovavirus JCV.
Authors: Feigenbaum L , Khalili K , Major E , Khoury G
Published: May 2006

Human papovavirus JCV is associated with the human demyelinating disorder progressive multifocal leukoencephalopathy. In tissue culture, the virus is largely restricted to growth in primary human fetal glial cell. In this study, we demonstrate two levels of regulation of the viral host range. Expression of the early JCV mRNA, which encodes the essential viral protein, large tumor antigen (T antigen), depends on recognition of the early enhancer/promoter elements by tissue-specific factors found in both human and rodent glial cells. In the presence of JCV T antigen, viral DNA replication requires a species-specific factor, presumably a component of DNA polymerase, which is found in a wide range of primate cells. We further demonstrate that simian virus 40 T antigen has sufficient homology to efficiently substitute for the analogous JCV protein in initiating viral DNA replication.
Soluble factors stimulating secretory protein translocation in bacteria and yeast can substitute for each other.
Authors: Fecycz I T , Blobel G
Published: May 2006

mRNA for prepro-alpha-factor (pp alpha), a yeast secretory glycoprotein, was translated in a wheat germ cell-free system that was posttranslationally supplemented either with inverted vesicles from the plasma membrane of Escherichia coli (INV) or with microsomes from Saccharomyces cerevisiae. A postribosomal supernatant (PRS) from E. coli was found to stimulate translocation of pp alpha across the INV membrane. A yeast PRS could substitute for its E. coli counterpart. Likewise, an E. coli PRS could substitute for a yeast PRS and stimulate translocation of pp alpha across yeast microsomal membranes.
Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast.
Authors: Sumrada R A , Cooper T G
Published: May 2006

Expression of the yeast arginase gene (CAR1) responds to both induction and nitrogen catabolite repression. Regulation is mediated through sequences that both positively and negatively modulate CAR1 transcription. A short sequence, 5'-TAGCCGCCGAGGG-3', possessing characteristics of a repressor binding site, plays a central role in the induction process. A fragment containing this upstream repression sequence (URS1) repressed gene expression when placed either 5' or 3' to the upstream activation sequences of the heterologous gene CYC1. Action of the URS and its cognate repressor was overcome by CAR1 induction when the URS was situated cis to the CAR1 flanking sequences. This was not observed, however, when it was situated downstream of a heterologous CYC1 upstream activation sequence indicating that URS function is specifically neutralized by cis-acting elements associated with CAR1 induction. Searches of sequences in various gene banks revealed that URS1-like sequences occur ubiquitously in genetic regulatory regions including those of bacteriophage lambda, yeast, mammalian, and viral genes. In a significant number of cases the sequence is contained in a region associated with negative control of yeast gene regulation. These data suggest the URS identified in this work is a generic repressor target site that apparently has been conserved during the evolution of transcriptional regulatory systems.
Separations of open-circular DNA using pulsed-field electrophoresis.
Authors: Levene S D , Zimm B H
Published: May 2006

The effect of high electric fields on the gel-electrophoretic mobility of open-circular DNA in agarose differs dramatically from that on linear molecules of the same molecular weight. At high fields, sufficiently large circular forms are prevented from migrating into the gel whereas linear molecules and smaller circular DNAs migrate normally. This effect is strongly field dependent, affecting circular molecules of decreasing size with increasing field strength. We have studied this effect with a series of plasmid DNAs ranging from 2.9 to 56 kilobase pairs using continuous and reversing-pulse electric fields. Application of reversing pulses abolishes the effect under certain conditions and supports the model for the gel electrophoresis of open-circular DNA where circular forms are trapped by engaging the free end of an agarose gel fiber.
Specific binding of a fungal glucan phytoalexin elicitor to membrane fractions from soybean
Glycine max
Authors: Schmidt Walter E. , Ebel Jürgen
Published: May 2006

Treatment of soybean tissues with elicitors results in the production of phytoalexins, one of a number of inducible plant defense reactions against microbial infections. The present study uses a β-1,3-[
3
H]glucan elicitor fraction from
Phytophthora megasperma
f. sp.
glycinea
, a fungal pathogen of soybean, to identify putative elicitor targets in soybean tissues. Use of the radiolabeled elicitor disclosed saturable high-affinity elicitor binding site(s) in membrane fractions of soybean roots. Highest binding activity is associated with a plasma membrane-enriched fraction. The apparent
K
d
value for β-glucan elicitor binding is ≈0.2 × 10
-6
M and the maximum number of binding sites is 0.5 pmol per mg of protein. Competition studies with the [
3
H]glucan elicitor and a number of polysaccharides demonstrate that only polysaccharides of a branched β-glucan type effectively displace the radiolabeled ligand from membrane binding. Differential displacing activity of the glucans on
P. megasperma
elicitor binding corresponds closely to their respective ability to elicit phytoalexin production in a cotyledon bioassay.
Bacteriophage lambda cloning system for the construction of directional cDNA libraries.
Authors: Meissner P S , Sisk W P , Berman M L
Published: May 2006

We have developed a bacteriophage lambda cloning vector, lambda ORF8, that can be used for the construction of cDNA libraries. The wild-type lambda genome contains five BamHI, five EcoRI, and seven HindIII restriction sites that have all been removed from the genome of lambda ORF8. Sites for these endonucleases are present within the multiple cloning site of lambda ORF8. We report a method for preparing cDNAs that can be cloned in a single orientation in our phage vector. The method utilizes the synthesis of double-stranded cDNA, including priming of first-strand synthesis by oligo(dT). After completion of second-strand synthesis, a bifunctional oligodeoxynucleotide linker is ligated to the cDNA fragments. This linker, which contains a BamHI restriction site, will create a HindIII restriction site when ligated to the 3' end of cDNA fragments. Subsequent treatment of methylated cDNA with HindIII and BamHI endonucleases allows these fragments to be cloned directionally into lambda ORF8. To demonstrate the utility of this cloning system, we prepared a library from 5 micrograms of mRNA isolated from phytohemagglutinin-stimulated human peripheral blood lymphocytes. The primary library contained 2 X 10(8) plaque-forming phage, at least 80% of which contain inserts. A portion of the library was examined for the presence of gamma-interferon-related clones to verify the method had generated a library that was representative of phytohemagglutinin-stimulated peripheral blood lymphocytes. This simple and efficient cDNA cloning system significantly reduces the amount of RNA and effort required for the preparation of large directionally cloned libraries.
Profile analysis: detection of distantly related proteins.
Authors: Gribskov M , McLachlan A D , Eisenberg D
Published: May 2006

Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), which is created from a group of sequences previously aligned by structural or sequence similarity. The similarity of any other sequence (target) to the group of aligned sequences (probe) can be tested by comparing the target to the profile using dynamic programming algorithms. The profile method differs in two major respects from methods of sequence comparison in common use: (i) Any number of known sequences can be used to construct the profile, allowing more information to be used in the testing of the target than is possible with pairwise alignment methods. (ii) The profile includes the penalties for insertion or deletion at each position, which allow one to include the probe secondary structure in the testing scheme. Tests with globin and immunoglobulin sequences show that profile analysis can distinguish all members of these families from all other sequences in a database containing 3800 protein sequences.
Human alpha 2-HS-glycoprotein: the A and B chains with a connecting sequence are encoded by a single mRNA transcript.
Authors: Lee C C , Bowman B H , Yang F M
Published: May 2006

The alpha 2-HS-glycoprotein (AHSG) is a plasma protein reported to play roles in bone mineralization and in the immune response. It is composed of two subunits, the A and B chains. Recombinant plasmids containing human cDNA AHSG have been isolated by screening an adult human liver library with a mixed oligonucleotide probe. The cDNA clones containing AHSG inserts span approximately 1.5 kilobase pairs and include the entire AHSG coding sequence, demonstrating that the A and B chains are encoded by a single mRNA transcript. The cDNA sequence predicts an 18-amino-acid signal peptide, followed by the A-chain sequence of AHSG. A heretofore unseen connecting sequence of 40 amino acids was deduced between the A- and B-chain sequences. The connecting sequence demonstrates the unique amino acid doublets and collagen triplets found in the A and B chains; it is not homologous with other reported amino acid sequences. The connecting sequence may be cleaved in a posttranslational step by limited proteolysis before mature AHSG is released into the circulation or may vary in its presence because of alternative processing. The AHSG cDNA was utilized for mapping the AHSG gene to the 3q21----qter region of human chromosome 3. The availability of the AHSG cDNA clone will facilitate the analysis of its genetic control and gene expression during development and bone formation.
The gluconate operon gnt of Bacillus subtilis encodes its own transcriptional negative regulator.
Authors: Fujita Y , Fujita T
Published: May 2006

The gluconate (gnt) operon of Bacillus subtilis consists of four gnt genes; the second and third genes code for gluconate kinase (gluconokinase, EC 2.7.1.12) and gluconate permease, respectively. A fragment carrying the promoter of this operon (gnt promoter) and the first gene (gntR) was subcloned into a promoter probe vector (pPL603B). Repression of the expression of cat-86 gene, encoded in the vector portion of a constructed plasmid (pgnt21), that is under the control of the gnt promoter was removed by gluconate. The results of deletion analysis and of insertional inactivation of the gntR gene cloned in pgnt21 suggested that the product of the gntR gene, actually synthesized as a 29-kDa protein in vivo, is involved in repression of the gnt promoter. A 4-base-pair insertional mutation within the gntR gene constructed in vitro was introduced into the B. subtilis chromosomal gnt operon by use of linkage of the 4 base pairs to gntK10 in transformation. The introduced mutation gntR1 caused the constitutive expression of the gluconate kinase and gluconate permease genes. S1 nuclease analysis indicated that the mRNA of this operon is synthesized in the gntR1 strain and amounts of mRNA are not changed very much by gluconate, which acts as an inducer in the wild-type gene. These results strongly indicate that the gntR gene codes for a transcriptional negative regulator for the gnt operon.
Tenascin is a stromal marker for epithelial malignancy in the mammary gland.
Authors: Mackie E J , Chiquet-Ehrismann R , Pearson C A , Inaguma Y , Taya K , Kawarada Y , Sakakura T
Published: May 2006

Tenascin is an extracellular matrix glycoprotein that is not present in the normal mature rat mammary gland. The distribution of tenascin was examined by immunohistochemistry in mammary tumors from carcinogen-treated and untreated rats, in virus-induced mammary tumors from mice, and in a variety of mammary gland lesions from humans. Tenascin was detectable in the stroma of the malignant but not of the benign tumors from all species. An inhibition ELISA, testing homogenates of rat tumors, confirmed that tenascin was present in malignant but not in benign tumors. Thus, tenascin was consistently found to be a stromal marker for epithelial malignancy in the mammary gland. It is concluded that tenascin may be involved in the interactions between the epithelial and mesenchyme-derived (stromal) components of the mammary gland, which are known to influence epithelial carcinogenesis in this organ.