bluuebunny/crossref_metadata_2025 huggingface dataset:
Properties of the duplex DNA-dependent ATPase activity of Escherichia coli RecA protein and its role in branch migration.
Authors: Kowalczykowski S C , Clow J , Krupp R A
Published: May 2006

We have investigated the double-stranded DNA (dsDNA)-dependent ATPase activity of recA protein. This activity is distinguished from the single-stranded DNA (ssDNA)-dependent ATPase activity by the presence of a pronounced lag time before the onset of steady-state ATP hydrolysis. During the lag phase there is little ATP hydrolysis. The duration of the lag phase, referred to as the lag time, is found to increase with the thermal stability of the dsDNA substrate. Increasing either the MgCl2 or NaCl concentration increases the lag time, whereas increasing the temperature decreases the lag time. The lag time shows little dependence on recA protein concentration but is strongly dependent on ATP concentration. After the lag phase, a steady-state ATP hydrolysis rate is achieved that approaches the rate observed with ssDNA. The steady-state phase of the reaction is proportional to the concentration of recA protein-DNA complex and shows saturation behavior at approximately equal to 5 +/- 1 base pairs per recA protein monomer. These results suggest that the lag phase represents a rate-limiting step in the dsDNA-dependent ATP hydrolysis reaction that requires a structural transition in the dsDNA and that involves a ternary complex of ATP, recA protein, and DNA. We propose that this transition involves the transient denaturation of the dsDNA to form regions of ssDNA. Elsewhere we demonstrate that the dsDNA-dependent ATPase activity is proportional to the rate of recA protein-catalyzed branch migration. We suggest that this activity is responsible for a polar polymerization that drives the branch migration reaction.
Purification, properties, and immunocytochemical localization of human liver peroxisomal enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase.
Authors: Reddy M K , Usuda N , Reddy M N , Kuczmarski E R , Rao M S , Reddy J K
Published: May 2006

A molecular understanding of genetic disease in which peroxisomal functions are impaired depends on analysis of the structure of normal and mutant enzymes of peroxisomes. We report experiments describing the isolation, characterization, and immunocytochemical localization of enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme (PBE) of the peroxisomal fatty acid beta-oxidation system from normal human liver and compared it with that of rat liver enzyme. The human enzyme, purified approximately equal to 2300-fold by ion-exchange chromatography, is homogeneous as judged by NaDodSO4/PAGE. This PBE is localized exclusively in the matrix of peroxisomes in liver cells by the protein A/gold immunocytochemical method. The human PBE is similar to rat enzyme in size (Mr, approximately equal to 79,000), isoelectric point (pI, 9.8), pH optima, molecular structure as observed by rotary shadowing, and peptide pattern on NaDodSO4/PAGE after proteolytic digestion with Staphylococcus aureus V8 protease. The human and rat enzymes differed in their immunological properties by having partial identity with each other; this is reflected in their slightly dissimilar composition of the amino acids aspartic acid, threonine, glutamic acid, tyrosine, and glycine. COOH-terminal amino acid were similar for both the enzymes: -Gly-Ser-Leu-Ile-COOH. These results suggest that the human and rat liver PBE may be different in their amino acid sequences at their antigenic sites.
Cell patterning in pigment-chimeric eyes in Xenopus: germinal transplants and their contributions to growth of the pigmented retinal epithelium.
Authors: Hunt R K , Cohen J S , Mason B J
Published: May 2006

We have examined the process by which small groups of pigmented germinal cells transplanted orthotopically from stage 30-38 donor embryos into stage 28-38 albino hosts contribute new postmitotic cells to the pigmented retinal epithelium of the growing larval eye in Xenopus. In the great majority of chimeric eyes, the transplant healed to occupy a small arc-territory at the intended dorsal or anterior position on the host germinal zone. Over the course of subsequent weeks, the transplanted germinal cells added new mitotically quiescent cells to the distal rim of the pigmented retinal epithelium and so gave rise to an elongating black sector on the growing larval eye. Cellular details at the boundaries of the graft-derived sector were stable over time; the accumulation of such landmarks provided a summary record--in the proximodistal axis of the older eye--of the growth history of the transplant. Case-to-case variation among both groups of transplants suggested a measure of indeterminancy in the details of germinal cell growth.
Nucleoside triphosphate-dependent DNA-binding properties of mos protein.
Authors: Seth A , Priel E , Vande Woude G F
Published: May 2006

We have previously shown that the mos gene product, p40mos, produced in Escherichia coli binds ATP and has ATPase activity. In the present study, we investigated the DNA-binding properties of p40mos and two mos deletion mutant proteins. Nitrocellulose blot protein-DNA binding assays showed that p40mos binds DNA in the presence of Mg2+-ATP and certain other nucleoside triphosphates. Ninety percent of the p40mos-bound DNA is dissociated if the complex is washed in the presence of 1 M NaCl or in the absence of ATP. p40mos-DNA binding is not observed in the presence of AMP or the nonhydrolyzable ATP analog adenosine 5'-[beta, gamma-methylene]-triphosphate; however, in the presence of ADP, p40mos binds DNA at 20% of the level that is observed with ATP. An N-terminal-deletion mutant protein, p19mos, has no DNA-binding activity, whereas a C-terminal-deletion mutant protein, p25mos, does. p25mos contains the ATP-binding domain, binds DNA in the presence of either ADP or ATP, and shows 5% and 45% binding (relative to that in the presence of ATP) in the presence of AMP and adenosine 5'-[beta, gamma-methylene]triphosphate, respectively. These results suggest that the N-terminal domain of p40mos is responsible for nucleoside triphosphate-mediated DNA binding. We also observed differential histone-DNA binding in the presence and absence of ATP.
Spectrum of cisplatin-induced mutations in Escherichia coli.
Authors: Burnouf D , Duane M , Fuchs R P
Published: May 2006

Using a forward-mutation assay based on the inactivation of the tetracycline-resistance gene located on plasmid pBR322, we have determined the mutation spectrum induced in Escherichia coli by cisplatin [cis-diamminedichloroplatinum(II)], a widely used antitumor drug. Cisplatin is known to form mainly intrastrand diadducts at ApG and GpG sites. We found that cisplatin efficiently induces mutations in an SOS-dependent way (i.e., dependent upon UV irradiation of the host bacteria). More than 90% of the mutations are single-base-pair substitutions occurring at the potential sites of cisplatin adducts (ApG and GpG). Taking into account the relative proportions of ApG and GpG adducts, we found that the ApG adducts are at least 5 times more mutagenic than the GpG adducts. Moreover, a strong mutation specificity was seen at the 5' side of the ApG adducts (A X T----T X A transversions). The observation that most mutations occur at the 5' end of the adduct at both ApG and GpG sites is discussed in relation to recent structural data.
The reciprocal effects of epsilon-aminohexanoic acid and chloride ion on the activation of human [Glu1]plasminogen by human urokinase.
Authors: Urano T , Chibber B A , Castellino F J
Published: May 2006

The activation of human [Glu1]plasminogen [( Glu1]Pg) by high-molecular-weight two-chain human urinary urokinase [EC 3.4.21.31) and low-molecular-weight two-chain human urinary urokinase is inhibited by Cl- at physiological concentrations and stimulated by epsilon-aminohexanoic acid (epsilon Ahx; epsilon-aminocaproic acid). The inhibition by Cl- does not occur in the presence of concentrations of epsilon Ahx that saturate the acid's weak binding sites on [Glu1]Pg, and the stimulation by epsilon Ahx is maximally exhibited in the presence of Cl-. We have used intrinsic fluorescence measurements with [Glu1]Pg to show that the conformational alteration and the concomitant increase in activation rate that accompanies epsilon Ahx-binding to [Glu1]Pg in the presence of Cl- does not occur in the same manner without Cl-. Further, the decrease in the intrinsic fluorescence that is attendant to Cl- binding to [Glu1]Pg in the absence of epsilon Ahx is not observed in the presence of this effector molecule. Analyses of the results of this manuscript strongly indicate that a conformation of [Glu1]Pg that is not optimal for its activation by urokinase is adopted in the presence of Cl-, and this is relieved by epsilon Ahx. This has important implications in the inhibition of [Glu1]Pg activation in the solution phase of blood plasma and in the large acceleration of this process when plasminogen is bound to physiological positive effectors via its epsilon Ahx-binding site(s).
Structural basis of human erythrocyte glucose transporter function in proteoliposome vesicles: circular dichroism measurements.
Authors: Chin J J , Jung E K , Chen V , Jung C Y
Published: May 2006

The secondary structural compositions of the human erythrocyte glucose transporter in proteoliposome vesicles were assessed on the basis of circular dichroism (CD) spectra measured in the absence and in the presence of D-glucose or an inhibitor, cytochalasin B. We designed and used a scattered-light-collecting device, which corrects CD spectra for optical artifacts originating from light scattering. Relative contents of eight types of secondary structure were estimated by using basis spectra generated by the eigenvector method based on CD spectra of 15 proteins of known structure. Results indicate that the glucose transporter is composed of approximately 82% alpha-helices, 10% beta-turns, and 8% other random structure, with no beta-strands. In the presence of an excess of D-glucose, the alpha-helical content is reduced by more than 10% and there is a significant increase in the random structure content. Cytochalasin B does not appear to affect the secondary structural composition of the transporter to any significant degree.
Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters.
Authors: Menzel R , Gellert M
Published: May 2006

Expression of the genes determining the subunits of Escherichia coli DNA gyrase (gyrA and gyrB) is known to be induced by relaxation of the template DNA. In this paper we report a deletion analysis of the gyrA and gyrB promoter regions. We find that a DNA sequence 20 base pairs long that includes the -10 consensus region, the transcription start point, and the first few transcribed bases is responsible for the property of induction by DNA relaxation. We propose a model for relaxation-stimulated transcription in which promoter clearance is the rate-limiting step.
DNA segment containing C beta 1, a gene for the constant region of the beta chain of the T-cell antigen receptor, was inserted into chromosome 6 in cells from one patient with human T-cell leukemia.
Authors: Ino T , Kurosawa Y , Yoshida M C , Hirano M
Published: May 2006

DNA rearrangements that occurred in the vicinity of T-cell antigen receptor beta-chain gene clusters residing on chromosome 7 were examined in human T-cell acute lymphoblastic leukemia cells. In one patient, it was observed that, for the T-cell receptor beta-chain genes, a D beta 1-J beta 2.3 (where D is diversity and J is joining) junction was found on one chromosome, while the other chromosome kept the germ-line configuration. If this D beta-J beta junction was formed by the customary deletion mechanism, the C beta 1 gene (where C is constant) located between the D beta 1 and J beta 2.3 loci should have disappeared from this chromosome. The C beta 1 gene indeed was absent from the rearranged chromosome 7, but it was found on chromosome 6 as an inserted segment. The implications of the observations are discussed.
T
-equivariant
K
-theory of generalized flag varieties
Authors: Kostant Bertram , Kumar Shrawan
Published: May 2006

Let
G
be a Kac—Moody group with Borel subgroup
B
and compact maximal torus
T
. Analogous to Kostant and Kumar [Kostant, B. & Kumar, S. (1986)
Proc. Natl. Acad. Sci. USA
83, 1543-1545], we define a certain ring
Y
, purely in terms of the Weyl group
W
(associated to
G
) and its action on
T
. By dualizing
Y
we get another ring Ψ, which, we prove, is “canonically” isomorphic with the
T
-equivariant
K
-theory

K
T

(
G
/
B
) of
G
/
B
. Now

K
T

(
G
/
B
), apart from being an algebra over

K
T

(pt.) ≈
A
(
T
), also has a Weyl group action and, moreover,

K
T

(
G
/
B
) admits certain operators {

D
w

}
w
[unk]
W
similar to the Demazure operators defined on
A
(
T
). We prove that these structures on

K
T

(
G
/
B
) come naturally from the ring
Y
. By “evaluating” the
A
(
T
)-module Ψ at 1, we recover
K
(
G
/
B
) together with the above-mentioned structures. We believe that many of the results of this paper are new in the finite case (i.e.,
G
is a finite-dimensional semisimple group over C) as well.
Amino acid substitutions in genetic variants of human serum albumin and in sequences inferred from molecular cloning.
Authors: Takahashi N , Takahashi Y , Blumberg B S , Putnam F W
Published: May 2006

The structural changes in four genetic variants of human serum albumin were analyzed by tandem high-pressure liquid chromatography (HPLC) of the tryptic peptides, HPLC mapping and isoelectric focusing of the CNBr fragments, and amino acid sequence analysis of the purified peptides. Lysine-372 of normal (common) albumin A was changed to glutamic acid both in albumin Naskapi, a widespread polymorphic variant of North American Indians, and in albumin Mersin found in Eti Turks. The two variants also exhibited anomalous migration in NaDodSO4/PAGE, which is attributed to a conformational change. The identity of albumins Naskapi and Mersin may have originated through descent from a common mid-Asiatic founder of the two migrating ethnic groups, or it may represent identical but independent mutations of the albumin gene. In albumin Adana, from Eti Turks, the substitution site was not identified but was localized to the region from positions 447 through 548. The substitution of aspartic acid-550 by glycine was found in albumin Mexico-2 from four individuals of the Pima tribe. Although only single-point substitutions have been found in these and in certain other genetic variants of human albumin, five differences exist in the amino acid sequences inferred from cDNA sequences by workers in three other laboratories. However, our results on albumin A and on 14 different genetic variants accord with the amino acid sequence of albumin deduced from the genomic sequence. The apparent amino acid substitutions inferred from comparison of individual cDNA sequences probably reflect artifacts in cloning or in cDNA sequence analysis rather than polymorphism of the coding sections of the albumin gene.
Increased biological activity of deglycosylated recombinant human granulocyte/macrophage colony-stimulating factor produced by yeast or animal cells.
Authors: Moonen P , Mermod J J , Ernst J F , Hirschi M , DeLamarter J F
Published: May 2006

Human granulocyte/macrophage colony-stimulating factor (hGM-CSF) produced by several recombinant sources including Escherichia coli, yeast, and animal cells was studied. Recombinant animal cells produced hGM-CSF in low quantities and in multiple forms of varying size. Mammalian hGM-CSF was purified 200,000-fold using immunoaffinity and lectin chromatography. Partially purified proteins produced in yeast and mammalian cells were assayed for the effects of deglycosylation. Following enzymatic deglycosylation, immunoreactivity was measured by radioimmunoassay and biological activity was measured in vitro on responsive human primary cells. Removal of N-linked oligosaccharides from both proteins increased their immunoreactivities by 4- to 8-fold. Removal of these oligosaccharides also increased their specific biological activities about 20-fold, to reach approximately the specific activity of recombinant hGM-CSF from E. coli. The E. coli produced-protein--lacking any carbohydrate--had by far the highest specific activity observed for the recombinant hGM-CSFs.
Inhibition of development in Myxococcus xanthus by monoclonal antibody 1604.
Authors: Gill J S , Jarvis B W , Dworkin M
Published: May 2006

Monoclonal antibody (mAb) 1604 is directed against a cell surface antigen of Myxococcus xanthus. Purified antibody 1604 inhibited development of M. xanthus under conditions of submerged culture procedure otherwise leading to fruiting body formation. Intact molecules of mAb 1604, as well as its Fab fragments, inhibited developmental aggregation, autolysis, fruiting body formation, and sporulation. The addition of relatively small amounts of antibody every 4 hr was much more effective than a single large dose given at the onset of development. The inhibitory action of mAb 1604 on development was reversible after prolonged incubation of the antibody with cells; this was probably due to proteolytic degradation of the antibody. The effect of mAb 1604 on submerged bacterial development was neutralized by affinity-purified 1604 cell surface antigen. Another antibody, mAb 2788, directed against an M. xanthus cell surface antigen, did not block development. These data suggest that 1604 cell surface antigens is involved in contact-mediated cell interactions in M. xanthus.
Cloning of a brain protein identified by autoantibodies from a patient with paraneoplastic cerebellar degeneration.
Authors: Dropcho E J , Chen Y T , Posner J B , Old L J
Published: May 2006

Autoantibodies directed against neuronal proteins have been identified in some patients with paraneoplastic cerebellar degeneration. To identify the molecular targets for these autoantibodies, we constructed a lambda gt11 cDNA expression library from human cerebellum and screened the library with IgG from a patient with paraneoplastic cerebellar degeneration. A single clone, pCDR2, produced a fusion protein that reacted strongly with the patient's IgG. The isolated pCDR2 clone was used to identify six overlapping cDNA clones. Sequencing of the pCDR clones revealed a distinctive pattern consisting of a unit of 18 nucleotides (6 amino acids) repeated in tandem along the entire cDNA sequence. This sequence is unlike any previously described eukaryotic gene. Southern blot analysis was consistent with single-copy representation of the CDR (cerebellar degeneration-related) gene in the human and mouse genome. RNA blotting studies with normal tissues showed expression of the CDR gene to be largely restricted to brain. Expression of the CDR message was also noted in cell lines derived from cancers of neuroectodermal, kidney, and lung origin.
Induction and regulation of mRNA encoding 26-kDa protein in human cell lines treated with recombinant human tumor necrosis factor.
Authors: Defilippi P , Poupart P , Tavernier J , Fiers W , Content J
Published: May 2006

A 26-kDa protein, originally described in human fibroblasts superinduced for interferon beta (IFN-beta) production, and termed IFN-beta 2 by other investigators, is induced by cycloheximide and by a 22-kDa, interleukin 1 (IL-1)-related factor. Although the structure and sequence of the corresponding gene show nonhomology with the IFN-beta gene, the gene is identical to that of B-cell stimulatory factor 2, a human interleukin, and displays a very potent growth and differentiation factor activity for B lymphocytes. In this work we show that IL-1 beta and tumor necrosis factor (TNF) strongly induce the 26-kDa protein in FS-4 fibroblasts and in some transformed cell lines. Addition of cycloheximide to recombinant (r)IL-1 beta and rTNF further enhances the level of 26-kDa-protein mRNA. We determined the kinetics of induction and the amounts of rTNF and rIL-1 beta required for optimal induction of this mRNA in FS-4 cells and in HeLa H21 cells and found that rIL-1 beta is a more efficient inducer of 26-kDa protein mRNA than is TNF. By analyzing the inducibility of the 26-kDa protein gene by rTNF and rIL-1 beta in a series of transformed cell lines that differ in their sensitivity to the cytotoxic action of TNF, we report a direct correlation between the 26-kDa protein mRNA expression and the resistance of these cells to the cytotoxic effect of TNF.
Secretion of follicle-stimulating hormone and production of inhibin are reciprocally related.
Authors: Ying S Y , Czvik J , Becker A , Ling N , Ueno N , Guillemin R
Published: May 2006

The production of inhibin in cultured granulosa cells from immature hypophysectomized, estrogen-treated rats and Sertoli cells from normal animals was determined by a specific radioimmunoassay using an antiserum against a synthetic replicate of [Tyr30]inhibin alpha-chain-(1-30). The amount of immunoreactive inhibin detected in the spent media of these cells is in proportion to the density of cells plated and the concentration of exogenously added follicle-stimulating hormone (FSH). In the presence of the estrogen precursor androstenedione (10(-7) M), FSH, but not luteinizing hormone, produced a dose-dependent increase in inhibin during 2-day culture of granulosa cells. In the absence of the estrogen precursor, similar but somewhat diminished inhibin production in responding to FSH was observed. Exogenously added estrogen potentiated the FSH-mediated release of inhibin in the absence of androstenedione. Neither androstenedione nor estradiol added to the cultured Sertoli cells had effect on inhibin production. A preparation of pure inhibin isolated on the basis of an in vitro bioassay and characterized chemically specifically suppressed serum FSH but not luteinizing hormone, when it was injected (24 micrograms per injection, two injections) into acutely ovariectomized rats. Thus, inhibin secreted by the granulosa and Sertoli cells specifically suppresses the secretion of pituitary FSH, and in turn FSH is primarily responsible for the inhibin production in these gonadal cells, as in a classical negative-feedback relationship.
Molecular structure of surfactant-coated surfaces
Authors: Garoff S.
Published: May 2006

The structure of surfactants on solid surfaces arises from the competition between the molecular forces that drive the formation of bulk phases of these molecules and the constraints of the solid interface. These monolayers exhibit bond-oriented ordering and undergo both reversible and irreversible phase transformations.
RepA and DnaA proteins are required for initiation of R1 plasmid replication in vitro and interact with the oriR sequence.
Authors: Masai H , Arai K
Published: May 2006

RepA, an initiation protein of R1 plasmid replication, was purified from an Escherichia coli strain overproducing the protein. The purified RepA protein specifically initiated replication in vitro of plasmid DNA bearing the replication origin of R1 plasmid (oriR). The replication, strictly dependent on added RepA protein, was independent of host RNA polymerase but required other host replication functions (DnaB and DnaC proteins, the single-stranded-DNA-binding protein SSB, and DNA gyrase). The replication was also completely dependent on the host DnaA function. In filter binding assays in high salt (0.5 M KCl) conditions, RepA specifically binds to both supercoiled and linear plasmid DNA containing the oriR sequence, whereas it binds to nonspecific DNA in low salt. DNase I-protection studies on a linearized DNA fragment revealed that DnaA protein specifically binds to a 9-base-pair DnaA-recognition sequence ("DnaA box") within oriR only when RepA is bound to the sequence immediately downstream of the DnaA box. These results indicate that initiation of R1 plasmid replication is triggered by interaction of RepA and DnaA proteins with the oriR sequence.
Human plasma apolipoprotein C-II: total solid-phase synthesis and chemical and biological characterization.
Authors: Fairwell T , Hospattankar A V , Brewer H B , Khan S A
Published: May 2006

The complete amino acid sequence of human plasma apolipoprotein C-II (apoC-II) has been synthesized chemically by the solid-phase method using phenylacetamidomethyl-resin. All amino acids were coupled to the peptide-resin in the presence of 1-hydroxybenzotriazole; tert-butyloxycarbonyl-protected amino acids with the appropriate side-chain-protecting groups that are stable to the reaction conditions used in the solid-phase methodology were used. After cleavage and deprotection, the crude apoC-II was purified by ion-exchange chromatography and then by reverse-phase high-performance liquid chromatography. The purified apolipoprotein was found to elute as a single peak under various chromatographic conditions, and the overall yield of the final purified protein was 20.7%. Synthetic apoC-II was characterized by several complementary analytical techniques including amino acid composition, Edman phenylisothiocyanate degradation, polyacrylamide gel electrophoresis, and high-performance liquid chromatography. The final product was found to be homogeneous and to activate normal human post-heparin lipase to the same extent as native apoC-II. The synthetic protein is also equally immunoreactive as native apoC-II.
Modification of DNA ends can decrease end joining relative to homologous recombination in mammalian cells.
Authors: Chang X B , Wilson J H
Published: May 2006

In animal cells, exogenous DNA recombines into random chromosomal sites much more frequently than it recombines into homologous sites. Free DNA ends are "recombinogenic" in both processes. To test the effects of specific ends on analogous extrachromosomal processes, we constructed a linear genome of simian virus 40 with terminal repeated sequences. After transfection into monkey cells, the model substrate can circularize by end joining (analogous to random integration) or by homologous recombination between its terminal repeats (analogous to targeted recombination). Since the two types of recombination are in competition with one another, the ratio of homologous-recombination to end-join products is a sensitive indicator of the differential effects of specific ends. Substrates with blunt ends, complementary sticky ends, or mismatched ends generated the same ratio of homologous-recombination to end-join products. However, addition of dideoxynucleotides to the 3' hydroxyls of the substrate decreased the frequency of end joining by a factor of 5-6 relative to homologous recombination. Thus, the frequency of end joining can be decreased relative to that of homologous recombination by modification of the ends of the input DNA. These results suggest an approach to altering the ratio of random to targeted integration in mammalian cells.
Active transport of messenger ribonucleoprotein particles in a reconstituted cell-free system.
Authors: French B T , Schumm D E , Webb T E
Published: May 2006

The ability of a reconstituted cell-free system to transport mRNA as a ribonucleoprotein particle has been examined. Poly(A) messenger ribonucleoproteins (mRNPs), UV cross-linked after release from isolated liver nuclei in a cell-free system, exhibited a buoyant density of 1.33 g/cm3 in cesium sulfate and 1.47 g/cm3 in cesium chloride, values identical to those of poly(A) mRNP isolated directly from liver polysomes. Furthermore, the in vivo and in vitro transported mRNP showed a similar degree of resistance to RNase digestion and had sedimentation coefficients approximately 2.5 times that of the isolated mRNA. Release of both total mRNA and alpha 2 mu-globulin mRNA was proportional to the concentration of a specific cytoplasmic protein. Removal of the transport proteins from the cytosol with streptomycin sulfate provided a basal system incapable of supporting the active transport of alpha 2 mu-globulin mRNA. Hybridization of released RNA with a recombinant probe specific for intron 6 of alpha 2 mu-globulin showed that intron sequences were retained within the nucleus under optimal alpha 2 mu-globulin mRNA transport conditions and that the transported alpha 2 mu-globulin mRNA was of mature size.
Trigger factor: a soluble protein that folds pro-OmpA into a membrane-assembly-competent form.
Authors: Crooke E , Wickner W
Published: May 2006

Pro-OmpA that is synthesized in vitro can assemble into bacterial inner membrane vesicles in the presence of ATP and NADH. We have purified pro-OmpA to determine which additional soluble proteins are necessary for its membrane assembly. [35S]Pro-OmpA was bound to Sepharose-linked antibody to OmpA, then eluted with 8 M urea and chromatographed on an anion-exchange resin in 8 M urea. This pro-OmpA is purified 2000-fold and is radiochemically pure. After dialysis, it is soluble but incompetent for membrane assembly. Addition of an Escherichia coli cytoplasmic fraction (S100) to the assembly reaction does not allow translocation. However, when S100 is added to pro-OmpA prior to dialysis, full assembly competence is restored, suggesting that a soluble factor, termed "trigger factor," triggers the folding of pro-OmpA into an assembly-competent form as the urea is removed. We noted that, prior to the last purification step, the immunoaffinity-purified pro-OmpA was partially competent for membrane assembly without addition of trigger factor. To test whether trigger factor had bound to the antibody column by means of its association with pro-OmpA, the crude pro-OmpA was acid-denatured prior to immunoadsorption. In this experiment, the trigger factor did not bind to the anti-OmpA column, and S100 was required for renaturation of this [35S]pro-OmpA. As suggested by this experiment, the crude [35S]pro-OmpA was in a complex with other proteins. Sedimentation velocity studies showed that the trigger factor has an apparent molecular weight of approximately 60,000. We propose that it is required for translocation-competent folding of pro-OmpA and other precursor proteins.
Spermatid-specific expression of protamine 1 in transgenic mice.
Authors: Peschon J J , Behringer R R , Brinster R L , Palmiter R D
Published: May 2006

Protamines are abundant basic proteins involved in the condensation of sperm chromatin. In the mouse, protamine genes are transcribed postmeiotically in round spermatids. We have cloned and sequenced the mouse protamine 1 gene. Ten lines of transgenic mice harboring marked protamine 1 sequences were generated by microinjection of fertilized eggs. Transcription of the transgene is restricted to round spermatids and in several cases exceeds that of the endogenous gene. The cis-acting sequences required for tissue-specific protamine expression reside on a 2.4-kilobase restriction fragment. Prospects for using transgenic mice to address fundamental questions of male germ-cell development are discussed.
The lens protein alpha A-crystallin of the blind mole rat, Spalax ehrenbergi: evolutionary change and functional constraints.
Authors: Hendriks W , Leunissen J , Nevo E , Bloemendal H , de Jong W W
Published: May 2006

The complete structure of the single-copy alpha A-crystallin gene of the blind mole rat (Spalax ehrenbergi) has been determined in order to elucidate the evolutionary effects of the loss of vision on a lens-specific protein and its gene. The alpha A-crystallin gene appears to have all the necessary transcriptional and translational signal sequences to be expressed in the rudimentary lens of the mole rat and gives rise to probably two protein products by means of alternative splicing, as in rodents with normal vision. Comparisons of the blind mole rat alpha A-crystallin sequence with alpha A sequences from other rodents reveal a considerable acceleration of the substitution rate at nonsynonymous positions in the mole rate lineage, which reflects a relaxation of selective constraints, but the acceleration is not to the extent that might be expected if the gene were now without any function. The remaining evolutionary constraints still imposed upon the mole rat alpha A-crystallin gene may possibly reflect the need for alpha-crystallin expression as an indispensable component in the developmental program of the atrophied eye.
Simulation of photochemical hole-burning experiments on photosynthetic reaction centers
Authors: Won Youngdo , Friesner Richard A.
Published: May 2006

An effective Hamiltonian formalism is used to calculate the homogeneous linewidth of long-wavelength absorption in the photosynthetic reaction center. Agreement with the experimental values of ≈400 cm
-1
for the hole width of the 990-nm band of
Rhodopseudomonas viridis
is obtained. The anomalously (two orders of magnitude) large width is explained in terms of resonant coupling to charge transfer states. These results support a dynamical model of primary charge separation [Friesner, R. & Wertheimer, R. (1982)
Proc. Natl. Acad. Sci USA
79, 2138-2142] in which such resonant coupling was also concluded to be important.
Purification and characterization of an activity from Saccharomyces cerevisiae that catalyzes homologous pairing and strand exchange.
Authors: Kolodner R , Evans D H , Morrison P T
Published: May 2006

An activity that catalyzes the formation of joint molecules from linear M13mp19 replicative form DNA and circular M13mp19 viral DNA was purified 1000- to 2000-fold from mitotic Saccharomyces cerevisiae cells. The activity appeared to reside in a Mr 132,000 polypeptide. The reaction required that the substrates be homologous and also required Mg2+. There was no requirement for ATP. The reaction required stoichiometric amounts of protein and showed a cooperative dependence on protein concentration. Electron microscopic analysis of the joint molecules indicated they were formed by displacement of one strand of the linear duplex by the single-stranded circular molecule. This analysis also showed that heteroduplex formation started at the 3'-homologous end of the linear duplex strand followed by extension of the hybrid region toward the 5'-homologous end of the linear duplex strand (3'-to-5' direction).
T-cell receptor genes in autoimmune mice: T-cell subsets have unexpected T-cell receptor gene programs.
Authors: Hashimoto Y , Yui K , Littman D , Greene M I
Published: May 2006

Two unique cell subsets have been identified in the autoimmune-prone MRL/MP lpr/lpr and C3H/HeJ gld/gld murine strains that have the Lyt-2-,L3T4-,Thy-1+, and Lyt-2-,L3T4-,Ia-,Thy-1- phenotypes, respectively. We have now found that these cells express T-cell receptor proteins on their surface. Our observations further indicate that the expression of the Thy-1 antigen does not correlate with the expression of alpha-chain and beta-chain T-cell receptor polypeptides. Interestingly, T-cell receptor gamma-chain RNA expression may be influenced or correlate with Thy-1 molecular expression. These studies indicate unusual relationships of different cell-surface structures that may reflect unexpected developmental programs.
Role of antibodies to murine leukemia virus p15E transmembrane protein in immunotherapy against AKR leukemia: a model for studies in human acquired immunodeficiency syndrome.
Authors: Thiel H J , Schwarz H , Fischinger P , Bolognesi D , Schäfer W
Published: May 2006

Previous studies have demonstrated that the onset of AKR leukemia could be dramatically delayed and the overall incidence significantly reduced following treatment with high-titered heterologous antibodies directed against the gp71 major glycoprotein of the virus. However, to be maximally successful, the treatment had to be initiated during the postnatal period of the AKR mouse, encompassing a narrow window representing approximately the first 3 days of life. In the present study we sought to extend this barrier by including antibodies directed against a second envelope component of the virion, the transmembrane protein, p15E. We demonstrate that although neither antibodies to gp71 nor antibodies to p15E could influence the course of leukemia development when applied individually later in life, a combination of the two antibodies was effective even if given as late as 5 months after birth. The significance of these studies is discussed in relation to human retrovirus-associated diseases.
Endogenous leukotriene D4 formation during anaphylactic shock in the guinea pig.
Authors: Keppler A , Orning L , Bernström K , Hammarström S
Published: May 2006

Experiments on the metabolism and excretion of i.v. administered selectively labeled [3H8]leukotriene C4 in bile duct-cannulated guinea pigs indicated predominantly biliary excretion of tritium. The major leukotriene metabolite in bile was identified as leukotriene D4. By monitoring leukotriene excretion radioimmunochromatographically, it was shown that guinea pigs suffering from anaphylactic shock produce leukotriene D4 endogenously. Immunological challenge of animals sensitized to ovalbumin was accompanied by an increase of biliary leukotriene D4 concentrations from 10 +/- 1 to 86 +/- 10 nM (mean +/- SEM, n = 5, P less than 0.001). When considering that bile flow was decreased to about half after challenge, the excretion rate of leukotriene D4 in bile increased from 0.88 +/- 0.16 before to 3.18 +/- 0.38 pmol X min-1 X kg-1 after challenge (mean +/- SEM, n = 5, P less than 0.002). It is concluded that systemic anaphylaxis in the guinea pig is associated with endogenous generation of leukotriene C4 (up to 1 nmol/kg during a 30-min period after the challenge.
Antithymocyte globulin stimulates human hematopoietic progenitor cells.
Authors: Huang A T , Mold N G , Zhang S F
Published: May 2006

Antithymocyte globulin (ATG), a horse antihuman thymus antiserum highly effective in the majority of patients with aplastic anemia, was studied for its in vitro effects on hematopoietic progenitor cells. Marrow cells isolated by an immunoadherence technique with the HPCA-1 (human progenitor cell antigen) monoclonal antibody after removal of contaminating T cells and macrophages formed erythroid colonies in methyl cellulose media in the presence of ATG at concentrations of 25-50 micrograms/ml. ATG also stimulated continuous production of hemoglobin-containing erythroid colonies beyond 35 days of culture when it was added to the culture weekly. ATG also had an indirect effect on myeloid (granulocytic and macrophagic) colony growth in vitro. At a concentration of 10 micrograms/ml, ATG stimulated late but not early myeloid progenitor cells to form mature colonies. This effect required the participation of lymphocytes containing the Leu-11 antigen and macrophages or supernatant fluids made from these two types of cells that had been preincubated with ATG for 3 hr and then cultured for 5 additional days. The supernatant fluids produced in such a manner showed characteristics similar to granulocyte colony-stimulating factor and had an activity peak that eluted at a volume corresponding to a 20,000 Da molecular mass protein by high-resolution liquid chromatography.
Intracellular free calcium concentration measured with 19F NMR spectroscopy in intact ferret hearts.
Authors: Marban E , Kitakaze M , Kusuoka H , Porterfield J K , Yue D T , Chacko V P
Published: May 2006

Changes in the intracellular free Ca2+ concentration, [Ca2+]i, mediate excitation-contraction coupling in the heart and contribute to cellular injury during ischemia and reperfusion. To study these processes directly, we measured [Ca2+]i in perfused ferret (Mustela putorius furo) hearts using 19F NMR spectroscopy to detect the 5,5'-difluoro derivative of the Ca2+ chelator 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA). To load cells, hearts were perfused with the acetoxymethyl ester derivative of 5,5'-F2-BAPTA. We measured 19F NMR spectra and left ventricular pressure simultaneously, at rest and during pacing at various external Ca concentrations [( Ca]o). Although contractile force was attenuated by the Ca2+ buffering properties of 5,5'-F2-BAPTA, the decrease in pressure could be overcome by raising [Ca]o. Our mean value of 104 nM for [Ca2+]i at rest in the perfused heart agrees well with previous measurements in isolated ventricular muscle. During pacing at 0.6-4 Hz, time-averaged [Ca2+]i increased; the effect of pacing was augmented by increasing [Ca]o. [Ca2+]i more than tripled during 10-20 min of global ischemia, and returned toward control levels upon reperfusion. This approach promises to be particularly useful in investigating the physiology of intact hearts and the pathophysiology of alterations in the coronary circulation.
Confidence interval for the number of selectively neutral amino acid polymorphisms.
Authors: Sawyer S A , Dykhuizen D E , Hartl D L
Published: May 2006

A statistical approach to the analysis of DNA sequences has been developed, which provides a confidence interval estimate for the proportion of naturally occurring amino acid polymorphisms that are selectively neutral. When applied to the gnd gene coding for 6-phosphogluconate dehydrogenase in a sample of seven natural isolates of Escherichia coli, the method indicates that the proportion of observed amino acid polymorphisms that are selectively neutral is unlikely to be greater than 49% (upper 95% confidence limit). On the other hand, the observations are also consistent with a model in which all of the observed amino acid substitutions are mildly deleterious with an average selection coefficient approximating 1.6 X 10(-7). Various models for the distribution of configurations at silent sites are also investigated.
Coordinated action of IgE and a B-cell-stimulatory factor on the CD23 receptor molecule up-regulates B-lymphocyte growth.
Authors: Guy G R , Gordon J
Published: May 2006

The CD23 (BLAST-2) antigen, recently identified as the low-affinity IgE receptor of B lymphocytes, has also been implicated as the focus for growth-promoting signals delivered to activated B cells by a low molecular weight B-cell growth factor (BCGF). Here we show that IgE and BCGF can coordinate B-lymphocyte growth through their opposing effects on the CD23 molecule. While the activation of purified quiescent B cells with phorbol 12-myristate 13-acetate led to the induction of 45-kDa CD23 at the surface membrane, the inclusion of IgE increased CD23 expression by a factor of approximately equal to 5. The addition of BCGF resulted in the rapid release of a 35-kDa form of CD23 from the cell surface. This shed molecule is associated with autocrine growth factor activity. Substantially more of this material was generated by BCGF acting on cells that had been stimulated in the presence of IgE. The combined effects of IgE and BCGF on DNA synthesis in activated B cells were more than additive. IgE similarly augmented the stimulatory capacity of a CD23 antibody that mimics the biological actions of BCGF. Binding of the anti-receptor antibody to its 45-kDa target at the B-cell surface also prompted the release of the 35-kDa soluble species. These results demonstrate a pleiotropy in the CD23 molecule with regard to both ligand binding and the subsequent behavior of the receptor. The ability of this single receptor to orchestrate a B-lymphocyte response through a variety of ligands and its role in normal and transformed autocrine growth are discussed.
A monoclonal antibody against a family of nuclear pore proteins (nucleoporins): O-linked N-acetylglucosamine is part of the immunodeterminant.
Authors: Park M K , D'Onofrio M , Willingham M C , Hanover J A
Published: May 2006

Using nuclear envelopes from Chinese hamster ovary (CHO) cells as an antigen, a mouse monoclonal antibody (IgM; designated mAb CHON211) that specifically binds to components of the nuclear pore complex (nucleoporins) was isolated. Immunofluorescence localization of the antigen recognized by mAb CHON211 revealed a punctate pattern restricted to the nuclear envelope; this pattern changed dramatically during the cell cycle. When examined by electron microscopy, the antigen was largely restricted to the nucleoplasmic and cytoplasmic faces of the nuclear pore complex. Immunoblots showed that mAb CHON211 bound to a series of polypeptides enriched in the nuclear envelope fraction with apparent molecular masses ranging from 110 to 35 kDa. Using galactosyltransferase and the lectin wheat germ agglutinin as probes, we have previously shown that proteins bearing O-linked N-acetylglucosamine (GlcNAc) are restricted to the cytoplasmic and nucleoplasmic faces of the nuclear pore complex. The nuclear membrane proteins recognized by mAb CHON211 had properties very similar to those identified by galactosyltransferase and wheat germ agglutinin labeling. Removal of O-linked GlcNAc residues with beta-hexosaminidase greatly reduced the binding of mAb CHON211, strongly suggesting that O-linked GlcNAc moieties are part of the immunodeterminant. This monoclonal antibody defines a new family of antigens that are restricted to the nuclear pore and bear a common modification: O-linked GlcNAc. mAb CHON211 will be useful for defining the role of the nucleoporins in nucleo-cytoplasmic exchange.
Biosynthesis of vitamin B12: concerning the origin of the methine protons of the corrin nucleus.
Authors: Scott A I , Kajiwara M , Santander P J
Published: May 2006

13C NMR spectroscopy has been used to locate six deuterium atoms incorporated biosynthetically on the periphery of the corrin nucleus of vitamin B12 (cyanocobalamin) derived from cells of Propionibacterium shermanii grown in a medium containing 50% 2H2O and 13C-enriched delta-aminolevulinic acid. The implications of these results for the mechanism of vitamin B12 biosynthesis are discussed, and it is concluded that the same oxidation level of the intermediates is maintained throughout the biosynthetic pathway, from delta-aminolevulinic acid to corrin.
Overproduction and purification of the
luxR
gene product: Transcriptional activator of the
Vibrio fischeri
luminescence system
Authors: Kaplan Heidi B. , Greenberg E. P.
Published: May 2006

Expression of
Vibrio fischeri
luminescence genes requires an inducer, termed autoinducer, and a positive regulatory element, the
luxR
gene product. A plasmid containing
luxR
under control of a
tac
promoter was engineered to overproduce this gene product. The overproduced
luxR
gene product was active
in vivo
, and its apparent monomeric molecular weight was indistinguishable from that of the protein encoded by
luxR
under control of its own promoter (
M
r
27,000). The new
tac-luxR
construct directed the synthesis of large quantities of the
luxR
gene product in induced
Escherichia coli
cells lacking other
lux
genes. In the presence of the other
lux
genes, overexpression of the
tac-luxR
construct was not detected. The overproduced
luxR
gene product, which formed cytoplasmic inclusion bodies, was purified and used in subsequent studies. Nonequilibrium pH gradient electrophoresis indicated that the protein was basic, and the amino-terminal 15 amino acids were sequenced. DNA-binding activity was detected by membrane filter binding assays; under the conditions used, the binding was not
lux
DNA-specific. Binding of tritium-labeled autoinducer to the
luxR
gene product was not detected, and autoinducer enhancement of the binding of the
luxR
gene product to DNA could not be detected reproducibly.