bluuebunny/crossref_metadata_2025 huggingface dataset:
Down-regulation of a member of the S100 gene family in mammary carcinoma cells and reexpression by azadeoxycytidine treatment.
Authors: Lee S W , Tomasetto C , Swisshelm K , Keyomarsi K , Sager R
Published: May 2006

A cDNA clone, designated CaN19 (originally called clone 19), isolated by subtractive hybridization, contains sequences that are preferentially expressed in normal mammary epithelial cells but not in breast tumor cells. Comparison of its deduced amino acid sequence with sequences in the GenBank data base revealed similarity with the S100 protein family, a group of small Ca(2+)-binding modulator proteins involved in cell cycle progression and cell differentiation. CaN19 expression is down-regulated in normal cells by A23187, a calcium ionophore, suggesting that its regulation is calcium-dependent. We have assigned CaN19 to human chromosome 1q21-q24, a region containing four other S100-related genes. In contrast to CaN19 mRNA expression, most members of the S100 protein family are activated or overexpressed in tumor cells. Synchronization experiments by growth-factor deprivation demonstrated a biphasic induction of CaN19 expression in normal cells, approximately 2-fold in early G1 phase and another 2- to 3-fold at the G1/S boundary. Exposure of mammary tumor cells to 5-aza-2'-deoxycytidine, an inhibitor of DNA methylation, reactivated the expression of CaN19 mRNA.
Tolerance induction by thymic medullary epithelium.
Authors: Hoffmann M W , Allison J , Miller J F
Published: May 2006

To study the role of thymic medullary epithelium in tolerance induction, the third and fourth branchial clefts of embryos from E mu-Kb transgenic mice, which express the major histocompatibility complex class I antigen H-2Kb exclusively on medullary thymic epithelium, were grafted to athymic nude mice. The grafts differentiated into tissue that morphologically resembled normal thymus. These grafts expressed the H-2Kb antigen appropriately and gave rise to a functional T cell repertoire. In vivo tolerance to H-2Kb disparate skin grafts was invariably found in mice expressing H-2Kb in the medulla or in both medulla and cortex of C57BL/6 branchial cleft-grafted controls. In marked contrast, in vitro cytotoxicity assays demonstrated reactivity toward H-2Kb in the presence of interleukin 2, and limiting-dilution analyses showed similar frequencies of cytolytic T cell precursors reactive to H-2Kb and to third-party stimulators. Medullary epithelium can, therefore, induce split tolerance, in which in vivo tolerance is accompanied by strong in vitro responses in the presence of interleukin 2.
Genetic structure of forensic populations.
Authors: Morton N E
Published: May 2006

DNA-based identification depends on the probability that two different individuals have the same phenotype, which is given by kinship theory. Together with the large and consistent body of evidence on human population structure, kinship theory provides a sound basis for forensic use of DNA markers.
What is the optimum size for the genetic alphabet?
Authors: Szathmáry E
Published: May 2006

An important question in biology is why the genetic alphabet is made of just two base pairs (G.C and A.T). This is particularly interesting because of the recent demonstration [Piccirilli, J. A., Krauch, T., Moroney, S. E. & Benner, S. A. (1990) Nature (London) 343, 33-37] that the alphabet can in principle be larger. It is possible to explain the size of the present genetic alphabet as a frozen character state that was an evolutionary optimum in an RNA world when nucleic acids functioned both for storing genetic information and for expressing information as enzymatically active RNA molecules--i.e., ribozymes. A previous model [Szathmáry, E. (1991) Proc. R. Soc. London Ser. B 245, 91-99] has described the principle of this approach. The present paper confirms and extends these results by showing explicitly the ways in which copying fidelity and metabolic efficiency change with the size of the genetic alphabet.
Nerve growth factor-induced synaptogenesis and hypertrophy of cortical cholinergic terminals.
Authors: Garofalo L , Ribeiro-da-Silva A , Cuello A C
Published: May 2006

In this study light and EM quantitative analysis were used to examine whether exogenous nerve growth factor (NGF) could affect terminal fields and synaptic connections in the adult rat brain in vivo. Adult rats received, immediately after unilateral decortication, 2.5S NGF (12 micrograms/day) or vehicle intracerebroventricularly for 7 days. Thirty days after the lesion cholinergic fiber length was quantified, using image analysis, in the remaining cortical area adjacent to the lesion site in each animal. Rats that had received vehicle showed a significantly reduced cortical choline acetyl-transferase-immunoreactive fiber network in the remaining cortex when compared with control animals. By contrast, the network in lesioned rats that had received 2.5S NGF was not different from control animals. Furthermore, the number of cortical choline acetyltransferase-immunoreactive varicosities, which decreased in vehicle-treated lesioned rats, significantly increased above control in lesioned rats that had received 2.5S NGF. At the ultrastructural level, 30 days after the lesion, animals that had received vehicle showed shrunken cholinergic boutons in cortical layer V and fewer synapses compared with control animals. Exogenous NGF, administered to lesioned rats, increased to supernormal levels both size of cholinergic boutons and number of synaptic contacts. These parameters were unaltered in unlesioned rats treated with NGF. This study demonstrates that exogenous NGF can cause significant compensatory changes in terminal fields and synaptic connections in the adult fully differentiated central nervous system.
Murine monoclonal anti-idiotope antibody breaks unresponsiveness and induces a specific antibody response to human melanoma-associated proteoglycan antigen in cynomolgus monkeys.
Authors: Chattopadhyay P , Starkey J , Morrow W J , Raychaudhuri S
Published: May 2006

The mouse monoclonal antibody MEM136 (mAb1) is directed against an epitope on human melanoma-associated proteoglycan antigen (MPG). This epitope is also present on various normal human and subhuman tissues. A monoclonal murine anti-idiotope (anti-Id) antibody (mAb2), designated I-Mel-2, was generated against MEM136 and used as a surrogate antigen for the MPG molecule. I-Mel-2 was tested in cynomolgus monkeys (Macaca fascicularis) for its ability to induce anti-MPG humoral responses. All monkeys immunized with Ab2 developed specific anti-anti-idiotype (Ab3) responses that were capable of inhibiting binding of Ab2 to Ab1. Furthermore, I-Mel-2 immune monkey serum contained anti-MPG antibodies (Ab1') that bound to MPG-positive but not to MPG-negative melanoma cell lines. Monkeys immunized with Colo38 melanoma cells (membrane-bound MPG antigen) did not contain anti-MPG antibodies that inhibited the binding of two distinct anti-MPG mAb 125I-labeled MEM136 or 125I-labeled 225.28 to Colo38 cells. The induction of anti-MPG responses in monkeys did not cause any apparent side effects in animals, despite the fact that the MPG antigen is expressed by many normal tissues. The affinity-purified, I-Mel-2 idiotype-specific, Ab3 immunoprecipitated MPG antigen from melanoma cells. Furthermore, the I-Mel-2-induced Ab3 inhibited melanoma cell invasion in an in vitro assay, implying that these antibodies have biological significance.
Retinoic acid mimics transforming growth factor beta in the regulation of human immunodeficiency virus expression in monocytic cells.
Authors: Poli G , Kinter A L , Justement J S , Bressler P , Kehrl J H , Fauci A S
Published: May 2006

Retinoic acid (RA) exerts potent suppressive and upregulatory effects on human immunodeficiency virus (HIV) expression in mononuclear phagocytes, strikingly similar to the effects of the cytokine transforming growth factor beta (TGF-beta). RA significantly inhibited phorbol ester-mediated, but not tumor necrosis factor alpha-mediated, induction of HIV transcription in the chronically infected promonocytic U1 cell line. RA and TGF-beta also completely suppressed the induction of virus production in U1 cells by interleukin 6 alone or in combination with glucocorticoids, which predominantly upregulate virus expression at the posttranscriptional level. Despite the close parallel to TGF-beta-induced effects, no evidence was obtained that RA mediated its effect by inducing secretion of active TGF-beta 1, -beta 2, or -beta 3. As with chronically infected U1 cells, similar inhibitory effects were also observed in primary monocyte-derived macrophages previously infected with HIV and then exposed to either RA or TGF-beta. In contrast, stimulation of monocyte-derived macrophages or U937 cells (the parental cell line of U1) with either RA or TGF-beta prior to in vitro infection resulted in the enhancement of virus production. Given the already successful use of retinoids in the treatment of several malignancies and the present demonstration of their capability of blocking the induction of HIV expression in infected mononuclear phagocytes, it would be of interest to pursue the potential role of this class of compounds in the development of strategies aimed at the pharmacologic regulation of HIV expression.
Regulation of hepatitis B virus gene expression by its two enhancers.
Authors: Su H , Yee J K
Published: May 2006

Hepatitis B virus (HBV) infection causes acute and chronic hepatitis and is closely associated with the development of hepatocellular carcinoma. The principal site of HBV infection is liver, and HBV actively replicates in hepatocytes. Two regions of the HBV genome have been shown previously to display properties of a transcriptional enhancer. In this study, we show that either of the two HBV enhancers can activate all three major HBV promoters in several human hepatoma lines, and the cooperative action of the two enhancers ultimately affects overall activity of the three promoters. In addition, our data suggest that HBV gene expression may be differentially regulated by its enhancers. HBV infection causes chronic liver inflammation and hepatocyte regeneration. It has been proposed that progressive accumulation of mutations during the regenerative hyperplasia may lead to alterations in the differentiation state of hepatocytes. Thus, the development of two differentially regulated enhancers may reflect a strategy of HBV to replicate efficiently in less differentiated hepatocytes during hepatocyte regeneration or hepatocarcinogenesis.
High-affinity ouabain binding by yeast cells expressing Na+, K(+)-ATPase alpha subunits and the gastric H+, K(+)-ATPase beta subunit.
Authors: Eakle K A , Kim K S , Kabalin M A , Farley R A
Published: May 2006

Recently, a beta subunit for the rat gastric H+,K(+)-ATPase (HK beta), which is structurally similar to the beta subunit of Na+, K(+)-ATPase, has been cloned and characterized. Using heterologous expression in yeast, we have tested the specificity of beta subunit assembly with different isoforms of the alpha subunit of Na+, K(+)-ATPase. Coexpression in yeast cells of the HK beta with both the sheep alpha 1 subunit and the rat alpha 3 subunit isoforms of Na+, K(+)-ATPase (alpha 1 and alpha 3, respectively) leads to the appearance of high-affinity ouabain-binding sites in yeast membranes. These ouabain-binding sites (alpha 1 plus HK beta, alpha 3 plus HK beta) have a high affinity for ouabain (Kd, 5-10 nM) and are expressed at levels similar to those formed with the rat beta 1 subunit of Na+, K(+)-ATPase (beta 1) (alpha 1 plus beta 1 or alpha 3 plus beta 1). Potassium acts as a specific antagonist of ouabain binding by alpha 1 plus HK beta and alpha 3 plus HK beta just like sodium pumps formed with beta 1. Sodium pumps formed with the HK beta, however, show quantitative differences in their affinity for ouabain and in the antagonism of K+ for ouabain binding. These data suggest that the structure of the beta subunit may play a role in sodium pump function.
Plasma membrane inositol 1,4,5-trisphosphate receptor of lymphocytes: selective enrichment in sialic acid and unique binding specificity.
Authors: Khan A A , Steiner J P , Snyder S H
Published: May 2006

The inositol 1,4,5-trisphosphate receptor (IP3R) associated with plasma membranes of lymphocytes differs in terminal sugar content and binding specificity from the cerebellar receptor, which is localized to endoplasmic reticulum. Lectin column chromatography reveals that 30% of IP3R in the thymus contains sialic acid, reflecting a plasma membrane association, in contrast to 5% of cerebellar IP3R. IP3R in thymus and plasma membrane fractions of Jurkat lymphocytes differs from IP3R of Jurkat microsomes and cerebellum in inositol phosphate specificity. The plasma membrane IP3R has lower affinity for IP3 but higher affinity for inositol 1,3,4,5-tetrakisphosphate, which may reflect a unique regulation of calcium at the plasma membrane by inositol phosphates.
An 11-base-pair DNA sequence motif apparently unique to the human interleukin 4 gene confers responsiveness to T-cell activation signals.
Authors: Abe E , De Waal Malefyt R , Matsuda I , Arai K , Arai N
Published: May 2006

We have identified a DNA segment that confers responsiveness to antigen stimulation signals on the human interleukin (IL) 4 gene in Jurkat cells. The human IL-4 gene, of 10 kilobases, is composed of four exons and three introns. A cis-acting element (P sequence) resides in the 5' upstream region; no additional DNA segments with enhancer activity were identified in the human IL-4 gene. For further mapping purposes, a fusion promoter was constructed with the granulocyte/macrophage colony-stimulating factor basic promoter containing 60 base pairs of sequence upstream from the cap site of the mouse granulocyte/macrophage colony-stimulating factor gene and various lengths of the 5' upstream sequence of the IL-4 gene. The P sequence was located between positions -79 and -69 relative to the transcription start site of the human IL-4 gene, and this location was confirmed by base-substitution mutations. The plasmids carrying multiple copies of the P sequence showed higher responsiveness to the stimulation. The binding protein(s) that recognize the P sequence of the IL-4 gene were identified by DNA-mobility-shift assays. The binding of NF(P) (a DNA binding protein that specifically recognizes the P sequence) to the P sequence was abolished when oligonucleotides carrying base substitutions were used, indicating that the NF(P) interaction is sequence-specific and that binding specificity of the protein paralleled the sequence requirements for IL-4 expression in vivo. The P sequence does not share homology with the 5' upstream sequence of the IL-2 gene, even though surrounding sequences of the IL-4 gene share high homology with the IL-2 gene. We conclude that a different set of proteins recognize IL-2 and IL-4 genes.
On the nature of global classification
Authors: Wheelis Mark L. , Kandler Otto , Woese Carl R.
Published: May 2006

Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classificagtion. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimentions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted.
Theory of hydrophobicity: Transient cavities in molecular liquids
Authors: Pratt Lawrence R. , Pohorille Andrew
Published: May 2006

Observation of the size distribution of transient cavities in computer simulations of water,
n
-hexane, and
n
-dodecane under benchtop conditions shows that the sizes of cavities are more sharply defined in liquid water but the most-probable-size cavities are about the same size in each of these liquids. The calculated solvent atomic density in contact with these cavities shows that water applies more force per unit area of cavity surface than do the hydrocarbon liquids. This contact density, or “squeezing” force, reaches a maximum near cavity diameters of 2.4 Å. The results for liquid water are compared to the predictions of simple theories and, in addition, to results for a reference simple liquid. The numerical data for water at a range of temperatures are analyzed to extract a surface free energy contribution to the work of formation of atomic-size cavities. Comparison with the liquid-vapor interfacial tensions of the model liquids studies here indicates that the surface free energies extracted for atomic-size cavities cannot be accurately identified with the macroscopic surface tensions of the systems.
On the identity of the major postsynaptic density protein.
Authors: Wu K , Huang Y , Adler J , Black I B
Published: May 2006

Increasing evidence suggests that the postsynaptic density (PSD) plays a critical role in synaptic communication and plasticity. The major PSD protein (mPSDp), a calcium/calmodulin-dependent protein kinase, appears to be central to PSD function. The mPSDp has long been considered identical to the alpha subunit of the soluble calmodulin kinase II (alpha-CKII). However, mPSDp and alpha-CKII do differ in solubility and antigenicity, raising the possibility that the two proteins are distinct. To further define the relationship between the two proteins, we purified the mPSDp to homogeneity from adult rat cerebral cortex and compared the proteins. In contrast to alpha-CKII, the purified mPSDp was insoluble in high concentrations of salt, various detergents, chelators of divalent cations, and the strong denaturant guanidine hydrochloride. The pI value of the mPSDp was 6.2, whereas that of alpha-CKII was 6.7-7.2. The purified mPSDp bound calmodulin in the presence of Ca2+ and was autophosphorylated in a Ca2+/calmodulin-dependent manner. Polyclonal antiserum raised against mPSDp (anti-mPSDp) recognized purified mPSDp or mPSDp in synaptic membrane, indicating immunologic specificity among the synaptic proteins. Anti-mPSDp did not recognize alpha-CKII, whereas anti-alpha-CKII antibodies reacted only weakly with mPSDp, suggesting that the proteins are distinct but structurally similar. Moreover, sequence analysis of protease V8-digested polypeptides revealed that there was at least an 8-amino acid sequence, MLKVPNIS, that is not present in alpha-CKII. Finally, HPLC analysis of V8-digested fragments of mPSDp and alpha-CKII in parallel revealed dissimilar peptide patterns. Thus our observations suggest that mPSDp and alpha-CKII are similar but not identical. The unique physicochemical and structural properties of the mPSDp may provide insights into molecular mechanisms mediating synaptic plasticity.
Mammalian neurotrophin-4: structure, chromosomal localization, tissue distribution, and receptor specificity.
Authors: Ip N Y , Ibáñez C F , Nye S H , McClain J , Jones P F , Gies D R , Belluscio L , Le Beau M M , Espinosa R , Squinto S P
Published: May 2006

Nerve growth factor, brain-derived neurotrophic factor, and neurotrophin-3 (NT-3) are the three members of the neurotrophin family known to exist in mammals. Recently, a fourth neurotrophin (designated neurotrophin-4 or NT-4), which shares all of the features found in the mammalian neurotrophins, has been identified in Xenopus and viper. We used sequences specific to the Xenopus/viper NT-4 to isolate a neurotrophin from both human and rat genomic DNA that appears to represent the mammalian counterpart of Xenopus/viper NT-4. Human NT-4 as well as a human NT-4 pseudogene colocalize to chromosome 19 band q13.3. Mammalian NT-4 has many unusual features compared to the previously identified neurotrophins and is less conserved evolutionarily than the other neurotrophins. However, mammalian NT-4 displays bioactivity and trk receptor specificity similar to that of Xenopus NT-4.
Independent domain folding of Pseudomonas exotoxin and single-chain immunotoxins: influence of interdomain connections.
Authors: Brinkmann U , Buchner J , Pastan I
Published: May 2006

We have studied the refolding of completely unfolded and reduced Pseudomonas exotoxin (PE) and of recombinant single-chain immunotoxins made with monoclonal antibody B3 that are composed of a heavy-chain variable region connected by a flexible linker to the corresponding light-chain variable region (Fv), which is in turn fused to a truncated form of PE. We have found by direct activity assays that different functional domains of these multifunctional proteins fold independently with different kinetics. The ADP-ribosylation domain of PE and of the recombinant immunotoxin fold rapidly, whereas the assembly of the binding and/or translocation domains is regained more slowly. The complete refolding of native PE occurs more rapidly than the refolding of the recombinant immunotoxins. To determine the influence of the connector region between the B3(Fv) moiety and the toxin on the folding process of the recombinant immunotoxin B3(Fv)-PE38KDEL, we have made two different mutations in the peptide that connects the single-chain Fv domain to domain II of PE. These molecules show different folding kinetics, differences in their propensity to aggregate, and different yields of correctly folded molecules. A mutation that decreases aggregation increases the rate of formation and the yield of active immunotoxin molecules.
Interaction of immune sera with synthetic peptides corresponding to the structural protein region of hepatitis C virus.
Authors: Ching W M , Wychowski C , Beach M J , Wang H , Davies C L , Carl M , Bradley D W , Alter H J , Feinstone S M , Shih J W
Published: May 2006

Comparison of the deduced amino acid sequence from the structural region of the Hutchinson strain of hepatitis C virus (HCV-H) with four other HCV isolates clearly divides the five isolates into two groups based on sequence homology. The first group includes HCV-H, HCV-1, and HC-J1, while the second includes HCV-J1 and HC-J4. Among the five isolates the first 190 residues (putative nucleocapsid) are highly conserved whereas residues 196-513 exhibit significant diversity and include a hypervariable region encompassing residues 386-404. A series of overlapping decapeptides were synthesized by solid-phase pin technology according to sequence from HCV-H (amino acids 1-513), HC-J4 (amino acids 181-513), and regions from the three other isolates which exhibited sequence variation. A modified ELISA was used to measure immunoreactivity of sera from clinical posttransfusion cases and experimentally infected chimpanzees. Comparison of pre- and postinfection samples revealed 16 clusters of immunoreactive peptides within the structural region, none of which was found in the hypervariable region. Only one cluster (amino acids 73-89) was recognized by all human and chimpanzee sera. Clear variation in the immune response was observed between individuals, although no obvious difference in reactivity between acute and chronic cases was observed. Within individual profiles, the reactivity to each peptide cluster and the total number of reactive clusters increased over time.
Susceptibility testing by polymerase chain reaction DNA quantitation: a method to measure drug resistance of human immunodeficiency virus type 1 isolates.
Authors: Eron J J , Gorczyca P , Kaplan J C , D'Aquila R T
Published: May 2006

Polymerase chain reaction (PCR) DNA quantitation (PDQ) susceptibility testing rapidly and directly measures nucleoside sensitivity of human immunodeficiency virus type 1 (HIV-1) isolates. PCR is used to quantitate the amount of HIV-1 DNA synthesized after in vitro infection of peripheral blood mononuclear cells. The relative amounts of HIV-1 DNA in cell lysates from cultures maintained at different drug concentrations reflect drug inhibition of virus replication. The results of PDQ susceptibility testing of 2- or 3-day cultures are supported by assays measuring HIV-1 p24 antigen production in supernatants of 7- or 10-day cultures. DNA sequence analyses to identify mutations in the reverse transcriptase gene that cause resistance to 3'-azido-3'-deoxythymidine also support the PDQ results. With the PDQ method, both infectivity titration and susceptibility testing can be performed on supernatants from primary cultures of peripheral blood mononuclear cells. PDQ susceptibility testing should facilitate epidemiologic studies of the clinical significance of drug-resistant HIV-1 isolates.
Expression of human factor IX in mice after injection of genetically modified myoblasts.
Authors: Yao S N , Kurachi K
Published: May 2006

Hemophilia B is an X chromosome-linked recessive bleeding disorder. To develop a somatic gene therapy for this disease, we have examined whether mouse skeletal myoblasts can serve as efficient vehicles for systemic delivery of recombinant factor IX. When mouse myoblasts (C2C12) transduced with a Moloney murine leukemia virus-based vector containing the bacterial beta-galactosidase gene were injected into mouse skeletal muscles, they fused with the existing and regenerating myofibers and continued to express beta-galactosidase. C2C12 myoblasts that were infected with recombinant retroviruses containing a human factor IX cDNA secreted biologically active human factor IX cDNA secreted biologically active human factor IX into the culture medium at a rate of 2.6 micrograms per 10(6) cells per day. Myotubes derived from these cells in culture continued to express human factor IX (0.68 micrograms/day from myotubes derived from 10(6) C2C12 cells). After injection of the transduced C2C12 myoblasts into skeletal muscles of mice, the systemic level of recombinant human factor IX was found to be as high as approximately 1 microgram/ml of serum. These results provide the rationale for using skeletal myoblasts as an efficient gene delivery vehicle in the somatic gene therapy for hemophilia B.
The threshold induction temperature of the 90-kDa heat shock protein is subject to acclimatization in eurythermal goby fishes (genus Gillichthys).
Authors: Dietz T J , Somero G N
Published: May 2006

Two extremely eurythermal goby fishes, Gillichthys mirabilis and Gillichthys seta, which encounter habitat temperature variations of approximately 30 degrees C, showed seasonal acclimatization of endogenous levels and of onset temperatures for enhanced synthesis of a 90-kDa-class heat shock protein (HSP90). Summer-acclimatized fishes had higher levels of HSP90 in brain tissue than winter-acclimatized specimens, as shown by Western blot analysis. For winter-acclimatized fishes, increased synthesis of HSP90 was observed when the temperature was raised from a control temperature (18 degrees C) to 28 degrees C. For summer-acclimatized fish, no significantly increased synthesis of HSP90 occurred until the experimental temperature was raised to 32 degrees C. These data suggest that the threshold temperature at which enhanced expression of HSP-encoding genes occurs is not hard-wired genetically but may be subject to acclimatization. A causal relationship between seasonal changes in steady-state levels of HSP90 and the threshold temperature for enhanced HSP90 synthesis is discussed in terms of existing models for the regulation of HSP gene expression.
A viral protease-mediated cleavage of the transmembrane glycoprotein of Mason-Pfizer monkey virus can be suppressed by mutations within the matrix protein.
Authors: Brody B A , Rhee S S , Sommerfelt M A , Hunter E
Published: May 2006

The envelope glycoprotein precursor of retroviruses undergoes proteolytic cleavage in the Golgi complex to yield the mature surface and transmembrane (TM) glycoproteins of the virus. We report here that the TM glycoprotein of Mason-Pfizer monkey virus undergoes a second proteolytic processing event during a late maturation step that can follow virus release and Gag polyprotein cleavage. Cleavage results in the conversion of the cell-associated TM glycoprotein (gp22) to a virus-associated gp20. Processing continues after virus release and yields virions that contain predominantly gp20. A mutation within the active site of the Mason-Pfizer monkey virus aspartyl protease was shown to block both TM glycoprotein cleavage and the processing of the Gag polyprotein precursor. The role of the viral protease in cleavage of the TM glycoprotein localizes the cleavage site to the cytoplasmic domain of this protein. Surprisingly, point mutations within the matrix (MA) coding region of the gag gene can affect the extent to which gp22 is processed to gp20 and in one case [p10(MA)-A79V] results in greater than 90% inhibition of gp22 cleavage. The data provide genetic evidence of a specific interaction between the capsid proteins and the cytoplasmic domain of the TM glycoprotein of a retrovirus. This interaction is required for cytoplasmic domain cleavage to occur and may play a critical role in virus assembly and viral infectivity.
The DnaK chaperone modulates the heat shock response of Escherichia coli by binding to the sigma 32 transcription factor.
Authors: Liberek K , Galitski T P , Zylicz M , Georgopoulos C
Published: May 2006

The heat shock response and the heat shock proteins have been conserved across evolution. In Escherichia coli, the heat shock response is positively regulated by the sigma 32 transcriptional factor and negatively regulated by a subset of the heat shock proteins themselves. In an effort to understand the regulation of the heat shock response, we have purified the sigma 32 polypeptide to homogeneity. During the purification procedure, we found that a large fraction of the overexpressed sigma 32 polypeptide copurified with the universally conserved DnaK heat shock protein (the prokaryotic equivalent of the 70-kDa heat shock protein, HSP70). Further experiments established that purified sigma 32 bound to DnaK and that this complex was disrupted in the presence of ATP. Consistent with the fact that dnaK756 mutant bacteria overexpress heat shock proteins at all temperatures, purified DnaK756 mutant protein did not appreciably bind to sigma 32.
RNA polymerase-associated transcription specificity factor encoded by vaccinia virus.
Authors: Ahn B Y , Moss B
Published: May 2006

Vaccinia virus encodes a multisubunit DNA-dependent RNA polymerase (EC 2.7.7.6) that is packaged in the infectious virus particle. This polymerase was found to contain a submolar polypeptide of approximately 85 kDa in addition to the core subunits, which consist of two larger and several smaller polypeptides. The polymerase containing the 85-kDa polypeptide was separated from the core polymerase by column chromatography. Although the core polymerase actively transcribed heterologous single-stranded DNA, only the form with the associated 85-kDa polypeptide could act in conjunction with an early stage-specific factor to transcribe double-stranded DNA containing a vaccinia virus early promoter. Peptide sequencing established that the RNA polymerase-associated 85-kDa protein was derived from the vaccinia virus H4L open reading frame, which encodes a 94-kDa polypeptide that we named RAP94. RAP94 is not closely related to prokaryotic sigma 70 or eukaryotic RAP30 RNA polymerase-binding proteins, although there are short regions of sequence similarity. The specific association of RAP94 with viral RNA polymerase was corroborated with antibody raised to a recombinant fusion protein. Unlike the previously defined subunits of vaccinia virus RNA polymerase, RAP94 is synthesized exclusively late in infection, and synthesis could be prevented by a DNA replication inhibitor. The role of RAP94 in mediating specific transcription was demonstrated by using an extract from cells in which the H4L open reading frame had been transiently expressed.
Reversible steps in the bacteriorhodopsin photocycle.
Authors: Lozier R H , Xie A , Hofrichter J , Clore G M
Published: May 2006

The absorbance changes that accompany the light-driven proton-pumping cycle of bacteriorhodopsin measured over a broad range of times, wavelengths, temperatures, and pH values have been globally fitted to the kinetic model K in equilibrium with L in equilibrium with X in equilibrium with M in equilibrium with N in equilibrium with O----bR. A remarkably good fit to the data was obtained by optimizing the rate constants at 20 degrees C and the corresponding activation energies at each pH value, together with the extinction coefficients for each intermediate, which were assumed to be independent of both pH and temperature. Back-reactions are included for all but the last step of the cycle and are found to be essential for fitting the data. The rates of these reactions are large, and the analogous irreversible model produced significantly worse fits to the data. Small systematic differences between the fit and the experimental data associated with the X, M, and O intermediates, together with the inability of the model to produce spectra for the X and M intermediates consistent with their assignment as molecular species, indicate that this model must be an incomplete description of the photocycle. We suggest that these problems arise from the presence of additional occupied states that are difficult to distinguish on the basis of their visible absorption spectra alone.
Human linear B-cell epitopes encoded by the hepatitis E virus include determinants in the RNA-dependent RNA polymerase.
Authors: Kaur M , Hyams K C , Purdy M A , Krawczynski K , Ching W M , Fry K E , Reyes G R , Bradley D W , Carl M
Published: May 2006

Hepatitis E virus is responsible for both sporadic and epidemic hepatitis in developing countries. The nonenveloped virus is 27-34 nm in diameter and has been shown to contain a single-strand, positive-sense, polyadenylylated RNA genome of approximately 7.5 kilobases. The nucleotide sequence of the Burma strain of hepatitis E virus has been reported and three open reading frames (ORFs) have been identified. The deduced amino acid sequence from each of these ORFs was used to synthesize overlapping peptides (decamers overlapping at every fourth amino acid) on a solid phase. These peptides were then tested in an ELISA with pooled acute-phase sera from known cases of enterically transmitted non-A, non-B hepatitis collected in the Sudan. Linear B-cell epitopes were identified in all three ORFs. Epitopes were identified throughout the polyprotein encoded by ORF1, but they appeared to be particularly concentrated in the region of the RNA-dependent RNA polymerase. Distinct epitopes were identified in the presumed structural protein encoded by ORF2, and one epitope was identified close to the carboxyl terminus of the protein encoded by ORF3. These data precisely pinpoint linear B-cell epitopes recognized by antibodies from patients with acute hepatitis E and identify an antibody response directed against the RNA-dependent RNA polymerase.
Does nitric oxide mediate the increases in cerebral blood flow elicited by hypercapnia?
Authors: Iadecola C
Published: May 2006

The endothelium-derived relaxing factor (EDRF), probably nitric oxide (NO) or a closely related compound (EDRF/NO), is a potent vasodilator that appears to regulate vascular tone in several vascular beds. I have investigated whether EDRF/NO is also involved in the regulation of the cerebral circulation--in particular, whether EDRF/NO participates in the increases in cerebral blood flow elicited by hypercapnia. Rats were anesthetized with halothane, 1-2% (vol/vol), paralyzed, and artificially ventilated. Arterial pressure was monitored and blood gases were controlled. Cerebral blood flow was continuously monitored through a cranial window over the sensory cortex by a laser-Doppler probe. The window was superfused with Ringer's solution (pH 7.3-7.4 at 37 degrees C). During superfusion with Ringer's solution, hypercapnia (PCO2 = 55.8 +/- 0.8 mmHg) increased cerebral blood flow by 121 +/- 6% (n = 27; P less than 0.001; analysis of variance). Topical superfusion with the NO synthase inhibitors N omega-nitro-L-arginine (1 mM) attenuated the cerebrovasodilation by 93 +/- 6% (n = 8). In contrast, the vasodilation elicited by topical papaverine (1 mM) was not affected by N omega-nitro-L-arginine (n = 10). Application of N omega-nitro-D-arginine (1 mM) did not affect the cerebrovasodilation elicited by hypercapnia (P greater than 0.05; n = 8). N omega-Methyl-L-arginine (1 mM) attenuated the cerebrovasodilation elicited by hypercapnia by 44 +/- 4% (n = 8; P less than 0.001), an effect completely reversed by coapplication of L-arginine (10 mM; P greater than 0.05; n = 13). These findings indicate that the powerful effects of CO2 on the cerebral circulation are mediated by arginine-derived EDRF/NO. EDRF/NO is an important molecular signal whose actions may also include the regulation cerebral circulation.
Mutations in the bovine leukemia virus Tax protein can abrogate the long terminal repeat-directed transactivating activity without concomitant loss of transforming potential.
Authors: Willems L , Grimonpont C , Heremans H , Rebeyrotte N , Chen G , Portetelle D , Burny A , Kettmann R
Published: May 2006

The bovine leukemia virus Tax protein transactivates gene expression directed by the viral long terminal repeat (LTR) and contributes to immortalization of primary cells. Theoretical analysis of the protein sequence revealed the presence of a putative zinc finger structure at its amino end. Selected mutations in that region completely abolished transactivation, demonstrating its importance for LTR-directed gene regulation. However, these mutations did not interfere with the ability of tax to bind zinc or to contribute to immortalization of primary cells. Thus, transactivation of bovine leukemia virus LTR and target cell transformation are independent functions of Tax and involve different functional domains of the protein.
RAG-2 expression is not essential for chicken immunoglobulin gene conversion.
Authors: Takeda S , Masteller E L , Thompson C B , Buerstedde J M
Published: May 2006

Chicken B cells diversify their immunoglobulin genes by gene conversion in the bursa of Fabricius. The avian leukosis virus-induced B-cell line DT40 continues to diversify its immunoglobulin light chain locus by gene conversion during in vitro passage. Since a variable(diversity)joining recombination-activating gene, RAG-2, is specifically expressed in chicken B cells undergoing immunoglobulin gene conversion, it has been suggested that RAG-2 may be involved in the immunoglobulin gene conversion process. We previously reported high ratios of targeted to random integration after transfection of genomic DNA constructs into DT40. This allows us to easily investigate the function of a gene product by gene disruption. We show here that subclones of DT40 maintain the ability to diversify their immunoglobulin light chain locus by gene conversion even after both copies of the RAG-2 coding regions are deleted. These results demonstrate that the RAG-2 product is not required for gene conversion activity in the immunoglobulin light chain locus.
Casimir energy for dielectrics.
Authors: Schwinger J
Published: May 2006

A treatment in terms of two scalar fields supplies the electromagnetic energy of attraction between two similar dielectric slabs with parallel plane interfaces.
Intrinsic pulsatile secretory activity of immortalized luteinizing hormone-releasing hormone-secreting neurons.
Authors: Wetsel W C , Valença M M , Merchenthaler I , Liposits Z , López F J , Weiner R I , Mellon P L , Negro-Vilar A
Published: May 2006

Mammalian reproduction is dependent upon intermittent delivery of luteinizing hormone-releasing hormone (LHRH) to the anterior pituitary. This mode of secretion is required to sensitize maximally the gonadotrophs to LHRH stimulation and to regulate gonadotropin gene expression. While LHRH secretion is pulsatile in nature, the origin of the pulse generator is unknown. In this report, we show that this oscillator could be located within the LHRH neuronal network. When immortalized LHRH neurons are placed into a perifusion system, LHRH is secreted into the medium in a pulsatile fashion under basal conditions. LHRH secretion and the number of LHRH pulses are reduced when calcium is removed from the medium. Perifusion also influences pro-LHRH processing, since the molar ratio of its processed products varies dramatically when the cells are transferred from a static system. Several different cellular mechanisms may underlie these changes in secretion and processing. Lucifer yellow experiments reveal that some cells are dye-coupled. Hence, these cells could be electrically coupled through gap junctions such that secretion from individual cells could be coordinated. Secretion could also be synchronized through the observed synapse-like contacts. These contacts could perform a negative-feedback role to regulate not only the amount of LHRH released but also the molecular forms secreted. The organization of LHRH neurons into interconnected clusters could serve to coordinate LHRH secretion from individual cells and, thereby, orchestrate functions in vivo as diverse as the onset of puberty, the timing of ovulation, and the duration of lactational infertility.
The type 1 human immunodeficiency virus Tat binding protein is a transcriptional activator belonging to an additional family of evolutionarily conserved genes.
Authors: Ohana B , Moore P A , Ruben S M , Southgate C D , Green M R , Rosen C A
Published: May 2006

The type 1 human immunodeficiency virus Tat protein is a powerful transcriptional activator when bound to an RNA structure (TAR) present at the extreme 5' terminus of viral mRNA. Since transcriptional activation requires binding of Tat to RNA, it has been suggested that Tat enhances initiation or elongation through a direct interaction with cellular transcription factors. Here we show through protein fusion experiments that the previously identified cellular Tat binding protein, TBP-1, although unable to bind DNA, is a strong transcriptional activator when brought into proximity of several promoter elements. Transcriptional activity depends upon the integrity of at least two highly conserved domains: one resembling a nucleotide-binding motif and the other motif common to proteins with helicase activity. Our studies further reveal that TBP-1 represents one member of a large, highly conserved gene family that encodes proteins demonstrating strong amino acid conservation across species. Finally, we identified a second family member that, although 77% similar to TBP-1, does not activate transcription from the promoters examined. This finding, together with the observation that TBP-1 does not activate each promoter examined, suggests that this gene family may encode promoter-specific transcriptional activators.
Selection of T lymphocytes bearing limited T-cell receptor beta chains in the response to a human pathogen.
Authors: Wang X H , Ohmen J D , Uyemura K , Rea T H , Kronenberg M , Modlin R L
Published: May 2006

Delayed-type hypersensitivity (DTH) is a classic measure of T-cell responsiveness to foreign antigen. To estimate the extent of the T-cell repertoire in the DTH response to a human pathogen, we measured T-cell receptor (TCR) beta-chain variable-region (V beta) gene usage in reversal reactions in leprosy. Reversal reactions represent naturally occurring DTH responses in leprosy, in which augmentation of T-cell responses to Mycobacterium leprae is concomitant with clearance of bacilli from lesions. T cells using the V beta 6-, V beta 12-, V beta 14-, and V beta 19-encoded TCRs were strikingly overrepresented in the lesions of patients as compared to blood and pre-DTH lesions from the same individuals. Furthermore, these data indicate a possible association between the predominant expression of a V beta gene segment in lesions and the major histocompatibility complex class II haplotype of the individual. V beta 6 was prominent in the lesions of four patients who were DR15, a marker of resistance in leprosy infection. Sequence analysis of V beta 6 TCRs showed frequent use of V beta 6.1 and J beta 2.7 gene segments and a conserved amino acid motif in the V-J junction in a reversal-reaction lesion, but not in blood from the same patient. The limited TCR repertoire expressed by the infiltrating T cells suggests that a limited set of antigens is recognized in the DTH response to a human pathogen. We suggest that the mechanism by which major histocompatibility complex haplotype influences DTH in this disease involves the presentation of specific peptides, with subsequent selection of specific TCRs followed by local oligoclonal expansion.
Functional interaction of heat shock protein GroEL with an RNase E-like activity in Escherichia coli.
Authors: Sohlberg B , Lundberg U , Hartl F U , von Gabain A
Published: May 2006

The highly specific endoribonuclease activities of RNase E (which processes ribosomal 9S RNA into p5S RNA) and RNase K (which initiates decay of the ompA mRNA) are inferred to play a central role in RNA processing and mRNA decay in Escherichia coli. In vivo both activities are affected by a conditional mutation of the ams/rne gene that seems to be complemented at nonpermissive temperatures by a fragment of the groEL gene. Analysis of the relationship between the two nucleases and the heat shock protein revealed that GroEL interacts functionally with an RNase E-like activity but not with an RNase K activity, a groEL mutation affected 9S RNA processing but not ompA mRNA cleavage, RNase E activity could be precipitated with an antibody against GroEL, and a highly purified GroEL preparation contained RNase E activity but not RNase K activity. When purifying RNase E activity, we obtained a preparation containing two major proteins of 60 and 17 kDa. The size and the N-terminal sequence identified the 60-kDa protein as GroEL.
High-frequency genetic reversion mediated by a DNA duplication: the mouse pink-eyed unstable mutation.
Authors: Gondo Y , Gardner J M , Nakatsu Y , Durham-Pierre D , Deveau S A , Kuper C , Brilliant M H
Published: May 2006

The mouse pink-eyed unstable (p(un)) mutation, affecting coat color, exhibits one of the highest reported reversion frequencies of any mammalian mutation and is associated with a duplication of genomic DNA at the p locus. In this study, genomic clones containing the boundaries of the p(un) duplication were isolated and characterized. The structure of these sequences and their wild-type and revertant counterparts were analyzed by restriction mapping, PCR product analysis, DNA sequence analysis, and pulsed-field gel electrophoresis. DNA from p(un) was distinguished from wild-type and revertant DNA by a head-to-tail tandem duplication of approximately 70 kilobases. No differences were detected between revertant and wild-type DNAs. Thus, the reversion in phenotype of p(un) mice is coupled with the loss of one copy of an approximately 70-kilobase duplicated segment. Testable models are presented to account for p(un) reversion.