bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoaffinity labeling of ATP and NAD+ binding sites on recombinant human interleukin 2.
Authors: Campbell S , Kim H , Doukas M , Haley B
Published: May 2006

Interleukin 2 (IL-2) is a T-cell-derived lymphokine critical in the activation and proliferation of T cells, B cells, and lymphokine-activated killer cells. It is a glycoprotein of approximately 15,500 daltons that is synthesized and secreted after activation by antigen or mitogen. By using the analogs 8-azidoadenosine 5'-[gamma-32P]triphosphate [( gamma-32P]8N3ATP) and nicotinamide 2-azidoadenine [adenylate-32P]dinucleotide [( alpha-32P]2N3NAD+) as photoaffinity probes, we have detected specific, metal ion-requiring nucleotide binding sites on recombinant human IL-2 (rhIL-2). The specificity of these nucleotide interactions with rhIL-2 was demonstrated by saturation effects and by competition by the parent nucleotides at physiologically relevant concentrations. Saturation of photoinsertion into rhIL-2 occurred at 50 microM [gamma-32P]8N3ATP; a half-maximal decrease of its photoinsertion at 10 microM was obtained with 22 microM ATP. Saturation of photoinsertion with [alpha-32P]2N3NAD+ was observed at 180 microM; a half-maximal decrease of its photoinsertion at 10 microM was effected by 10 microM NAD+ and by 5 microM 3-aminobenzamide. The extent of photoinsertion of both photoprobes into rhIL-2 varied with the presence of different divalent metal ions. rhIL-2 photolabeling with [gamma-32P]8N3ATP appeared to be dependent on the presence of metal ion. It was effectively labeled in the presence of Mg2+ and photoinsertion was increased with the addition of Zn2+ at micromolar concentrations. Also, rhIL-2 underwent slow autophosphorylation by an intramolecular mechanism using [gamma-32P]8N3ATP as well as nonphotoactive nuceotide. The biological significance of these interactions is unknown, but their specificity suggests that nucleotide binding may be involved in the bioactivity of IL-2.
Pseudomonas chromosomal replication origins: a bacterial class distinct from Escherichia coli-type origins.
Authors: Yee T W , Smith D W
Published: May 2006

The bacterial origins of DNA replication have been isolated from Pseudomonas aeruginosa and Pseudomonas putida. These origins comprise a second class of bacterial origins distinct from enteric-type origins: both origins function in both Pseudomonas species, and neither functions in Escherichia coli; enteric origins do not function in either pseudomonad. Both cloned sequences hybridize to chromosomal fragments that show properties expected of replication origins. These origin plasmids are highly unstable, are present at low copy number, and show mutual incompatibility properties. DNA sequence analysis shows that both origins contain several 9-base-pair (bp) E. coli DnaA protein binding sites; four of these are conserved in position and orientation, two of which resemble the R1 and R4 sites of the E. coli origin. Conserved 13-bp direct repeats adjacent to the analogous R1 site are also found. No GATC sites are in the P. aeruginosa origin and only four are in the P. putida origin; no other 4-bp sequence is present in high abundance. Both origins are found between sequences similar to the E. coli and Bacillus subtilis dnaA, dnaN, rpmH, and rnpA genes, a gene organization identical to that for B. subtilis and unlike that of E. coli. A second autonomously replicating sequence was obtained from P. aeruginosa that has some properties of bacterial origins.
Are many Z-DNA binding proteins actually phospholipid-binding proteins?
Authors: Krishna P , Kennedy B P , Waisman D M , van de Sande J H , McGhee J D
Published: May 2006

We used a Z-DNA affinity column to isolate a collection of Z-DNA binding proteins from a high salt extract of Escherichia coli. We identified one of the major Z-DNA binding proteins of this fraction, not as a protein involved in gene regulation or genetic recombination, but rather as an outer membrane porin protein. We then showed that several other known phospholipid-binding proteins (bovine lung annexins and human serum lipoproteins) also bind much more tightly to Z-DNA than to B-DNA. In all cases, this Z-DNA binding was strongly blocked by competition with acidic phospholipids, such as cardiolipin. Our results raise the question whether many of the Z-DNA binding proteins previously isolated are actually phospholipid-binding proteins.
Silencing of human immunodeficiency virus long terminal repeat expression by an adenovirus E1a mutant.
Authors: Ventura A M , Arens M Q , Srinivasan A , Chinnadurai G
Published: May 2006

Gene expression from the human immunodeficiency virus (HIV) long terminal repeat (LTR) is strongly stimulated by the viral tat gene. The HIV LTR is also activated by several physical and chemical agents and heterologous viral genes, including adenovirus E1a. As E1a has separable transcriptional activation and repression functions, we examined the negative regulatory effects of E1a on the expression of the HIV LTR by using a trans-dominant E1a mutant. Mutant hr5 strongly suppressed the basal activity of the LTR as well as trans-activation of the LTR by heterologous agents such as the cytomegalovirus immediate early gene or DNA-damaging agents such as mitomycin C and UV irradiation. In addition, hr5 also caused significant suppression of tat gene-mediated trans-activation. The suppression of HIV LTR expression by hr5 appears to be mediated, at least in part, by the repression of the HIV enhancer, as the activity of an enhancer test system composed of the human T-cell leukemia virus I LTR containing an HIV-1 enhancer substitution was severely repressed by hr5. Cotransfection of HIV-1 proviral DNA with hr5 DNA resulted in a significant reduction of HIV production.
Identification and mapping of a common proviral integration site Fli-1 in erythroleukemia cells induced by Friend murine leukemia virus.
Authors: Ben-David Y , Giddens E B , Bernstein A
Published: May 2006

Friend murine leukemia virus (F-MuLV) induces erythroleukemia when inoculated into newborn BALB/c or NIH/Swiss mice. We have molecularly cloned F-MuLV host cell DNA junction fragments from an erythroleukemia cell line induced by F-MuLV to identify cellular genes involved in the leukemogenic process. One particular proviral integration site, Fli-1, is rearranged in 75% (9/12) of independently isolated erythroleukemia cell lines derived from either BALB/c or NIH/Swiss mice inoculated at birth with F-MuLV. Other hematopoietic neoplasms induced by F-MuLV, including myeloid (granulocytic) and lymphoid tumors, did not show rearrangements of the Fli-1 locus. Similarly, none of 35 erythroleukemia cell lines induced by the Friend virus complexes (FV-A and FV-P) was rearranged at the Fli-1 locus. In contrast, no rearrangements were detected at the Sfpi-1 locus, a preferred site of integration in either FV-P- or FV-A-induced leukemias. Using recombinant inbred mice, the Fli-1 locus was situated on mouse chromosome 9 close to the cellular protooncogene c-ets-1. DNA and RNA analysis suggests, however, that Fli-1 is different from ets-1. Thus, Fli-1 appears to define a distinct locus specifically involved in the induction of erythroid leukemias by F-MuLV.
Potential for two isoforms of the A1 ribonucleoprotein in Xenopus laevis.
Authors: Kay B K , Sawhney R K , Wilson S H
Published: May 2006

We have identified the Xenopus cognates for the RNA-binding protein A1. This protein has previously been shown to be one of the components of the heterogeneous nuclear ribonucleoprotein (hnRNP) complex in rat and human cells. We have isolated several Xenopus clones from oocyte, tailbud embryo, and leg muscle cDNA libraries and determined their nucleotide sequences. Potentially, two different A1 isoforms are expressed in Xenopus; they have been termed XA1a and XA1b. Besides insertions and deletions, the XA1a protein sequence is 92% identical to the rat protein and suggests very similar secondary structures. There are two segments in the COOH-terminal domain where deletions or insertions are apparent: the rat protein does not have a 48-residue sequence that is present in the frog protein, and the frog protein does not have a 12-residue sequence that is present in the rat protein. We have confirmed that the XA1a protein is larger than rat A1 by in vitro transcription, translation, and gel electrophoresis. The second isoform, XA1b, is very similar to the XA1a isoform, except it has a different COOH terminus due to the absence of a 73-nucleotide region from its cDNA clones. Transcripts representing both isoforms have been detected in various Xenopus RNA preparations by polymerase chain reaction experiments with A1-specific oligonucleotides. Our findings suggest that the isoforms are encoded by one or two genes and are the result of alternative splicing. We discuss the biological implications of having two forms of the A1 component of hnRNP particles.
Callosal projections in rat somatosensory cortex are altered by early removal of afferent input.
Authors: Koralek K A , Killackey H P
Published: May 2006

During the first postnatal week, the distribution of callosal projection neurons in the rat somatosensory cortex changes from a uniform to a discontinuous pattern. To determine if this change is influenced by afferent inputs to the somatosensory cortex, the effect of both early unilateral infraorbital nerve section and unilateral removal of the dorsal thalamus on the distribution of callosal projections in rat somatosensory cortex was examined. One month after either of the above manipulations at birth, the tangential distribution of callosal projections in the somatosensory cortex was examined using the combined retrograde and anterograde transport of horseradish peroxidase. Both manipulations alter the distribution of callosal projection neurons and terminations in the somatosensory cortex. After infraorbital nerve section, the distribution of callosal projections is altered in the contralateral primary somatosensory cortex. The abnormalities observed are consistent with the altered distribution of thalamocortical projections. In addition, consistent abnormalities were observed in the pattern of callosal projections of the second somatosensory area of both hemispheres. Most notably, they are absent in a portion of the region that contains the representation of the mystacial vibrissae and sinus hairs in this area. Thalamic ablation resulted in highly aberrant patterns of callosal projections in the somatosensory cortex on the operated side, where abnormal bands and clusters of callosal projections were observed in apparently random locations. These results are interpreted as evidence that both peripheral and central inputs influence the maturational changes in the distribution of callosal projection neurons.
Cross-linking Fc receptors stimulate splenic non-B, non-T cells to secrete interleukin 4 and other lymphokines.
Authors: Ben-Sasson S Z , Le Gros G , Conrad D H , Finkelman F D , Paul W E
Published: May 2006

Spleen cell populations depleted of both B and T lymphocytes produce interleukin 4 (IL-4) in response to stimulation with immunoglobulins bound to the surface of culture dishes. In the presence of interleukin 3 (IL-3), plate-bound (PB) IgE and PB-IgG1, IgG2a, and IgG2b are excellent stimulants, whereas PB-IgA and PB-IgM fail to stimulate IL-4 production. In the absence of IL-3, PB-IgE stimulates relatively modest production of IL-4, whereas PB-IgG2a generally does not. The response to PB-IgE is inhibited by soluble IgE; antibody to Fc gamma receptor II inhibits the response to PB-IgG2a. Thus, separate receptors mediate these stimulations, and Fc receptor cross-linkage is required for IL-4 production. Depletion of cells expressing asialo-GM1 does not diminish IL-4 production in response to PB immunoglobulins, indicating that natural killer cells are not essential for non-B, non-T cell production of IL-4. In addition to IL-4, non-B, non-T cells produce IL-3, but no detectable interleukin 2 or interferon gamma. Non-B, non-T cells may be an important source of lymphokines in a variety of immune responses and may serve to amplify the effects of T cells of the TH2 type.
Transforming growth factor beta 1 regulates production of acute-phase proteins.
Authors: Mackiewicz A , Ganapathi M K , Schultz D , Brabenec A , Weinstein J , Kelley M F , Kushner I
Published: May 2006

We explored the possible role of transforming growth factor beta 1 (TGF-beta), a cytokine that appears to be an important modulator of inflammation and tissue repair, in regulation of human plasma protein synthesis during the acute-phase response. In Hep 3B cells, TGF-beta led to increased secretion of the positive acute-phase proteins alpha 1-protease inhibitor and alpha 1-antichymotrypsin and decreased secretion of the negative acute-phase protein albumin. In Hep G2 cells, after incubation with TGF-beta, the same changes in secretion of alpha 1-protease inhibitor, alpha 1-antichymotrypsin, and albumin were observed, as well as decreased secretion of both the negative acute-phase protein alpha-fetoprotein and the positive acute-phase protein fibrinogen. In addition, TGF-beta modulated the effects of interleukin 6; these cytokines, in combination, were additive in inducing synthesis and secretion of alpha 1-protease inhibitor and alpha 1-antichymotrypsin and in decreasing secretion of albumin and alpha-fetoprotein. TGF-beta inhibited the induction of fibrinogen caused by interleukin 6. The effects on alpha 1-protease inhibitor were confirmed by metabolic labeling in Hep 3B cells and by demonstrating increased accumulation of specific mRNA in Hep G2 cells, and the effects on fibrinogen were confirmed in Hep 3B cells by studies of mRNA for the alpha chain of fibrinogen. TGF-beta had no effect on haptoglobin or alpha 1-acid glycoprotein secretion, either directly or in the presence of interleukin 6, which is capable of inducing these proteins. These studies demonstrate that TGF-beta can affect hepatic synthesis and secretion of a subset of acute-phase proteins, both directly and by modulating the effect of interleukin 6. The affected group of plasma proteins is distinct from those affected by other recognized acute-phase protein-inducing cytokines. These findings support the view that combinations of cytokines mediate the response of the hepatocyte to inflammatory stimuli.
Protein N-myristoylation in Escherichia coli: reconstitution of a eukaryotic protein modification in bacteria.
Authors: Duronio R J , Jackson-Machelski E , Heuckeroth R O , Olins P O , Devine C S , Yonemoto W , Slice L W , Taylor S S , Gordon J I
Published: May 2006

Protein N-myristoylation refers to the covalent attachment of a myristoyl group (C14:0), via amide linkage, to the NH2-terminal glycine residue of certain cellular and viral proteins. Myristoyl-CoA:protein N-myristoyltransferase (NMT) catalyzes this cotranslational modification. We have developed a system for studying the substrate requirements and biological effects of protein N-myristoylation as well as NMT structure-activity relationships. Expression of the yeast NMT1 gene in Escherichia coli, a bacterium that has no endogenous NMT activity, results in production of the intact 53-kDa NMT polypeptide as well as a truncated polypeptide derived from proteolytic removal of its NH2-terminal 39 amino acids. Each E. coli-synthesized NMT species has fatty acid and peptide substrate specificities that are indistinguishable from those of NMT recovered from Saccharomyces cerevisiae, suggesting that the NH2-terminal domain of this enzyme is not required for its catalytic activity. By using a dual plasmid system, N-myristoylation of a mammalian protein was reconstituted in E. coli by simultaneous expression of the yeast NMT1 gene and a murine cDNA encoding the catalytic (C) subunit of cAMP-dependent protein kinase (PK-A). The fatty acid specificity of N-myristoylation was preserved in this system: [9,10(n)-3H]myristate but not [9,10(n)3H]palmitate was efficiently linked to Gly-1 of the C subunit. [13,14(n)-3H]10-Propoxydecanoic acid, a heteroatom-containing analog of myristic acid with reduced hydrophobicity but similar chain length, was an effective alternative substrate for NMT that also could be incorporated into the C subunit of PK-A. Such analogs have recently been shown to inhibit replication of certain retroviruses that depend upon linkage of a myristoyl group to their gag polyprotein precursors (e.g., the Pr55gag of human immunodeficiency virus type 1). A major advantage of the bacterial system over eukaryotic systems is the absence of endogenous NMT and substrates, providing a more straightforward way of preparing myristoylated, analog-substituted, and nonmyristoylated forms of a given protein for comparison of their structural and functional properties. The system should facilitate screening of enzyme inhibitors as well as alternative NMT fatty acid substrates for their ability to be incorporated into a specific target protein. Our experimental system may prove useful for recapitulating other eukaryotic protein modifications in E. coli so that structure-activity relationships of modifying enzymes and their substrates can be more readily assessed.
Chromosomal organization of adrenergic receptor genes.
Authors: Yang-Feng T L , Xue F Y , Zhong W W , Cotecchia S , Frielle T , Caron M G , Lefkowitz R J , Francke U
Published: May 2006

The adrenergic receptors (ARs) (subtypes alpha 1, alpha 2, beta 1, and beta 2) are a prototypic family of guanine nucleotide binding regulatory protein-coupled receptors that mediate the physiological effects of the hormone epinephrine and the neurotransmitter norepinephrine. We have previously assigned the genes for beta 2- and alpha 2-AR to human chromosomes 5 and 10, respectively. By Southern analysis of somatic cell hybrids and in situ chromosomal hybridization, we have now mapped the alpha 1-AR gene to chromosome 5q32----q34, the same position as beta 2-AR, and the beta 1-AR gene to chromosome 10q24----q26, the region where alpha 2-AR is located. In mouse, both alpha 2- and beta 1-AR genes were assigned to chromosome 19, and the alpha 1-AR locus was localized to chromosome 11. Pulsed field gel electrophoresis has shown that the alpha 1- and beta 2-AR genes in humans are within 300 kilobases (kb) and the distance between the alpha 2- and beta 1-AR genes is less than 225 kb. The proximity of these two pairs of AR genes and the sequence similarity that exists among all the ARs strongly suggest that they are evolutionarily related. Moreover, they likely arose from a common ancestral receptor gene and subsequently diverged through gene duplication and chromosomal duplication to perform their distinctive roles in mediating the physiological effects of catecholamines. The AR genes thus provide a paradigm for understanding the evolution of such structurally conserved yet functionally divergent families of receptor molecules.
Functional dissection of a mouse ribosomal protein promoter: significance of the polypyrimidine initiator and an element in the TATA-box region.
Authors: Hariharan N , Perry R P
Published: May 2006

All of the mammalian ribosomal protein (rp) genes examined to date initiate transcription with high precision despite the fact that they do not contain a well-defined TATA box. The initiation sites are situated within polypyrimidine tracts that are flanked by both upstream and intragenic promoter elements. In the TATA-box region of each rp promoter, there is a functionally critical element with nuclear factor binding specificity that is distinct from that of a conventional TATA box. To understand how the various elements contribute to rp promoter function, we have used site-specific mutagenesis-transfection protocols and factor binding analyses to evaluate the significance of the polypyrimidine initiator and the TATA-box counterpart for efficient and accurate transcription of the rpS16 gene. Our results indicate (i) that the polypyrimidine initiator sequence critically defines the position of the transcriptional start site, whereas a much less specific sequence is sufficient to satisfy the efficiency requirement; (ii) that an uninterrupted stretch of pyrimidines in the initiator region is not necessary for efficient transcription of rpS16 gene; and (iii) that the TATA-box counterpart or even a substituted conventional TATA box primarily influences promoter efficiency. The great diversity of promoter design, which is becoming evident as more RNA polymerase II promoters are being carefully dissected, suggests that the requirements for building a functional initiation complex may be much more flexible than was previously appreciated.
Initiation of protein synthesis from a termination codon.
Authors: Varshney U , RajBhandary U L
Published: May 2006

We show that the amber termination codon UAG can initiate protein synthesis in Escherichia coli. We mutated the initiation codon AUG of the chloramphenicol acetyltransferase (CAT) gene to UAG (CATam1) and translated mRNA derived from the mutant CAT gene in E. coli S-30 extracts. A full-length CAT polypeptide was synthesized in the presence of tRNA(fMetCUA), a mutant E. coli initiator tRNA which has a change in the anticodon sequence from CAU to CUA. Addition of purified E. coli glutaminyl-tRNA synthetase substantially stimulated synthesis of the CAT polypeptide. Thus, initiation of protein synthesis with UAG and tRNA(fMetCUA) most likely occurs with glutamine and not methionine. The UAG codon also initiates protein synthesis in vivo. To eliminate a weak secondary site of initiation from AUC, the fifth codon, we further mutagenized the CATam1 gene at codons 2 (GAG----GAC) and 5 (AUC----ACC). Transformation of E. coli with the resultant CATam1.2.5 gene yielded transformants that synthesized CAT polypeptide and were resistant to chloramphenicol only when they were also transformed with the mutant tRNA(fMetCUA) gene. Immunoblot analyses and assays for CAT enzyme activity in extracts from transformed cells indicate that initiation from UAG is efficient, 60-70% of that obtained from AUG. Initiation of protein synthesis from UAG using a mutant initiator tRNA allows tightly regulated expression of specific genes. This may be generally useful for overproduction in E. coli and other eubacteria of proteins which are toxic to these cells.
Transforming growth factor beta decreases the immunogenicity of rat islet xenografts (rat to mouse) and prevents rejection in association with treatment of the recipient with a monoclonal antibody to interferon gamma.
Authors: Carel J C , Schreiber R D , Falqui L , Lacy P E
Published: May 2006

Culture of rat islets of Langerhans for 1 week at 37 degrees C with recombinant transforming growth factor beta prolonged the survival of islet xenografts transplanted into diabetic mouse recipients. Treatment of diabetic recipients with a neutralizing monoclonal antibody to murine interferon gamma did not affect the survival of islet xenografts cultured 7 days in control medium. However, treatment of donor islets with transforming growth factor beta in combination with treatment of diabetic recipients with interferon gamma antibody produced a 75% survival of the islet xenografts at 100 days. Fifty percent of the recipients who had accepted their graft for more than 100 days were immune unresponsive to a transplant of freshly isolated islets from the same donor strain.
Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra.
Authors: Smith J , Kuczera K , Karplus M
Published: May 2006

Molecular dynamics simulations are used to calculate the incoherent neutron scattering spectra of myoglobin between 80 K and 325 K and compared with experimental data. There is good agreement over the entire temperature range for the elastic, quasi-elastic, and inelastic components of the scattering. This provides support for the accuracy of the simulations of the internal motions that make the dominant contributions to the atomic displacements on a time scale of 0.3-100 ps (100-0.3 cm-1). Analysis of the simulations shows that at low temperatures a harmonic description of the molecule is appropriate and that the molecule is trapped in localized regions of conformational space. At higher temperatures the scattering arises from a combination of vibrations within wells (substates) and transitions between them; the latter contribute to the quasi-elastic scattering.
Electron microscopy of small nuclear ribonucleoprotein (snRNP) particles U2 and U5: evidence for a common structure-determining principle in the major U snRNP family.
Authors: Kastner B , Bach M , Lührmann R
Published: May 2006

We have studied by electron microscopy the structures of native small nuclear ribonucleoprotein (snRNP) particles U2 and U5 from HeLa cells. The structure of native U2 snRNP is characterized by a main body 8 nm in diameter with one additional domain about 4 nm long and 6 nm wide. Electron micrographs show that the 20S U5 snRNP, which contains at least seven U5-specific proteins in addition to the common proteins, has an elongated structure measuring 20-23 nm in length and 11-14 nm in width. Two main structural domains can be distinguished: a small head and a large elongated body about twice the size of the head. In addition to the head, the body of the 20S U5 snRNP possesses three short protuberances. The U2 and U5 core RNP particles--that is, of the snRNPs U2 and U5 without the snRNP-specific proteins, look much simpler and smaller under the electron microscope. They both are round in shape with a diameter of approximately 8 nm. With respect to their size, appearance, and fine structure, the U2 and U5 snRNP cores not only closely resemble each other but also share these properties with the core domain of U1 snRNP. We propose that the characteristic shape of each of the major snRNP species U1, U2, U4/U6, and U5 is determined by (i) a core domain containing the proteins that are common to all members of this family, which has the same shape for each member, and (ii) peripheral structures, which for snRNPs U1, U2, and U5 arise from the specific proteins, that give each of these snRNP species its characteristic shape.
Reversible ADP-ribosylation is demonstrated to be a regulatory mechanism in prokaryotes by heterologous expression.
Authors: Fu H , Burris R H , Roberts G P
Published: May 2006

The primary product of biological nitrogen fixation, ammonia, reversibly regulates nitrogenase activity in a variety of diazotrophs by a process called "NH4(+)-switch-off/on." Strong correlative evidence from work in Azospirillum lipoferum and Rhodospirillum rubrum indicates that this regulation involves both the inactivation of dinitrogenase reductase by dinitrogenase reductase ADP-ribosyltransferase and the reactivation by dinitrogenase reductase activating glycohydrolase. The genes encoding these two enzymes, draT and draG, have been cloned from these two organisms, so that direct genetic evidence can be marshaled to test this model in vivo. The draT/G system has been transferred to and monitored in the enteric nitrogen-fixing bacterium Klebsiella pneumoniae, an organism normally devoid of such a regulatory mechanism. The expressed draT and draG genes allowed K. pneumoniae to respond to NH4Cl with a reversible regulation of nitrogenase activity that was correlated with the reversible ADP-ribosylation of dinitrogenase reductase in vivo. Thus, the expression of draT and draG genes in K. pneumoniae is necessary and sufficient to support NH4(+)-switch-off/on, and ADP-ribosylation serves as a reversible regulatory mechanism for controlling nitrogenase activity in prokaryotes.
Application of scanning electrochemical microscopy to biological samples.
Authors: Lee C , Kwak J , Bard A J
Published: May 2006

The scanning electrochemical microscope can be used in the feedback mode in two-dimensional scans over biological substrates to obtain topographic information at the micrometer level. In this mode, the effect of distance between a substrate (either conductive or insulating) and a scanning ultramicroelectrode tip on the electrolytic current flowing at the tip is recorded as a function of the tip x-y position. Scans of the upper surface of a grass leaf and the lower surface of a Ligustrum sinensis leaf (which show open stomata structures) immersed in aqueous solution are shown. Scans of the upper surface of an elodea leaf in the dark and under irradiation, where the tip reaction is the reduction of oxygen produced by photosynthesis, demonstrate the possibility of obtaining information about the distribution of reaction sites on the substrate surface.
Zones of sharp genetic change in Europe are also linguistic boundaries.
Authors: Barbujani G , Sokal R R
Published: May 2006

A newly elaborated method, "Wombling," for detecting regions of abrupt change in biological variables was applied to 63 human allele frequencies in Europe. Of the 33 gene-frequency boundaries discovered in this way, 31 are coincident with linguistic boundaries marking contiguous regions of different language families, languages, or dialects. The remaining two boundaries (through Iceland and Greece) separate descendants of different ethnic or geographical provenance but lack modern linguistic correlates. These findings support a model of genetic differentiation in Europe in which the genetic structure of the population is determined mainly by gene flow and admixture, rather than by adaptation to varying environmental conditions. Of the 33 boundaries, 27 reflect diverse population origins at often distant locations. Language affiliation of European populations plays a major role in maintaining and probably causing genetic differences.
Limited sequence heterogeneity among biologically distinct human immunodeficiency virus type 1 isolates from individuals involved in a clustered infectious outbreak.
Authors: McNearney T , Westervelt P , Thielan B J , Trowbridge D B , Garcia J , Whittier R , Ratner L
Published: May 2006

Human immunodeficiency virus type 1 isolates were obtained over a 3-year period from blood, brain, and lung of three patients in a clustered infectious outbreak. This included a blood donor who was initially asymptomatic but subsequently developed AIDS-related complex and two neonatal transfusion recipients who developed AIDS. Isolates from brain and lung replicated to greater than 30-fold higher levels in primary monocyte cultures than did those from blood; no growth differences on primary lymphocytes were observed. Thirteen clones were obtained from seven isolates, and env sequences were determined. The predicted amino acid sequences among these clones differed by only 0.01% but differed by 15-27% when compared to previously sequenced isolates from other patients. The level of envelope amino acid sequence divergence noted among these isolates is considerably lower than that previously reported for other human immunodeficiency virus isolates. No differences in the envelope unique to lung or brain isolates compared to blood isolates were noted. This study provides evidence that mutations in the envelope may not be necessary for disease progression and that other portions of the viral genome may contribute to cell-specific tropism.
Defective cAMP-dependent phosphorylation of intact T lymphocytes in active systemic lupus erythematosus.
Authors: Hasler P , Schultz L A , Kammer G M
Published: May 2006

The present study was undertaken to establish whether cAMP-dependent phosphorylation of endogenous substrates is impaired in T lymphocytes from subjects with active systemic lupus erythematosus (SLE). In normal human T lymphocytes, the cell-permeable cAMP analog, N6,O2'-dibutyryladenosine 3',5'-cyclic monophosphate, induced phosphorylation of substrates with molecular masses of 17.5, 23/25, 33.5 kDa on one-dimensional SDS/PAGE. Maximal phosphorylation occurred at 60 min. In contrast to healthy T cells, the extent of substrate phosphorylation achieved in active SLE T cells (n = 8) was only 15% at 60 min in the 17.5-kDa substrate, 21% in the 23/25-kDa substrate, and 9% in the 33.5-kDa substrate. The rheumatic disease controls (rheumatoid arthritis; primary Sjögren syndrome; n = 8) exhibited a mean 72%, 124%, and 85%, respectively, of phosphorylation observed in healthy T cells. Because the only known mechanism by which cAMP acts is via cAMP-dependent protein kinase (protein kinase A), these data raise the possibility of a defect at the level of this kinase in SLE T lymphocytes.
Calcium flux mediated by purified inositol 1,4,5-trisphosphate receptor in reconstituted lipid vesicles is allosterically regulated by adenine nucleotides.
Authors: Ferris C D , Huganir R L , Snyder S H
Published: May 2006

When incorporated into lipid vesicles, the purified inositol 1,4,5-trisphosphate (IP3) receptor protein mediates 45Ca2+ flux. We observe a potent, selective allosteric regulation by ATP of IP3 actions on Ca2+ flux. The action of ATP is selective for adenine nucleotides with ADP and AMP less potent and GTP inactive. At 1-10 microM, ATP increases maximal IP3-induced flux by 50% with no change in IP3 potency. The enhancing effect of ATP diminishes between 0.1 and 1 mM. Concentration-response curves are steep for both the increasing and the decreasing effects of ATP on IP3 actions, suggesting a physiological regulatory role of ATP in IP3-induced Ca2+ release. Diminishing local ATP concentrations coincident with filling of Ca2+ stores by the Ca2(+)-ATPase may enhance IP3 release of Ca2+, an effect that would decline as ATP returns to physiological levels. ATP regulation of Ca2+ release may also play a role in oscillations of intracellular Ca2+ concentration.
Suppression of tumor-forming ability and related traits in MCF-7 human breast cancer cells by fusion with immortal mammary epithelial cells.
Authors: Zajchowski D A , Band V , Trask D K , Kling D , Connolly J L , Sager R
Published: May 2006

Somatic cell hybrids between MCF-7 human breast cancer cells and normal immortalized human mammary epithelial cells have been obtained by polyethylene glycol-mediated cell fusion. The hybrid cells are suppressed in their ability to form tumors in nude mice, as well as in traits specific to the tumorigenic MCF-7 parent: growth factor independence, tumor necrosis factor sensitivity, and pS2 gene expression. In addition, they display other characteristics of the "normal" parent, including increased expression relative to the MCF-7 cells of the genes for the extracellular matrix component fibronectin, the intermediate filament keratin 5, and the angiogenesis inhibitor thrombospondin. The levels of keratins 8 and 18 also resemble those of the nontumorigenic parent. These results provide evidence for the existence of tumor suppressor gene products in immortal mammary epithelial cells. We propose a characteristic "suppressed" tumor cell phenotype, which encompasses altered cytoarchitecture, angiogenesis capabilities, and growth factor requirements.
Proteinaceous inhibitors of phospholipase A2 purified from inflammatory sites in rats.
Authors: Suwa Y , Kudo I , Imaizumi A , Okada M , Kamimura T , Suzuki Y , Chang H W , Hara S , Inoue K
Published: May 2006

We have purified two phospholipase A2 inhibitory proteins (37 and 33 kDa) from peritoneal fluid of dexamethasone-treated rats. The extracellular phospholipase A2 found in inflammatory sites differed from the exocrine phospholipase A2 in susceptibility to these endogenous inhibitors; both proteins inhibited the activity of the extracellular phospholipase A2 purified from sites of inflammation but did not affect appreciably the activity of either porcine pancreatic or Naja naja venom phospholipase A2. The amino acid sequence of the NH2-terminal portion of the purified proteins did not resemble that of lipocortins so far reported, but it was almost identical to that of parts of human or mouse complement component C3. These findings may indicate that degraded products of C3 are involved in the regulation of activity of a class of mammalian phospholipase A2.
Biophysical and biological activity of a synthetic 8.7-kDa hydrophobic pulmonary surfactant protein SP-B.
Authors: Sarin V K , Gupta S , Leung T K , Taylor V E , Ohning B L , Whitsett J A , Fox J L
Published: May 2006

We have synthesized pulmonary surfactant apoprotein SP-B peptides by solid-phase chemistry and demonstrated their ability to enhance the surface-active properties of synthetic lipid mixtures. The synthetic peptides were reactive with antiserum generated against the native bovine surfactant peptide. Both peptides conferred surfactant-like properties to synthetic lipid mixtures as assessed by a Wilhelmy balance and pulsating bubble surfactometer. Likewise, mixtures of synthetic SP-B peptides and lipid restored compliance of isolated surfactant-deficient rat lungs. This work demonstrates the utility of SP-B as a functional component of pulmonary surfactant mixtures for treatment of respiratory distress syndrome or other disorders characterized by surfactant deficiency.
Acetylcholine release from intrahippocampal septal grafts is under control of the host brain.
Authors: Nilsson O G , Kalén P , Rosengren E , Björklund A
Published: May 2006

The activity of intrahippocampal transplants of cholinergic neurons was monitored by microdialysis in awake, freely moving rats. Fetal septal-diagonal band tissue was implanted into rats with a complete transection of the fimbria-fornix cholinergic pathway either as a cell suspension injected into the hippocampus or as a solid graft implanted in the lesion cavity. The grafts restored baseline acetylcholine release in the graft-reinnervated hippocampus to normal or supranormal levels. The graft-derived acetylcholine release was dependent on intact axonal impulse flow, and it was markedly increased during behavioral activation by sensory stimulation or by electrical stimulation of the lateral habenula. The results demonstrate that the septal grafts, despite their ectopic location, can become functionally integrated with the host brain and that the activity of the transplanted cholinergic neurons can be modulated from the host brain during ongoing behavior. Anatomical observations, using immunohistochemistry and retrograde tracing, indicate that direct or indirect brainstem afferents to the graft could mediate this functional integration. Host afferent control of the graft may thus play a role in the recovery of lesion-induced functional deficits seen with these types of transplants.
An S1 nuclease-sensitive homopurine/homopyrimidine domain in the c-Ki-ras promoter interacts with a nuclear factor.
Authors: Hoffman E K , Trusko S P , Murphy M , George D L
Published: May 2006

To gain insight into the normal controls mediating expression of the c-Ki-ras protooncogene, we have identified DNA sequence elements within its promoter that are essential for transcriptional activity. Transient expression assays using the bacterial chloramphenicol acetyltransferase gene were used initially to localize regions directing primary promoter function. Stepwise deletion of 5' promoter sequences resulted in a gradual decrease in the ability to drive transcription of the reporter gene, suggesting that this promoter is composed of multiple cis-acting elements. Gel mobility-shift and DNase protection studies involving a 166-base-pair DNA fragment allowed the identification of protein-binding sites corresponding to these multiple regulatory elements. One element demonstrating particular transcriptional influence exists as a homopurine/homopyrimidine-rich region that in vitro exhibits S1 nuclease sensitivity and binds at least one nuclear protein. Data from competition binding experiments suggest that this nuclear factor may be influential in the regulation of other essential growth-control genes as well.
Overexpressed human metallothionein IIA gene protects Chinese hamster ovary cells from killing by alkylating agents.
Authors: Kaina B , Lohrer H , Karin M , Herrlich P
Published: May 2006

Experiments were designed to detect survival advantages that cells gain by overexpressing metallothionein (MT). Chinese hamster ovary K1-2 cells and an x-ray-sensitive derivative were transfected with a bovine papillomavirus (BPV)-linked construct carrying the human metallothionein IIA (hMT-IIA) gene. Transfectants survived 40-fold higher levels of cadmium chloride, harbored at least 30 copies of hMT-IIA, and contained 25- to 166-fold more MT than the parent cells. Even under conditions of reduced glutathione synthesis, the transfectants were not more resistant to the lethal effects of ionizing radiation and bleomycin than the parent cells. Thus free radicals generated by these agents cannot be scavenged efficiently by MT in vivo. The hMT-IIA transfectants, however, but not control transfectants harboring a BPV-MT promoter-neo construct, tolerated significantly higher doses of the alkylating agents N-methyl-N-nitrosourea and N-methyl-N'-nitro-N-nitrosoguanidine. Resistance and MT overexpression occurred irrespective of selection and cultivation in cadmium and zinc. There was no increase in resistance to methyl methanesulfonate and N-hydroxyethyl-N-chloroethylnitrosourea. MT did not affect the degree of overall DNA methylation after N-methyl-N-nitrosourea treatment nor the level of O6-methylguanine-DNA methyltransferase. The results suggest that MT participates as a cofactor or regulatory element in repair or tolerance of toxic alkylation lesions.
Glucocorticoid up-regulation of high-affinity interleukin 6 receptors on human epithelial cells.
Authors: Snyers L , De Wit L , Content J
Published: May 2006

Interleukin 6 (IL-6) is a potent pleiotropic cytokine, known, among others, to stimulate immunoglobulin production by B cells and to trigger acute-phase protein synthesis by hepatocytes. Similar to IL-1, it is produced by monocytes and macrophages following an inflammatory challenge. Analysis of IL-6 receptor (IL-6R) expression on different human cell lines indicates that dexamethasone could up-regulate the number of IL-6R on one epithelial cell line (UAC) and on two hepatoma cell lines (HepG2 and Hep3B). This effect was confirmed by Scatchard analysis of binding experiments, using [35S]methionine and [35S]cysteine metabolically labeled IL-6. It was confirmed at the level of mRNA expression by Northern blot analysis. These results provide evidence for a link between IL-6 and glucocorticoids. They could represent an example of a system in which one role of glucocorticoids is to define more accurately the target of cytokines, and they could explain, at least partly, the frequently observed synergy between IL-6 and glucocorticoids, notably in the case of hepatocytes.
The second zinc-finger domain of poly(ADP-ribose) polymerase determines specificity for single-stranded breaks in DNA.
Authors: Gradwohl G , Ménissier de Murcia J M , Molinete M , Simonin F , Koken M , Hoeijmakers J H , de Murcia G
Published: May 2006

Poly(ADP-ribose) polymerase (EC 2.4.2.30) is a zinc-binding protein that specifically binds to a DNA strand break in a zinc-dependent manner. We describe here the cloning and expression in Escherichia coli of a cDNA fragment encoding the two putative zinc fingers (FI and FII) domain of the human poly(ADP-ribose) polymerase. Using site-directed mutagenesis, we identified the amino acids involved in metal coordination and analyzed the consequence of altering the proposed zinc-finger structures on DNA binding. Disruption of the metal binding ability of the second zinc finger, FII, dramatically reduced target DNA binding. In contrast, when the postulated Zn(II) ligands of FI were mutated, the DNA binding activity was only slightly affected. DNase I protection studies showed that the FII is involved in the specific recognition of a DNA strand break. These results demonstrate that poly(ADP-ribose) polymerase contains a type of zinc finger that differs from previously recognized classes in terms of both structure and function.
T-cell receptor gamma delta and gamma transgenic mice suggest a role of a gamma gene silencer in the generation of alpha beta T cells.
Authors: Ishida I , Verbeek S , Bonneville M , Itohara S , Berns A , Tonegawa S
Published: May 2006

A T lymphocyte expresses on its surface one of two types of antigen receptor, T-cell receptor alpha beta or T-cell receptor gamma delta, encoded by a pair of somatically rearranged alpha and beta or gamma and delta genes. It has been suggested that alpha beta T cells are generated only from precursor T cells that failed to rearrange gamma and delta genes in a functional form. However, we found that transgenic mice constructed with functionally rearranged gamma and delta genes produce a normal number of alpha beta T cells. The transgene gamma present in these alpha beta T cells is repressed apparently through an associated cis DNA element (silencer). We propose that some T-cell precursors are committed to generate alpha beta T cells independent of the rearrangement status of their gamma gene and that this commitment involves activation of a factor(s) that interacts with the gamma gene-associated silencer.
A mutant neomycin phosphotransferase II gene reduces the resistance of transformants to antibiotic selection pressure.
Authors: Yenofsky R L , Fine M , Pellow J W
Published: May 2006

The neo (neomycin-resistance) gene of transposon Tn5 encodes the enzyme neomycin phosphotransferase II (EC 2.7.1.95), which confers resistance to various aminoglycoside antibiotics, including kanamycin and G418. The gene is widely used as a selectable marker in the transformation of organisms as diverse as bacteria, yeast, plants, and animals. We found a mutation that involves a glutamic to aspartic acid conversion at residue 182 in the protein encoded by the chimeric neomycin phosphotransferase II genes of several commonly used transformation vectors. The mutation substantially reduces phosphotransferase activity but does not appear to affect the stability of the neomycin phosphotransferase II mRNA or protein. Plants and bacteria transformed with the mutant gene are less resistant to antibiotics than those transformed with the normal gene. A simple restriction endonuclease digestion distinguishes between the mutant and the normal gene.
Cell-specific expression in transgenic plants reveals nonoverlapping roles for chloroplast and cytosolic glutamine synthetase.
Authors: Edwards J W , Walker E L , Coruzzi G M
Published: May 2006

Chloroplast and cytosolic isoforms of glutamine synthetase (GS; EC 6.3.1.2) are encoded by separate nuclear genes in plants. Here we report that the promoters for chloroplast GS2 and cytosolic GS3A of Pisum sativum confer nonoverlapping, cell-specific expression patterns on the beta-glucuronidase (GUS) reporter gene in transgenic tobacco. The promoter for chloroplast GS2 directs GUS expression within photosynthetic cell types (e.g., palisade parenchymal cells of the leaf blade, chlorenchymal cells of the midrib and stem, and photosynthetic cells of tobacco cotyledons). The promoter for chloroplast GS2 retains the ability to confer light-regulated gene expression in the heterologous transgenic tobacco system in a manner analogous to the light-regulated expression of the cognate gene for chloroplast GS2 in pea. These expression patterns reflect the physiological role of the chloroplast GS2 isoform in the assimilation of ammonia generated by nitrite reduction and photorespiration. In contrast, the promoter for cytosolic GS3A directs expression of GUS specifically within the phloem elements in all organs of mature plants. This phloem-specific expression pattern suggests that the cytosolic GS3A isoenzyme functions to generate glutamine for intercellular nitrogen transport. In germinating seedlings, the intense expression of the cytosolic GS3A-GUS transgene in the vasculature of cotyledons reveals a role for cytosolic GS in the mobilization of seed storage reserves. The distinct, cell-specific patterns of expression conferred by the promoters for chloroplast GS2 and cytosolic GS3A indicate that the corresponding GS isoforms perform separate metabolic functions.