bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of a human intracisternal retroviral particle associated with CD4+ T-cell deficiency.
Authors: Gupta S , Ribak C E , Gollapudi S , Kim C H , Salahuddin S Z
Published: May 2006

A number of non-human-immunodeficiency-virus (HIV) type 1 disorders are associated with CD4+ T-cell deficiency and dysfunction. However, the etiopathogenesis of CD4+ T-cell immunodeficiency in these disease states remains unclear. Human intracisternal retroviral (HICRV) particles were detected in a lymphoblastoid cell line exposed to mononuclear cells from a patient with severe CD4+ T-cell deficiency without risk factors for HIV infection. Ultrastructurally, the HICRV is distinct from HIV-1, HIV-2, human T-lymphotropic virus (HTLV) type I, and HTLV-II. Supernatants of activated mononuclear cells showed significant reverse transcriptase activity that was predominantly Mn2+ dependent. The patient's mononuclear cells were negative for HIV-1, HIV-2, HTLV-I, and HTLV-II proviruses as demonstrated by the lack of amplification by PCR. Also, the patient's serum was negative for antibodies to HIV-1, HTLV-I, and HTLV-II and for HIV-1 p24 antigen; however, serum was positive for antibodies against the HICRV as demonstrated by Western blot. Similar HICRV particles were detected in a lymphoblastoid cell line exposed to mononuclear cells from the patient's daughter, who showed CD4+ T-cell dysfunction. The HICRV may be associated with CD4+ T-cell immunodeficiency and dysfunction in patients without risk for HIV-1, HIV-2, HTLV-I, and HTLV-II.
In vivo self-association of the Drosophila rel-protein dorsal.
Authors: Govind S , Whalen A M , Steward R
Published: May 2006

The Drosophila morphogen dorsal, KBF1, NF-kappa B, and the proto-oncogene c-rel belong to the rel family of transcription factors whose function is regulated post-translationally by selective nuclear import. In the early Drosophila embryo, dorsal protein is proposed to be retained in the cytoplasm through its interaction with cactus protein. The maternal dorsal group genes constitute a signal transduction pathway, which results in targeting cytoplasmic dorsal protein into the nuclei of the syncytial blastoderm embryo, in a ventral-to-dorsal gradient. The asymmetric transcriptional regulation of zygotic genes along the dorsoventral axis by the dorsal morphogen gradient establishes embryonic dorsoventral polarity. In the lymphocytes, the functional equivalent of cactus is I kappa B, which appears to retain NF-kappa B in the cytoplasm. This retention is relieved by extracellular signals in tissue culture. NF-kappa B and rel proteins each are known to function as oligomeric complexes. Here we present genetic and biochemical evidence for the existence and functional importance of an oligomeric dorsal complex in vivo.
Cationic lipids direct a viral glycoprotein into the class I major histocompatibility complex antigen-presentation pathway.
Authors: Walker C , Selby M , Erickson A , Cataldo D , Valensi J P , Van Nest G V
Published: May 2006

Recombinant glycoprotein B (gB) of herpes simplex virus (HSV) was processed and presented by class I major histocompatibility complex (MHC) molecules after delivery into cells by using N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium methyl sulfate (DOTAP), a commercially available cationic lipid used for DNA transfection. Cells treated with DOTAP-associated gB were susceptible to lysis by class I MHC-restricted, HSV-specific cytotoxic T lymphocytes (CTL), and the treated cells restimulated memory gB-specific CTL activity in spleen cells from HSV-infected mice. gB-specific CTL responses were detected in mice immunized with recombinant gB and DOTAP but not in those receiving gB emulsified in complete Freund's adjuvant. Thus, cationic lipids may facilitate induction of CD8+ T-cell responses in vaccinations with recombinant antigens, and they may serve as readily available reagents for dissecting class I MHC immunity to viruses and other intracellular pathogens.
Alloantigen recognition by two human natural killer cell clones is associated with HLA-C or a closely linked gene.
Authors: Colonna M , Spies T , Strominger J L , Ciccone E , Moretta A , Moretta L , Pende D , Viale O
Published: May 2006

Human natural killer (NK) cells with the CD3- CD16+ phenotype recognize allospecificities on normal T-cell blasts. The NK-defined specificity 1 (NK-1) is recessively inherited and has been mapped to the major histocompatibility complex between the complement gene cluster and HLA-A. A gene for NK-1, however, has not been identified. Here we demonstrate that NK-1 and the recently defined NK specificity 2 (NK-2) are reciprocally associated with homozygosity for a diallelic polymorphism at amino acid positions 77 and 80 in the putative peptide-binding site of HLA-C (P less than 10(-5)). NK-cell recognition of allogeneic cells may, therefore, be controlled by HLA-C itself or by a closely linked gene(s), which dominantly prevents (resistance alleles) or recessively permits (susceptibility alleles) recognition of still-unknown target determinants.
Targeted cleavage of mRNA by human RNase P.
Authors: Yuan Y , Hwang E S , Altman S
Published: May 2006

Ribonuclease P from Escherichia coli can cleave RNAs in simple, hydrogen-bonded complexes of two oligoribonucleotides that resemble the aminoacyl stem and 5' leader sequence of tRNA precursors. RNase P from human (HeLa) cells cannot catalyze the cleavage in vitro of the 5'-proximal oligoribonucleotide that contains the leader sequence in such simple complexes but can do so when the 3'-proximal oligoribonucleotide (external guide sequence) is altered to resemble three-quarters of a tRNA molecule. In such a complex, the efficiency of cleavage of the mRNA for chloramphenicol acetyltransferase, as the 5'-proximal oligoribonucleotide, depends on the structural details of the external guide sequence and on the choice of target site within the mRNA. The presence of the appropriately designed external guide sequence in cells in tissue culture reduces chloramphenicol acetyltransferase activity and the level of the corresponding intact mRNA in the cells. Thus, it appears that the use of such external guide sequences may provide a general technique for gene inactivation.
Characterization of a metabotropic glutamate receptor: direct negative coupling to adenylyl cyclase and involvement of a pertussis toxin-sensitive G protein.
Authors: Prezeau L , Manzoni O , Homburger V , Sladeczek F , Curry K , Bockaert J
Published: May 2006

We have characterized a G-protein-coupled glutamate receptor in primary cultures of striatal neurons. Glutamate, quisqualate, or trans-1-aminocyclopentane-1,3-dicarboxylate inhibited by 30-40% either forskolin-stimulated cAMP production in intact cells or forskolin plus vasoactive intestinal peptide-activated adenylyl cyclase assayed in neuronal membrane preparations. These inhibitory effects were suppressed after treatment of striatal neurons with Bordetella pertussis toxin, suggesting the involvement of a heterotrimeric guanine nucleotide-binding protein (G protein) of the G(i)/G(o) subtype. The pharmacological profile of this glutamate receptor negatively coupled to adenylyl cyclase was different from that of the metabotropic Qp glutamate receptor coupled to phospholipase C in striatal neurons and from that of the recently cloned "mGluR2" glutamate receptor, which is negatively coupled to adenylyl cyclase when expressed in non-neuronal cells.
Reactions depending on iron sulfide and linking geochemistry with biochemistry.
Authors: Blöchl E , Keller M , Wachtershäuser G , Stetter K O
Published: May 2006

Iron sulfide gives rise to unusual reducing reactions: some dependent on FeS/H2S synergism [NO-3 --> NH3; HC(three bonds)CH--> H2C=CH2, H3C-CH3; -CH2-CO- --> -CH=CH-, -CH2-CH2-; HS-CH2-COOH --> CH3-COOH; others dependent on FeS alone [HS-CH2-CH2-X --> CH2=CH2 (where X = OH, SH, or NH2)]. The experimental conditions are geochemically plausible: 100 degrees C, aqueous, nearly neutral, and fastidiously anaerobic. These reactions establish additional facts of soil chemistry, organic geochemistry, and the global nitrogen cycle. Further, they point to the common evolutionary denominator of geochemistry and biochemistry.
The p50 subunit of NF-kappa B associates with the NF-IL6 transcription factor.
Authors: LeClair K P , Blanar M A , Sharp P A
Published: May 2006

The NF-kappa B-p50 polypeptide, a member of the Rel family of transcription factors, was produced as a fusion protein containing amino-terminal peptide additions that facilitate purification and detection with a monoclonal antibody and specific radiolabeling by phosphorylation in vitro. The 32P-labeled NK-kappa B-p50 fusion polypeptide was used as the probe in Western blotting experiments and in screenings of a bacteriophage expression library to isolate cDNAs encoding interacting protein domains. As expected, cDNAs encoding proteins of the Rel family were identified. Surprisingly, the 32P-labeled NF-kappa B protein also specifically bound to proteins encoded by cDNAs for the human NF-IL6 transcription factor. The NF-kappa B-p50 and NF-IL6 proteins directly interact, and the Rel homology domain and leucine-zipper motif, respectively, are important for this interaction. Since induction of the NF-kappa B and NF-IL6 factors are important events in immune and acute-phase responses, this interaction could permit coregulation of genes.
Molecular structure of Ti8C12 and related complexes.
Authors: Pauling L
Published: May 2006

Application of valence-bond theory leads to the assignment to the molecule Ti8C12 of a cubic structure, point group Ohm3m, with 8 Ti at the cube corners, +/-(x x x, x, x x [symbol, see text]) where x = 1.78 A, and with 12 C in pairs in the cube faces, +/-(0 y z, [symbol, see text], 0, y z [symbol, see text]) where y = 1.78 A and z = 0.71 A. The Ti-C and C-C bonds have bond number 4/3, corresponding to resonance of single and double bonds in 2:1 ratio.
Phorbol ester stimulates a protein-tyrosine/threonine kinase that phosphorylates and activates the Erk-1 gene product.
Authors: Alessandrini A , Crews C M , Erikson R L
Published: May 2006

The regulation of the Erk (extracellular-signal-regulated kinase) gene-encoded protein kinase activity by reversible phosphorylation has been reported to involve either an activator of autophosphorylation or an upstream protein kinase. In this communication we describe assays utilizing the Erk-1 protein fused to glutathione S-transferase that permit the identification of protein kinase(s) that phosphorylate and activate the myelin basic protein kinase activity encoded by the Erk-1 gene. A phorbol ester-stimulated protein kinase activity was identified that phosphorylated a kinase-negative Erk-1 gene product on tyrosine and threonine. The protein kinase phosphorylated and activated wild-type protein expressed in bacteria from 20- to 50-fold. The activation of the Erk-1-encoded myelin basic protein kinase required ATP and correlated directly with the degree of phosphorylation on the same amino acid residues previously shown to be phosphorylated in vivo. Conversion of the tyrosine site of phosphorylation to phenylalanine yielded an Erk-1 gene product that could not be activated. Similar results were obtained when the threonine site was mutated to valine. It is likely that the phorbol ester-stimulated protein-tyrosine/threonine kinase(s) is an up-stream target for multiple extracellular signals.
Inhibition of human immunodeficiency virus and growth of infected T cells by the immunosuppressive drugs cyclosporin A and FK 506.
Authors: Karpas A , Lowdell M , Jacobson S K , Hill F
Published: May 2006

The effects of the immunosuppressive drugs cyclosporin A and FK 506 were studied on cells chronically infected with human immunodeficiency virus type 1 (HIV-1) as well as on uninfected and newly infected cells. When cells chronically infected with HIV-1 or with HIV-2 were cocultivated with uninfected cells in the presence of cyclosporin A or FK 506 there was a delay in the formation of syncytia and of cytopathic effects. This inhibitory effect was not due to decreased membrane expression of CD4. In addition, there was an approximately 100-fold reduction in the yield of infectious HIV-1 when the infected cells were grown in the presence of these drugs, a finding consistent with other evidence of decreased HIV expression. Both drugs were found to inhibit the growth of chronically infected cells at concentrations that did not inhibit the growth of the uninfected cells. These results, demonstrating that cyclosporin A and FK 506 interfere with HIV production and selectively inhibit the growth of infected cells, suggest that they may be useful in the treatment of this infection and indicate further cellular targets for antiviral agents.
3'-Azido-3'-deoxythymidine-induced reduction in the ability of uninfected CD4-expressing cells to participate in syncytium formation.
Authors: Buckheit R W , Germany-Decker J , Qualls-Goodwin K , Bowdon B J , Shannon W M
Published: May 2006

A cocultivation assay system consisting of uninfected human T cells and cells chronically infected with human immunodeficiency virus type 1 has been used to investigate syncytium formation in short-term assays. Continuous treatment or short-term pretreatment of uninfected CD4-expressing human T-cell lines with 3'-azido-3'-deoxythymidine (AZT) reduces the ability of these cells to participate in syncytium formation when mixed with chronically infected cells. The effect of AZT on syncytium formation is observed both as a reduction in the number of syncytia and as a reduction in the size of the syncytia that are detected. This syncytium-reducing effect of AZT is dose and time dependent and does not result from a modulation of CD4 antigen expression on the cell surface of uninfected, treated cells. Maximum syncytium reduction is observed with the continuous presence of AZT; however, pretreatment for times as short as 15 min results in a significant reduction in syncytium formation. Since reverse transcription is not required for efficient syncytium formation, the syncytium-reducing effect of AZT on uninfected human cells may represent an antiviral property of AZT with important therapeutic potential.
Heterogeneity of immunoglobulin-associated molecules on human B cells identified by monoclonal antibodies.
Authors: Nakamura T , Kubagawa H , Cooper M D
Published: May 2006

Two covalently linked transmembrane molecules, encoded in mice by the mb-1 and B29 genes, have been defined as integral components of the antibody receptor units expressed on B cells. We have produced monoclonal antibodies against an exposed extracellular epitope on the putative human equivalent of the mouse B29 product. These antibodies, CB3-1 and -2, were used to show that cytoplasmic expression of this molecule begins in human pro-B cells (terminal deoxynucleotidyltransferase-positive, mu chain-negative), whereas surface expression coincides strictly with surface immunoglobulin expression of all isotypes. Immunochemical analysis of the human immunoglobulin-associated molecules revealed greater molecular heterogeneity than has been noted for the murine analogues. This molecular heterogeneity of immunoglobulin-associated molecules varied as a function of differentiation stage and the immunoglobulin isotypes expressed by B-lineage cells. Our data support the hypothesis that biochemical heterogeneity of the surface immunoglobulin-associated molecules may contribute to the variability in biological effects of antigen receptor crosslinkage on B cells of different maturational stages. Because the CB3 antibodies are capable of down-modulating the antigen receptors on all B cells, they may prove therapeutically useful as universal B-cell suppressants.
Hippocampal glucocorticoid receptor activation enhances voltage-dependent Ca2+ conductances: relevance to brain aging.
Authors: Kerr D S , Campbell L W , Thibault O , Landfield P W
Published: May 2006

Glucocorticoids (GCs) activate several biochemical/molecular processes in the hippocampus through two receptor types. In addition, GCs influence cognitive behaviors and hippocampal neural activity and can also increase the rate of aging-dependent cell loss in the hippocampus. However, the ionic mechanisms through which GCs modulate hippocampal neuronal function are not well understood. We report here direct evidence that activation of cytosolic steroid receptors, specifically of the type II GC receptor, can enhance voltage-dependent Ca2+ conductances in brain neurons. Ca2+ current was assessed by current-clamp measures of Ca2+ action potentials and by sharp electrode voltage-clamp analyses of voltage-sensitive currents in cesium-, tetrodotoxin-, and tetraethylammonium-treated CA1 neurons in hippocampal slices. Both Ca2+ action potentials and voltage-activated Ca2+ currents (N- and L-like) were increased by 2-hr exposure to the synthetic GC receptor agonist, RU 28362. This effect of RU 28362 was blocked by coincubation with cycloheximide, indicating that the GC receptor-Ca2+ channel interaction depends on de novo protein synthesis. Dysregulated calcium homeostasis is also viewed as a candidate mechanism in brain aging. Thus, present results are consistent with the hypothesis that excessive GC-receptor activation and resultant increased Ca2+ influx may be two sequential phases of a brain-aging process that results initially in impairment of function and eventually in neuronal loss.
Convergent evolution among immunoglobulin G-binding bacterial proteins.
Authors: Frick I M , Wikström M , Forsén S , Drakenberg T , Gomi H , Sjöbring U , Björck L
Published: May 2006

Protein G, a bacterial cell-wall protein with high affinity for the constant region of IgG (IgGFc) antibodies, contains homologous repeats responsible for the interaction with IgGFc. A synthetic peptide corresponding to an 11-amino acid-long sequence in the COOH-terminal region of the repeats was found to bind to IgGFc and block the interaction with protein G. Moreover, two other IgGFc-binding bacterial proteins (proteins A and H), which do not contain any sequences homologous to the peptide, were also inhibited in their interactions with IgGFc by the peptide. Finally, a decapeptide based on a sequence in IgGFc blocked the binding of all three proteins to IgGFc. This unusually clear example of convergent evolution emphasizes the complexity of protein-protein interactions and suggests that bacterial surface-protein interaction with host protein adds selective advantages to the microorganism.
Mechanism of hormone-stimulated lipolysis in adipocytes: translocation of hormone-sensitive lipase to the lipid storage droplet.
Authors: Egan J J , Greenberg A S , Chang M K , Wek S A , Moos M C , Londos C
Published: May 2006

Hormone-sensitive lipase activity (HSL), which is found in the supernatant of centrifuged homogenates of lipolytically quiet isolated rat adipocytes, was greatly reduced in or absent from the supernatant of lipolytically stimulated cells. The lipase was purified 100- to 250-fold from the supernatant of lipolytically quiet cells to 10-20% purity by a single passage over phenyl-Sepharose resin with high (greater than 70%) activity yields. Western blotting of adipocyte homogenate fractions with polyclonal antiserum raised against HSL showed that the enzyme shifted quantitatively from the supernatant of control cells to the floating "fat cake" of lipolytically stimulated cells. A similar shift to the fat cake was observed when cells were disrupted by hypotonic lysis and centrifugation rather than by homogenization. We propose that upon lipolytic activation of adipocytes and phosphorylation of HSL by cAMP-dependent protein kinase, the critical event is not an increase in catalytic activity (i.e., turnover number) but a translocation of the lipase to its substrate at the surface of the lipid storage droplet.
Effects of cyclosporin A and FK506 on Fc epsilon receptor type I-initiated increases in cytokine mRNA in mouse bone marrow-derived progenitor mast cells: resistance to FK506 is associated with a deficiency in FK506-binding protein FKBP12.
Authors: Kaye R E , Fruman D A , Bierer B E , Albers M W , Zydowsky L D , Ho S I , Jin Y J , Castells M C , Schreiber S L , Walsh C T
Published: May 2006

The inhibitory effects of cyclosporin A (CsA) and FK506 on Fc epsilon receptor type I-initiated increases in cytokine mRNA and the expression of their intracellular binding proteins were studied in interleukin 3 (IL-3)-dependent, mouse bone marrow-derived mast cells (BMMCs). In BMMCs sensitized with IgE anti-trinitrophenyl, CsA inhibited trinitrophenylated bovine serum albumin-induced increases in mRNA for IL-1 beta, tumor necrosis factor alpha (TNF-alpha), and IL-6 in a dose-related manner (IC50 values of 4, 65, and 130 nM, respectively). FK506 did not inhibit hapten-specific increases of mRNA for TNF-alpha or IL-6, and for IL-1 beta the IC50 was greater than 50-fold higher than that of CsA. Neither agent inhibited exocytosis of the endogenous secretory granule mediators beta-hexosaminidase and histamine at the IC50 values for inhibition of increases in cytokine mRNA. BMMCs expressed cyclophilin, and CsA inhibited the phosphatase activity of cellular calcineurin with an IC50 of approximately 8 nM. That CsA inhibited IL-1 beta mRNA accumulation in IgE-activated BMMCs with an IC50 similar to that for inhibition of calcineurin activity, whereas the IC50 values were approximately 20-fold higher for the inhibition of TNF-alpha and IL-6 mRNA, suggests that the induction of TNF-alpha and IL-6 is less dependent upon calcineurin activity than is the induction of IL-1 beta. BMMCs were deficient in the 12-kDa FK506-binding protein FKBP12, but not FKBP13, as assessed by RNA and protein blot analyses. FK506 did not inhibit calcineurin phosphatase activity in BMMCs, even at drug concentrations of 1000 nM. The resistance of BMMCs to inhibition of Fc epsilon receptor type I-mediated increases in cytokine mRNA by FK506 is most likely due to their deficiency of FKBP12 and the related inability to inhibit the activity of calcineurin.
Unusually high conservation of untranslated sequences in cDNAs for Trimeresurus flavoviridis phospholipase A2 isozymes.
Authors: Ogawa T , Oda N , Nakashima K , Sasaki H , Hattori M , Sakaki Y , Kihara H , Ohno M
Published: May 2006

As a step toward understanding the structure and function of phospholipases A2 (PLA2s), we isolated and sequenced several cDNAs encoding Trimeresurus flavoviridis venom PLA2 isozymes including two [Lys49]PLA2s called basic proteins I and II, [Thr37]PLA2, and PLX'-PLA2. Comparison of the nucleotide sequences of these cDNAs with the previously isolated [Asp49]PLA2 cDNA revealed some interesting findings from the viewpoint of evolution. First, the homologies of the 5' and 3' untranslated regions (98% and 89%, respectively) were much higher than that of the protein-coding regions (67%). The predicted secondary structure showed the characteristic stem-loop structures for both the untranslated regions of the mRNAs, suggesting that these regions play some functional role(s) in translation or stability of mRNAs. Second, base substitutions appeared to have occurred at similar rates for the three positions of codons among these PLA2s. The results are discussed in terms of evolution of PLA2s. Northern blot analysis showed that these PLA2s are specific to venom gland.
A membrane-based force generation mechanism in auditory sensory cells.
Authors: Kalinec F , Holley M C , Iwasa K H , Lim D J , Kachar B
Published: May 2006

Auditory outer hair cells can elongate and shorten at acoustic frequencies in response to changes of plasma membrane potential. We show that this fast bidirectional contractile activity consists of an electromechanical transduction process that occurs at the lateral plasma membrane and can be activated and analyzed independently in small membrane patches inside a patch electrode. Bidirectional forces are generated by increases and decreases in membrane area in response to hyperpolarization and depolarization, respectively. We suggest that the force generation mechanism is driven by voltage-dependent conformational changes within a dense array of large transmembrane proteins associated with the site of electromechanical transduction.
The Enhancer of split [E(spl)] locus of Drosophila encodes seven independent helix-loop-helix proteins.
Authors: Delidakis C , Artavanis-Tsakonas S
Published: May 2006

The E(spl) locus is thought to participate in a cell interaction mechanism that controls the choice of many cell fates during Drosophila development, including the segregation of neural precursors. Previous studies have demonstrated that E(spl) is defined by two groups of closely related transcripts, (i) a cluster of three transcripts encoding proteins bearing a helix-loop-helix (HLH) motif and (ii) a single-copy gene encoding a nuclear protein containing repeated motifs first identified in the beta subunit of guanine nucleotide-binding proteins. Both groups interact genetically with the Notch locus, which codes for a transmembrane protein. We report the structure of four additional HLH-encoding genes that reside in the E(spl) complex and provide evidence that we have now identified all the remaining members of the E(spl) HLH cluster.
Independent origins of New Zealand moas and kiwis.
Authors: Cooper A , Mourer-Chauviré C , Chambers G K , von Haeseler A , Wilson A C , Pääbo S
Published: May 2006

Two groups of flightless ratite birds existed in New Zealand during the Pleistocene: the kiwis and the moas. The latter are now extinct but formerly included 11 species. We have enzymatically amplified and sequenced approximately 400 base pairs of the mitochondrial 12S rRNA gene from bones and soft tissue remains of four species of moas as well as eight other species of ratite birds and a tinamou. Contrary to expectation, the phylogenetic analysis shows that the kiwis are more closely related to Australian and African ratities than to the moas. Thus, New Zealand probably was colonized twice by ancestors of ratite birds.
A 2-O-methylfucose moiety is present in the lipo-oligosaccharide nodulation signal of Bradyrhizobium japonicum.
Authors: Sanjuan J , Carlson R W , Spaink H P , Bhat U R , Barbour W M , Glushka J , Stacey G
Published: May 2006

Bradyrhizobium japonicum is a soil bacterium that forms nitrogen-fixing nodules on the roots of the agronomically important legume soybean. Microscopic observation of plant roots showed that butanol extract of B. japonicum strain USDA110 cultures induced for nod gene expression elicited root hair deformation, an early event in the nodulation process. The metabolite produced by B. japonicum responsible for root hair deformation activity was purified. Chemical analysis of the compound revealed it to be a pentasaccharide of N-acetylglucosamine modified by a C18:1 fatty acyl chain at the nonreducing end. In these respects, the B. japonicum metabolite is similar to the lipo-oligosaccharide signals described from Rhizobium species. However, the B. japonicum compound is unique in that an additional sugar, 2-O-methylfucose, is linked to the reducing end. Comparative analysis of the B. japonicum Nod metabolite and those characterized from Rhizobium species suggests that the presence of the fucosyl residue plays an important role in the specificity of the B. japonicum-soybean symbiosis. The availability of the purified B. japonicum nodulation signal should greatly facilitate further studies of soybean nodulation.
Coupling between gene expression and DNA synthesis early during development in Bacillus subtilis.
Authors: Ireton K , Grossman A D
Published: May 2006

Endospore formation in the bacterium Bacillus subtilis involves generation of two cell types, each with different developmental fates. Each cell type contains an active chromosome, and treatments that inhibit DNA synthesis at the beginning of development inhibit spore formation. We describe experiments demonstrating that gene expression early during sporulation is coupled to DNA synthesis. Expression of several genes that are induced early during sporulation, before the formation of two cell types, is inhibited when DNA synthesis is inhibited. Genes that are affected require the transcription factor encoded by spo0A for normal induction. Spo0A protein is normally activated early in development by a multicomponent phosphorylation pathway, or phospho-relay. Altered function mutations in spo0A that bypass the need for the phospho-relay allow early sporulation gene expression, even when DNA synthesis is inhibited. These results indicate that inhibition of DNA synthesis prevents activation of the Spo0A transcription factor by inhibiting a step in the phospho-relay. It seems likely that coupling early developmental gene expression to DNA synthesis is a general mechanism to prevent inappropriate or unnecessary gene expression.
Molecular cloning and characterization of additional factors that bind to the interferon-alpha/beta response element B of the murine (2'-5')oligoadenylate synthetase ME-12 gene.
Authors: Yan C , Tamm I
Published: May 2006

The function of interferon (IFN) response elements (IREs) may be classified into two classes according to the location of the IRE in the polymerase II transcription promoter: located upstream of the core promoter, or located within the core promoter. Thus, the IRE-binding factors (IREBFs) can serve as sequence-specific transcription factors that activate IFN-inducible gene transcription and they can participate in preinitiation complex formation. In the murine and human (2'-5')oligoadenylate synthetase genes the IRE is located within the core promoter region. For this reason, it is important to isolate cDNAs encoding protein factors that can bind to this IRE and determine their functional roles in the regulation of expression of the IFN-inducible (2'-5')oligoadenylate synthetase gene. We have isolated three groups of cDNAs that encode IREBFs. Here we report on clone 38 cDNA, which contains an open reading frame encoding a protein of 277 amino acids that is designated IREBF-2. The C terminus of IREBF-2 is extremely proline-rich and contains a high percentage of short-armed amino acids. IREBF-2 shares marked similarity with some gene products of the herpes group of viruses. These gene products are potent transcription activators. IREBF-2 is constitutively expressed in BALB/c 3T3 cells.
Analysis of the association of peptides of optimal length to class I molecules on the surface of cells.
Authors: Rock K L , Rothstein L , Benacerraf B
Published: May 2006

The association of major histocompatibility complex (MHC) class I molecules on the surface of cells with synthetic antigenic peptides of eight or nine amino acid residues was examined. Peptides were synthesized that correspond to the antigenic sequences from ovalbumin and influenza nucleoprotein believed to be naturally processed and presented by cells with Kb and Db MHC class I molecules, respectively. Consistent with the results of others, these peptides were 10(3)-10(5) times more active in stimulating specific T cells as compared to peptides of longer sequences. When cells are incubated with these peptides at less than 0.01-0.1 microM, the association of the peptides with class I molecules is dependent on (i) the reassociation of free beta 2-microglobulin from the extracellular fluids, (ii) a process that requires cells to be metabolically active, or (iii) stabilization of class I heterodimers by chemical crosslinking. In contrast, when cells are incubated with these peptides at greater than 0.1-1.0 microM, the peptides associate with class I molecules in the absence of exogenous beta 2-microglobulin, energy, or chemical crosslinking. Antigen competition experiments suggest that the class I molecules that bind peptides offered at high concentration become only transiently receptive to binding peptide. The concentration of peptides required for presentation to T cells under these conditions corresponds to those that stabilize Kb molecules on the surface of RMA-S mutant cells in the absence of exogenous beta 2-microglobulin. These results support the concept that the receptivity of class I molecules on cells is determined by the dissociation of beta 2-microglobulin from MHC class I that lacks bound peptides.
Inositol polyphosphate receptor and clathrin assembly protein AP-2 are related proteins that form potassium-selective ion channels in planar lipid bilayers.
Authors: Timerman A P , Mayrleitner M M , Lukas T J , Chadwick C C , Saito A , Watterson D M , Schindler H , Fleischer S
Published: May 2006

We have previously described an inositol polyphosphate receptor (IPxRec), purified from detergent-solubilized bovine cerebellum microsomes, that displays potassium ion channel activity in planar lipid bilayers. We now find that the IPxRec is closely related to clathrin assembly protein AP-2. The IPxRec and AP-2 purified from bovine brain clathrin-coated vesicles share several structural and functional features: (i) similar subunit composition; each has four major polypeptides that have similar mobility (Mr values of 111,000, 100,000, 50,000, and 17,000) and relative intensity by SDS/PAGE analysis; (ii) similar size as studied by molecular sieve chromatography (Mr 400,000); (iii) identical N-terminal amino acid sequences for the Mr 50,000 subunits and Mr 111,000/100,000 doublets; (iv) immunoreactivity of the AP-2 Mr 111,000/100,000 doublet to polyclonal antibodies affinity purified against the doublet proteins of the IPxRec; (v) display of the in vitro diagnostic feature of assembly proteins--i.e., they induce the assembly of clathrin cages; and (vi) ion channel activity selective for potassium ions with the same unitary conductance when incorporated into planar lipid bilayers. One difference was found. AP-2 channels were not blocked by inositol 1,3,4,5-tetraphosphate as reported for IPx receptor channels. These studies suggest a possible connection between the IPx signaling pathways and receptor-mediated endocytosis.
Proposed acquisition of an animal protein domain by bacteria.
Authors: Bork P , Doolittle R F
Published: May 2006

A systematic screen of a protein sequence data base confirms that the fibronectin type III (Fn3) domain is widely distributed among animal proteins and occurs also in several bacterial carbohydrate-splitting enzymes. The motif has yet to be identified in proteins from plants or fungi. All indications are that the bacterial sequences are much too similar to the animal type to be the result of conventional vertical descent. Rather, it is likely that the bacterial units were initially acquired from an animal source and are being spread further by horizontal transfers between distantly related bacteria.
Glucocorticoid-induced formation of tight junctions in mouse mammary epithelial cells in vitro.
Authors: Zettl K S , Sjaastad M D , Riskin P M , Parry G , Machen T E , Firestone G L
Published: May 2006

Phenotypically stable cultures of untransformed mouse mammary epithelial cells (denoted 31EG4) were established and utilized to investigate the lactogenic hormone (glucocorticoids, insulin, and prolactin) regulation of tight junction formation. When 31EG4 cells were grown on permeable supports for 4 days in medium containing the synthetic glucocorticoid dexamethasone and insulin, confluent cell monolayers obtained a transepithelial electrical resistance (TER) of 1000-3000 omega.cm2. In contrast, over the same time period, confluent monolayers treated with insulin or insulin and prolactin maintained a low TER (35-150 omega.cm2). Consistent with the formation of tight junctions, apical to basolateral paracellular permeability was decreased from 12% to 1% for [14C]mannitol and 3.3% to 0.3% for [3H]inulin when cells were cultured in dexamethasone. This effect of dexamethasone on TER required extracellular calcium, de novo protein synthesis, dose-dependently correlated with glucocorticoid receptor occupancy, and was not due to an increase in cell density. As shown by direct and indirect immunofluorescence microscopy, dexamethasone treatment did not modulate the production or location of filamentous actin, the tight junction protein ZO-1, or the cell adhesion protein E-cadherin. Our results suggest that glucocorticoids play a fundamental role in the function and maintenance of cell-cell contact in the mammary epithelia by inducing the formation of tight junctions.
Anion sensitivity and spectral tuning of cone visual pigments in situ.
Authors: Kleinschmidt J , Harosi F I
Published: May 2006

We tested the effect of anions on the absorbance spectrum of native visual pigments as measured by microspectrophotometry in individual cone outer segments of four species of fish and one species of amphibian. In all species tested, the long-wavelength-absorbing cone pigments were anion sensitive, and their lambda max could be tuned over a range of 55 nm depending on the identity of the anion present. Cl- and Br- were the only anions that produced native pigment spectra by red shifting lambda max from its value under anion-free conditions. Lyotropic anions such as NO3-, SCN-, BF4-, and ClO4- caused substantial and graded blue shifts of lambda max. The apparent Kd of binding sites on the pigment for Cl- and for ClO4- was approximately 2 mM. Taken together with previous findings on three visual pigments from the reptilian, avian, and amphibian classes, our results support the hypothesis that all long-wavelength-absorbing vertebrate visual pigments are spectrally tuned in part through the binding of a chloride ion. We propose that the site of anion tuning is near the protonated Schiff base of the chromophore, whose counterion may be complex and include Cl- as an exchangeable anion. This counterion configuration may resemble the one present in the light-driven Cl- pump halorhodopsin.
Solution of the discrete Plateau problem.
Authors: Hu T C , Kahng A B , Robins G
Published: May 2006

We solve a discrete version of the classic Plateau problem, which asks for a minimal surface spanning a given curve. Our algorithm is based on a network-flow formulation that finds minimal slabs, intuitively corresponding to minimal "surfaces" of prescribed thickness. We let the slab thickness approach zero in order to obtain the desired minimal surface.
Recombinant human Fab fragments neutralize human type 1 immunodeficiency virus in vitro.
Authors: Barbas C F , Björling E , Chiodi F , Dunlop N , Cababa D , Jones T M , Zebedee S L , Persson M A , Nara P L , Norrby E
Published: May 2006

A panel of 20 recombinant Fab fragments reactive with the surface glycoprotein gp120 of human type 1 immunodeficiency virus (HIV-1) were examined for their ability to neutralize MN and IIIB strains of the virus. Neutralization was determined as the ability of the Fab fragments to inhibit infection as measured in both a p24 ELISA and a syncytium-formation assay. One group of closely sequence-related Fab fragments was found to neutralize virus in both assays with a 50% neutralization titer at approximately 1 micrograms/ml. Another Fab neutralized in the p24 ELISA but not in the syncytium assay. The other Fab fragments showed weak or no neutralizing ability. The results imply that virion aggregation or crosslinking of gp120 molecules on the virion surface is not an absolute requirement for HIV-1 neutralization. Further, all of the Fab fragments were shown to be competitive with soluble CD4 for binding to gp120 and yet few neutralized the virus effectively, implying that the mechanism of neutralization in this case may not involve receptor blocking. The observation of a preponderance of high-affinity Fab fragments with poor or no neutralizing ability could have implications for vaccine strategies.
5'-Azido-[3,6-3H2]-1-napthylphthalamic acid, a photoactivatable probe for naphthylphthalamic acid receptor proteins from higher plants: identification of a 23-kDa protein from maize coleoptile plasma membranes.
Authors: Zettl R , Feldwisch J , Boland W , Schell J , Palme K
Published: May 2006

1-Naphthylphthalamic acid (NPA) is a specific inhibitor of polar auxin transport that blocks carrier-mediated auxin efflux from plant cells. To allow identification of the NPA receptor thought to be part of the auxin efflux carrier, we have synthesized a tritiated, photolabile NPA analogue, 5'-azido-[3,6-3H2]NPA ([3H2]N3NPA). This analogue was used to identify NPA-binding proteins in fractions highly enriched for plasma membrane vesicles isolated from maize coleoptiles (Zea mays L.). Competition studies showed that binding of [3H2]N3NPA to maize plasma membrane vesicles was blocked by nonradioactive NPA but not by benzoic acid. After incubation of plasma membrane vesicles with [3H2]N3NPA and exposure to UV light, we observed specific photoaffinity labeling of a protein with an apparent molecular mass of 23 kDa. Pretreatment of the plasma membrane vesicles with indole-3-acetic acid or with the auxin-transport inhibitors NPA and 2,3,5-triiodobenzoic acid strongly reduced specific labeling of this protein. This 23-kDa protein was also labeled by addition of 5-azido-[7-3H]indole-3-acetic acid to plasma membranes prior to exposure to UV light. The 23-kDa protein was solubilized from plasma membranes by 1% Triton X-100. The possibility that this 23-kDa polypeptide is part of the auxin efflux carrier system is discussed.
Mutagenesis of some conserved residues in human 5-lipoxygenase: effects on enzyme activity.
Authors: Zhang Y Y , Rådmark O , Samuelsson B
Published: May 2006

Recombinant human 5-lipoxygenase (arachidonate:oxygen 5-oxidoreductase, EC 1.13.11.34) was expressed in Escherichia coli. In incubations of E. coli supernatants with arachidonic acid, 5-hydroxy-7,9,11,14-eicosatetraenoic acid and leukotriene A4 were formed, while incubation with 8,11,14-eicosatrienoic acid gave 8-hydroxy-9,11,14-eicosatrienoic acid. Six conserved histidine residues in 5-lipoxygenase were subjected to site-directed mutagenesis. Exchanges of His-367, -372, or -551 gave mutants for which no enzyme activities were detectable. On the other hand, exchanges of His-362, -390, or -399 gave mutants that were enzymatically active, but less so than the nonmutated control. For two of these (exchanges of His-390 or -399), the activities of the mutants were dependent on the expression temperature. Thus, the histidines in the first group (His-367, -372, -551) were crucial for 5-lipoxygenase activity, possibly because of a function of these residues as metal ligands. Mutagenesis aimed at two other conserved elements in 5-lipoxygenase, Gln-558 and the C terminus, gave mutated proteins with only a small residual activity (substitution of Gln-558), or with no detectable activity (deletion of six C-terminal amino acids), indicating that these regions are important for the function of 5-lipoxygenase.
Purification and characterization of a mammalian myosin I.
Authors: Barylko B , Wagner M C , Reizes O , Albanesi J P
Published: May 2006

Myosin I, an actin-dependent force-generating enzyme, has been purified from three mammalian sources: bovine adrenal medulla, adrenal cortex, and brain. The purification procedure includes extraction of tissue with ATP at low ionic strength and coprecipitation with actin, followed by gel filtration on Sepharose 4B, anion-exchange chromatography on Q Sepharose, and affinity chromatography on ATP-agarose. Mammalian myosin I molecules are composed of a heavy chain of 116 kDa and multiple low molecular weight polypeptides identified as calmodulin. The structural and enzymatic properties of adrenal medulla myosin I were further characterized. This enzyme exhibits high K+,EDTA- and Ca(2+)-ATPase specific activities (about 0.2 mumol.min-1 per mg of protein), whereas the Mg(2+)-ATPase activity is very low (1-3 nmol.min-1.mg-1). The Mg(2+)-ATPase of medulla myosin I is activated by F-actin in a Ca(2+)-dependent manner: activity is stimulated 40-fold in the presence of EGTA and 90-fold in the presence of 10 microM Ca2+. Two structural domains of the myosin I heavy chain were identified. A 74-kDa chymotryptic fragment contains the catalytic site, while a 36-kDa polypeptide contains the calmodulin-binding sites. These results indicate that mammalian myosin I is more closely related to myosin I from the avian intestinal brush border than to the enzymes isolated from the protozoans Acanthamoeba and Dictyostelium.
Truncated staphylococcal nuclease is compact but disordered.
Authors: Flanagan J M , Kataoka M , Shortle D , Engelman D M
Published: May 2006

Deletion of 13 amino acids from the carboxyl terminus of the 149-amino acid staphylococcal nuclease molecule results in a denatured, partly unfolded molecule that lacks persistent secondary structure but is compact under physiological conditions. Since the modification is a carboxyl-terminal deletion, it is argued that the state resembles a peptide emerging from the ribosome just before the complete folding pathway is initiated. In this paper, we characterize the molecule by nuclear magnetic resonance, circular dichroism, and small-angle x-ray scattering measurements. The truncated nuclease shows wild-type levels of activity in the presence of calcium and is found to fold into a native-like conformation in the presence of 3',5'-bisphospho-2'-deoxythymidine, a potent inhibitor. Thus, the truncated molecule retains the capacity to fold. Our results suggest that extensive solvent exclusion generates a compact polypeptide chain prior to the development of persistent secondary structural features as a protein folds during biosynthesis.
A 5' to 3' exonuclease functionally interacts with calf DNA polymerase epsilon.
Authors: Siegal G , Turchi J J , Myers T W , Bambara R A
Published: May 2006

Analysis of fractions containing purified DNA polymerase epsilon from calf thymus has revealed the presence of a 5' to 3' exonuclease activity that is specific for a single strand of duplex DNA. This activity is capable of degrading a 3'-labeled oligonucleotide hybridized to M13mp18 DNA. When a second oligonucleotide primer is annealed 3 bases upstream, degradation of the downstream primer is strictly dependent on DNA synthesis from the upstream primer. Replacement of the downstream primer by an oligoribonucleotide of identical sequence results in a similar pattern of exonucleolytic activity. The activity has been highly purified and found to cosediment in glycerol gradients with a peptide of 56 kDa as judged by SDS/PAGE analysis. Effects of calf DNA polymerase alpha and delta on exonuclease activity are also observed but with differences in the pattern of products.
Spontaneous insertion of polypeptide chains into membranes: a Monte Carlo model.
Authors: Milik M , Skolnick J
Published: May 2006

The Monte Carlo dynamics method was used to examine the process of protein insertion into model cell membranes. The water and lipid environments were taken into account via an effective medium approximation based on coordinate-dependent hydrophobic and hydrogen bond potentials. The polypeptide chain was represented in a full-backbone atom representation as a chain of diamond lattice vectors. The simulations support the idea that to a good approximation insertion may be depicted as a spontaneous thermodynamic process. The mechanism of membrane insertion of a simple lattice protein chain exhibits many features of theoretical predictions and is in good accord with experimental data. In the model, insertion begins with adsorption of the chain onto the interface, followed by the formation of helical fragments. These fragments, having partially saturated internal hydrogen bonds, can be transported into the lipid phase and then form transbilayer structures.