bluuebunny/crossref_metadata_2025 huggingface dataset:
Nitric oxide production in islets from nonobese diabetic mice: aminoguanidine-sensitive and -resistant stages in the immunological diabetic process.
Authors: Corbett J A , Mikhael A , Shimizu J , Frederick K , Misko T P , McDaniel M L , Kanagawa O , Unanue E R
Published: May 2006

The role of nitric oxide (NO.) in the development of immunologically induced diabetes was examined. Transfer of spleen cells obtained from diabetic female nonobese diabetic (NOD) mice to nondiabetic irradiated males induced diabetes 11-13 days after transfer. Islets isolated from recipient male mice produced NO. in a time-dependent fashion. The production of nitrite was initially detected at day 6 after transfer, with increasing levels by days 9 and 13. Under similar conditions glucose-induced insulin secretion by isolated NOD mouse islets was irreversibly reduced by approximately 40% at days 6, 9, and 13 after transfer of spleen cells. The number of islets harvested per pancreas by the 9th and 13th day after transfer was decreased by 20-25% as compared to controls. Treatment of male NOD mice with aminoguanidine, an inhibitor of the inducible form of NO. synthase, reduced the production of NO. in islets and delayed the development of diabetes by 3-8 days. The temporary inhibition by aminoguanidine was dependent on both inhibitor concentration and number of spleen cells transferred. These results indicate that NO. is produced in NOD islets as a result of an immunological diabetogenic process and suggests a role of this compound in the immunological diabetic process.
Favored and suppressed patterns of hydrophobic and nonhydrophobic amino acids in protein sequences.
Authors: Vazquez S , Thomas C , Lew R A , Humphreys R E
Published: May 2006

Hydrophobic amino acids of the group Leu, Ile, Val, Phe, and Met (LIVFM) are distributed in favored or suppressed patterns within protein sequences. The frequencies of all five-position combinations of [symbol: see text] = LIVFM and [symbol: see text] = non-LIVFM residues were analyzed in 48 proteins of known crystallographic structure. Some motifs were strongly preferred or suppressed; e.g., [symbol: see text] was favored (z = 3.5), while [symbol: see text] was suppressed (z = -3.4). In longer patterns, [symbol: see text] followed by [symbol: see text] and one [symbol: see text] was favored ([symbol: see text], z = 5.1), while conversion of the single hydrophobic residue to a pair was not ([symbol: see text], z = 0.8). Distributions of certain non-LIVFM amino acids around [symbol: see text] positions in strongly favored patterns were also favored or disfavored (Asp, Glu, Lys, Arg, Asn, Cys, Tyr, and Pro; for each magnitude of z > 2.0). While the strongly favored pattern [symbol: see text] was found in both alpha-helical and beta-strand sequences, it associated significantly with alpha-helices (z = 3.6 for the second-position alpha-helical phi and psi angles) but not with beta-strands (z = -1.1). Certain motifs of LIVFM and non-LIVFM residues might be selected if they lead efficiently to the local nucleations hypothesized to characterize molten globule intermediates in the folding of proteins.
Evidence that transporters associated with antigen processing translocate a major histocompatibility complex class I-binding peptide into the endoplasmic reticulum in an ATP-dependent manner.
Authors: Androlewicz M J , Anderson K S , Cresswell P
Published: May 2006

We have investigated the role of the putative peptide transporters associated with antigen processing (TAP) by using a permeabilized-cell system. The main objective was to determine whether these molecules, which bear homology to the ATP-binding cassette family of transporters, translocate antigenic peptides across the endoplasmic reticulum membrane for assembly with major histocompatibility complex (MHC) class I molecules and beta 2-microglobulin light chain. The pore-forming toxin streptolysin O was used to generate permeabilized cells, and peptide translocation was determined by measuring the amount of added radiolabeled peptide bound to endogenous class I molecules. No radiolabeled peptide was associated with MHC class I glycoproteins from unpermeabilized cells. We found that efficient peptide binding to MHC class I molecules in permeabilized cells is both transporter dependent and ATP dependent. In antigen-processing mutant cells lacking a functional transporter, uptake occurs only through a less-efficient transporter and ATP-independent pathway. In addition, short peptides (8-10 amino acids) known to bind MHC class I molecules compete efficiently with a radiolabeled peptide for TAP-dependent translocation, whereas longer peptides and a peptide derived from an endoplasmic reticulum signal sequence do not compete efficiently. This result indicates that the optimal substrates for TAP possess the characteristics of MHC-binding peptides.
Use of a reporter transgene to generate arabidopsis mutants in ubiquitin-dependent protein degradation.
Authors: Bachmair A , Becker F , Schell J
Published: May 2006

Ubiquitin-dependent proteolysis is a major proteolytic pathway in the cytoplasm and nucleus of eukaryotic cells. We introduced a gene encoding a substrate for this pathway into the genome of Arabidopsis thaliana. The transgene codes for a hybrid protein consisting of dihydrofolate reductase (DHFR, EC 1.5.1.3) fused to a degradation signal that is specifically recognized by components of the ubiquitin-dependent proteolysis pathway. Elevated concentrations of the DHFR protein confer resistance to the drug methotrexate, but rapid degradation prevents accumulation of the protein in the plant. Therefore, transgenic A. thaliana lines expressing the DHFR fusion protein are methotrexate-sensitive. Selection for mutants resistant to methotrexate resulted in plants impaired in degradation of the DHFR model substrate, as shown by an increase in protein level in the mutants.
A localized differentiation-inducing-factor sink in the front of the Dictyostelium slug.
Authors: Kay R R , Large S , Traynor D , Nayler O
Published: May 2006

Differentiation-inducing factor 1 [DIF-1; 1-(3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl)-hexan-1-one] induces stalk cell differentiation during Dictyostelium development. It is present as a gradient in the multicellular slug, its lowest concentration being in the anterior. Here we demonstrate the existence of a localized sink for DIF-1, also in the anterior of the slug, which could be responsible for generating the DIF-1 gradient. DIF-1 is metabolized extensively by developing cells, initially by a mono-dechlorination. We used an enzyme assay for DIF-1 dechlorinase to examine its distribution in the slug. DIF-1 dechlorinase activity is 30-fold higher in prestalk cells (largely anterior) compared with prespore cells (posterior) when these are separated from each other on Percoll density gradients. Dissection experiments showed that DIF-1 dechlorinase is 25-fold enriched in the anterior 13% of the slug compared with the rest. These experiments also showed that DIF-1 dechlorinase is more anterior-enriched than the standard prestalk markers, the ecmA and ecmB mRNAs. When cut from a slug, both prestalk and prespore fragments regulate to restore the missing cell type. Prespore fragments rapidly regain (by 30 min) a DIF-1 sink in their anteriors, and prestalk fragments restore a posterior zone with low DIF-1 dechlorinase by 4 hr after cutting. The reappearance of the DIF-1 sink in the anterior of prespore fragments is accomplished without detectable cell sorting and may, therefore, be in response to positional signals. Finally, a localized sink may provide a general way of producing a gradient of a signal substance in a developing embryo.
Molecular evolution of the myosin family: relationships derived from comparisons of amino acid sequences.
Authors: Goodson H V , Spudich J A
Published: May 2006

To examine the evolutionary relationships between members of the myosin family, we have used two different phylogenetic methods, distance matrix and maximum parsimony, to analyze all available myosin head sequences. We find that there are at least three equally divergent classes of myosin, demonstrating that the current classification of myosin into only two classes needs to be reexamined. In the myosin II class, smooth muscle myosin is more closely related to nonmuscle myosin than to striated muscle myosin, implying that smooth muscle and skeletal muscle myosins were independently derived from nonmuscle myosin and suggesting that similarities between these types of muscle are the result of convergent evolution. The grouping of head sequences produced by phylogenetic analysis is consistent with classifications based on enzymology and structural localization and is generally consistent with grouping based on common tail structure elements. This result demonstrates that specific head sequences are tightly coupled to specific tail sequences throughout evolution and challenges the idea that myosin heads are freely interchangeable units whose unique function is determined only by the tail structure to which it is attached.
Acute hypoxia increases ornithine decarboxylase activity and polyamine concentrations in fetal rat brain.
Authors: Longo L D , Packianathan S , McQueary J A , Stagg R B , Byus C V , Cain C D
Published: May 2006

The cellular responses to hypoxia are poorly understood. To test the hypothesis that ornithine decarboxylase (ODC; L-ornithine carboxy-lyase; EC 4.1.1.17) activity and polyamine concentrations change in response to acute hypoxia, we performed the following studies. Pregnant Sprague-Dawley rats inspired various O2 concentrations (9-21%) for various time periods (0.5-48 h) from days 15 to 21 of gestation. In fetal brains we measured the activity of ODC, ODC mRNA, and polyamines. In response to 4-h acute mild hypoxia, ODC activity in fetal rat brain (cerebrum, cerebellum, and hippocampus) increased to 330-450% from control values (P < 0.001), after which it declined to control levels in 6-8 h. The 4-h ODC response varied inversely with inspired O2 concentration and was not mimicked by beta 2 agonist or blocked by beta 2-antagonist administration. The ODC response was associated with an increase in fetal brain putrescine concentration to 190% above control at 4-6 h (P < 0.01) and an increase in the polyamines spermidine and spermine to about 115% above control at 6-8 h. We also observed that ODC mRNA increased significantly after 2-4 h of hypoxia. ODC activity and polyamine concentrations appear to be useful enzymatic markers for fetal brain hypoxia. The magnitude and time course of the acute hypoxic ODC increase were similar to responses to extracellular signals that result in differentiation or cell growth. Thus, the well-defined and regulated ODC activity response may represent a protective mechanism in brain to hypoxia.
An in vitro system for human cytomegalovirus immediate early 2 protein (IE2)-mediated site-dependent repression of transcription and direct binding of IE2 to the major immediate early promoter.
Authors: Macias M P , Stinski M F
Published: May 2006

In vivo, negative autoregulation of the strong major immediate early promoter (MIEP) of human cytomegalovirus requires the viral immediate early 2 protein (IE2) and a cis element located from position -13 through position -1 relative to the transcription start site. We have established an in vitro transcription system that reproduces the specificity of IE2-mediated negative autoregulation. The carboxyl-terminal 290-amino acid fragment of IE2 was purified as a bacterial fusion protein. Addition of this chimeric protein to the cell-free system specifically repressed transcription from the MIEP containing the wild-type cis-acting repressor element but not from a mutated template in which the cis element had been replaced by heterologous DNA. Control protein and a mutant IE2 fusion protein containing two specific amino acid substitutions in a putative zinc finger motif did not repress the MIEP in vitro. Using conditions defined by this functional assay, we demonstrated by mobility-shift experiments that IE2 binds directly and specifically to DNA bearing the cis-acting repressor element. In addition, IE2 bound to the MIEP in the in vitro transcription reaction mixture.
Effects of Mn2+ and Mg2+ on assimilation of NO3- and NH4+ by soil microorganisms.
Authors: McCarty G W , Bremner J M
Published: May 2006

Although it has been demonstrated that Mn2+ and Mg2+ can influence the activity of glutamine synthetase in various organisms, there is little information concerning the effects of these cations on the activity of this enzyme in soil microorganisms or on ability of these microorganisms to assimilate NO3- and NH4+. We studied the effects of different concentrations of Mn2+ and Mg2+ on assimilatory NO3- reduction and NH4+ assimilation in cultures of two microorganisms commonly found in soil [Pseudomonas fluorescens (ATCC 13525) and Azotobacter chroococcum (ATCC 9043)] and in an enrichment culture of soil microorganisms. We found that Mn2+ strongly inhibited NH4+ assimilation by soil microorganisms and blocked the inhibitory effect of NH4+ on assimilatory NO3- reductase (ANR) activity, thereby uncoupling ANR activity from nitrogen assimilation and causing the NH4+ formed by ANR activity to be released to the environment. Mg2+ counteracted the effect of Mn2+ on microbial metabolism of nitrogen, which suggests that the overall effect of these cations on nitrogen assimilation by soil microorganisms will depend on the ratio of their concentrations in soil.
The t-complex polypeptide 1 complex is a chaperonin for tubulin and actin in vivo.
Authors: Sternlicht H , Farr G W , Sternlicht M L , Driscoll J K , Willison K , Yaffe M B
Published: May 2006

A role in folding newly translated cytoskeletal proteins in the cytosol of eukaryotes has been proposed for t-complex polypeptide 1 (TCP1). In this study, we investigated tubulin and actin biogenesis in Chinese hamster ovary (CHO) cells. When extracts of pulse-labeled cells were analyzed by anion-exchange and size-exclusion chromatography, newly synthesized alpha-tubulin, beta-tubulin, and actin were observed to enter a large molecular mass complex (approximately 900 kDa). These proteins were released from this complex capable, in the case of tubulin, of forming heterodimers. The large molecular mass complexes coeluted with TCP1 and could be immunoprecipitated by using an anti-TCP1 antibody. These findings demonstrate that there is a cytosolic pathway for folding tubulin and actin in vivo that involves the TCP1 complex.
Measurement of the g-tensor of the P700+. signal from deuterated cyanobacterial photosystem I particles.
Authors: Prisner T F , McDermott A E , Un S , Norris J R , Thurnauer M C , Griffin R G
Published: May 2006

We report high-field continuous wave EPR spectra of P700+. in preparations obtained from deuterated cyanobacteria (Synechococcus lividus). Measurements were performed with photosystem I (PS-I) preparations, whole cells from cyanobacteria grown in 2H2O, and photosystem II (PS-II) preparations, as well as with protonated PS-I preparations. Because of the significantly improved resolution of our 140-GHz spectrometer (as compared with X- or Q-band EPR) the principal values of the g-tensor of the primary donor P700+. could be resolved and measured with high accuracy as g11 = 2.00304, g22 = 2.00262, and g33 = 2.00232. Other signals arising from Mn2+ and a dark signal from PS-II at g approximately 2.00266 are distinguished from the P700+. g-tensor powder pattern. The measured g values are compared with those of several bacterial reaction center donors.
A light stabilizer (Tinuvin 770) that elutes from polypropylene plastic tubes is a potent L-type Ca(2+)-channel blocker.
Authors: Glossmann H , Hering S , Savchenko A , Berger W , Friedrich K , Garcia M L , Goetz M A , Liesch J M , Zink D L , Kaczorowski G J
Published: May 2006

A pharmacologically active agent was easily extracted by aqueous or organic solvents from laboratory plastic tubes (Falcon Blue Max) and has been chemically identified as bis(2,2,6,6-tetramethyl-4-piperidyl) sebacate. This compound (approximately 12 micrograms per tube approximately 25 nmol) blocked 1,4-dihydropyridine-sensitive 45Ca2+ uptake into GH3 cells with an IC50 value of 3.6 microM, inhibited Sr2+ currents through L-type Ca2+ channels in A7r5 smooth-muscle cells in whole-cell patch-clamp experiments after extracellular application, and affected the high-affinity binding of Ca2+ entry-blocker ligands to a variety of preparations. Bis(2,2,6,6-tetramethyl-4-piperidyl) sebacate is a highly potent (IC50 values < 10 nM) inhibitor at the phenylalkylamine- and benzothiazepine-selective drug-binding domains of the alpha 1 subunit of L-type Ca2+ channels. This compound behaves as a heterotropic allosteric regulator for the 1,4-dihydropyridine-selective domain in purified Ca(2+)-channel preparations from rabbit skeletal muscle. (+)-Tetrandrine stimulation of 1,4-dihydropyridine binding to the membrane-bound L-type Ca2+ channel is inhibited by the compound in a competitive manner (Ki value = 6.8 nM). Bis(2,2,6,6-tetramethyl-4-piperidyl) sebacate is therefore classified as the prototype of another class of L-type Ca(2+)-channel blockers that binds to the alpha 1 subunit at the drug-binding domains selective for (+)-tetrandrine or (+)-cis-diltiazem. This compound is identical to Tinuvin 770, which is used worldwide as a light stabilizer for polyolefins.
An accuracy center in the ribosome conserved over 2 billion years.
Authors: Alksne L E , Anthony R A , Liebman S W , Warner J R
Published: May 2006

The accuracy of translation in Escherichia coli is profoundly influenced by three interacting ribosomal proteins, S12, S4, and S5. Mutations at lysine-42 of S12, originally isolated as causing resistance to streptomycin, increase accuracy. Countervailing "ribosomal ambiguity mutations" (ram) in S4 or S5 decrease accuracy. In the eukaryotic ribosome of Saccharomyces cerevisiae, mutations in SUP46 and SUP44, encoding the proteins equivalent to S4 and S5, lead to omnipotent suppression--i.e., to less accurate translation. The evolution of ribosomal protein S12 can be traced, by comparison with archaebacteria and Tetrahymena, to S28 of S. cerevisiae, even though the two proteins share only very limited regions of homology. However, one region that has been conserved contains a lysine residue whose mutation leads to increased accuracy in E. coli. We have introduced into S28 of yeast the same amino acid substitutions that led to the original streptomycin-resistant mutations in E. coli. We find that they have a profound effect on the accuracy of translation and interact with SUP44 and SUP46, just as predicted from the E. coli model. Thus, the interplay of these three proteins to provide the optimal level of accuracy of translation has been conserved during the 2 billion years of evolution that separate E. coli from S. cerevisiae.
A single-base-pair mutation changes the specificities of both a transcription activation protein and its binding site.
Authors: Retallack D M , Johnson L L , Ziegler S F , Strauch M A , Friedman D I
Published: May 2006

The C1 protein of bacteriophage P22 binds to a unique site in the -35 region of the PRE promoter and activates transcription of the phage c2 repressor gene. This -35 target has an approximate direct repeat that overlaps the 5' end of the c1 coding region. We have isolated a single-base-pair mutation in this region that changes the PRE -35 target as well as the amino-terminal region of the C1 protein. Although the mutant C1 protein activates the mutant PRE promoter, it fails to activate the wild-type PRE promoter. This suggests that a single-base-pair mutation changes the specificities of both a protein and its target site. These studies also indicate that C1 binding to DNA is influenced by contacts made through residues near the amino terminus.
An Abd transgene prevents diabetes in nonobese diabetic mice by inducing regulatory T cells.
Authors: Singer S M , Tisch R , Yang X D , McDevitt H O
Published: May 2006

Susceptibility to the human autoimmune disease insulin-dependent diabetes mellitus is strongly associated with particular haplotypes of the major histocompatibility complex (MHC). Similarly, in a spontaneous animal model of this disease, the nonobese diabetic (NOD) mouse, the genes of the MHC play an important role in the development of diabetes. We have produced transgenic NOD mice that express the class II MHC molecule I-Ad in addition to the endogenous I-Ag7 molecules in order to study the role of these molecules in the disease process. Although the inflammatory lesions within the islets of Langerhans in the pancreas appear similar in transgenic and nontransgenic animals, transgenic mice develop diabetes with greatly diminished frequency compared to their nontransgenic littermates (10% of transgenic females by 30 weeks of age compared to 45% of nontransgenic females). Furthermore, adoptive transfer experiments show that T cells present in the transgenic mice are able to interfere with the diabetogenic process caused by T cells from nontransgenic mice. Thus, the mechanism by which I-Ad molecules protect mice from diabetes includes selecting in the thymus and/or inducing in the periphery T cells capable of inhibiting diabetes development.
Tissue-specific light-regulated expression directed by the promoter of a C4 gene, maize pyruvate,orthophosphate dikinase, in a C3 plant, rice.
Authors: Matsuoka M , Tada Y , Fujimura T , Kano-Murakami Y
Published: May 2006

Pyruvate,orthophosphate dikinase (PPDK; EC 2.7.9.1) activity is abundant in leaves of C4 plants, while it is difficult to detect in leaves of C3 plants. Recent studies have indicated that C3 plants have a gene encoding PPDK, with a structure similar to that of PPDK in C4 plants. However, low expression makes PPDK detection difficult in C3 plants. This finding suggests that high PPDK expression in C4 plants is due to regulatory mechanisms which are not operative in C3 plants. We have introduced a chimeric gene consisting of the gene encoding beta-glucuronidase (GUS; EC 3.2.1.31) controlled by the PPDK promoter from a C4 plant, maize, into a C3 cereal, rice. The chimeric gene was exclusively expressed in photosynthetic organs, leaf blades and sheaths, and not in roots or stems. Histochemical analysis of GUS activity demonstrated high expression of the chimeric gene in photosynthetic organs, localized in mesophyll cells, and no or very low activity in other cells. GUS expression was also regulated by light in that it was low in etiolated leaves and was enhanced by illumination. These observations indicate that the mechanisms responsible for cell-specific and light-inducible regulation of PPDK observed in C4 plants are also present in C3 plants. We directly tested whether rice has DNA-binding protein(s) which interact with a previously identified cis-acting element of the C4-type gene. Gel retardation assays indicate the presence in rice of a protein which binds this element and is similar to a maize nuclear protein which binds PPDK in maize. Taken together, these results indicate that the regulatory system which controls PPDK expression in maize is not unique to C4 plants.
Changes in intra- or extracellular pH do not mediate P-glycoprotein-dependent multidrug resistance.
Authors: Altenberg G A , Young G , Horton J K , Glass D , Belli J A , Reuss L
Published: May 2006

P-glycoprotein (Pgp)-mediated multidrug resistance (MDR) is thought to result from active extrusion of lipid-soluble, titratable chemotherapeutic agents. Given the lack of demonstration of coupling between ATP hydrolysis and drug transport, the resistance to chemically unrelated compounds, and findings of elevated intracellular pH (pHi), it has been proposed that reduced intracellular accumulation of drugs in MDR is due to changes in the pH difference across the plasma membrane. Elevation of pHi or decrease in local extracellular pH (pHo) could reduce the intracellular accumulation of the protonated chemotherapeutic drugs and account for Pgp-mediated MDR. Alternatively, changes in pHi or pHo could increase drug efflux by other mechanisms, such as coupled transport involving H+ or OH-, or allosteric effects on Pgp or other proteins. Both mechanisms could operate independently of the charge of the substrate. The possibility of a role of pHi in drug efflux is important to test because of the clinical significance of the phenomenon of MDR of tumors. We tested this hypothesis and found that MDR can occur in cells with low, normal, or high pHi. Further, resistant cells exhibited reduced steady-state drug accumulation and increased efflux without changes in local pHo. Finally, acute changes in pHi had no appreciable effect on Pgp-mediated drug efflux. We conclude that Pgp-mediated MDR is not a consequence of changes in pHi or pHo.
Beet western yellows virus-associated RNA: an independently replicating RNA that stimulates virus accumulation.
Authors: Passmore B K , Sanger M , Chin L S , Falk B W , Bruening G
Published: May 2006

Infections of plants by subviral RNA agents, alone or in association with virus genomic RNA molecules, are well known. The ST9 strain of beet western yellows virus encapsidates not only the 5.6-kilobase genomic RNA that is typical of luteoviruses, but also a 2.8-kilobase-associated RNA that has a distinct nucleotide sequence. The ST9-associated RNA has been postulated to be a satellite RNA, which by definition would be capable of replicating only in coinfections with beet western yellows virus or closely related viruses. To characterize the associated RNA, we inoculated protoplasts and leaves with in vitro transcripts of the virus genomic RNA and the ST9-associated RNA separately and in combination. Surprisingly, the ST9-associated RNA alone replicated efficiently in both protoplasts and leaves, and it stimulated accumulation of the virus genomic RNA in protoplasts. Thus, the ST9-associated RNA is a newly discovered type of plant infectious agent, which depends on its associated virus, beet western yellows virus, for encapsidation but not for replication.
Cationic drug analysis using matrix-assisted laser desorption/ionization mass spectrometry: application to influx kinetics, multidrug resistance, and intracellular chemical change.
Authors: Rideout D , Bustamante A , Siuzdak G
Published: May 2006

Highly sensitive and convenient analysis of intracellular cationic drugs has been achieved by applying matrix-assisted laser desorption/ionization mass spectrometry (MALD-MS). Tetraphenylphosphonium cation was readily identified and quantified (using methyltriphenylphosphonium cation as an internal standard) at subpicomole levels in crude lysate from < 4 x 10(3) FaDu human hypopharyngeal carcinoma cells. A quantitative MALD-MS time course for tetraphenylphosphonium cation accumulation into FaDu cells was comparable to a time course using scintillation counting with tritiated tetraphenylphosphonium. MALD-MS was also capable of demonstrating the reduced accumulation of the cationic drug rhodamine-123 by DoxR MCF7, a multiply drug-resistant human breast adenocarcinoma cell line, relative to the nonresistant parent line MCF7. In addition, MALD-MS was used to follow a chemical reaction inside intact FaDu cells: the formation of a hydrazone (II-51) from benzaldehyde and an acylhydrazide, 5-[tris(4-dimethylaminophenyl)phosphonio]pentanoyl hydrazide (II-25). These results suggest that MALD-MS may provide a rapid and practical alternative to existing methods for the analysis of cationic drugs, toxins, and their metabolites in cells and tissues.
Capelli's theory, Koszul maps, and superalgebras.
Authors: Brini A , Teolis A G
Published: May 2006

The straightening laws for the enveloping algebra Ukappa(pl(L)) of the general linear Lie superalgebra of a finite dimensional Z2-graded vector space are investigated. An isomorphism Psi from the supersymmetric algebra Super[L L] of pl(L) to Ukappa(pl(L)) is introduced; the isomorphism Psi maps each bitableau of Super[L L] to the Young-Capelli bitableau of Ukappa(pl(L)) parametrized by the same pair of Young diagrams, both in the permanental case and in the determinantal case. The map Psi is shown to be the inverse of the isomorphism introduced by Koszul [Koszul, J. P. (1981) C.R. Acad. Sci. Paris 292, 139-141]. The set of all costandard determinantal Young-Capelli bitableaux is a basis of Ukappa(pl(L)); this basis acts in a triangular way on the basis of Super[L L]given by the set of all standard permanental bitableaux.
Protein kinase A antagonizes platelet-derived growth factor-induced signaling by mitogen-activated protein kinase in human arterial smooth muscle cells.
Authors: Graves L M , Bornfeldt K E , Raines E W , Potts B C , Macdonald S G , Ross R , Krebs E G
Published: May 2006

Stimulation of aortic smooth muscle cells with platelet-derived growth factor BB homodimer (PDGF-BB) leads to the rapid activation of mitogen-activated protein kinase (MAPK) and MAPK kinase (MAPKK). Compounds that increase cAMP and activate protein kinase A (PKA)--prostaglandin E2, isoproterenol, cholera toxin, and forskolin--were found to inhibit the PDGF-BB-induced activation of MAPKK and MAPK. Forskolin, but not the inactive analogue 1,9-dideoxyforskolin, inhibited PDGF-BB-stimulated MAPKK and MAPK activation in a dose-dependent manner. PKA antagonism of MAPK signaling was observed at all doses of PDGF-BB or PDGF-AA. PKA did not inhibit MAPKK and MAPK activity in vitro, and MAPKK and MAPK from extracts of forskolin-treated cells could be activated normally with purified Raf-1 and MAPKK, respectively, suggesting that PKA blocked signaling upstream of MAPKK. Neither PDGF-BB-stimulated tyrosine autophosphorylation of the PDGF receptor beta subunit nor inositol monophosphate accumulation was affected by increased PKA activity, suggesting that PKA inhibits events downstream of the PDGF receptor. This study provides an example of cross talk between two important signaling systems activated by physiological stimuli in smooth muscle cells--namely, the PKA pathway and the growth factor-activated MAPK cascade.
Split decomposition: a technique to analyze viral evolution.
Authors: Dopazo J , Dress A , von Haeseler A
Published: May 2006

A clustering technique allowing a restricted amount of overlapping and based on an abstract theory of coherent decompositions of finite metrics is used to analyze the evolution of foot-and-mouth disease viruses. The emerging picture is compatible with the existence of viral populations with a quasispecies structure and illustrates various forms of evolution of this virus family. In addition, it allows the correlation of these forms with geographic occurrence.
Fibroblasts can induce thymocyte positive selection in vivo.
Authors: Hugo P , Kappler J W , McCormack J E , Marrack P
Published: May 2006

During development in the thymus, thymocytes bearing alpha beta T-cell receptors are selected to mature if the receptors they bear are able to interact in some way with major histocompatibility complex (MHC) proteins expressed on thymic stromal cells. It has been shown that thymus cortical epithelial cells are usually the cells presenting the MHC molecules involved in this process of so-called positive selection. Here we tested the ability of fibroblasts to mediate positive selection in vivo. Fibroblasts transfected with the genes for the MHC I-Ab proteins were injected intrathymically into irradiated H-2k animals reconstituted with H-2bxk F1 fetal liver cells. Eight weeks later, the recipient mice were immunized and shown to contain peptide-specific I-Ab-restricted T cells. This demonstrates the ability of I-Ab-transfected fibroblasts to participate in positive selection. Thus a cell type that is not specialized to process and present antigens in the context of MHC class II molecules can mediate positive selection when transfected with an appropriate MHC molecule. The data also support the idea that the ability to mediate positive selection may not be limited to thymic cortical epithelium.
Overview of imaging science.
Authors: Beck R N
Published: May 2006

The traditional disciplines of science are grounded in the observation and measurement of object properties. Recent advances in digital computer technology have spawned numerous computer-based imaging systems that extend the range of observation and measurement into realms that would otherwise be inaccessible. More importantly, the same set of principles, concepts, strategies, and methods may be used to address the generic issues involved in the production and use of all digitized images. Recognition of this fact is giving rise to the new discipline of imaging science, with its own intellectual agenda.
Crystal structure of a bacterial sialidase (from Salmonella typhimurium LT2) shows the same fold as an influenza virus neuraminidase.
Authors: Crennell S J , Garman E F , Laver W G , Vimr E R , Taylor G L
Published: May 2006

Sialidases (EC 3.2.1.18 or neuraminidases) remove sialic acid from sialoglycoconjugates, are widely distributed in nature, and have been implicated in the pathogenesis of many diseases. The three-dimensional structure of influenza virus sialidase is known, and we now report the three-dimensional structure of a bacterial sialidase, from Salmonella typhimurium LT2, at 2.0-A resolution and the structure of its complex with the inhibitor 2-deoxy-2,3-dehydro-N-acetylneuraminic acid at 2.2-A resolution. The viral enzyme is a tetramer; the bacterial enzyme, a monomer. Although the monomers are of similar size (approximately 380 residues), the sequence similarity is low (approximately 15%). The viral enzyme contains at least eight disulfide bridges, conserved in all strains, and binds Ca2+, which enhances activity; the bacterial enzyme contains one disulfide and does not bind Ca2+. Comparison of the two structures shows a remarkable similarity both in the general fold and in the spatial arrangement of the catalytic residues. However, an rms fit of 3.1 A between 264 C alpha atoms of the S. typhimurium enzyme and those from an influenza A virus reflects some major differences in the fold. In common with the viral enzyme, the bacterial enzyme active site consists of an arginine triad, a hydrophobic pocket, and a key tyrosine and glutamic acid, but differences in the interactions with the O4 and glycerol groups of the inhibitor reflect differing kinetics and substrate preferences of the two enzymes. The repeating "Asp-box" motifs observed among the nonviral sialidase sequences occur at topologically equivalent positions on the outside of the structure. Implications of the structure for the catalytic mechanism, evolution, and secretion of the enzyme are discussed.
Specific prolongation of allograft survival by a T-cell-receptor-derived peptide.
Authors: Goss J A , Alexander-Miller M A , Gorka J , Flye M W , Connolly J M , Hansen T H
Published: May 2006

Allograft rejection results from the specific recognition by host CD8+ T cells of allogeneic major histocompatibility complex (MHC) molecules on the tissue graft. The specificity of this cellular response is determined by the molecular interaction of the T-cell receptor (TCR) on host T cells with the MHC molecule and its bound ligand on the grafted tissue. To better understand the precise manner by which the TCR interacts with the MHC-peptide complex and how to therapeutically intervene, we have studied the allogeneic response to the mouse class I MHC molecule Ld. In this report, the therapeutic potential of a synthetic peptide derived from the TCR V beta 8 variable region that predominates in responses to Ld was tested. This V beta 8-derived peptide was found to dramatically and specifically block the in vivo and in vitro allogeneic response to Ld. Furthermore, this specific blocking is not dependent upon the presence of V beta 8+ effector cells nor does the V beta 8 peptide bind to the Ld ligand binding cleft. We propose that this peptide functions as an antagonist, competing with the native TCR for recognition of the Ld molecule.
Formation of the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase by a disorder-order transition from the unactivated to the activated form.
Authors: Schreuder H A , Knight S , Curmi P M , Andersson I , Cascio D , Brändén C I , Eisenberg D
Published: May 2006

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the key first step in photosynthetic CO2 fixation, the reaction that incorporates CO2 into sugar. In this study, refined crystal structures of unactivated tobacco RuBisCO and activated RuBisCO from spinach and tobacco, in complex with the reaction-intermediate analog 2-carboxyarabinitol 1,5-bisphosphate (CABP), are compared. Both plant enzymes are hexadecameric complexes of eight large and eight small subunits with a total relative molecular mass of approximately 550,000. The comparison of activated and unactivated forms of RuBisCO provides insight into the dynamics of action of this enzyme. The catalytic site, which is open to the solvent in the unactivated enzyme, becomes shielded in the activated CABP complex. This shielding is accomplished by a 12-A movement of the active-site "loop 6" (residues 331-338) and a disorder-order transition of three loops near the active-site entrance, the N terminus, the C terminus, and a loop comprising residues 64-68. All these residues belong to the catalytic large subunit. Domain rotations of about 2 degrees are observed, also tightening the active-site cleft. These observations provide an explanation for the extremely tight binding (Kd < or = 10(-11) M) of the CABP molecule. A striking correlation exists between crystallographic temperature factors in the activated enzyme and the magnitude of the atomic movement upon activation.
Isolation of peptides that inhibit binding of basic fibroblast growth factor to its receptor from a random phage-epitope library.
Authors: Yayon A , Aviezer D , Safran M , Gross J L , Heldman Y , Cabilly S , Givol D , Katchalski-Katzir E
Published: May 2006

Basic fibroblast growth factor (bFGF) is known to bind to its cell-surface receptors with high affinity and in a heparin-dependent manner. In an attempt to predict the receptor recognition site on bFGF we screened phage-epitope libraries with monoclonal antibodies DG2 and DE6, which inhibit bFGF binding to its receptor. On the affinity-isolated phages, we identified several peptide sequences as the putative antibody-binding epitopes on bFGF. The identified library epitopes shared the consensus sequence Pro-(Pro/Ser)-Gly-His-(Tyr/Phe)-Lys, corresponding to two continuous protein sequences of bFGF: Pro-Pro-Gly-His-Phe-Lys and Arg-Thr-Gly-Gln-Tyr-Lys at amino acids 13-18 and 120-125 of bFGF, respectively. Synthetic peptides of the corresponding phage epitopes or of the above bFGF sequences specifically inhibited binding of the antibodies to bFGF, blocked binding of bFGF to its high-affinity receptor, and inhibited basal and bFGF-induced proliferation of vascular endothelial cells at submicromolar peptide concentrations. The potent inhibition of bFGF binding and biological activity by peptides recognized by the antibodies suggests that these sequences are functionally involved in receptor binding and may constitute part of the receptor-binding determinants on bFGF.
RNA fingerprinting using arbitrarily primed PCR identifies differentially regulated RNAs in mink lung (Mv1Lu) cells growth arrested by transforming growth factor beta 1.
Authors: Ralph D , McClelland M , Welsh J
Published: May 2006

RNA fingerprinting using arbitrarily primed PCR (RAP) samples an RNA population and allows the detection of differentially expressed genes between two or more populations. This method was applied to mink lung epithelial cells, which respond to treatment with transforming growth factor beta (TGF-beta) by undergoing cell cycle arrest at or near the G1/S-phase boundary. The steady-state abundances of approximately 200 RNAs were surveyed, a few of which displayed differential regulation in response to TGF-beta 1. Three products were isolated, cloned, and sequenced. One differentially regulated RNA corresponded to cyclin A, a gene known to be required for the progression of mammalian fibroblasts through S phase. Northern blot analysis confirmed that the cyclin A mRNA steady-state abundance decreased dramatically in response to a 24-hr TGF-beta 1 treatment and also in response to cell cycle arrest caused by contact inhibition. A second RAP product corresponded to a previously unknown 7.5-kb mRNA, the level of which decreased dramatically in response to TGF-beta 1 treatment. Unlike the cyclin A mRNA, the abundance of this transcript did not decrease in response to growth arrest induced by contact inhibition. A third RAP product corresponded to the mRNA for osteonectin, an extracellular matrix protein. The abundance of this mRNA increased at least 2-fold during TGF-beta 1 treatment. This observation is consistent with other reports of increases in extracellular matrix proteins during TGF-beta treatment. RAP should be able to identify many of the genes that change in steady-state expression during the cell cycle.
Characterization of broken DNA molecules associated with V(D)J recombination.
Authors: Roth D B , Zhu C , Gellert M
Published: May 2006

We previously demonstrated that DNA molecules with double-strand breaks at variable-(diversity)-joining [V(D)J] recombination signal sequences are relatively abundant in mouse thymocytes. This abundance strongly suggests that the mechanism of V(D)J recombination involves double-strand cleavage at recombination signals. As a first step toward understanding the mechanism of cleavage, we used a sensitive PCR assay to characterize the structure of one class of cleavage products, the signal ends, in detail. Here we demonstrate that most of these ends are blunt and terminate in 5' phosphoryl groups. Virtually all of the flush signal ends are full length. A minor subpopulation of broken ends terminates in short single-strand extensions. We have found no evidence for covalent DNA-protein linkages involving the signal ends. These data allow further refinement of the double-strand cleavage model for V(D)J recombination.
Efficacy of beta 1-adrenergic receptors is lower than that of beta 2-adrenergic receptors.
Authors: Levy F O , Zhu X , Kaumann A J , Birnbaumer L
Published: May 2006

We investigated the relative activity at which fully occupied human beta 1- and beta 2-adrenergic receptors (beta 1AR and beta 2AR) activate the stimulatory G protein (Gs)/adenylyl cyclase (AC) system in isolated membranes. The receptors were cloned and coexpressed in permanent cell lines at beta 1/beta 2 ratios that varied from 1:2 to 3:1 and at total receptor abundance that ranged from 8 to 2200 fmol/mg of membrane protein. Cell lines expressing beta 1AR or beta 2AR alone were also obtained. Competitive inhibition of isoproterenol-stimulated AC activity by the beta 2-selective antagonist ICI 118551 showed in all cases that maximal stimulation elicited by beta 1AR was lower than when it was elicited by equivalent densities of beta 2AR. This was especially noticeable at limiting concentrations of receptor, where the beta 1AR-mediated effect was < 10% of that mediated by beta 2AR. At receptor concentrations > 1000 fmol/mg of protein, stimulation by beta 2AR appeared to reach a maximum, while stimulation by beta 1AR continued to increase, so that at 3200 fmol/mg, beta 1AR-stimulated activity was 80% of beta 2AR-stimulated activity. It is clear that the degree to which a given receptor system is able to activate the Gs/AC system depends not only on its abundance but also on an activity parameter determined by the nature of the receptor, which we refer to as receptor efficacy. For human beta ARs, this efficacy parameter is much lower for the beta 1 subtype than for its beta 2 counterpart. The more effective stimulation of AC through beta 2AR than through beta 1AR is an inherent property of the receptor and not the cell in which it is expressed.
Highly identical cassettes of gene regulatory elements, genomically repetitive and present in RNA.
Authors: Nemer M , Bai G , Stuebing E W
Published: May 2006

A region in the first intron of a metallothionein-encoding gene of the sea urchin Strongylocentrotus purpuratus (SpMTA gene) regulates its 5' promoter activity. Within this region is a 290-bp cassette of six sequence motifs that are present in other genes in this species and posited to operate as regulatory elements. The cassette, present at high multiplicity in the genome, was used to screen genomic DNA clones. Of these, six diverse individuals were partially sequenced and found to have segments 94% identical to the 290-bp cassette in the SpMTA gene. Their next 80 bp diverged from the SpMTA sequence but were highly identical among the six non-SpMTA clones and contained an additional regulatory motif. These diverse clones thus contained 370-bp cassettes of an overall 94% sequence identity and an apparent content of seven regulatory elements. The regulatory cassettes were transposon-like, insofar as the termini of the highly identical regions consisted of 24- to 25-bp inverted repeats, bracketed by 6- to 9-bp direct repeats in the divergent regions. In addition to being in transcripts of the SpMTA intron, the cassette was found in other sea urchin embryo poly(A)+ RNAs, in eggs and embryos, and enriched in pluteus ectoderm. The cassette sequence was present in moderate abundance in transcripts in both sense and antisense orientation. We report the presence of a transposon-like cassette of regulatory elements that is also represented in RNA, which potentially could function differently from previously described transposons.
Rapid assembly of the bacteriophage T4 core replication complex on a linear primer/template construct.
Authors: Kaboord B F , Benkovic S J
Published: May 2006

DNA synthesis on a primed DNA substrate by bacteriophage T4 requires the assembly of a core replication complex consisting of the T4 DNA polymerase, a single-stranded binding protein (32 protein), and the accessory proteins 44/62 and 45. In this paper, we demonstrate the successful assembly of this core complex on a short linear primer/template system at levels of accessory proteins equivalent to the concentration of primer 3' ends. The key to this assembly is the presence of streptavidin molecules bound at each end of the DNA substrate via biotin moieties incorporated into the template strand. Streptavidin serves to block the ends of the primer/template, thus preventing translocation of the accessory proteins away from the site of assembly and their subsequent dissociation from the ends of the primer/template. Complex assembly on this substrate requires ATP and the presence of both the 44/62 and 45 proteins. The time required for assembly of a full enzyme equivalent of complex in our system is approximately 2 s.
Mechanism for the T4 lymphopenia of AIDS Silvio Micali
Authors: Micali Silvio
Published: May 2006

I suggest that the T4 lymphopenia of AIDS may be caused by antibodies raised against the human immunodeficiency virus that block the generation of T4 cells.