bluuebunny/crossref_metadata_2025 huggingface dataset:
Charge pair model of bioenergetics: redox enzymes.
Authors: Kemeny G , Mahanti S D
Published: May 2006

A model of electron transfer between redox enzymes is constructed on the assumption that the apoenzyme contains orientable units, which are tentatively identified with flipping amino acids. The model is based on the entatic state hypothesis, and the rate of electron transfer is derived.
Natural antibodies in sera from healthy humans to antigens on surfaces of type C RNA viruses and cells from primates.
Authors: Aoki T , Walling M J , Bushar G S , Liu M , Hsu K C
Published: May 2006

Sera from healthy humans contained naturally occurring antibody against group- or subgroup-specific antigen on the envelope of the following type C viruses isolated from primates: gibbon ape leukemia virus, simian (woolly monkey) sarcoma virus, baboon endogenous type C virus, and putative human type C viruses [HL23V isolated from blood cells of a patient with acute myelogenous leukemia (HL23) and HEL-12V from human embryonic diploid cells (CIH-32)]. Two sera also reacted with C57BL/6 mouse leukemia induced by Friend virus. These results were obtained by indirect immunoelectron microscopy with various virus-producing cells and by absorption tests using as targets gibbon lymphosarcoma cells that release gibbon ape leukemia virus. In a previous report, the presence of natural antibody in sera from healthy gibbon apes was demonstrated. When the specificities of the human and gibbon natural antibodies were compared, the human natural antibody reacted with two nonproducing culture cell lines of human lymphocytic leukemia (CEM-A and MOLT) and with human embryonic diploid (CIH-1(V-) cells [which became type C virus-producing CIH-32(V+) cells after many passages], but did not react with normal gibbon spleen monolayer cells. In contrast, gibbon natural antibody showed no reaction with CEM-A, MOLT, and CIH-1(V-) cells but reacted with gibbon spleen monolayer cells. Neither human nor gibbon natural antibody that was reactive with gibbon ape leukemia virus crossreacted with feline leukemia virus and mouse wild-type AKR leukemia virus. The gibbon lymphosarcoma cells releasing gibbon ape leukemia virus were used in a screening study of sera from healthy humans. Out of 72 sera screened by indirect immunoelectron microscopy using this system, 55 were positive (76%), i.e., 26 out of 35 males (74%) and 29 out of 37 females (78%). The highest incidence of antibody production was in 1- to 10-year-olds and 31- to 40-year-olds, with the adults exhibiting higher levels. Differences in incidence of natural antibody were not found to be sex-linked. These findings suggest that type C RNA viruses related to the gibbon ape leukemia virus and simian (woolly monkey) sarcoma virus family as well as the baboon endogenous type C virus family may be widespread in humans.
Medium-induced radiationless transitions and effect of solvent on radiationless transitions
Authors: Lin S. H. , Lee S. T. , Yoon Y. H. , Eyring H.
Published: May 2006

The purpose of this paper has been to investigate the effect of solvent on radiationless transitions. Two types of the solvent effect have been studied: one is the so-called medium-induced radiationless transition, i.e., the radiationless transition induced by the interaction between the solute and solvent, and the other is the effect of solvent on the radiationless transition through the change in energy gap induced by the solute-solvent interaction.
Bernstein polynomials and Milnor algebras
Authors: Kochman Fred
Published: May 2006

Let
f
be an analytic germ on C

n
+1

. Then there is an analytic linear partial differential operator
P
with polynomial dependence on
s
, and a polynomial
b
(
s
), such that
Pf

s
+1

=
b
(
s
)

f
s

. This paper contains a simple existence proof and geometric interpretation in the case when
f
has an isolated critical zero at the origin, and is contained in its Jacobian ideal of first partial derivatives.
Myosin-mediated Ca++-regulation of actomyosin-adenosinetriphosphatase from porcine aorta.
Authors: Frederiksen D W
Published: May 2006

The nature of the Ca++-sensitive regulatory system for contraction of vascular smooth muscle is considered in detail. Smooth muscle actomyosin prepared from the medial layer of porcine aorta is analyzed chemically and its ATPase (adenosinetriphosphatase, EC 3.6.1.14) activities are investigated. The Mg++-ATPase of this vascular actomyosin is sensitive to the concentration of calcium in the range from 0.1 mM to 10 nM. The calcium sensitivity is maintained in the presence of excess pure actin from skeletal muscle and is abolished in the presence of pure skeletal myosin. It is concluded that the regulatory properties of this natural actomyosin from smooth muscle are in the myosin portion of the protein complex and are not bound to actin-tropomyosin as in skeletal muscle.
Transfer of tRNAs to somatic cells mediated by Sendai-virus-induced fusion.
Authors: Kaltoft K , Zeuthen J , Engbaek F , Piper P W , Celis J E
Published: May 2006

tRNAs from yeast (tRNAPhe and 4S RNA) and Escherichia coli (suIII+ tRNAITyr) have been transferred to mouse cells by means of a two-step transfer procedure [Loyter, Zakai, and Kulka (1975) J. Cell Biol. 66, 292-304; Schlegel and Rechsteiner (1975) Cell 5, 371-379]. In the first stage of the transfer tRNAs were incorporated into rabbit red blood cells (RBCs). Thereafter, the loaded erythrocytes were fused with recipient mouse cells by means of Sendai virus. At least 0.3-0.4% of the total input of tRNA used to load the RBCs could be transferred to mouse cells. Of the tRNA incorporated in the mouse cells, at least 50% could be recovered in the form of intact tRNA molecules when yeast 4S RNA was used. With E. coli suIII+ tRNAITyr a rather smaller proportion of the tRNA remained intact (33%). Although the loading of tRNA into RBCs is not essential for its uptake, we find that the transfer is four times more efficient with RBCs as a vehicle for the injection. Significantly, a fraction (2%) of the recipient cells possessed much more incorporated tRNA than the average cell when Sendai virus and loaded RBCs were used. Such cells were not found in control experiments in which tRNA uptake was induced by Sendai virus alone.
Increased ion permeability of planar lipid bilayer membranes after treatment with the C5b-9 cytolytic attack mechanism of complement.
Authors: Michaels D W , Abramovitz A S , Hammer C H , Mayer M M
Published: May 2006

The ion permeability of planar lipid bilayers, as measured electrically, was found to increase modestly upon treatment with purified complement complex C5b,6 and complement components C7 and C8. The subsequent addition C9 greatly amplified this change. No permeability changes occurred when components were added individually to the membrane, or when they were used in paired combinations, or when C5b, C7, C8, and C9 were admixed prior to addition. Thus, there is a significant parallel between the permeability changes induced in the model membrane and damage produced in biological membranes by the C5b-9 complement attack sequence. The efficiency of membrane action by C5b-9 was critically dependent on the order in whcih components were added to the membrane. There were also differences in the electrical properties of membranes treated with C5b-8 and C5b-9, though in both cases the enhanced bilayer permeability is best attributed to the formation of trans-membrane channels. Collectively, the data are consistent with the hypothesis that the mechanism of membrane action by complement involves the production of a stable channel across the lipid bilayer, resulting in cell death by colloid-osmotic lysis.
The unusual Favorskii-Nazarov reaction of dicyclopropyl ketone
Authors: Olah George A. , Prakash G. K. Surya , Liang Gao
Published: May 2006

Dicyclopropyl ketone under Favorskii-Nazarov reaction conditions neither gave tetracyclopropylethylene glycol nor 1,1,4,4-tetracyclopropyl-1,4-butanediol by ether incorporation as expected. The hitherto unknown 1,1,5-tricyclopropyl-1-hydroxypentan-5-one is obtained, presumably through the intermediacy of a dianion which nucleophilically attacks the neutral ketone through the cleavage of the cyclopropyl bond.
DNA dependent synthesis of protein L12 from escherichia coli ribosomes, in vitro.
Authors: Chu F , Kung H F , Caldwell P , Weissbach H , Brot N
Published: May 2006

The in vitro synthesis of ribosomal protein L12 has been obtained in a coupled system with DNA extracted from the transducing phage lambdarifd18 as template. In addition, a second protein (molecular weight of 16,000) with immunological, chemical, and ribosome-binding characteristics similar to L12 is formed in this in vitro system. The synthesis of both proteins is depressed by one-half when guanosine-5'-diphosphate-3'-diphosphate is added to the reaction mixture.
Identification of an intracellular precursor to DNA excreted by human lymphocytes.
Authors: Rogers J C
Published: May 2006

Phytohemagglutinin-stimulated human peripheral blood lymphocytes in vitro synthesize DNA that is excreted into the culture medium. When such cells are pulse-labeled with [3H]thymidine during the peak of DNA synthesis on day 3 of culture, then cultured for 3 more days in the absence of isotope, labeled DNA moves slowly into the Hirt supernatant cell fraction from the pellet fraction containing chromosomal DNA,and then into the culture medium. The number of copies of excreted DNA sequences in the Hirt pellet fraction was determined for lymphocytes harvested on days 3,4, and 6 after stimulation and compared to the number found in resting lymphocyte DNA and in placenta DNA. While resting lymphocyte and placenta DNAs contain one to two copies of sequences similar to excreted DNA per haploid genome, stimulated lymphocytes on days 3 and 4 of culture contain 3- to 4-fold more copies; by day 6 of culture, stimulated lymphocytes contain only 1- to 2-fold more copies than resting lymphocytes. Thus, phytohemagglutinin induces lymphocytes to selectively replicate several copies of a limited portion of their genome, copies which are then excreted into the culture medium. As determined by reassociation kinetics analysis, a high-molecular-weight DNA fraction from the Hirt supernatant contains sequences found in excreted DNA. This DNA may represent an intermediate formed prior to release of excreted sequences from the cells.
Bandage-backfall reaction: occurs in infancy, hypothalamic damage, and catalepsy.
Authors: Teitelbaum P , Wolgin D L , De Ryck M , Marin O S
Published: May 2006

In cataleptic clinging, produced either by catecholamine-blocking drugs or lateral hypothalamic damage in adult cats, rats, or monkeys, bandaging the face and neck causes the head to fall backwards.Early in development, a similar reaction can be seen in normal undrugged infants.
Anesthetic stimulation of insect water receptors.
Authors: Dethier V G , Goldrich-Rachman N
Published: May 2006

Halothane, chloroform, and carbon tetrachloride, in the vapor and liquid phases, stimulate the water receptor of the blowfly Phormia regina. There are three successive phases of response to long-lasting stimulation by halothane: stimulation of the water receptor for the first 19 sec, narcosis for the next 80 sec, and stimulation of all receptors after 80 sec. The behavior of the fly is correlated with these phases. A thirsty fly extends its proboscis and attempts to drink during the first phase, withdraws its proboscis during the second, and extends in a manner characteristic of aversion in the third. A water-satiated fly responds only in the third phase. These results indicate that both the labeled line and the across-fiber hypothesis of sensory coding apply to the blowfly. At the level of sensory transduction the data do not rule out the possibility that streaming potentials are normally involved in stimulation of the water receptor. They are also consistent with a hypothesis that neutral narcotics stimulate the water receptor by facilitating the passage of sodium ions through the dendritic membrane.
Rhodopsin in model membranes: charge displacements in interfacial layers.
Authors: Trissl H W , Darszon A , Montal M
Published: May 2006

A model membrane was developed in which interfacial layers of rhodopsin were reoriented onto one side of a thin Teflon film separating two aqueous compartments. Flashes evoked fast photoelectric signals (1 ms) that originated from capacitative charge displacements of oriented rhodopsin upon bleaching. The photoelectric responses of rhodopsin in the model membrane are compared with the early receptor potential of photoreceptor cells; it is concluded that the signals in both systems originate from the same mechanism.
Convex programs having some linear constraints
Authors: Duffin R. J.
Published: May 2006

The problem of concern is the minimization of a convex function over a normed space (such as a Hilbert space) subject to the constraints that a number of other convex functions are not positive. As is well known, there is a dual maximization problem involving Lagrange multipliers. Some of the constraint functions are linear, and so the Uzawa, Stoer, and Witzgall form of the Slater constraint qualifications is appropriate. A short elementary proof is given that the infimum of the first problem is equal to the supremum of the second problem.
Gravitational interaction of hadrons: Band-spinor representations of
GL(n,R)
Authors: Ne'eman Yuval
Published: May 2006

We demonstrate the existence of double-valued linear (infinite) spinorial representations of the group of general coordinate transformations. We discuss the topology of the group of general coordinate transformations and its subgroups
GA(nR), GL(n,R), SL(nr)
for
n
= 2,3,4, and the existence of a double covering. We present the construction of band-spinor representations of
GL(n,R)
in terms of Harish-Chandra modules.

It is suggested that hadrons interact with gravitation as band-spinors of that type. In the metric-affine extension of general relativity, the hadron intrinsic hypermomentum is minimally coupled to the connection, in addition to the coupling of the energy momentum tensor to the vierbeins. The relativistic conservation of intrinsic hypermomentum fits the observed regularities of hadrons:
SU
(6) (∼ spin independence), scaling, and complex-
J
trajectories. The latter correspond to volume-preserving deformations (confinement?) exciting rotational bands.
Action of nucleotide phosphotransferase of Escherichia coli on nicotinamide riboside and nicotinamide mononucleotide.
Authors: Brunngraber E F , Chargaff E
Published: May 2006

The action of the nucleotide phosphotransferase of Escherichia coli on nicotinamide riboside and on its 5'-phosphate results in the addition of one phosphate moiety to each of the substrates. Although the proof is not conclusive, it is likely that the phosphate group is transferred to the 3'-hydroxyl of the ribose. This is in contrast to the behavior of the enzyme toward NAD in which only the adenylic acid portion is phosphorylated enzymically.
Synthesis of phiX174 viral DNA in vitro depends on phiX replicative form DNA.
Authors: Sumida-Yasumoto C , Hurwitz J
Published: May 2006

A cell-free system that catalyzes phiX174 replicative form I (supercoiled circular duplex, RFI)-dependent phiX174 DNA synthesis has been isolated from Escherichia coli infected with phiX174 phage. The products formed with such preparations are viral strands as judged by hybridization to poly(U,G) followed by equilibrium centrifugation in CsCl. This phiX174 DNA-synthesizing involves formation of DNA-protein complexes that sediment in neutral sucrose with S values of 50, 60-70, and higher. The 50S complex contained a rolling-circle replicative intermediate DNA with an extended tail of single-stranded viral DNA. The DNA contained in the 60-70S region was a mixture of circular and linear single-stranded DNA, RFI, and RFII with an extended single-stranded tail. Such complexes have been isolated during in vivo progeny phiX174 DNA synthesis [Fujisawa, H. & Hayashi, M. (1976) J. Vriol. 19,409]. In vitro, maximal phiX174 DNA synthesis was shown to require the genetically defined proteins E. coli dna B, dna C, dna G, dna Z, rep. phiX174 gene A product, and other phiX174 coded proteins. The synthesis of phiX174 DNA is ATP-dependent and is inhibited by nalidixic acid and novobiocin but is resistant to rifampicin.
Chemical basis for brain-specific serine transfer RNAs.
Authors: Rogg H , Müller P , Keith G , Staehelin M
Published: May 2006

Serine tRNA from rat brain can be resolved into six isoaccepting species. Three of these species show the same chromatographic behavior as the seryl tRNAs from other rat organs, whereas the remaining species appear to be specific for brain. The isoacceptor tRNAs were purified to homogeneity by chromatography on benzoylated DEAE-cellulose followed by reversed-phase chromatography. We found that the additional species of serine tRNA in brain differ from their counterparts derived from other rat organs by a lack of a specific guanosine ribose-methylation in the dihydrouridine loop. In addition, when total liver tRNA was compared with total brain tRNA, the same degree of undermethylation with respect to 2'-O-methylguanosine was found as a general phenomenon.
Steroidogenic activity of fragments of adrenocorticotropin with arginine in residue positions 3 and 5.
Authors: Jean-Baptiste E , Draper M W , Rizack M A
Published: May 2006

The maximal steroidogenic response (Smax) to adrenocorticotropin (ACTH) is enhanced by the substitution of arginine in position 3. Though the Smax of adrenocorticotropin-(3-10)-octapeptide [ACTH-(3-10)] is only 20% of ACTH-(1-24) in isolated rabbit adrenal cells and 10% in rat cells, [Arg3]ACTH-(3-10) has an Smax comparable to that of the longer peptide. Activity determined from the midpoints of dose-response curves (A50), however, is several orders of magnitude less. The Smax of ACTH-(4-10) is not significantly different from that of the 3-10 analog. Substitution of arginine in the 5 position of ACTH-(4-10) decreases activity for rabbit cells, but does not affect activity for rat cells. The substitution of arginine in the 5 position of ACTH-(1-20) markedly decreases Smax in rabbit but not rat cells. The Smax of [Arg 3,5)]ACTH-(3-10), containing both substitutions, is greater than that of ACTH-(3-10), but much less than that of [Arg3]acth-(3-10) in both species studied. These findings contrast with those in the rabbit adipocyte, where both arginine-containing ACTH analogs have enhanced activity and the effects of both substitutions in a single peptide are additive.
Activation of guanylate cyclase by superoxide dismutase and hydroxyl radical: a physiological regulator of guanosine 3',5'-monophosphate formation.
Authors: Mittal C K , Murad F
Published: May 2006

Partially purified soluble rat liver guanylate cyclase [GTP pyrophosphate-lyase (cyclizing), EC 4.6.1.2] was activated by superoxide dismutase (superoxide: superoxide oxidoreductase, EC 1.15.1.1). This activation was prevented with KCN or glutathione, inhibitors of superoxide dismutase. Guanylate cyclase preparations formed superoxide ion. Activation by superoxide dismutase was further enhanced by the addition of nitrate reductase. Although guanylate cyclase activity was much greater with Mn2+ than with Mg2+ as sole cation cofactor, activation with superoxide dismutase was not observed when Mn2+ was included in incubations. Catalase also decreased the activation induced with superoxide dismutase. Thus, activation required the formation of both superoxide ion and H2O2 in incubations. Activation of guanylate cyclase could not be achieved by the addition of H2O2 alone. Scavengers of hydroxyl radicals prevented the activation. It is proposed that superoxide ion and hydrogen peroxide can lead to the formation of hydroxyl radicals that activate guanylate cyclase. This mechanism of activation can explain numerous observations of altered guanylate cyclase activity and cyclic GMP accumulation in tissues with oxidizing and reducing agents. This mechanism will also permit physiological regulation of guanylate cyclase and cyclic GMP formation when there is altered redox or free radical formation in tissues in response to hormones, other agents, and processes.
Induction of DNA synthesis in BALB/c 3T3 cells by serum components: Reevaluation of the commitment process
Authors: Pledger W. J. , Stiles C. D. , Antoniades H. N. , Scher C. D.
Published: May 2006

Serum contains a growth factor derived from platelets and also growth factors derived from platelet-poor plasma. Extracts of heated (100°) human platelets function synergistically with platelet-poor plasma to induce DNA synthesis in quiescent, density-inhibited BALB/c 3T3 cells. Platelet-poor plasma alone did not induce DNA synthesis. Cells exposed to platelet extracts became competent to enter the cell cycle, but the rate of entry into the S phase depended upon the concentration of platelet-poor plasma. The time required for the induction of this competent state was a function of the concentration of the platelet extract. A 2-hr exposure to 100 μg of the platelet extract at 37° caused the entire cell population to become competent to enter the S phase. At 4° or 25° the cells did not become competent to synthesize DNA. The platelet extract-induced competent state was stable for at least 13 hr after removal of the platelet extract; however, in the absence of platelet-poor plasma, these competent cells did not progress through the cell cycle. The addition of an optimal concentration of platelet-poor plasma (5%) to these competent cells initiated cell cycle traverse with a rapid, first-order entry of cells into the S phase beginning 12 hr after addition of the plasma. The addition of a suboptimal concentration of the plasma (0.25%) did not increase the rate of cell entry into the S phase. Thus, the induction of DNA synthesis in quiescent BALB/c 3T3 cells can be resolved into at least two phases, controlled by different serum components: (
i
) competence, induced by the platelet-derived growth factor; and (
ii
) progression of competent cells into the cell cycle, mediated by factors in platelet-poor plasma.
Specific factors influencing histotypic aggregation of chick embryo hepatocytes.
Authors: Sankaran L , Proffitt R T , Petersen J R , Pogell B M
Published: May 2006

Conditions are described for the reproducible assay of substances affecting the in vitro rate of aggregation of isolated chick embryo hepatocytes. Two low molecular weight (less than 1000) fractions--one that promotes hepatocyte aggregation (HAP) and the other that inhibits this stimulation (HAI)--have been isolated and partially purified from adult chicken liver. One major active component of HAP was identified as taurine (2-aminoethanesulfonate). The presence of HAP during the entire time of assay was required for largest aggregate formation. HAP had no effect on aggregation of chick embryo neural retina, kidney, or heart cells. Our results and the fact that puromycin completely inhibits aggregate formation suggest that HAP and HAI influence the specific synthesis and interaction of membrane macromolecules involved in the aggregation process.
Cystinotic fibroblasts accumulate cystine from intracellular protein degradation.
Authors: Thoene J G , Oshima R G , Ritchie D G , Schneider J A
Published: May 2006

Fibroblasts derived from patients with cystinosis, an autosomal recessive condition, accumulate the disulfide amino acid cystine within lysosomes. The metabolic defect leading to the cystine accumulation and the source from which the cystine is derived are unknown. In this report we present data showing that cystine in these cells accumulates from the degradation of endogenous protein. This conclusion is based upon: (i) no demonstrable synthesis of cystine from serine; (ii) no difference in cystine reaccumulation between glutathione-depleted and non-glutathione-depleted cystinotic cells; (iii) recovery of labeled cystine only when the protein pool is labeled; (iv) reversible inhibition of cystine reaccumulation by known inhibitors of lysosomal protein degradation (chloroquine and NH4Cl).
Identification of amber and ochre mutants of the human virus Ad2+ND1.
Authors: Gesteland R F , Wills N , Lewis J B , Grodzicker T
Published: May 2006

Although human adenoviruses grow poorly in monkey cells, this defect can be overcome either by coinfection of cells with simian virus 40 (SV40) or by insertion of the relevant portion of the SV40 genome into the adenovirus genome to form an adenovirus-SV40 hybrid virus. The nondefective adenovirus-2-SV40 hybrid virus, Ad2+ND1, contains an insertion of 17% of the SV40 genome, which codes for at least part of a 30,000 dalton protein. A set of Ad2+ND1 host-range mutants that have lost the ability to grow in monkey cells and behave as point mutants fail to synthesize the 30,000 dalton ND1 protein. Translation in vitro of SV40-specific mRNA from mutant-infected cells produces unique short polypeptides instead of the 30,000 dalton protein. Here we show that this set of host-range mutants includes both ochre and amber nonsense mutations. When the SV40-specific mRNA from the host-range mutants is translated in vitro to produce the polypeptide fragments, yeast suppressor tRNA can partially restore synthesis of wild-type-size 30,000 dalton protein. By this assay, one mutant is ochre and two are amber.
Enzyme replacement therapy in Gaucher's disease: preliminary clinical trial of a new enzyme preparation.
Authors: Beutler E , Dale G L , Guinto D E , Kuhl W
Published: May 2006

A patient with far-advanced adult type Gaucher's disease was treated with solubilized, highly purified placental glucocerebrosidase administered after entrapment in human erythrocytes or by direct intravenous injection. In some instances the enzyme-containing erythrocytes were coated with gamma globulin. No toxic side effects were observed after enzyme infusion. There were suggestive, but not conclusive, findings that enzyme infusion may have been beneficial. After therapy, there was a decrease in transfusion requirement, some improvement of liver function, possible decrease in liver size, and relief of subjective symptoms. Erythrocyte and plasma glucocerebroside levels were unchanged during therapy, but there was a possibly significant decrease in leukocyte and platelet levels of the glycolipid. No changes occurred in serum acid phosphatase or angiotensin-converting enzyme activity.
Regulatory function of simian virus 40 DNA replication for late viral gene expression.
Authors: Graessmann A , Graessmann M , Mueller C
Published: May 2006

Inhibition of simian virus 40 (SV40) DNA synthesis prevents late but not early viral gene expression in infected cells. To test whether the late SV40 template specificity is elicited by replicative intermediate DNA molecules (RI-DNA), we isolated subcellular fractions containing RI-DNA from SV-40-infected monkey cells and microinjected these preparations into various cell lines under conditions in which viral DNA synthesis was blocked. Late SV40 gene expression (V-antigen synthesis) was obtained by microinjection of wild-type RI-DNA or temperature-sensitive mutant A7 RI-DNA preparations at 37 degrees or 41.5 degrees, respectively, while SV40 native superhelical DNA (DNA I) at a 10-fold higher concentration failed to induce V-antigen synthesis under the restrictive conditions. V-antigen synthesis was also obtained by microinjection of partially denatured SV40 DNA or a high number of randomly nicked DNA molecules (DNA II) in the absence of DNA synthesis; both single-stranded regions and nicks are specific features of RI-DNA molecules.
Analytical and graphical examination of strong binding by half-of-sites in proteins: Illustration with aspartate transcarbamylase
Authors: Klotz Irving M. , Hunston Donald L.
Published: May 2006

In multiple binding of ligands to a protein, the binding sites may seem to behave as if they are partitioned equally between two modalities. This paper analyzes three different molecular situations in which two actual assemblages appear: (
i
) two classes of sites exist at the outset in the ligand-free macromolecule; (
ii
) all sites are initially identical but after half are occupied, the affinity of the residual ones is altered; (
iii
) all sites are initially identical but they interact in a pairwise manner. The contours of affinity profiles—graphs of normalized stoichiometric binding constants (

iK
i

) versus stoichiometric step number
i
—are examined for each situation to provide a basis for discriminating among them. Proper procedures for evaluating the site binding constants are then described. To illustrate these procedures, published experimental data for two real systems, binding of substrate or modifier by the enzyme aspartate transcarbamylase (carbamoylphosphate: L-aspartate carbamoyltransferase, EC 2.1.3.2), are scrutinized and the meaning of the calculated binding parameters is examined. The results demonstrate concretely that site binding constants cannot be specified without assuming a particular molecular model, but the stoichiometric constants can be assigned unambiguously without regard to the type of behavior at the individual sites.
Emission Mössbauer study of the stereochemical trigger that initiates cooperative interaction of hemoglobin subunits.
Authors: Srivastava T S , Tyagi S , Nath A
Published: May 2006

An important feature of Perutz's trigger mechanism for cooperativity in the reversible oxygenation of hemoglobin (Hb) is the tension along the histidine--metal linkage in deoxyHb and deoxycobaltohemoglobin (deoxy CoHb), supposedly due to the pull exerted by the globin on the metal atom. We have attempted to verify the existence of this pull by studying the emission Mössbauer spectra of deoxy 57CoHb and oxy 57 CoHb at different temperatures. The emission Mössbauer spectrum for none of the cobalt Hbs agrees with the absorption spectrum of the corresponding iron analog and, moreover, the spectrum of deoxy 57CoHb is characteristic of the intermediate-spin iron. These observations indicate that the daughter 57Fe atom is "frozen" almost in the same spatial situation as that of the parent 57Co. The protein is apparently holding the cobalt atom in position rather rigidly and, after the electron-capture decay of the 57Co atom, the protein does not permit the daughter 57Fe to move to a position characteristic of the iron atom.
On subthreshold solutions of the Hodgkin-Huxley equations.
Authors: Sirovich L , Knight B W
Published: May 2006

Subthreshold solutions of the Hodgkin-Huxley equations are considered here by means of the linearized forms of these equations. An asymptotic theory is obtained, based on dimensional analysis and scaling arguments. Explicit expressions for the crest speed are obtained and are shown to be in good agreement with experiment, with computation, and with an exact asymptotic value which is also obtained here.
Netropsin-poly(dA-dT) complex in solution: structure and dynamics of antibiotic-free base pair regions and those centered on bound netropsin.
Authors: Patel D J , Canuel L L
Published: May 2006

The biphasic duplex-to-strand transition for the netropsin.poly(dA-dT) complex, phosphate/drug mole ratio (P/D) = 50, has been investigated by high-resolution proton nuclear magnetic resonance (NMR) spectroscopy at the nonexchangeable base and sugar protons in 0.1 M cacodylate solution. The NMR spectral parameters monitor the structure and dynamics of the opening of antibiotic-free base pair regions (55 degrees-65 degrees) and the opening of base regions centered on bound netropsin (90 degrees-100 degrees). The gradual addition of netropsin to poly(dA-dT) results in structural perturbations extending into the antibiotic-free base pair regions that begin to level off above 0.02 antibiotic molecules per polynucleotide phosphate (P/D = 50). The NMR chemical shift parameters at the antibiotic-free base pair regions in the P/D = 50 complex suggest changes in the glycosidic torsion angles of the deoxyadenosine and thymidine residues and less pronounced changes in the base pair overlap geometries. The dissociation rates of the antibiotic-free base pair regions are at least an order of magnitude slower in the P/D = 50 netropsin.poly(dA-dT) complex compared to related parameters for poly(dA-dT) and the P/D = 50 ethidium bromide-poly(dA-dT) complex. There is decreased segmental mobility at the antibiotic-free strand regions in the temperature range (65 degrees-90 degrees) between the two transitions in the biphasic melting curve of the P/D = 50 netropsin-poly(dA-dT) complex. Netropsin stabilizes at least five base pairs, with their center at its binding site.
Minimal coupling and the symplectic mechanics of a classical particle in the presence of a Yang-Mills field
Authors: Sternberg Shlomo
Published: May 2006

This note is to show how to use symplectic geometry to write equations of motion of a “classical particle” in the presence of a Yang-Mills field, for any gauge group,
G
, and any differentiable manifold,
M
. In the case that
M
is Minkowski space and
G
=
U
(1), the equations reduce to the Lorentz equations for a charged particle in an electromagnetic field. Our procedure in the general case uses the connection form as defined on the principle bundle to introduce a symplectic structure on certain associated bundles and is automatically gauge invariant.
2'-Deoxy-2'-azidocytidine inhibits the initiation of polyoma DNA synthesis.
Authors: Bjursell G , Skoog L , Thelander L , Söderman G
Published: May 2006

2'-Deoxy-2'-azidocytidine, a nucleoside analogue, inhibits polyoma DNA synthesis. The inhibition results in a 5.5-fold decrease in the amount of replicating intermediates, as detected by electron microscopy. The results indicate that replication is inhibited at an early step, possibly in the initiation of new rounds of replication. In contrast, the effect on the elongation of DNA chains appears to be less pronounced. As a result of the inhibition, polyoma DNA molecules at an early stage of replication accumulate in the nuclei. Upon incubation of such nuclei, DNA synthesis is induced in these molecules. The replication starts from the normal origin and elongation proceeds bidirectionally at a rate close to that observed during in vivo conditions. Analysis of polyoma DNA replication in nuclei isolated from control cells indicates that both initiation and termination of replication are impaired under in vitro conditions.
Experimental evidence for a kinetic and electrochemical memory in enzyme membranes.
Authors: Thomas D , Barbotin J N , David A , Hervagault J F , Romette J L
Published: May 2006

The existence of hysteresis phenomena in artificial enzyme membranes due to the coupling of simple kinetic enzyme properties with diffusion transport processes is reported. The intramembrane pH of a urease coating on the surface of a glass pH electrode exhibits a hysteresis loop when the pH of the bulk solution varies cyclically. The steady-state potential of a urease membrane, as a function of the substrate concentration in the bulk solution, also exhibits a memory effect. The influence of the membrane's history on its overall behavior is visualized by electron microscopy. We interpret the results in terms of a coupling between the enzyme reactions and diffusion processes, without taking into account molecular effects.
Asymmetric binding of the inhibitor di(adenosine-5′) pentaphosphate (Ap
5
A) to adenylate kinase
Authors: Nageswara Rao B. D. , Cohn Mildred
Published: May 2006

The effect of binding diadenosine pentaphosphate (Ap
5
A) to adenylate kinase (ATP:AMP phosphotransferase; EC 2.7.4.3) has been investigated by
31
P nuclear magnetic resonance. The symmetric molecule, Ap
5
A, is a potent inhibitor of the adenylate kinase reaction, 2 ADP ⇄ ATP + AMP. Free Ap
5
A has two groups of signals in its
31
P nuclear magnetic resonance spectrum centered at 11.1 and 22.8 parts/million (ppm) upfield from 85% H
3
PO
4
that are assigned to the end (1-P and 5-P) and middle (2-, 3-, and 4-P) phosphates, respectively. Addition of Mg
2+
shifts the centers of these resonances to 11.7 and 22.3 ppm. The spectrum of Ap
5
A bound to porcine adenylate kinase shows five groups of signals centered at 10.9, 11.9, 20.5, 22.7, and 24.0 ppm; the resonances at 11.1 ppm (1-P and 5-P) and at 22.8 ppm (2-P and 4-P) are now clearly split, indicating asymmetric binding of Ap
5
A to the enzyme. The asymmetry is strikingly enhanced in enzyme-bound MgAp
5
A, which has resonances at 10.5, 12.5, 18.6, 22.7, and 25.6 ppm. By the addition of Mn
2+
to the enzyme·MgAp
5
A complex, the observed signals in increasing order of shifts were tentatively assigned to 1-P, 5-P, 4-P, 3-P, and 2-P, where the 3-, 4-, and 5-P positions correspond to the ATP-binding site on the enzyme. The asymmetry introduced in the phosphate chain of enzyme·MgAp
5
A is indicated by the
31
P chemical shift of 7 ppm between 2- and 4-P, which is one of the largest thus far observed for phosphate substrates bound noncovalently to enzymes.
Regulation of proline oxidase activity by lactate.
Authors: Kowaloff E M , Phang J M , Granger A S , Downing S J
Published: May 2006

We found that proline oxidase, the first enzyme of the proline degradative pathway, is inhibited by lactate. The Km of the enzyme for proline increases with increasing concentrations of lactate. Since proline can be a source for gluconeogenesis, regulation of proline degradation by lactate may serve as a mechanism for allocation of metabolic fuel sources. The marked inhibition of proline oxidase at levels of lactate that commonly occur in both genetic and acquired lactic acidosis may cause the previously unexplained hyperprolinemia seen in these metabolic disorders.
mRNA-dependent in vitro synthesis of ribosomal proteins L12 and L10 and elongation factor Tu.
Authors: Chu F , Caldwell P , Weissbach H , Brot N
Published: May 2006

RNA extracted from growing Escherichia coli can direct the in vitro synthesis of ribosomal proteins L12 and L10 and elongation factor Tu when an E. coli system is used. The synthesized L12 can be bound to L12-depleted ribosomes and the synthesized elongation factor Tu can form complexes with both elongation factor Ts and GDP. Guanosine 5'-diphosphate 3'-diphosphate has no effect on the synthesis of these proteins from an RNA template but inhibits their synthesis when a DNA template is used.
Regulation of synthesis and activity of a mutant RNA polymerase in Escherichia coli.
Authors: Dennis P P
Published: May 2006

The expression of the genes specifying the beta and beta' subunits of RNA polymerase (nucleosidetriphosphate: RNA nucleotidyltransferase, EC 2.7.7.6) was examined in an Escherichia coli strain bearing a temperature-sensitive mutation in the beta' subunit gene. A shift to 42 degrees results in a restriction of RNA chain initiation and a cessation of RNA synthesis. A shift to 39 degrees results in only partial restriction, allowing RNA and protein synthesis to continue. The partial restriction produces a 5- to 6-fold increase in the relative transcription rate of the beta and beta' genes and a concomitant increase in the relative synthesis rate of the beta and beta' proteins. The transcription rate of ribosomal protein genes was also increased somewhat. These results indicate that the genes specifying the beta and beta' subunits of RNA polymerase are regulated at the level of transcription and that this regulation is related to the transcription of ribosomal protein genes. Furthermore, the results indicate that this regulation of the beta and beta' RNA polymerase subunit genes is somehow triggered by a reduction in the ability of RNA polymerase to initiate transcription on the bacterial chromosome.
Nucleotide sequence of a mutant eukaryotic gene: the yeast tyrosine-inserting ochre suppressor SUP4-o.
Authors: Goodman H M , Olson M V , Hall B D
Published: May 2006

One of the eight endonuclease EcoRI fragments of yeast DNA that hybridize to yeast tRNATyr has been identified with the genetically defined nonsense-suppressor locus SUP4. This identification was achieved by analyzing the meiotic linkage between the genetic determinant for the SUP4 phenotype and that for an electrophoretic variant of the EcoRI fragment. The SUP4 gene was then cloned from an ochre-suppressing yeast strain and analyzed by DNA sequencing. A wild-type SUP4 gene and two other genetically unidentified tRNATyr genes were also sequenced. The sequence of the ochre suppressor differs from that of the wild-type genes by virtue of a G.C leads to T.A transversion in the base pair that codes for the wobble position base of the tRNATyr anticodon. All four genes contain, immediately to the 3' side of the anticodon triplet, a 14 base pair tract that is not present in mature tRNATyr. Although the four genes, which represent three unlinked chromosomal loci, all encode the same mature tRNA sequence, there is virtually no observable sequence homology between the three loci in the region preceding the 5' end of the mature tRNATyr sequences.
Muscarinic acetylcholine receptors of the developing retina.
Authors: Sugiyama H , Daniels M P , Nirenberg M
Published: May 2006

Six- and 13-day chicken embryo retinas contain 10 and 320 fmol per mg of protein of specific binding sites for 3-[3H]quinuclidinyl benzilate, a ligand of muscarinic acetylcholine receptors. Most of the receptors of 13-day embryo retina were found, by autoradiography, to be localized in two sharp bands within the inner synaptic layer of the retina. In the adult, the receptors were found almost exclusively in three bands in the inner synaptic layer of the retina. A possible mechanism for generating sets of stratified or columnar neurons and relating one set to another is proposed.
Catecholamine binding to the beta-adrenergic receptor.
Authors: Lefkowitz R J , Williams L T
Published: May 2006

The adenylate cyclase-coupled beta-adrenergic receptors of frog erythrocyte membranes have been identified by direct radioligand binding techniques using the potent catecholamine agonist (+/-)[3H]hydroxybenzylisproterenol (2-[3, 4-dihydroxyphenyl]-2-hydroxy-1', 1'-dimethyl-2'-[4-hydroxyphenyl]-diethylamine). The successful experimental conditions included the use of (i) high concentrations of catechol and ascorbic acid to suppress nonreceptor binding, (ii) a very potent radiolabeled catecholamine (10 times more potent than isoproterenol), and (iii) membranes rich in binding sites for beta-adrenergic receptors. Thus, previous problems in accomplishing successful catecholamine binding to the beta-receptors have been overcome. The binding sites identified with (+/-)[3H]hydroxybenzylisoproterenol in the erythrocyte membranes have all the characteristics expected of true beta-adrenergic receptors. These include rapidity of binding, saturability, specificity for beta-agonists and antagonists, and stereospecificity [(-)isomers more potent than (+)isomers]. Physiologically inactive compounds containing a catechol moiety do not compete for occupancy of these binding sites. Dissociation of the radiolabeled agonist from the receptors is slow and incomplete in the absence of guanine nucleotides. In the presence of nucleotide, however, dissociation is rapid and complete. beta-Adrenergic agonists and antagonists compete for the (+/-)[3H]hydroxybenzylisoproterenol binding sites in a fashion parallel to their competition for the receptors, as previously delineated with the beta-adrenergic antagonist (-)[3H]dihydroalprenolol.
Assembly of tobacco mosaic virus in vitro: elongation of partially reconstituted RNA.
Authors: Ohno T , Takahashi M , Okada Y
Published: May 2006

It was reported that the rate of elongation of partially reconstituted RNA, if prepared without centrifugation, showed dependency upon the state of protein aggregation like that found when free RNA was used as the nucleic acid source [Butler, P. J. G. (1974) J. Mol. Biol. 82, 333-341]. Butler concluded from this result that disks are the kinetically favored protein source for the elongation of the tobacco mosaic virus rod. We show that partially reconstituted RNA prepared without centrifugation always contains a significant amount of free RNA and conclude that the dependency of its elongation rate upon the state of protein aggregation is due to contamination of his partially reconstituted RNA preparation by free RNA. The elongation rate of partially reconstituted RNA, which had been pelleted and contained no free RNA, was found to be about the same regardless of the state of aggregation of the added protein.
Free calcium increases explosively in activating medaka eggs.
Authors: Ridgway E B , Gilkey J C , Jaffe L F
Published: May 2006

We have used the calcium-specific light-emitting protein aequorin to follow changes in free calcium concentration during fertilization and cleavage of eggs from medaka, a fresh-water fish. Aequorin-injected medaka eggs show a very low resting glow before they are fertilized, indicating a low calcium concentration in the resting state. Upon activation by sperm, the calcium-mediated light emission increases to a level some 10,000 times the resting level with a 1 to 2 sec time constant for an e-fold increase, and then slowly retruns to the resting level. Upon activation by the ionophore A23187, the early rise in luminescence is much slower, but once a threshold has been reached the subsequent rise becomes as rapid as the normal sperm-induced response. We infer that the explosive rise in calcium involves calcium-stimulated calcium release, and that a sperm normally triggers this rise by somehow inducing a more modest and localized rise in calcium.
Structure of human plasma low-density lipoproteins: molecular organization of the central core.
Authors: Atkinson D , Deckelbaum R J , Small D M , Shipley G G
Published: May 2006

Human plasma low density lipoprotein (LDL) exhibits a thermal transition over the temperature range 20-40 degrees. This transition is associated with a structural change within the lipoprotein particle and is reflected in the small-angle x-ray scattering profiles from LDL. The scattering profile of the quasispherical LDL particle at 10 degrees shows a relatively intense maximum at 1/36 A-1 which is absent from the scattering of LDL at 45 degrees. Theoretical calculations, using model electron density distributions, have been carried out to describe the packing of arrangement of the cholesterol esters, based on perturbations of the molecular packing of crystalline cholesteryl myristate, adequately reproduces the high relative intensity of the x-ray scattering maximum at 1/36 A-1. The perturbations of the packing in the crystal structure of cholesteryl myristate involve "melting" of the hydrocarbon chains of the esters together with translations of pairs of molecules parallel to the molecular long axis. The interaction of opposing steroid moieties, with C18 and C19 angular methyl groups interlocked, exhibited in the crystal structure is retained in the perturbed arrangement. At 45 degrees, thermally induced disorder of this arrangement averages the electron density of the central core. The x-ray scattering profiles of particles with a homogeneous electron density in the core region do not show a high relative intensity of the subsidiary maxima in the 1/36 A-1 region, in agreement with experimental observation. The results of these calculations support the concept that the thermal transition observed for LDL is due to a smectic leads to disordered transition of the cholesterol esters in the core of the LDL particle.
Isolation and characterization of conditional-lethal rho mutants of Escherichia coli.
Authors: Inoko H , Shigesada K , Imai M
Published: May 2006

Temperature-sensitive nitA (rho) mutants of E. coli were isolated; one of them was characterized as an amber mutant. These strains show the Nit phenotype (transcription of phage lambda DNA independent of the N gene) at low temperatures and are inviable at high temperatures. The mutated sites appear to be between cya and metE on the chromosome. Temperature-sensitive nitA bacteria not only permit leftward transcription of the lambda genome at a high rate in the absence of the lambda N protein, but also allow lambda growth at low temperatures. At high temperatures, phages lambda and T4 are incapable of normal development in these cells, while growth of T7 is not affected. The production of thermally unstable rho by the nitA temperature-sensitive mutant suggests that nitA is the structural gene for rho.