bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient electric dichroism of rod-like DNA molecules.
Authors: Hogan M , Dattagupta N , Crothers D M
Published: May 2006

We report transient electric dichroism studies on monodisperse rod-like DNA molecules. By using restriction fragments and DNAs of known length, it is shown that the orientation time is accurately predicted by the theoretically calculated rotational diffusion coefficient. The field dependence of the steady-state dichroism values is not consistent with the induced electric dipole orientation mechanism, and the time dependence is not consistent with the presence of a permanent dipole moment. In order to explain the dependence of the dichroism on the electric field, the ionic strength of the medium, and the length of the macromolecule, we propose a new model in which anisotropic ion flow produces an asymmetric ion atmosphere around the polyelectrolyte, resulting in an orienting torque. From the limiting dichroism at high field, we estimate that the DNA bases are inclined at an angle of 73 degrees or less relative to the helix axis, in good agreement with the revised model of B-form DNA suggested by Levitt, in which the base pairs have a propeller-like twist. Our results establish transient electric dichroism measurements as a technique well suited for study of alterations in the length and base pair inclination of rod-like DNA molecules.
Electron microscopic determination of the binding sites of ribosomal proteins S4 and S8 on 16S RNA.
Authors: Cole M D , Beer M , Koller T , Strycharz W A , Nomura M
Published: May 2006

Specific complexes.early in the assembly of Escherichia coli ribosomes were examined in the electron microscope. Complexes between ribosomal protein S4 or S8 and 16S RNA were fixed gently with formaldehyde and then denatured for protein-free spreading. Binding of each protein was found to preserve an easily recognized configuration in the RNA that allows the sites of protein binding to be determined. S8--16S RNA complexes have a single hairpin loop near the middle of the 16S RNA, 798 +/- 21 bases from one end and 657 +/- 26 bases from the other. S4-16S RNA complexes have two adjacent loops at one end with 250--450 bases. This structure probably arises from the simultaneous binding of S4 to three noncontiguous sites on the RNA. Measurements of these complexes place the binding sites near the 5' end, at more than one site 250--585 nucleotides from the 5' end and 645 +/- 45 bases from the 3' end. The latter site has not been recognized previously as a distinct S4 binding site. This approach allows the binding sites to be determined without knowledge of the nucleotide sequence and gives insight into the configuration of the rRNA in the assembling ribisome.
Modification of DNA by the benzo[a]pyrene metabolite diol-epoxide r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene.
Authors: Kakefuda T , Yamamoto H
Published: May 2006

The structural modification of double-stranded circular DNA of simian virus 40 and plasmid ColE1 by in vitro binding of r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene was studied. Stepwise hydrolysis with endonuclease S1 and DNase followed by DNA base analysis by thin-layer chromatography provided evidence that binding to adenine caused the local denaturation of DNA, whereas the more than 10-fold greater binding to guanine did not create such local denaturation. Of the two synthetic double-stranded polymers, poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC), bound to the diol-epoxide, only the former showed a marked hydrolysis after endonuclease S1 treatment, whereas binding occurred 24-fold more on the latter.
Mutation affecting thermostability of sigma subunit of Escherichia coli RNA polymerase lies near the dnaG locus at about 66 min on the E. coli genetic map.
Authors: Gross C , Hoffman J , Ward C , Hager D , Burdick G , Berger H , Burgess R
Published: May 2006

The Escherichia coli strain, ts-rnp5, originally described in 1975 by G. D. Burdick and H. Berger, is shown to possess an RNA polymerase (RNA nucleotidyltransferase) sigma subunit with an activity 4--6 times less thermostable at 45 degrees than sigma from wild-type strains. This defect remains associated with the sigma polypeptide through a variety of purification stages, including renaturation of sigma after its elution from sodium dodecyl sulfate/polyacrylamide gels. The mutation responsible for decreased thermostability of sigma, called rpoD1, cotransduces with dnaG and therefore is located at about 66 min of the E. coli genetic map.
Demonstration of biological activity of brain gastrin-like peptidic material in the human: its relationship with the COOH-terminal octapeptide of cholecystokinin.
Authors: Robberecht P , Deschodt-Lanckman M , Vanderhaeghen J J
Published: May 2006

The previously described peptide material that reacts with antibodies to gastrin and is found in the central nervous system of various vertebrates is present in only the 100,000 X g pellet of postmortem human cerebral cortical grey matter. This immunoreactive material, extractable in boiling water, is biologically active on rat pancreatic preparations. On the basis of size, charge, immunological specificity, and patterns of biological activity, most of this material is closely related to the COOH-terminal octapeptide of cholecystokinin in its complete, sulfated biologically active form.
Abnormal cellular localization of thyroglobulin mRNA associated with hereditary congenital goiter and thyroglobulin deficiency.
Authors: Van Voorthuizen W F , Dinsart C , Flavell R A , DeVijlder J J , Vassart G
Published: May 2006

The goiters in a breed of hypothyroid goats contain only minute amounts of thyroblobulin-related antigens (0.01% of normal value). We have analyzed these goiters for the presence of mRNA coding for thyroglobulin. Using DNA complementary to beef 33S thyroglobulin mRNA as a probe, we found that the mRNA sequence is present in the goat goiter but at a concentration 1/10-1/40 that of normal goat thyroid. Hybrids of cDNA with either goiter or normal thyroid RNA exhibited identical sharp melting curves which suggests that the same RNA sequence is responsible for hybridization in both tissues. Normal goat thyroid contains a population of large membrane-bound polysomes engaged in throglobulin synthesis. In contrast, such polysomes are absent in the goiter. In regard to subcellular distribution, the relative amount of the thyroglobulin mRNA sequences from the goiter in nuclear RNA was 42% of normal, in cytoplasmic RNA was 7% of normal, and in the membrane fraction was only 1-2% of normal. Our results suggest that the lack of thyroglobulin in these goiters is due to a defect in thyroglobulin mRNA which leads to aberrant processing and/or transport of it from its site of synthesis to the endoplasmic reticulum.
A polypeptide in eukaryotic initiation factors that crosslinks specifically to the 5'-terminal cap in mRNA.
Authors: Sonenberg N , Morgan M A , Merrick W C , Shatkin A J
Published: May 2006

Protein synthesis initiation factors prepared from rabbit reticulocyte and mouse ascites ribosomes were tested for the ability to crosslink to the 5' cap of mRNA. Crosslinking of one polypeptide of apparent molecular weight 24,000 was inhibited by the cap analogs, m7GMP and m7GDP, indicating a specific interaction with the cap. Although specific crosslinking of the 24,000 molecular weight polypeptide was found with eukaryotic initiation factor 3 and to a lesser extent with initiation factor 4B, both of these factors contained less than stoichiometric amounts of this polypeptide. The crosslinking method provides a highly sensitive and specific assay for cap-binding proteins and should facilitate their purification for functional studies.
Biogenesis of peroxisomes: intracellular site of synthesis of catalase and uricase.
Authors: Goldman B M , Blobel G
Published: May 2006

The intracellular site of synthesis of two peroxisomal enzymes of rat liver, uricase (urate:oxygen oxidoreductase, EC 1.7.3.3) and catalase (hydrogen peroxide:hydrogen peroxide oxidoreductase, EC 1.11.1.6), has been localized on free ribosomes and not membrane-bound ribosomes. Free polysomes and membrane-bound polysomes, prepared by classical cell fractionation techniques from rat liver, were incubated for protein synthesis in a cell-free system derived from rabbit reticulocytes. Characterization of the total translation products by polyacrylamide gel electrophoresis in sodium dodecyl sulfate, as well as by immunoprecipitation with anti-rat albumin anti-serum, confirmed that good separation of the two polysome classes was achieved. Uricase and catalase were immunoprecipitable from translation products directed by free polysomes or phenol-extracted free polysomal mRNA but not from products of membrane-bound polysomes. Furthermore, unlike albumin, nascent uricase and catalase were not cotranslationally segregated by dog pancreas microsomal membranes. The results indicate that uricase and catalase are transferred to the interior of peroxisomes by a post-translational mechanism; an hypothesis is formulated here for the biogenesis of peroxisomes.
Sanfilippo syndrome type C: deficiency of acetyl-CoA:alpha-glucosaminide N-acetyltransferase in skin fibroblasts.
Authors: Klein U , Kresse H , von Figura K
Published: May 2006

Removal of N-sulfated glucosamine residues during degradation of heparan sulfate is accomplished by the sequential action of three enzymes. Action of sulfamidase results in the formation of alpha-glucosaminide residues. Removal of these groups requires conversion to alpha-N-acetylglucosaminide by the action of an acetyltransferase in the presence of acetyl-CoA, followed by hydrolysis by alpha-N-acetylglucosaminidase. In fibroblast homogenates from three patients with Sanfilippo syndrome type C (mucopolysaccharidosis III C), a biochemical variant of the Sanfilippo syndrome, complete deficiency of the acetyl-CoA:alpha-glucosaminide N-acetyltransferase activity was detected. Activities of all lysosomal hydrolases known so far to degrade mucopolysaccharides, including those of sulfamidase and alpha-N-acetylglucosaminidase, were in the range of controls. Acetyl-CoA:alpha-glucosaminide N-acetyltransferase activity was normal in fibroblasts of patients with other genetic mucopolysaccharidoses, including Sanfilippo syndrome A and B.
Locality principle in wave mechanics
Authors: Kohn W. , Yaniv A.
Published: May 2006

This paper proves a locality principle for a wave-mechanical particle governed by the Schrödinger equation. It is shown that ρ(r,β), the Laplace transform of the local density of states
n
(r,
E
), depends significantly only on the potential
V
(r′) at points r′
near
r. The effect of changes of
V
(r′) at distant points r′ (|

x
i

′ -

x
i

| >
a
) on ρ(r,β) decay in a Gaussian fashion with
a
. This result sheds some light on the locality of physical properties of extended systems and provides general support for various local methods of calculation.
Stoichiometry of vectorial H
+
movements coupled to electron transport and to ATP synthesis in mitochondria
Authors: Alexandre Adolfo , Reynafarje Baltazar , Lehninger Albert L.
Published: May 2006

In order to verify more directly our earlier measurements showing that, on the average, close to four vectorial H
+
are rejected per pair of electrons passing each of the three energy-conserving sites of the mitochondrial electron transport chain, direct tests of the H
+
/2
e
-
ratio for sites 2 and 3 were carried out in the presence of permeant charge-compensating cations. Site 2 was examined by utilizing succinate as electron donor and ferricyanide as electron acceptor from mitochondrial cytochrome
c
; the directly measured H
+
/2
e
-
ratio was close to 4. Energy-conserving site 3 was isolated for study with ferrocyanide or ascorbate plus tetramethylphenylenediamine as electron donors to cytochrome
c
and with oxygen as electron acceptor. The directly measured H
+
/2
e
-
ratio for site 3 was close to 4. The H
+
/ATP ratio (number of vectorial H
+
ejected per ATP hydrolyzed) was determined with a new method in which the steady-state rates of both H
+
ejection and ATP hydrolysis were measured in the presence of K
+
+ valinomycin. The H
+
/ATP ratio was found to approach 3.0. A proton cycle for oxidative phosphorylation is proposed, in which four electrochemical H
+
equivalents are ejected per pair of electrons passing each energy-conserving site; three of the H
+
equivalents pass inward to derive ATP synthesis from ADP and phosphate and the fourth H
+
is used to bring about the energy-requiring electrogenic expulsion of ATP
4-
in exchange for extramitochondrial ADP
3-
, via the H
+
/H
2
PO
4
-
symporter.
Molecular nature of the complement lesion.
Authors: Bhakdi S , Tranum-Jensen J
Published: May 2006

The principle molecular event leading to membrane perturbation by complement is the assembly of the terminal five serum complement components (C5b-C9) into a macromolecular C5b-9 complex on the target membrane [Müller-Eberhard, H.-J. (1975) Ann. Rev. Biochem. 44, 697--723]. The present communication reports on the ability of purified C5b-9 complexes isolated from target membranes to become reincorporated into artificial lipid vesicles. The data indicate that the complex is a vertically oriented, hollow, cylindrical macromolecule possessing lipid-binding regions that enable one terminus to penetrate into the lipid bilayer. A transmembrane pore appears to be created at the attachment site of the C5b-9 complex.
Characterization of immunoglobulin from the Pacific hagfish, a primitive vertebrate
Authors: Raison Robert L. , Hull Charles J. , Hildemann William H.
Published: May 2006

Antibodies to group A streptococcal carbohydrate, demonstrable by radioimmunoassay, were elicited in Pacific hagfish,
Eptatretus stoutii
, after prolonged immunization with whole cell vaccine. This hagfish antibody, isolated by ion-exchange chromatography of immune serum, exhibited a single precipitin line after immunoelectrophoresis against rabbit antiserum to hagfish serum. The isolated antibodies retained high binding activity for the streptococcal carbohydrate, but lacked the natural hemagglutinating activity found in both nonimmune and immune sera. Analysis by gel filtration in neutral and dissociating buffers and by sodium dodecyl sulfate/polyacrylamide gel electrophoresis under nonreducing conditions indicated an intact molecule of molecular weight approximately 160,000 that may be noncovalently associated in a polymer of higher molecular weight. Heavy chains of mobility identical to that of murine μ chains and light chains of mobility significantly slower than murine λ chains were obtained after sodium dodecyl sulfate gel electrophoresis under reducing conditions. Instability of the tertiary structure of the antibody molecule was indicated by partial dissociation in buffers containing sodium dodecyl sulfate and by dissociation at low concentrations of reducing agent. In contrast to its well-developed system of cell-mediated immunity, only a minimal system of circulating antibody production is evident in this primitive fish. No evidence for divergence of cyclostome lymphocytes into separate T- and B-cell systems has yet been discerned.
Histochemically distinct compartments in the striatum of human, monkeys, and cat demonstrated by acetylthiocholinesterase staining.
Authors: Graybiel A M , Ragsdale C W
Published: May 2006

We here report observations on the distribution of acetylcholinesterase (acetylcholine hydrolase, EC 3.1.1.7) in the striatum of the adult human, the rhesus monkey, and the cat. By the histochemical staining methods of Geneser-Jensen and Blackstad and of Karnovsky and Roots, compartments of low cholinesterase activity were identified in parts of the striatum in all three species. In frontal sections, these enzyme-poor zones appeared as a variable number of weakly stained approximately 0.5-mm-wide zones embedded in a darkly stained background. The zones varied in cross-sectional shape from round to elongated and were sometimes branched. They were most prominent in the head of the caudate nucleus. Three-dimensional reconstructions of serial sections through the caudate nucleus in the human and cat suggest that over distances of at least several millimeters, the zones of low enzyme activity form nearly continuous labyrinths.
Three-dimensional structure of thioredoxin induced by bacteriophage T4.
Authors: Söderberg B O , Sjöberg B M , Sonnerstam U , Brändén C I
Published: May 2006

The three-dimensional structure of thioredoxin from bacteriophage T4 has been determined from a 2.8-angstrom resolution electron density map. Phase angles for this map were determined from one heavy atom derivative and anomalous differences from cadmium in the native crystals. The molecule of 87 amino acid residues is built up from two simple folding units; a betaalphabeta unit from the amino end of the chain and a betabetaalpha unit from the carboxyl end. This structure is similar to that of thioredoxin from Escherichia coli in spite of their completely different amino acid sequences. The redox-active S--S bridge is part of a protrusion of the molecule as in E. coli thioredoxin, but with quite different surroundings. The structural differences in this region have been correlated to differences in specificity towards the enzyme ribonucleotide reductase from different species.
Hemoglobin switching in sheep: Only the γ gene is in the active conformation in fetal liver but all the β and γ genes are in the active conformation in bone marrow
Authors: Young Neal S. , Benz Edward J. , Kantor Judith A. , Kretschmer Peter , Nienhuis Arthur W.
Published: May 2006

Differential expression of the closely linked γ, β
A
(or β
B
), and β
C
globin genes in sheep results in the production of fetal hemoglobin (Hb F, α
2
γ
2
) during gestation and the adult hemoglobins (Hb A, α
2
β
2
A
, and Hb B, α
2
β
2
B
) after birth. Erythropoietic stress in certain animals leads to production of Hb C (α
2
β
2
C
). The molecular mechanism of differential expression of these genes in nuclei of fetal and adult erythroid cells has been investigated by analysis of their susceptibility to digestion by DNase I (genes that are in the conformation associated with active transcription are sensitive to this nuclease). The concentration of globin gene sequences in DNA from control and DNase I-digested nuclei was determined by annealing to synthetic DNAs and analogous cDNA probes derived from recombinant plasmids containing one of the sheep globin genes. In nuclei from sheep fetal liver erythroid cells, the γ genes but not the β genes were digested by DNase I; the γ locus was open but the β
A
or β
C
loci was closed, consistent with synthesis of only Hb F by these cells. DNase I digestion of nuclei from bone marrow of anemic sheep making only Hb C or Hb B resulted in equivalent digestion of the β and γ gene sequences, although γ mRNA was not detected in these cells. Digestion by DNase I did not decrease the globin gene sequence concentration in residual DNA of spleen nuclei. As a further control, DNA from digested bone marrow and spleen nuclei were shown to anneal equally well to a cDNA prepared from liver polysomal mRNA. Differential expression of the γ and β globin genes in sheep fetal erythroid cell appears to be based on differences in chromatin structure. The γ globin gene remains in the active conformation in adult erythroid cells; failure of γ mRNA to accumulate in these cells probably reflects transcriptional or post-transcriptional regulation.
DNA gyrase: subunit structure and ATPase activity of the purified enzyme.
Authors: Mizuuchi K , O'Dea M H , Gellert M
Published: May 2006

DNA gyrase has been purified to near homogeneity from Escherichia coli. The enzyme consists of two subunits of molecular weights 90,000 and 100,000 present in roughly equimolar amounts. The subunits can be identified as the products of two genes, determining resistance to coumermycin A1 and novobiocin (cou) and to nalidixic acid and oxolinic acid (nalA), respectively. These antibiotics were previously shown to be specific inhibitors of DNA gyrase. The ATPase activity of DNA gyrase is stimulated by double-stranded DNA and strongly inhibited by novobiocin but is relatively insensitive to oxolinic acid. Covalent attachment of an ATP derivative to the smaller (coumermycin-specific) subunit is also inhibited by novobiocin, suggesting that this drug interferes with the energy-coupling aspect of the DNA supercoiling reaction by blocking the access of ATP to the enzyme.
Temperature-sensitive Escherichia coli mutant producing a temperature-sensitive sigma subunit of DNA-dependent RNA polymerase.
Authors: Harris J D , Heilig J S , Martinez I I , Calendar R , Isaksson L A
Published: May 2006

A gene affecting the sigma subunit of DNA-dependent RNA polymerase is tightly linked to dnaG at 66 min on the Escherichia coli chromosome. In order to create an easily selectable marker in this region, we inserted transposon-10, which carries a gene determining resistance to tetracycline (tet) near 66 min, and the order tolC-dnaG-sigma-tet was determined. We used frequency of contransduction with tet as a criterion to screen a collection of spontaneous temperature-sensitive Escherichia coli mutants that might affect the sigma subunit. One such mutant was found to map at the sigma locus. The sigma subunit isolated from this mutant is unstable at 46 degrees C in vitro and has an altered electrophoretic mobility. The temperature sensitivity of RNA synthesis in this mutant indicates that most transcription in E. coli is sigma dependent.
alpha-Melanocyte stimulating hormone: immunohistochemical identification and mapping in neurons of rat brain.
Authors: Jacobowitz D M , O'Donohue T L
Published: May 2006

alpha-Melanocyte stimulating hormone (alpha-melanotropin) immunofluorescence was observed in rat brain by means of a highly specific and well-characterized antibody. The hormone was contained in arcuate nucleus cell bodies and in varicose fibers. Dense populations of hormone-containing fibers were present in the septum, the nucleus interstitialis stria terminalis, and the medial preoptic, anterior hypothalamic, dorsomedial, and periventricular nuclei. Moderate numbers of fibers were seen in the paraventricular and arcuate nuclei, the amygdala, the region of the tractus diagonalis, the mammillary body, the central gray, the cuneiform nucleus, and the nucleus of the solitary tract. There is an interesting correlation of alpha-melanocyte stimulating hormone fibers with regions of noradrenergic axonal projections and terminal fields.
The molecular mechanism of excitation in visual transduction and bacteriorhodopsin
Authors: Lewis Aaron
Published: May 2006

An electronic theory of excitation is proposed and described in terms of a three-dimensional excited/ground-state energy surface which elucidates the photochemical and excited-state dynamics of rhodopsins. In this theory the primary action of light is to produce significant electron redistribution in the retinal, thereby generating new interactions that vibrationally excite and perturb the ground-state protein conformation. Thus, light energy causes charge redistribution in the retinal and induces transient charge-density assisted bond rearrangements (such as proton translocation) in the protein structure which is stabilized by subsequent retinal structural alteration. In this theory the isoprenoid chain of the retinal is considered a structurally pliable molecular entity that can generate charge redistributions and can be subsequently achieve intermediate conformations or various isomeric states to minimize the energy of the new protein structure generated by light. Thus, the 11-
cis
to all
trans
isomerization of the retinylidene chromophore is not considered a primary mechanism of excitation. An alternate biological role for this molecular process (which is eventually completed in all photoreceptors but not in bacterial rhodopsins) is to provide the irreversibility needed for effective quantum detection on the time scale of a neural response. Finally, it will be demonstrated that this mechanism, which readily accounts for the photophysical and photochemical data, can also be restated in terms of the Monod, Wyman, and Changeux terminology suggesting that aggregates of these pigments may function allosterically.
Respective roles of short- and long-range interactions in protein folding.
Authors: Go N , Taketomi H
Published: May 2006

A lattice model of protein is studied by a Monte Carlo simulation method. The native conformation of the lattice protein molecule is stabilized by specific long-range and short-ranged interactions. By comparing results of simulation for different relative weights of the long- and short-range interactions, it is concluded that the specific long-range interactions are essential for highly cooperative stabilization of the native conformation and that the short-range interactions accelerate the folding and unfolding transitions.
On the process of cellular division in Escherichia coli: a series of mutants of E. coli altered in the penicillin-binding proteins.
Authors: Suzuki H , Nishimura Y , Hirota Y
Published: May 2006

A series of mutants defective in penicillin-binding components (or protein) (PBCs) was isolated from a collection of thermosensitive mutants of Escherichia coli. The mutants included mutations for each PBC (1 through 4) and a mutation in the activity of D-alanine carboxypeptidase 1a (PBC-5/6). PBC-1 was resolved into two components, PBC-1a and PBC-1b, which were the products of different genes referred to as ponA and ponB, respectively. No mutation examined in ponA-- or ponB--, by itself, was associated with a thermosensitive defect in growth. The mutants having ponB-- were hypersensitive to cephalosporins, which showed unusually high affinity to PBC-1a. Murein synthetic activity decreased markedly in cell-free preparations from the ponB-- mutant. The double mutation ponA-- ponB-- was found to be lethal. A mutant having ponAts and ponB-- revealed thermosensitivity of growth and lysed at the restrictive temperature. It is concluded that PBC-1a and PBC-1b could share a biochemical reaction necessary for cell elongation so that the function of either one may bypass the loss of the function of the other. With the series of mutants, the chromosomal locus of the gene for each PBC was mapped: ponA (PBC-1a) 73.5 min, ponB (PBC-1b) 3.3 min, rodA (PBC-2) 14.4 min, ftsI (PBC-3) 1.8 min, dacB (PBC-4) 68 min, and dacA (PBC-5/6) 13.7 min.
Purification and translation of zein messenger RNA from maize endosperm protein bodies
Authors: Burr B. , Burr F. A. , Rubenstein I. , Simon M. N.
Published: May 2006

The messenger RNAs coding for the zein storage protein have been purified from other contaminating RNAs. The average molecular lengths are 1.1-1.2 kilobases, as determined by polyacrylamide gel electrophoresis and by electron microscopy. Products of messenger-dependent protein synthesis
in vitro
appear to be 1100 and 2000 daltons heavier than the native polypeptides. Zein is like secretory proteins in having a precursor with an additional amino-terminal sequence. Although only one mRNA is seen in polyacrylamide gel electrophoresis, the combined size of the polypeptide products formed exceeds the coding capacity for one message of the size determined in this study. This suggests that there are at least two mRNAs of similar sizes for the zein polypeptides rather than one dicistronic message.
Antibody response of mice to chemically induced tumors.
Authors: Brown J P , Klitzman J M , Hellström I , Nowinski R C , Hellström K E
Published: May 2006

BALB/c mice immunized with syngeneic methylcholanthrene-induced fibrosarcomas did not have antibodies against the unique tumor-specific transplantation antigens, even though they were capable of rejecting a lethal dose of tumor cells. Endogenous murine leukemia virus antigens expressed by certain of the tumors did, however, elicit high titers of antibodies, accounting for serological crossreactions that occurred between those tumors.
Biological activity of purified simian virus 40 T antigen proteins.
Authors: Tjian R , Fey G , Graessmann A
Published: May 2006

Proteins related to simian virus 40 (SV40) T antigen uere isolated from cells infected with adenovirus 2/SV40 hybrids Ad2+D2 and Ad2+ND1 dp2 as well as from a line of human cells (SV80) transformed by SV40. The 96,000- and 107,000-dalton proteins of SV80 and Ad2+D2, after injection into the cytoplasm of cultured cells, rapidly accumulate in the nuclei, where they remain antigenically reactive for at least 20 hr and trigger DNA synthesis in quiescent cells. By contrast, the 23,000-dalton protein coded by Ad2+ND1 dp2 does not stimulate cellular DNA synthesis. However, all three purified proteins are able to provide helper function for the growth of adenovirus 2 in monkey cells. Thus, purified SV40 T antigen and proteins that share sequences with it retain the ability to carry out at least two functions associated with the product of the A gene of SV40.
Membrane lateral phase separations and chlortetracycline transport by
Bacillus megaterium
Authors: Dockter Michael E. , Trumble William R. , Magnuson James A.
Published: May 2006

Chlortetracycline, a fluorescent probe of its own active transport, has been used to study lateral phase separations of membrane lipid in
Bacillus megaterium
cells. Arrhenius plots of initial accumulation rates are triphasic, with transitions or characteristic temperatures of 20° and 9.5°. At the higher temperature, the mobility of the chloretracycline, as measured by fluorescence polarization, is markedly altered. Chlortetracycline transport exhibits saturation kinetics, and fluorescence energy transfer from protein to bound antibiotic can be observed.
N
-Phenyl-1-naphthylamine, a lipophilic fluorescent probe, responds to changes in the hydrophobic regions of the membrane that are distinct from membrane protein. The fluorescent properties of
N
-phenylnaphthylamine in partitioning and polarization experiments are altered most significantly at the lower characteristic temperature. No fluorescence energy transfer between
N
-phenylnaphthylamine and membrane protein or bound tetracycline can be detected. In correlative electron spin resonance experiments on the partitioning of a lipid-soluble spin label, the same characteristic temperatures detected in the fluorescence studies were measured. These data suggest that different probes may respond to either or both of the characteristic temperatures describing the lateral phase separation. Between these characteristic temperatures the chlortetracycline transport system is most intimately associated with relatively immobile lipids that are surrounded by a more mobile lipid phase.
Nonequilibrium entropy, Lyapounov variables, and ergodic properties of classical systems
Authors: Misra B.
Published: May 2006

We discuss the problem of defining (nonequilibrium) entropy in terms of the concepts of mechanics and of reconciling its
monotonic
increase with the Hamiltonian evolution of the dynamical system. This leads to investigating necessary and sufficient conditions for the existence of monotonically increasing quantities or the so-called
Lyapounov variables
of classical systems. It is found that the condition of “
mixing
” is necessary and the property of being K-
flow
is sufficient for the existence of a Lyapounov variable. The significance of the study of Lyapounov variables for the elucidation of the fundamental questions of statistical mechanics is briefly discussed. It is seen that every Lyapounov variable must fail to commute with at least some of the operators of multiplication by phase space functions. The uncertainty relations implied by this necessary noncommutativity would then set a limit on the simultaneous determination of entropy and trajectories in phase space. These considerations thus support and sharpen the view that the thermodynamical and the (microscopic) dynamical descriptions of classical systems could be consistently reconciled as being
complementary
descriptions analogous to the complementary descriptions encountered in quantum mechanics.
Regulation of Ca
2+
release from mitochondria by the oxidation-reduction state of pyridine nucleotides
Authors: Lehninger Albert L. , Vercesi Anibal , Bababunmi Enitan A.
Published: May 2006

Mitochondria from normal rat liver and heart, and also Ehrlich tumor cells, respiring on succinate as energy source in the presence of rotenone (to prevent net electron flow to oxygen from the endogenous pyridine nucleotides), rapidly take up Ca
2+
and retain it so long as the pyridine nucleotides are kept in the reduced state. When acetoacetate is added to bring the pyridine nucleotides into a more oxidized state, Ca
2+
is released to the medium. A subsequent addition of a reductant of the pyridine nucleotides such as β-hydroxybutyrate, glutamate, or isocitrate causes reuptake of the released Ca
2+
. Successive cycles of Ca
2+
release and uptake can be induced by shifting the redox state of the pyridine nucleotides to more oxidized and more reduced states, respectively. Similar observations were made when succinate oxidation was replaced as energy source by ascorbate oxidation or by the hydrolysis of ATP. These and other observations form the basis of a hypothesis for feedback regulation of Ca
2+
-dependent substrate- or energy-mobilizing enzymatic reactions by the uptake or release of mitochondrial Ca
2+
, mediated by the cytosolic phosphate potential and the ATP-dependent reduction of mitochondrial pyridine nucleotides by reversal of electron transport.
Identification of the principal aflatoxin B1-DNA adduct formed in vivo in rat liver.
Authors: Croy R G , Essigmann J M , Reinhold V N , Wogan G N
Published: May 2006

The products of in vivo covalent binding of activated aflatoxin B1 (AFB1) to DNA have been investigated in rats. The principal covalent product formed in liver DNA of rats treated with AFB1 has been identified as 2,3-dihydro-2-(N7-guanyl)-3-hydroxy-aflatoxin B1. This compound was isolated from the liver DNA of rats dosed with AFB1 (2.0 mg/kg) in sufficient quantity for characterization by physicochemical techniques, including field-desorption mass spectrometry. This information together with results of chemical methylation of the compound proved that the major adduct formed between DNA and AFB1 in vivo is identical to that produced in vitro when AFB1 is incubated with DNA in the presence of a rat liver microsomal activating system. Quantitative studies of formation of this compound revealed a dose-dependent relationship between the level of its occurence in liver DNA and AFB1 doses over the range 0.125-1.0 mg/kg.
Density-dependent regulation of growth of BSC-1 cells in cell culture: growth inhibitors formed by the cells.
Authors: Holley R W , Armour R , Baldwin J H
Published: May 2006

Inhibitors formed by a monkey epithelial cell line, BSC-1, play an important role in limiting growth at high cell densities. At least three inhibitors are formed: lactic acid, ammonia, and an unidentified inhibitor that may be an unstable protein. The unidentified inhibitor is destroyed by shaking the conditioned medium, by bubbling gas through the medium, or by heating or storing the medium in the absence of cells. The concentrations of lactic acid and ammonia that accumulate in conditioned medium inhibit growth when added to fresh medium. These results, together with earlier studies, indicate that density-dependent regulation of growth of BSC-1 cells results from the combined effects of (a) inhibitors formed by the cells, (b) decreased availability of receptor sites for serum growth factors as the cells become crowded, and (c) limiting concentrations of low molecular weight nutrients in the medium. In contrast, density-dependent regulation of growth in 3T3 mouse embryo fibroblasts results almost entirely from inactivation of serum factors.
Alternative mating strategies in the digger wasp
Philanthus zebratus
Cresson
Authors: Evans Howard E. , O'Neill Kevin M.
Published: May 2006

Males of at least six species of the digger wasp genus
Philanthus
are territorial, defending areas on the ground and evidently marking these with a pheromone. This is also true of
P. zebratus
at two widely separate localities in Colorado. However, males in an aggregation in Jackson Hole, Wyoming, are nonterritorial and participate in flights serving to intercept females leaving and entering the nesting area. The evidence suggests that this novel strategy may have arisen
de novo
as a result of unknown ecological and historical factors.
Organization of immunoglobulin heavy chain genes and allelic deletion model.
Authors: Honjo T , Kataoka t
Published: May 2006

We have assessed the number of times the gene sequence encoding constant regions of mouse immunoglobulin heavy chains gamma1, gamma2a, and gamma3 are represented in the mouse genome by hybridization kinetic analysis. All three genes are present at one copy each per haploid genome in normal tissues and myelomas producing IgM or IgG3. IgG1-producing myelomas, however, contain 1 copy each of the gamma1 and gamma2a genes and 0.5 copy of the gamma3 gene per haploid genome. IgG2b-producing myelomas contain 1 copy of the gamma2a gene and 0.5 copy each of the gamma1 and gamma3 genes per haploid genome. IgG2a-producing myelomas contain 1 copy of the gamma2a gene and 0.5 copy each of the gamma1 and gamma3 genes per haploid genome. In myelomas producing IgA, all three gamma genes are represented 0.5 times per haploid genome. In order to account for the results we propose an allelic deletion model: (i) The specific deletion of heavy chain constant region genes accompanies the recombination of a variable region gene to a constant region gene. (ii) The portion of the chromosome that resides between two joining sequences is excised out of the chromosome. (iii) The recombination occurs on one of the alleles. Based on this model we also propose that heavy chain genes are arranged on one chromosome in the following order; variable region genes, unknown spacer sequence, mu, gamma3, gamma1, gamma2b, gamma2a, and alpha.
Nature of the gel to liquid crystal transition of synthetic phosphatidylcholines.
Authors: Albon N , Sturtevant J M
Published: May 2006

High sensitivity differential scanning calorimetry is employed in the study of the gel to liquid crystal phase transition of a highly purified sample of dipalmitoylphosphatidylcholine in multilamellar bilayer suspension. It is concluded from the calorimetric data that the purity of the sample is better than 99.94 mol % and that the transition closely approximates an isothermal first-order transition.
Charge stabilization mechanism in the visual and purple membrane pigments.
Authors: Warshel A
Published: May 2006

The effects of charged groups of rhodopsin and bacteriorhodopsin on the potential energy surface of their chromophore are examined, taking into account the protein dielectric effect. It is found that the barriers for twisting double bonds of an isolated chromophore can be drastically reduced when the chromophore interacts with the protein charges. New types of local minima are found in the ground-state potential surface of the protein-chromophore complex. These minima correspond to "charge-stabilized intermediates" which are formed when a shift of the chromophore positive charge to the ring is stabilized by the ionization of a properly placed acidic group of the protein and by partial alternation of the bond lengths of the chromophore. It is suggested that the absorption of light by rhodopsin and bacteriorhodopsin may be used not only for isomerization about double bonds, but also for trapping such charge-stabilized intermediates. Thus, for example, it is concluded that prelumirhodopsin might be still in the cis configuration. Both the mechanism of the proton pump system of the purple membrane and the dark reaction of the visual and purple membrane pigments are considered. The connection between the finding of the present work and the mechanism of storage of light energy in photobiology is indicated.
Hapten mimic elicits antibodies recognizing prostaglandin E2.
Authors: Fitzpatrick F A , Bundy G L
Published: May 2006

Antibodies that recognized the prostaglandin (PG) E structure were elicited from rabbits. 9-Deoxy-9-methylene-PGF2alpha, a stable isosteric mimic of PGE2, was conjugated to two different protein immunogens and the immune response system was duped into producing antibodies with poor recognition for prostaglandins other than the hapten mimic (9-deoxy-9-methylene-PGF2alpha) and its isosteric counterparts (PGE1 and PGE2). With this procedure, crossreaction that would ordinarily arise from the chemical or metabolic instability of an authentic PGE2 immunogen was avoided. Antibodies raised against a keyhole limpet hemocyanin conjugate of 9-deoxy-9-methylene-PGF2alpha had an average intrinsic association constant, Ko = 2.6 X 10(9) liters.mole-1, for PGE2. Crossreaction was low for a number of related prostaglandins, and a sensitive radioimmunoassay procedure with a detection limit of 6 pg was developed.
Purification of the fusion protein of Sendai virus: analysis of the NH2-terminal sequence generated during precursor activation.
Authors: Gething M J , White J M , Waterfield M D
Published: May 2006

The two glycoproteins of Sendai virus, the hemagglutinin-neuraminidase and the fusion protein (F), were separated and purified by affinity chromatography on a Lens culinaris lectin-Sepharose column. F was shown to consist of two disulfide-bonded glycopolypeptide chains, F1 and F2, of molecular weights 51,000 and 11,000, each of which contained 15% carbohydrate by weight. Amino-terminal sequence analysis showed that F2 was blocked and that the hydrophobic sequence NH2-Phe-Phe-Gly-Ala-Val-Ile-Gly-Ile-Ile-Ala-Leu-Gly-Pro-Ala-Thr- was at the amino terminus of F1. This sequence shows identity at six positions with the hydrophobic amino-terminal sequence of the smaller glycopolypeptide chain, HA2, of the hemagglutinin of influenza virus. Both F1 and HA2 are formed by proteolytic cleavage of precursor glycoproteins (Fo, Sendai virus; HAo, influenza virus). Since these cleavages confer infectivity upon both Sendai and influenza viruses and the ability to induce cell-to-cell fusion upon Sendai virus, the hydrophobic NH2-terminal sequences on F1 and HA2 may play a role in fusion of viral and host-cell membranes.
"Panning" for lymphocytes: a method for cell selection.
Authors: Wysocki L J , Sato V L
Published: May 2006

We have developed a simple method for the fractionation of T and B lymphocytes. Plastic dishes coated with antibodies specific for mouse Ig selectively bind splenic B lymphocytes. The adherent cells are easily removed by gentle pipetting; both adherent and nonadherent populations retain immunologic function. In a typical experiment, when 3 X 10(7) splenic lymphocytes were added to a 100 X 15 mm plastic dish coated with microgram quantities of anti-Ig, 98 % of the nonadherent cells were Ig negative and 97% of the adherent cells were Ig positive. The method is sufficiently sensitive to allow detection and separation of cell types comprising as little as 2% of the total population and can be modified to allow the selection of cells by a double-antibody procedure. We believe that the plastic dish method will be generally useful for fractionating cells on the basis of their cell surface antigens.
Stimulation of fetal hemoglobin synthesis in baboons by hemolysis and hypoxia.
Authors: DeSimone J , Biel S I , Heller P
Published: May 2006

Fetal hemoglobin (Hb F) levels in the peripheral blood of baboons (Papio cynocephalus) increased from an average value of 0.78% to 18.1% during the recovery phase from phenylhydrazine-induced hemolytic anemia. A similar increase was observed in animals exposed to hypobaric hypoxia. Large individual variations in the maximal Hb F levels were observed which could not be correlated with the ages of the animals. Reinduction of hemolysis in two fully recovered animals resulted in Hb F levels that were of similar magnitude as in the preceding episode, suggesting the possibility of genetically determined individual variations in the rate of Hb F synthesis under the same conditions of erythropoietic stimulation. Reticulocytes from the animals subjected to hemolysis of hypobaric hypoxia synthesized similar absolute quantities of Hb F in vitro. The results of the present studies indicate that the physiological switch from the synthesis of Hb F to that of Hb A during ontogeny can be reversed in adult nonhuman primates by conditions of erythropoietic stress known to be associated with high erythropoietin levels. These findings open the possibility that Hb F synthesis in adult humans may be therapeutically modulated in individuals who might benefit from increased levels of Hb F, such as patients with sickle cell anemia.
Isolation and characterization of mitochondrial DNA from Chlamydomonas reinhardtii.
Authors: Ryan R , Grant D , Chiang K S , Swift H
Published: May 2006

Mitochondrial DNA (mtDNA) has been isolated from a mitochondrial pellet of Chlamydomonas reinhardtii. The mtDNA has a buoyant density of 1.706 g/ml in CsCl, a melting temperature of 87.9 degrees in standard saline citrate, and a nucleoside composition of 47.5% deoxyguanidine plus deoxycytidine with no odd nucleosides. Thermal denaturation and renaturation studies have shown that (i) mtDNA contains no extensive intramolecular heterogeneity nor significant base bias between the complementary polynucleotide chains and (ii) mtDNA renatures as a single homogeneous class with a kinetic complexity of 9.78 X 10(6) daltons. Although rare (less than or equal to 1%), both open and supercoiled circular mtDNA molecules have been observed in the electron microscope. Contour lengths of linear and open and closed circular molecules are all within the range of 4.0-5.4 micron with a mean of 4.67 +/- 0.30 micron. This size is similar to that of animal mtDNA but approximately 1/8 that of the higher plant mtDNAs. The magnitude of mtDNA reiteration in C. reinhardtii is estimated to be of the same order as that of chloroplast DNA.
Quota methods for congressional apportionment are still non-unique
Authors: Mayberry John P.
Published: May 2006

Balinski and Young described a “quota method” for congressional apportionment and recommended it as “the only method satisfying three essential axioms” [Balinski, M. L. & Young, H. P. (1974)
Proc. Natl. Acad. Sci. USA
71, 4602-4606]. This paper points out and repairs a slight defect in one of those axioms, producing a quota method slightly different from that described previously. It also presents an alternative to the “consistency” axiom of the paper and describes the “dual quota” method, uniquely satisfying the alternative axioms (which have exactly as much justification as the originals).