bluuebunny/crossref_metadata_2025 huggingface dataset:
Elucidating the structural chemistry of glycosaminoglycan recognition by protein C inhibitor.
Authors: Kuhn L A , Griffin J H , Fisher C L , Greengard J S , Bouma B N , España F , Tainer J A
Published: May 2006

Glycosaminoglycans (GAGs) including heparin accelerate the inhibition of serine proteases by serine protease inhibitors (serpins), an essential process in regulating blood coagulation. to analyze the molecular basis for GAG recognition by the plasma serpin protein C inhibitor (PCI; also known as plasminogen activator inhibitor 3), we have constructed a complete, energy-minimized, three-dimensional model of PCI by using the structure of homologous alpha 1-antitrypsin as a template. Sequence analysis, hydrogen-bonding environment, and shape complementarity suggested that the N-terminal residues of PCI, which are not homologous to those of alpha 1-antitrypsin, form an amphipathic alpha-helix, here designated A+ since it precedes the alpha 1-antitrypsin A helix. Electrostatic calculations revealed a single, highly positive surface region arising from both the A+ and H helices, suggesting that this two-helix motif is required for GAG binding by PCI. The dominant role of electrostatic interactions in PCI-heparin binding was confirmed by the strong ionic strength dependence of heparin stimulation. The involvement of the A+ helix in heparin binding was verified by demonstrating that an anti-PCI antibody that specifically binds the A+ peptide blocks heparin binding.
Direct structure analysis of a paraffin solid solution.
Authors: Dorset D L
Published: May 2006

Single microcrystals of a 1:1 solid solution of n-C32H66/n-C36H74 have been grown by epitaxial nucleation on benzoic acid, and 0kl electron diffraction patterns from them can be obtained with a lamellar spacing characteristic of the intermediate n-paraffin n-C34H70. This average structure is also indicated by indices (space group Pca21) for major intensities in this zone. Direct phasing of the intensity data is carried out by combined use of low-dose electron microscope lattice images (to assign values to the "lamellar" reflections) and three-phase structure invariant relationships (to find values for the "polyethylene" reflections). The computed electrostatic potential map closely resembles the crystal structure of n-C34H74, for which all 34 atom positions can be found. It is apparent, however, that lower atomic occupancies at the chain ends correspond to anticipated disorder at the lamellar interface. Structural refinement based on this occupancy results in a good match to the observed intensity data.
Changing the invariant proline-30 of rat and Drosophila melanogaster cytochromes c to alanine or valine destabilizes the heme crevice more than the overall conformation.
Authors: Koshy T I , Luntz T L , Schejter A , Margoliash E
Published: May 2006

Drosophila melanogaster and rat cytochromes c in which proline-30 was converted to alanine or valine were expressed in a strain of baker's yeast, Saccharomyces cerevisiae, where they sustained aerobic growth. The mutations had no significant effect on the spectra or redox potentials but altered drastically the stability of the bond between the methionine-80 sulfur and the heme iron, as judged by four criteria: (i) the alkaline pKa values of the 695-nm band of the ferric form of the mutant proteins decreased by almost 1 pH unit as compared to the wild types; (ii) the acid pKa values increased by 0.5 to 1.2 pH units; (iii) the 695-nm band half-disappeared at temperatures 10-20 degrees C lower in the mutant proteins than in the wild types; and (iv) the 695-nm band of the mutant proteins was susceptible to concentrations of urea that had little influence on their overall structure. The valine-substituted rat cytochrome c had properties intermediate between those of the wild type and the alanine mutant. The destabilized coordinative bond is located in space a long distance from the mutation site. It is suggested that the mutations weaken the hydrogen bond between the carbonyl of residue 30 and the imino group of the imidazole of histidine-18, modifying the bonding of the heme iron by that imidazole, which, in turn, through a trans effect, weakens the bond between the heme iron and the other axial ligand, the sulfur of methionine-80. Alternatively, the effect of the mutations may be propagated allosterically along the peptide chain.
Two genes encode factors with NF-kappa B- and H2TF1-like DNA-binding properties.
Authors: Rustgi A K , Van 't Veer L J , Bernards R
Published: May 2006

NF-kappa B and H2TF1 are transcription factors that bind to related DNA sequence motifs. NF-kappa B is a constitutive factor in mature B lymphocytes and is inducible in immature B cells and nonlymphoid cells. H2TF1 is a constitutive ubiquitous transcription factor that activates expression of major histocompatibility complex class I genes. We report here the isolation of two zinc finger genes. One, named MBP-2 (major histocompatibility complex-binding protein 2), encodes a factor that has DNA-binding properties similar, if not identical, to the H2TF1 transcription factor. The second, named KBP-1 (kappa-enhancer binding protein 1), encodes a factor that is similar to, but distinct from, NF-kappa B in its DNA-binding properties and methylation interference pattern, suggesting that at least two proteins can bind to the immunoglobulin kappa gene enhancer.
Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay.
Authors: Nickerson D A , Kaiser R , Lappin S , Stewart J , Hood L , Landegren U
Published: May 2006

DNA diagnostics, the detection of specific DNA sequences, will play an increasingly important role in medicine as the molecular basis of human disease is defined. Here, we demonstrate an automated, nonisotopic strategy for DNA diagnostics using amplification of target DNA segments by the polymerase chain reaction (PCR) and the discrimination of allelic sequence variants by a colorimetric oligonucleotide ligation assay (OLA). We have applied the automated PCR/OLA procedure to diagnosis of common genetic diseases, such as sickle cell anemia and cystic fibrosis (delta F508 mutation), and to genetic linkage mapping of gene segments in the human T-cell receptor beta-chain locus. The automated PCR/OLA strategy provides a rapid system for diagnosis of genetic, malignant, and infectious diseases as well as a powerful approach to genetic linkage mapping of chromosomes and forensic DNA typing.
Expression of chicken liver cell adhesion molecule fusion genes in transgenic mice.
Authors: Begemann M , Tan S S , Cunningham B A , Edelman G M
Published: May 2006

The tissue-specific expression of the chicken liver cell adhesion molecule (L-CAM) was studied by generating transgenic mice. The rat insulin II promoter was fused to a chicken L-CAM cDNA or to chicken genomic L-CAM sequences. Mice carrying the cDNA showed no expression of L-CAM. Mice carrying L-CAM genomic sequences showed expression in the beta cells of the pancreas, suggesting that sequences in introns or in flanking regions are required for expression. Murine L-CAM was undetectable in the beta cells of the pancreas of those transgenic mice expressing chicken L-CAM and thus appeared to be down-regulated, but expression of the mouse protein was not altered at other sites. Chicken L-CAM was also found in extrapancreatic tissues such as skin, kidney, liver, lung, intestine, blood vessels, and the choroid plexus and leptomeninges of the central nervous system. These findings raised the possibility that the chicken L-CAM gene contains cis regulatory elements that interfere with the specificity of a tissue-specific promoter such as the rat insulin promoter. To test this hypothesis, transgenic mice were produced with a construct containing the murine neurofilament promoter fused to genomic chicken L-CAM sequences. Chicken L-CAM was expressed in the brain and spinal cord, where L-CAM is not normally found, but it was also found in some nonneural tissues (kidney, liver, intestine, lung) in which L-CAM is normally expressed. The combined results suggest that tissue-specific cis-acting elements in the chicken L-CAM gene, when combined with heterologous promoters/enhancers, can generate novel patterns of gene expression.
Embryonic stem cell virus, a recombinant murine retrovirus with expression in embryonic stem cells.
Authors: Grez M , Akgün E , Hilberg F , Ostertag W
Published: May 2006

The expression of Moloney murine leukemia virus and vectors derived from it is restricted in undifferentiated mouse embryonal carcinoma and embryonal stem (ES) cells. We have developed a retroviral vector, the murine embryonic stem cell virus (MESV), that is active in embryonal carcinoma and ES cells. MESV was derived from a retroviral mutant [PCC4-cell-passaged myeloproliferative sarcoma virus (PCMV)] expressed in embryonal carcinoma cells but not in ES cells. The enhancer region of PCMV was shown to be functional in both cell types, but sequences within the 5' untranslated region of PCMV were found to restrict viral expression in ES cells. Replacement of this region by related sequences obtained from the dl-587rev retrovirus results in MESV, a modified PCMV virus that confers G418 resistance to fibroblasts and ES cells with similar efficiencies. Expression of MESV in ES cells is mediated by transcriptional regulatory elements within the 5' long terminal repeat of the viral genome.
Binocular competition in the control of geniculate cell size depends upon visual cortical N-methyl-D-aspartate receptor activation.
Authors: Bear M F , Colman H
Published: May 2006

The lateral geniculate nucleus relays visual information from the retina to cortex. One well-known anatomical consequence of monocular deprivation during early postnatal development is a shrinkage of neurons in the lamina of the lateral geniculate nucleus that receive input from the deprived eye. This is thought to reflect the competition of afferents subserving the two eyes, possibly at the level of the visual cortex. We find that blockade of N-methyl-D-aspartate receptors in kitten visual cortex disrupts this process of binocular competition. These data provide direct evidence that postsynaptic activation of cortical neurons is required for competitive changes in lateral geniculate cell size and suggest a role for N-methyl-D-aspartate receptors in anatomical as well as physiological plasticity in the mammalian visual system.
Mapping chromosome band 11q23 in human acute leukemia with biotinylated probes: identification of 11q23 translocation breakpoints with a yeast artificial chromosome.
Authors: Rowley J D , Diaz M O , Espinosa R , Patel Y D , van Melle E , Ziemin S , Taillon-Miller P , Lichter P , Evans G A , Kersey J H
Published: May 2006

Translocations involving chromosome 11, band q23, are frequent recurring abnormalities in human acute lymphoblastic and acute myeloid leukemia. We used 19 biotin-labeled probes derived from genes and anonymous cosmids for hybridization to metaphase chromosomes from leukemia cells that contained four translocations involving band 11q23: t(4;11)(q21;q23), t(6;11)(q27;q23), t(9;11)(p22;q23), and t(11;19)(q23;p13). The location of the cosmid probes relative to the breakpoint in 11q23 was the same in all translocations. Of the cosmid clones containing known genes, CD3D was proximal and PBGD, THY1, SRPR, and ETS1 were distal to the breakpoint on 11q23. Hybridization of genomic DNA from a yeast clone containing yeast artificial chromosomes (YACs), that carry 320 kilobases (kb) of human DNA including CD3D and CD3G genes, showed that the YACs were split in all four translocations. These results indicate that the breakpoint at 11q23 in each of these translocations occurs within the 320 kb encompassed by these YACs; whether the breakpoint within the YACs is precisely the same in the different translocations is presently unknown.
Site-specific cleavage of RNA by Fe(II).bleomycin.
Authors: Carter B J , de Vroom E , Long E C , van der Marel G A , van Boom J H , Hecht S M
Published: May 2006

Bleomycin is an antitumor agent whose activity has long been thought to derive from its ability to degrade DNA. Recent findings suggest that cellular RNA may be a therapeutically relevant locus. At micromolar concentrations, Fe(II)-bleomycin readily cleaved a Bacillus subtilis tRNAHis precursor in a highly selective fashion, but Escherichia coli tRNA(Tyr) precursor was largely unaffected even under more forcing conditions. Other substrates included an RNA transcript encoding a large segment of the reverse transcriptase from human immunodeficiency virus 1. RNA cleavage was oxidative, approximately 10-fold more selective than DNA cleavage, and largely unaffected by nonsubstrate RNAs. RNA sequence analysis suggested recognition of RNA tertiary structure, rather than recognition of specific sequences; subsets of nucleotides at the junction of single- and double-stranded regions were especially susceptible to cleavage. The ready accessibility of cellular RNAs to xenobiotic agents, the high selectivity of bleomycin action on RNAs, and the paucity of mechanisms for RNA repair suggest that RNA may be a therapeutically relevant target for bleomycin.
Beneficial effects of x-irradiation on recovery of lesioned mammalian central nervous tissue.
Authors: Kalderon N , Alfieri A A , Fuks Z
Published: May 2006

We examined the potential of x-irradiation, at clinical dose levels, to manipulate the cellular constituents and thereby change the consequences of transection injury to adult mammalian central nervous tissue (rat olfactory bulb). Irradiation resulted in reduction or elimination of reactive astrocytes at the site of incision provided that it was delivered within a defined time window postinjury. Under conditions optimal for the elimination of gliosis (15-18 days postinjury), irradiation of severed olfactory bulbs averted some of the degenerative consequences of lesion. We observed that irradiation was accompanied by prevention of tissue degeneration around the site of lesion, structural healing with maintenance of the typical cell lamination, and rescue of some axotomized mitral cells (principal bulb neurons). Thus radiation resulted in partial preservation of normal tissue morphology. It is postulated that intrusive cell populations are generated in response to injury and reactive astrocytes are one such group. Our results suggest that selective elimination of these cells by irradiation enabled some of the regenerative processes that are necessary for full recovery to maintain their courses. The cellular targets of these cells, their modes of intervention in recovery, and the potential role of irradiation as a therapeutic modality for injured central nervous system are discussed.
A long terminal repeat-containing retrotransposon is mobilized during hybrid dysgenesis in Drosophila virilis.
Authors: Scheinker V S , Lozovskaya E R , Bishop J G , Corces V G , Evgen'ev M B
Published: May 2006

A hybrid dysgenesis syndrome similar to those described in Drosophila melanogaster occurs in Drosophila virilis when a laboratory stock is crossed to a wild strain collected in the Batumi region of Georgia (U.S.S.R). Mutations in various loci obtained during these crosses are presumably induced by the insertion of DNA sequences. We have cloned an induced white mutation and characterized the insertion sequence responsible for the mutant phenotype. This sequence is a 10.6-kilobase (kb) transposable element we have named Ulysses. This element is flanked by unusually large 2.1-kb long terminal repeats. Ulysses also contains other landmarks characteristic of the retrotransposon family, such as a tRNA-binding site adjacent to the 5' long terminal repeat and open reading frames encoding putative products with homology to the reverse transcriptase, protease, and integrase domains typical of proteins encoded by vertebrate retroviruses. Some of the mutations obtained do not contain a copy of the Ulysses element at the mutant locus, suggesting that a different transposable element may be responsible for the mutation. Therefore, Ulysses may not be the primary cause of the entire dysgenic syndrome, and its mobilization may be the result of activation by an independent mobile element.
In vitro regulation of a SIN3-dependent DNA-binding activity by stimulatory and inhibitory factors.
Authors: Wang H , Stillman D J
Published: May 2006

The yeast SIN3 gene (also known as SDII, is a known negative regulator of the yeast HO gene. A DNA-binding activity, called SDP1, which binds to the HO promoter, is absent in extracts prepared from sin3 mutants and has been proposed to function as a repressor. We show that SIN3 does not encode SDP1 and that SDP1 DNA-binding activity is modulated in vitro by two factors, an inhibitory factor, I-SDP1, and a stimulatory factor, S-SDP1. I-SDP1 acts as an in vitro inhibitor of the SDP1 DNA-binding activity. Restoration of the DNA-binding activity is achieved by inclusion of a stimulatory factor, S-SDP1, which copurifies with the SIN3 protein. SDP1 DNA-binding activity was restored by treating a protein fraction containing SDP1 and I-SDP1 with the dissociating agent formamide.
Molecular cloning, functional expression, and chromosomal localization of mouse hepatocyte nuclear factor 1.
Authors: Kuo C J , Conley P B , Hsieh C L , Francke U , Crabtree G R
Published: May 2006

The homeodomain-containing transcription factor hepatocyte nuclear factor 1 (HNF-1) most likely plays an essential role during liver organogenesis by transactivating a family of greater than 15 predominantly hepatic genes. We have isolated cDNA clones encoding mouse HNF-1 and expressed them in monkey COS cells and in the human T-cell line Jurkat, producing HNF-1 DNA-binding activity as well as transactivation of reporter constructs containing multimerized HNF-1 binding sites. In addition, the HNF-1 gene was assigned by somatic cell hybrids and recombinant inbred strain mapping to mouse chromosome 5 near Bcd-1 and to human chromosome 12 region q22-qter, revealing a homologous chromosome region in these two species. The presence of HNF-1 mRNA in multiple endodermal tissues (liver, stomach, intestine) suggests that HNF-1 may constitute an early marker for endodermal, rather than hepatocyte, differentiation. Further, that HNF-1 DNA-binding and transcriptional activity can be conferred by transfecting the HNF-1 cDNA into several cell lines indicates that it is sufficient to activate transcription in the context of ubiquitously expressed factors.
Polyamines potentiate responses of N-methyl-D-aspartate receptors expressed in xenopus oocytes.
Authors: McGurk J F , Bennett M V , Zukin R S
Published: May 2006

Glutamate, the major excitatory neurotransmitter in the central nervous system, activates at least three types of channel-forming receptors defined by the selective agonists N-methyl-D-aspartate (NMDA), kainate, and quisqualate [or more selectively by alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)]. Activation of the NMDA receptor requires glycine as well as NMDA or glutamate. Recent studies have provided evidence that certain polyamines potentiate the binding by NMDA receptors of glycine and the open channel blocker MK-801. To determine whether polyamines alter channel opening, we examined their effects on rat brain glutamate receptors expressed in Xenopus oocytes. Our results demonstrate that spermine potentiates the response of the NMDA receptor but has no effect on responses to kainate and quisqualate. Furthermore, spermine increases the maximum response to NMDA and glycine and acts, at least in part, by increasing the apparent affinity of the NMDA receptor/channel complex for glycine. The present findings and the fact that polyamines are a natural constituent of brain suggest that polyamines may play a role in the regulation of glutamatergic transmission.
Activation of erythropoietin receptors by Friend viral gp55 and by erythropoietin and down-modulation by the murine Fv-2r resistance gene.
Authors: Hoatlin M E , Kozak S L , Lilly F , Chakraborti A , Kozak C A , Kabat D
Published: May 2006

The leukemogenic membrane glycoprotein (gp55) encoded by Friend spleen focus-forming virus appears to bind to erythropoietin receptors (EpoR) sto stimulate erythroblastosis [Li, J.-P., D'Andrea, A.D., Lodish, H.F. & Baltimore, D. (1990) Nature (London) 343, 762-764]. To directly compare the effects of gp55 with erythropoietin (Epo), we produced retrovirions that encode either gp55, Epo, or EpoR. After infection with EpoR virus, interleukin 3-dependent DA-3 cells bound 125I-labeled Epo and grew without interleukin 3 in the presence of Epo. These latter cells, but not parental DA-3 cells, became factor-independent after superinfection either with Epo virus or with Friend spleen focus-forming virus. In addition, Epo virus caused a disease in mice that mimicked Friend erythroleukemia. Although Fv-2r homozygotes are susceptible to all other retroviral diseases, they are resistant to both Epo viral and Friend viral erythroleukemias. These results indicate that both gp55 and Epo stimulate EpoR and that the Fv-2 gene encodes a protein that controls response to these ligands. However, the Fv-2 protein is not EpoR because the corresponding genes map to opposite ends of mouse chromosome 9. These results have important implications for understanding signal transduction by EpoR and the role of host genetic variation in controlling susceptibility to an oncogenic protein.
Dominant lethal mutations in a conserved loop in 16S rRNA.
Authors: Powers T , Noller H F
Published: May 2006

The 530 stem-loop region in 16S rRNA is among the most phylogenetically conserved structural elements in all rRNAs, yet its role in protein synthesis remains mysterious. G-530 is protected from kethoxal attack when tRNA, or its 15-nucleotide anticodon stem-loop fragment, is bound to the ribosomal A site. Based on presently available evidence, however, this region is believed to be too remote from the decoding site for this protection to be the result of direct contact. In this study, we use a conditional rRNA expression system to demonstrate that plasmid-encoded 16S rRNA genes carrying A, C, and T point mutations at position G-530 confer a dominant lethal phenotype when expressed in Escherichia coli. Analysis of the distribution of plasmid-encoded 16S rRNA in ribosomal particles, following induction of the A-530 mutation, shows that mutant rRNA is present both in 30S subunits and in 70S ribosomes. Little mutant rRNA is found in polyribosomes, however, indicating that the mutant ribosomes are severely impaired at the stage of polysome formation and/or stability. Detailed chemical probing of mutant ribosomal particles reveals no evidence of structural perturbation within the 16S rRNA. Taken together, these results argue for the direct participation of G-530 in ribosomal function and, furthermore, suggest that the dominant lethal phenotype caused by these mutations is due primarily to the mutant ribosomes blocking a crucial step in protein synthesis after translational initiation.
Insulin, oxytocin, and vasopressin stimulate protein kinase C activity in adipocyte plasma membranes.
Authors: Egan J J , Saltis J , Wek S A , Simpson I A , Londos C
Published: May 2006

Incubation of isolated rat adipocytes with insulin, vasopressin, or oxytocin increased plasma membrane-bound protein kinase C (PKC) activity by 100-400%. PKC activity was assayed by a procedure that is virtually background-free, thus permitting assay of protein kinase activity in highly diluted samples of solubilized membranes. Hormone-dependent increases in PKC activity were limited to plasma membranes. Stimulation of the kinase was half-maximal with 70 pM insulin, and the hormone effect was rapid. Oxytocin and vasopressin produced effects on PKC similar to insulin, but the magnitude of the vasopressin stimulation exhibited seasonal variations. Treatment of cells with phorbol 12-myristate 13-acetate (PMA) resulted in a loss of PKC activity from the cytosol and a gain in plasma membrane activity, indicative of translocation of the enzyme. With activity measurements it was not possible to determine if insulin stimulated a translocation of the kinase. However, Western blot analysis of plasma membranes with polyclonal antibodies directed against PKC suggest that at least some of the insulin-stimulated PKC activity resulted from enzyme translocation.
Synergistic fibrinolysis: combined effects of plasminogen activators and an antibody that inhibits alpha 2-antiplasmin.
Authors: Reed G L , Matsueda G R , Haber E
Published: May 2006

To improve the efficacy of plasminogen activators, we produced a monoclonal antibody (RWR) that inhibits human alpha 2-antiplasmin (alpha 2AP). In addition to inhibiting alpha 2AP in plasma, RWR binds to and inhibits fibrin cross-linked alpha 2AP and reproduces the "spontaneous" clot lysis that is the hallmark of human alpha 2AP deficiency. By inhibiting the inactivation of plasmin by alpha 2AP, RWR interacts synergistically with plasminogen activators to increase the potency (for 50% clot lysis) of urokinase by 80-fold, tissue plasminogen activator by 27-fold, and streptokinase by 20-fold. Yet, for a given amount of fibrinolysis, the combination of RWR and lower doses of plasminogen activator leads to less fibrinogen consumption than is obtained with higher, equipotent doses of plasminogen activator alone. These results suggest a strategy for increasing the efficacy of plasminogen activators. More generally, this approach to amplifying enzymatic activity by immunoneutralizing an inhibitor may be useful in other biologic processes that are rigidly governed by inhibitors.
Modulation of muscle gene expression in Caenorhabditis elegans: differential levels of transcripts, mRNAs, and polypeptides for thick filament proteins during nematode development.
Authors: Honda S , Epstein H F
Published: May 2006

The body-wall muscle cells of the nematode Caenorhabditis elegans produce thick filaments during embryonic, larval, and adult stages. These thick filaments contain two myosin isoforms, A and B, which assemble into different zones along the 10-microns lengths. Paramyosin, a protein homologous to myosin rods, forms a substratum for the myosins. The three filament proteins are encoded by different genes: myo-3 V (myosin heavy chain A), unc-54 I (myosin heavy chain B), and unc-15 I (paramyosin). The relative expression of these genes has been studied by run-on nuclear transcription in vitro, hybridization of accumulated mRNA, and immunochemical determination of specific polypeptide accumulation. In late larval nematodes (L4), the relative levels of nuclear run-on transcription per mol of probe are 6.4 unc-54:2.4 myo-3:1.0 unc-15. Similarly, the relative levels of immunospecific proteins are 4.5 unc-15:3.1 unc-54:1.0 myo-3. Most strikingly, the relative mRNA amounts are 50.0 unc-54:12.4 unc-15:1.0 myo-3. Thus, the orders of relative abundance and the quantitative relations of expression of the three functionally related genes change from transcriptional activities to final accumulated product of thick filament proteins. Modulation of the expression appears to involve processes affecting accumulation of mRNA and protein. The great difference in accumulation of the mRNAs for the two myosin heavy chain isoforms A and B may be related to the different roles of the myosins in thick filament assembly.
Coexpression of glutamine synthetase and carbamoylphosphate synthase I genes in pancreatic hepatocytes of rat.
Authors: Yeldandi A V , Tan X D , Dwivedi R S , Subbarao V , Smith D D , Scarpelli D G , Rao M S , Reddy J K
Published: May 2006

In the mammalian liver the distribution of ammonia-detoxifying enzymes, glutamine synthetase (GS) and carbamoylphosphate synthase I (ammonia) (CPS-I), is mutually exclusive in that these enzymes are expressed in two distinct populations of hepatocytes that are zonally demarcated in the liver acinus. In the present study we examined the distribution of GS and CPS-I in pancreatic hepatocytes to ascertain if the expression of these two genes in these hepatocytes is also mutually exclusive. Multiple foci of hepatocytes showing no clear acinar organization develop in the adult rat pancreas as a result of a change in the differentiation commitment after dietary copper deficiency. Unlike liver, GS and CPS-I are detected by immunofluorescence in all pancreatic hepatocytes. In situ hybridization revealed that all pancreatic hepatocytes contain GS and CPS-I mRNAs. The sizes of these two mRNAs in pancreas with hepatocytes are similar to those of the liver. The concomitant expression of GS and CPS-I genes in pancreatic hepatocytes may be attributed, in part, to the absence of portal blood supply to the pancreas vis-à-vis the lack of hormonal/metabolic gradients as well as to possible matrix homogeneity in the pancreas.
Fractal geometry of music.
Authors: Hsü K J , Hsü A J
Published: May 2006

Music critics have compared Bach's music to the precision of mathematics. What "mathematics" and what "precision" are the questions for a curious scientist. The purpose of this short note is to suggest that the mathematics is, at least in part, Mandelbrot's fractal geometry and the precision is the deviation from a log-log linear plot.
Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase.
Authors: Collyer C A , Blow D M
Published: May 2006

Crystallographic studies of D-xylose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5) incubated to equilibrium with substrate/product mixtures of xylose and xylulose show electron density for a bound intermediate. The accumulation of this bound intermediate shows that the mechanism is a non-Michaelis type. Carrell et al. [Carrell, H. L., Glusker, J. P., Burger, V., Manfre, F., Tritsch, D. & Biellmann, J.-F. (1989) Proc. Natl. Acad. Sci. USA 86, 4440-4444] and the present authors studied crystals of the enzyme-substrate complex under different conditions and made different interpretations of the substrate density, leading to different conclusions about the enzyme mechanism. All authors agree that the bound intermediate of the sugar is in an open-chain form. It is suggested that the higher-temperature study of Carrell et al. may have produced an equilibrium of multiple states, whose density fits poorly to the open-chain substrate, and led to incorrect interpretation. The two groups also bound different closed-ring sugar analogues to the enzyme, but these analogues bind differently. A possible explanation consistent with all the data is that the enzyme operates by a hydride shift mechanism.
FMS mutations in myelodysplastic, leukemic, and normal subjects.
Authors: Ridge S A , Worwood M , Oscier D , Jacobs A , Padua R A
Published: May 2006

The FMS gene encodes the functional cell surface receptor for colony-stimulating factor 1, the macrophage- and monocyte-specific growth factor. Codons 969 and 301 have been identified as potentially involved in promoting the transforming activity of FMS. Mutations at codon 301 are believed to lead to neoplastic transformation by ligand independence and constitutive tyrosine kinase activity of the receptor. The tyrosine residue at codon 969 has been shown to be involved in a negative regulatory activity, which is disrupted by amino acid substitutions. This study reports on the frequency of point mutations at these codons, in vivo, in human myeloid malignancies and in normal subjects. We studied 110 patients [67 with myelodysplasia (MDS) and 48 with acute myeloblastic leukemia (AML)], 5 patients being studied at the MDS and the later AML stage of the disease. There was a total incidence of 12.7% (14/110) with mutations in codon 969 and 1.8% (2/110) with mutations in codon 301. Two patients had mutations in the AML stage of the disease but not in the preceding MDS and one had a mutation in the MDS stage but not upon transformation of AML. This is consistent with the somatic origin of these mutations. FMS mutations were most prevalent (20%) in chronic myelomonocytic leukemia and AML type M4 (23%), both of which are characterized by monocytic differentiation. One of 51 normal subjects had a constitutional codon 969 mutation, which may represent a marker for predisposition to myeloid malignancy.
Site-specific excision from RNA by RNase H and mixed-phosphate-backbone oligodeoxynucleotides.
Authors: Agrawal S , Mayrand S H , Zamecnik P C , Pederson T
Published: May 2006

Oligodeoxynucleotides containing phosphodiester or modified internucleoside linkages were investigated with respect to their ability to be acted on by ribonuclease H activities present in a HeLa cell nuclear extract after hybridization with complementary sequences in RNA. Oligodeoxynucleotides complementary to nucleotides 2-14 of human U1 small nuclear RNA were investigated. Extensive cleavage of U1 RNA was observed with the unmodified oligodeoxynucleotide and with the phosphorothioate analogue but not with U1-complementary oligodeoxynucleotides containing methylphosphonate, phosphoro-N-morpholidate, or phosphoro-N-butylamidate internucleoside linkages. Additional experiments using a 514-nucleotide-long RNA substrate demonstrated the capacity of complementary phosphodiester- and phosphorothioate-linked oligodeoxynucleotides (but not ones containing methylphosphonate, phosphoro-N-morpholidate, or phosphoro-N-butylamidate linkages) to serve as RNase H targets when hybridized to an internal RNA site. Detailed comparisons revealed phosphodiester-linked oligodeoxynucleotides to be more efficient than the comparable phosphorothioate-linked oligomers with respect to RNase H action. Various pentadecamer oligodeoxynucleotides complementary to the 514-nucleotide-long test RNA and containing 2-6 consecutive phosphodiester- or phosphorothioate-linked nucleotides flanked by RNase H-resistant methylphosphonate linkages afforded precise "site-directed" RNase H excision within the DNA.RNA hybrid. These results serve to assort modified oligodeoxynucleotide-containing hybrids into RNase H-sensitive and -resistant classes and also provide clues as to how RNase H makes contact with the DNA strand in a DNA.RNA hybrid.
Genetic and molecular analysis of chlorambucil-induced germ-line mutations in the mouse.
Authors: Rinchik E M , Bangham J W , Hunsicker P R , Cacheiro N L , Kwon B S , Jackson I J , Russell L B
Published: May 2006

Eighteen variants recovered from specific locus mutation rate experiments involving the mutagen chlorambucil were subjected to several genetic and molecular analyses. Most mutations were found to be homozygous lethal. Because lethality is often presumptive evidence for multilocus-deletion events, 10 mutations were analyzed by Southern blot analysis with probes at, or closely linked to, several of the specific locus test markers, namely, albino (c), brown (b), and dilute (d). All eight mutations (two c; three b; two d; and one dilute-short ear [Df(d se)]) that arose in post-spermatogonial germ cells were deleted for DNA sequences. No evidence for deletion of two d-se region probes was obtained for the remaining two d mutations that arose in stem-cell spermatogonia. Six of the primary mutants also produced low litter sizes ("semisterility"). Karyotypic analysis has, to date, confirmed the presence of reciprocal translocations in four of the six. The high frequency of deletions and translocations among the mutations induced in post-spermatogonial stages by chlorambucil, combined with its overall high efficiency in inducing mutations in these stages, should make chlorambucil mutagenesis useful for generating experimentally valuable germ-line deletions throughout the mouse genome.
Expression of functional replication protein from tomato golden mosaic virus in transgenic tobacco plants.
Authors: Hanley-Bowdoin L , Elmer J S , Rogers S G
Published: May 2006

The A component of the bipartite genome of the geminivirus tomato golden mosaic virus (TGMV) encodes the viral protein (AL1) that is required for viral DNA replication. We have constructed transgenic Nicotiana benthamiana plants in which the AL1 open reading frame is transcribed under the control of the cauliflower mosaic virus 35S promoter. The transgenic plants, which were phenotypically normal, produced a single transcript from the 35S-AL1 construct and a 40-kDa protein that cross-reacted with a polyclonal antiserum raised against AL1 protein overproduced in Escherichia coli. Six of nine transgenic lines complemented a TGMV A variant with a mutation in AL1 when coinoculated with the B component of the TGMV genome. Single- and double-stranded forms of the B component were synthesized in leaf discs from a complementing, transgenic line in the absence of TGMV A. These results establish that the transgenic plants express functional AL1 protein and show that this viral protein is not only required, but sufficient, for single- and double-stranded replication of TGMV DNA in the presence of host proteins. These results also show that the AL1 protein is not by itself a determinant of disease or pathogenesis.
Maize chloroplast RNA polymerase: the 180-, 120-, and 38-kilodalton polypeptides are encoded in chloroplast genes.
Authors: Hu J , Bogorad L
Published: May 2006

Prominent polypeptides with apparent molecular masses of 180, 120, 85, and 38 kDa are found in an extensively purified preparation of maize chloroplast DNA-dependent RNA polymerase that retains the capacity to initiate transcription of the cloned chloroplast gene rbcL correctly and the requirement for a supercoiled DNA template for specific and active transcription. Amino-terminal amino acid sequences of the 180-, 120-, and 38-kDa polypeptides have been determined and found to correspond precisely to the sequences deduced from the 5' ends of the maize chloroplast rpoC2, rpoB, and rpoA genes, respectively. These experiments show that these chloroplast rpo genes encode the prominent polypeptides in the highly enriched maize chloroplast RNA polymerase preparation and support the conclusion that these polypeptides are functional components of the enzyme. The rpoB, rpoC1, and rpoC2 genes have been mapped on the maize chloroplast chromosome.
Frequency of intrachromosomal homologous recombination induced by UV radiation in normally repairing and excision repair-deficient human cells.
Authors: Tsujimura T , Maher V M , Godwin A R , Liskay R M , McCormick J J
Published: May 2006

To investigate the role of DNA damage and nucleotide excision repair in intrachromosomal homologous recombination, a plasmid containing duplicated copies of the gene coding for hygromycin resistance was introduced into the genome of a repair-proficient human cell line, KMST-6, and two repair-deficient lines, XP2OS(SV) from xeroderma pigmentosum complementation group A and XP2YO(SV) from complementation group F. Neither hygromycin-resistance gene codes for a functional enzyme because each contains an insertion/deletion mutation at a unique site, but recombination between the two defective genes can yield hygromycin-resistant cells. The rates of spontaneous recombination in normal and xeroderma pigmentosum cell strains containing the recombination substrate were found to be similar. The frequency of UV-induced recombination was determined for three of these cell strains. At low doses, the group A cell strain and the group F cell strain showed a significant increase in frequency of recombinants. The repair-proficient cell strain required 10- to 20-fold higher doses of UV to exhibit comparable increases in frequency of recombinants. These results suggest that unexcised DNA damage, rather than the excision repair process per se, stimulates such recombination.
The same target sequences are differentially important for activation of the interleukin 2 receptor alpha-chain gene in two distinct T-cell lines.
Authors: Toledano M B , Roman D G , Halden N F , Lin B B , Leonard W J
Published: May 2006

High-affinity receptors for interleukin 2 (IL-2) are expressed on T cells following activation. These receptors are composed of both alpha and beta chains. Expression of alpha chains and, therefore, expression of high-affinity receptors are critically regulated at the level of transcription initiation. We have further dissected the regulatory elements involved in controlling transcription of the IL-2 receptor alpha-chain (IL-2R alpha) gene. The IL-2R alpha promoter contains a kappa B site and binding sites for additional nuclear factors within a 50-base-pair region (positions -290 to -240 relative to the major transcription start site). These include one upstream of the kappa B site and one similar to the c-fos serum response element (SRE), which is downstream of the kappa B site. Mutation of the kappa B site decreases IL-2R alpha promoter activity in MT-2 cells (a T-cell line that has been transformed with human T-cell lymphotropic virus type I), but not in Jurkat cells (a T-cell leukemia line) that have been activated by phorbol 12-myristate 13-acetate (PMA). In contrast, mutation of a region upstream of the kappa B site decreases activity in PMA-induced Jurkat cells but increases activity in MT-2 cells. Mutation of the SRE-like site decreases activity in both cell types but the effect in PMA-induced Jurkat is more pronounced. Thus, these distinct cis-acting elements play different physiological roles in IL-2R alpha gene activation in MT-2 cells and PMA-induced Jurkat T cells. These studies provide direct evidence for a functionally significant SRE-like sequence in a gene other than c-fos and the actin genes and identify other elements that are critical for IL-2R alpha gene expression.
"Collective coding" of correlated cone signals in the retinal ganglion cell.
Authors: Tsukamoto Y , Smith R G , Sterling P
Published: May 2006

The signals in neighboring cones are partially correlated due to local correlations of luminance in the visual scene. By summing these partially correlated signals, the retinal ganglion cell improves its signal/noise ratio (compared to the signal/noise ratio in a cone) and expands the variance of its response to fill its dynamic range. Our computations prove that the optimal weighting function for this summation is dome-shaped. The computations also show that (assuming a particular space constant for the correlation function) ganglion cell collecting area and cone density are matched at all eccentricities such that the signal/noise ratio improves by a constant factor. The signal/noise improvement factor for beta ganglion cells in cat retina is about 4.
Characterization of the transverse relaxation rates in lipid bilayers.
Authors: Watnick P I , Dea P , Chan S I
Published: May 2006

The 2H NMR transverse relaxation rates of a deuterated phospholipid bilayer reflect slow motions in the bilayer membrane. A study of dimyristoyl lecithin specifically deuterated at several positions of the hydrocarbon chains indicates that these motions are cooperative and are confined to the hydrocarbon chains of the lipid bilayer. However, lipid head group interactions do play an important role in modulating the properties of the cooperative fluctuations of the hydrocarbon chains (director fluctuations), as evidenced by the effects of various lipid additives on the 2H NMR transverse relaxation rates of the dimyristoyl lecithin bilayer.
Molecular characterization of the terminal energy acceptor of cyanobacterial phycobilisomes.
Authors: Houmard J , Capuano V , Colombano M V , Coursin T , Tandeau de Marsac N
Published: May 2006

Cyanobacteria harvest light energy through multimolecular structures, the phycobilisomes, regularly arrayed at the surface of the photosynthetic membranes. Phycobilisomes consist of a central core from which rods radiate. A large polypeptide (LCM, 75-120 kDa) is postulated to act both as terminal energy acceptor and as a linker polypeptide that stabilizes the phycobilisome architecture. We report here the characterization of the gene (apcE) that encodes this LCM polypeptide in Calothrix sp. PCC 7601. It is located upstream from the genes encoding the major components of the phycobilisome core (allophycocyanin) and is part of the same operon. The deduced amino acid sequence shows that the N-terminal region of LCM shares homology with the other phycobiliprotein subunits and thus constitutes the chromoprotein domain. The other part of the molecule is made up of four repeated domains that are highly homologous to the N-terminal regions of the phycocyanin rod linker polypeptides. The predicted secondary structure of the different domains of the LCM is discussed in relation to the different roles and properties of this large molecule.
Increased platelet-derived growth factor A-chain expression in human uterine smooth muscle cells during the physiologic hypertrophy of pregnancy.
Authors: Mendoza A E , Young R , Orkin S H , Collins T
Published: May 2006

Platelet-derived growth factor (PDGF) has been implicated in the cell proliferation and directed cell movement in various physiologic and pathologic processes. To explore the role of PDGF in a reversible physiologic process, adaptation of the uterus to pregnancy, expression of PDGF in tissue sections of human gestational myometrium was demonstrated by immunohistochemical techniques and confirmed by nuclease protection analysis. Commensurate with an increase in immunoreactive PDGF expression in the myometrial smooth muscle cells, increased levels of PDGF A-chain mRNA, but not PDGF B-chain or PDGF B-type receptor transcripts, were seen in the gravid uterus relative to the nongravid uterus. The amount of A-chain transcript increased during gestation and diminished during the puerperium. These observations demonstrate PDGF polypeptide expression in situ and implicate PDGF in a normal physiologic process--uterine expansion during pregnancy.
Essential 170-kDa subunit for degradation of crystalline cellulose by Clostridium cellulovorans cellulase.
Authors: Shoseyov O , Doi R H
Published: May 2006

The cellulase complex from Clostridium cellulovorans has been purified and its subunit composition determined. The complex exhibits cellulase activity against crystalline cellulose as well as carboxymethylcellulase (CMCase) and cellobiohydrolase activities. Three major subunits are present with molecular masses of 170, 100, and 70 kDa. The 100-kDa subunit is the major CMCase, although at least four other, minor subunits show CMCase activity. The 170-kDa subunit has the highest affinity for cellulose, does not have detectable enzymatic activity, but is necessary for cellulase activity. Immunological studies indicate that the 170-kDa subunit is not required for binding of the catalytic subunits to cellulose and therefore does not function solely as an anchor protein. Thus this core subunit must have multiple functions. We propose a working hypothesis that the binding of the 170-kDa subunit converts the crystalline cellulose to a form that is capable of being hydrolyzed in a cooperative fashion by the associated catalytic subunits.
Structure of nogalamycin bound to a DNA hexamer.
Authors: Williams L D , Egli M , Qi G , Bash P , van der Marel G A , van Boom J H , Rich A , Frederick C A
Published: May 2006

The anthracycline antibiotic nogalamycin, which binds to DNA, is composed of a planar aglycone substituted on each end to form an unusual dumbbell-shaped molecule. At one end nogalamycin contains an uncharged nogalose sugar and a methyl ester. At the other end nogalamycin contains a positively charged bicyclo amino sugar. We report the crystal structure of nogalamycin bound to the self-complementary DNA hexamer d(m5CGTsAm5CG). In this complex, the cytosines are methylated at the 5 position and the DNA contains a phosphorothioate linkage at the TpA step. Two nogalamycin molecules bind to the 6-base-pair fragment of double-helical DNA. The drug has threaded between the phosphodiester backbones with three aromatic rings intercalated within the DNA. In the major groove, the bicyclo amino sugar forms two direct hydrogen bonds to span a CG base pair and interacts indirectly with the next base pair of the duplex via a water-mediated hydrogen bond. In the minor groove, a carbonyl oxygen of nogalamycin forms a hydrogen bond directly to N2 of a guanine. The DNA base pairs are severely buckled by up to 26 degrees and are also distorted in directions perpendicular to the Watson-Crick hydrogen bonds. This complex illustrates the deformable nature of DNA.