bluuebunny/crossref_metadata_2025 huggingface dataset:
Hirudin as a molecular probe for thrombin in vitro and during systemic coagulation in the pig.
Authors: Zoldhelyi P , Chesebro J H , Owen W G
Published: May 2006

The amount of thrombin active in vivo in the intravascular space (blood and endothelial surface), both basally and in experimental intravascular coagulation, is measured by way of the accessibility of thrombin to intravascular hirudin. Blood samples from pigs given intravenous 125I-labeled hirudin contain 125I-labeled hirudin-thrombin complex in concentrations indicative of a basal thrombin concentration in vivo of 0.5 nmol/liter. Intravenous infusion of Salmonella endotoxin elicits an increase in the circulating concentration of hirudin-thrombin complex that begins within 15 min and is 20-30 times basal after 4 hr. Induction of mild intravascular coagulation is evidenced by a modest reduction in plasma fibrinogen concentrations. It is concluded that there is a basal pool of hirudin-accessible thrombin in the intravascular space that, were it free in the plasma phase, would be sufficient in principle to sustain intravascular coagulation.
Identification and preliminary characterization of a protein motif related to the zinc finger.
Authors: Lovering R , Hanson I M , Borden K L , Martin S , O'Reilly N J , Evan G I , Rahman D , Pappin D J , Trowsdale J , Freemont P S
Published: May 2006

We have identified a protein motif, related to the zinc finger, which defines a newly discovered family of proteins. The motif was found in the sequence of the human RING1 gene, which is proximal to the major histocompatibility complex region on chromosome six. We propose naming this motif the "RING finger" and it is found in 27 proteins, all of which have putative DNA binding functions. We have synthesized a peptide corresponding to the RING1 motif and examined a number of properties, including metal and DNA binding. We provide evidence to support the suggestion that the RING finger motif is the DNA binding domain of this newly defined family of proteins.
Immunosuppressants implicate protein phosphatase regulation of K+ channels in guard cells.
Authors: Luan S , Li W , Rusnak F , Assmann S M , Schreiber S L
Published: May 2006

The elevation of Ca2+ levels in the cytoplasm inactivates inward-rectifying K+ channels that play a central role in regulating the apertures of stomatal pores in higher plants. However, the mechanism for the Ca(2+)-mediated inhibition of K(+)-channel function is unknown. Using patch-clamp techniques, we show that cyclophilin-cyclosporin A and FK506-binding protein-FK506 complexes, which are highly specific inhibitors of protein phosphatase 2B (calcineurin), block Ca(2+)-induced inactivation of K+ channels in Vicia faba guard cells. A constitutively active calcineurin fragment that is Ca(2+)-independent inhibits K(+)-channel activity in the absence of Ca2+. We have also identified an endogenous Ca(2+)-dependent phosphatase activity from V. faba that is inhibited by the cyclophilin-cyclosporin A and FK506-binding protein-FK506 complexes. Our findings implicate a Ca(2+)-dependent, calcineurin-like protein phosphatase in a Ca2+ signal-transduction pathway of higher plants.
Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data.
Authors: Vellieux F M , Hajdu J , Verlinde C L , Groendijk H , Read R J , Greenhough T J , Campbell J W , Kalk K H , Littlechild J A , Watson H C
Published: May 2006

The three-dimensional structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating), EC 1.12.1.12] from the sleeping-sickness parasite Trypanosoma brucei was solved by molecular replacement at 3.2-A resolution with an x-ray data set collected by the Laue method. For data collection, three crystals were exposed to the polychromatic synchrotron x-ray beam for a total of 20.5 sec. The structure was solved by using the Bacillus stearothermophilus enzyme model [Skarzyński, T., Moody, P. C. E. & Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187] with a partial data set which was 37% complete. The crystals contain six subunits per asymmetric unit, which allowed us to overcome the absence of > 60% of the reflections by 6-fold density averaging. After molecular dynamics refinement, the current molecular model has an R factor of 17.6%. Comparing the structure of the trypanosome enzyme with that of the homologous human muscle enzyme, which was determined at 2.4-A resolution, reveals important structural differences in the NAD binding region. These are of great interest for the design of specific inhibitors of the parasite enzyme.
Epitopic structure of Tn glycophorin A for an anti-Tn antibody (MLS 128).
Authors: Nakada H , Inoue M , Numata Y , Tanaka N , Funakoshi I , Fukui S , Mellors A , Yamashina I
Published: May 2006

Glycophorin A was digested with glycoprotease (Pasteurella haemolytica) and the digest was fractionated by a combination of high-pressure column chromatographies to produce the glycopeptides GPA-1 to GPA-6. Sequence analysis of the glycopeptides revealed that two serine residues (Ser-14 and Ser-15) are not glycosylated, Thr-17 and Ser-19 being glycosylated instead, in disagreement with the accepted structure. The glycopeptides thus obtained were treated with sialidase and beta-galactosidase. The Tn antigenicity, as assayed by the binding to a monoclonal anti-Tn antibody (MLS 128), was found exclusively in the glycopeptides including three (cluster I) or four (cluster II) consecutive residues of GalNAc-Ser/Thr, whereas the glycopeptide (GPA-2) containing two nonconsecutive GalNAc-Ser/Thr residues had practically no Tn antigenicity. The immunoreactivities of GPA-1 and GPA-3, containing both clusters I and II, and GPA-4, containing cluster II, were 63% (calcd. 67%), 81% (calcd. 86%), and 50% (calcd. 50%), respectively, of the immunoreactivity of GPA-5 or GPA-6, containing cluster I (the average being taken as the basis), based on the reactivity per GalNAc residue. These results indicate that clusters I and II react with the antibody to the same extent. The structure consisting of three consecutive glycosylated Ser/Thr residues may be essential for Tn antigenicity in the light of previous results for ovine submaxillary mucin.
Transfected cGMP-dependent protein kinase suppresses calcium transients by inhibition of inositol 1,4,5-trisphosphate production.
Authors: Ruth P , Wang G X , Boekhoff I , May B , Pfeifer A , Penner R , Korth M , Breer H , Hofmann F
Published: May 2006

cGMP is a key regulatory molecule in visual transduction, integration of neuronal response to excitatory neurotransmitters, relaxation of smooth muscle, intestinal secretion of water and salt, and reabsorption of sodium and water in the distal tubules of the nephron. Some of these cellular functions are associated with the activation of cGMP kinase and a decrease in cytosolic calcium levels ([Ca2+]i). The mechanism by which cGMP kinase lowers [Ca2+]i is controversial. We have used CHO cells stably transfected with cGMP kinase to test several of the proposed [Ca2+]i-lowering mechanisms. Thrombin induces a calcium transient in wild-type and cGMP kinase-expressing CHO cells by releasing calcium from intracellular stores. Preincubation of wild-type cells with 8-bromo-cGMP had no effect on the calcium transient, whereas 8-bromo-cGMP prevented the thrombin-stimulated calcium transient in cGMP kinase-expressing CHO cells. In both cell types 8-bromo-cGMP had no effect on [Ca2+]i transients induced by replacing extracellular sodium by tetramethylammonium, ruling out an effect of cGMP kinase on Ca(2+)-ATPases. However, cGMP kinase activation effectively suppressed thrombin-induced stimulation of inositol 1,4,5-trisphosphate production. These results show that cGMP kinase lowers [Ca2+]i by interfering with the inositol 1,4,5-trisphosphate synthesis.
Increased manganese superoxide dismutase expression suppresses the malignant phenotype of human melanoma cells.
Authors: Church S L , Grant J W , Ridnour L A , Oberley L W , Swanson P E , Meltzer P S , Trent J M
Published: May 2006

Introduction of a normal human chromosome 6 into human melanoma cell lines results in suppression of tumorigenicity. This suggests that a gene(s) on chromosome 6 controls the malignant phenotype of human melanoma. Because antioxidants can suppress the tumor-promotion phase of carcinogenesis, and because the antioxidant enzyme manganese superoxide dismutase (MnSOD) has been localized to a region of chromosome 6 frequently lost in melanomas, we have examined the effect of transfecting sense and antisense human MnSOD cDNAs into melanoma cell lines. Cell lines expressing abundant (+)-sense MnSOD-5 cDNAs significantly altered their phenotype in culture and lost their ability to form colonies in soft agar and tumors in nude mice. In contrast, the introduction of antisense MnSOD or +psv2neo had no effect on melanoma tumorigenicity. These findings indicate that stable transfection of MnSOD cDNA into melanoma cell lines exerts a biological effect that mimics that observed after introduction of an entire human chromosome 6.
Mapping cis-acting defects in promoters of transcriptionally silent DQA2, DQB2, and DOB genes.
Authors: Voliva C F , Tsang S , Peterlin B M
Published: May 2006

Defects in promoters of the nonexpressed DQA2, DQB2, and DOB genes from the class II major histo-compatibility complex were mapped by placing Z and X boxes of these silent genes into a synthetic DRA promoter. These conserved upstream sequences confer B-cell-specific and gamma-interferon-inducible expression to the DRA gene. Since DRA promoters containing the X box from the DQA2 gene and Z boxes from DQA2, DQB2, and DOB genes were neither expressed constitutively in B cells nor inducible by gamma interferon in fibroblastic cells, these conserved upstream sequences are implicated in the transcriptional defects of these silent genes.
Molecular cloning and expression of inducible nitric oxide synthase from human hepatocytes.
Authors: Geller D A , Lowenstein C J , Shapiro R A , Nussler A K , Di Silvio M , Wang S C , Nakayama D K , Simmons R L , Snyder S H , Billiar T R
Published: May 2006

Nitric oxide is a short-lived biologic mediator for diverse cell types. Synthesis of an inducible nitric oxide synthase (NOS) in murine macrophages is stimulated by lipopolysaccharide (LPS) and interferon gamma. In human hepatocytes, NOS activity is induced by treatment with a combination of tumor necrosis factor, interleukin 1, interferon gamma, and LPS. We now report the molecular cloning and expression of an inducible human hepatocyte NOS (hep-NOS) cDNA. hep-NOS has 80% amino acid sequence homology to macrophage NOS (mac-NOS). Like other NOS isoforms, recognition sites for FMN, FAD, and NADPH are present, as well as a consensus calmodulin binding site. NOS activity in human 293 kidney cells transfected with hep-NOS cDNA is diminished by Ca2+ chelation and a calmodulin antagonist, reflecting a Ca2+ dependence not evident for mac-NOS. Northern blot analysis with hep-NOS cDNA reveals a 4.5-kb mRNA in both human hepatocytes and aortic smooth muscle cells following stimulation with LPS and cytokines. Human genomic Southern blots probed with human hep-NOS and human endothelial NOS cDNA clones display different genomic restriction enzyme fragments, suggesting distinct gene products for these NOS isoforms. hep-NOS appears to be an inducible form of NOS that is distinct from mac-NOS as well as brain and endothelial NOS isozymes.
Expression of gonadotropin-releasing hormone receptors and autocrine regulation of neuropeptide release in immortalized hypothalamic neurons.
Authors: Krsmanović L Z , Stojilković S S , Mertz L M , Tomić M , Catt K J
Published: May 2006

The hypothalamic control of gonadotropin secretion is mediated by episodic basal secretion and midcycle ovulatory surges of gonadotropin-releasing hormone (GnRH), which interacts with specific plasma membrane receptors in pituitary gonadotrophs. Similar GnRH receptors and their mRNA transcripts were found to be expressed in immortalized hypothalamic neurons, which release GnRH in a pulsatile manner in vitro. Activation of these neuronal GnRH receptors elicited dose-related intracellular Ca2+ concentration responses that were dependent on calcium mobilization and entry and were inhibited by GnRH antagonists. Exposure of perifused neurons to a GnRH agonist analog caused a transient elevation of GnRH release and subsequent suppression of the basal pulsatile secretion. This was followed by dose-dependent induction of less frequent but larger GnRH pulses and ultimately by single massive episodes of GnRH release. The ability of GnRH to exert autocrine actions on its secretory neurons, and to promote episodic release and synchronized discharge of the neuropeptide, could reflect the operation of the endogenous pulse generator and the genesis of the preovulatory GnRH surge in vivo.
Increased intracellular Ca2+: a critical link in the pathophysiology of sepsis?
Authors: Song S K , Karl I E , Ackerman J J , Hotchkiss R S
Published: May 2006

Severe bloodstream-borne infection--i.e., sepsis--and the resulting multiorgan failure are now the most common cause of death in many intensive care units. One of the most fundamentally important and controversial issues concerning the pathophysiology of sepsis is the role of intracellular free calcium concentration ([Ca2+]i) in this disorder. Because of the critical role of calcium as an intracellular second messenger and as a potential cellular toxin, resolution of this issue is crucial. Using 19F NMR spectroscopy and the calcium indicator 5,5'-difluoro-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetate we demonstrate in the intact perfused organ, the rat thoracic aorta, that [Ca2+]i in aortic smooth muscle is increased > 2-fold during sepsis. Furthermore, we determined that sodium dantrolene, a drug that decreases release of calcium from the sarcoplasmic reticulum and that is lifesaving in malignant hyperthermia (a disorder due to increased [Ca2+]i), is able to reduce the elevated [Ca2+]i in sepsis to control values when added in vitro or when given in vivo to the animal. These results suggest that an increase in [Ca2+]i is an early event in sepsis and that increased [Ca2+]i may be responsible for, or contribute to, cellular injury. Dantrolene may offer a therapeutic strategy in the treatment of sepsis.
Molecular cloning, sequencing, tissue distribution, and functional expression of a Na+/H+ exchanger (NHE-2).
Authors: Collins J F , Honda T , Knobel S , Bulus N M , Conary J , DuBois R , Ghishan F K
Published: May 2006

The present studies demonstrate cloning, sequencing, tissue distribution, and functional expression of a Na+/H+ exchanger which was isolated from a rat intestinal cDNA library. The cloned cDNA recognizes two transcripts in poly(A)+ RNA from the stomach, jejunum, ileum, liver, large intestine, and uterus. Based on deduced amino acid sequences, this clone shares sequence homology with the other known Na+/H+ exchanger isoforms (NHE-1, NHE-3, and NHE-4) except for its 5' end. Overall, the protein exhibits 47.8%, 41.2%, and 56.2% amino acid sequence identity to NHE-1, NHE-3, and NHE-4, respectively. The hydropathy profile of the predicted protein shows 10 transmembrane domains, suggesting a protein with transport characteristics. The tissue distribution differs from that of the other Na+/H+ exchanger isoforms. The cDNA hybridizes to two closely related transcripts in the mRNA of these tissues, which suggests that the predominant transcript of this clone is alternatively spliced. Transfection of this cDNA into Na+/H+ exchanger-deficient mutant fibroblasts (PS120 cells) results in functional Na+/H+ exchange activity. These data suggest that we have cloned a member of the Na+/H+ exchanger family with tissue-specific expression. We suggest the designation of NHE-2 for this Na+/H+ exchanger.
Thymidine kinase mutants obtained by random sequence selection.
Authors: Munir K M , French D C , Loeb L A
Published: May 2006

Knowledge of the catalytic properties and structural information regarding the amino acid residues that comprise the active site of an enzyme allows one, in principle, to use site-specific mutagenesis to construct genes that encode enzymes with altered functions. However, such information about most enzymes is not known and the effects of specific amino acid substitutions are not generally predictable. An alternative approach is to substitute random nucleotides for key codons in a gene and to use genetic selection to identify new and interesting enzyme variants. We describe here the construction, selection, and characterization of herpes simplex virus type 1 thymidine kinase mutants either with different catalytic properties or with enhanced thermostability. From a library containing 2 x 10(6) plasmid-encoded herpes thymidine kinase genes, each with a different nucleotide sequence at the putative nucleoside binding site, we obtained 1540 active mutants. Using this library and one previously constructed, we identified by secondary selection Escherichia coli harboring thymidine kinase mutant clones that were unable to grow in the presence of concentrations of 3'-azido-3'-deoxythymidine (AZT) that permits colony formation by E. coli harboring the wild-type plasmid. Two of the mutant enzymes exhibited a reduced Km for AZT, one of which displayed a higher catalytic efficiency for AZT over thymidine relative to that of the wild type. We also identified one mutant with enhanced thermostability. These mutants may have clinical potential as the promise of gene therapy is increasingly becoming a reality.
Recombination sequence-binding protein in thymocytes undergoing T-cell receptor gene rearrangement.
Authors: Muegge K , West M , Durum S K
Published: May 2006

Rearrangement of T-cell antigen receptor and immunoglobulin genes occurs in immature lymphoid cells by an unknown mechanism. To identify components of the rearrangement machinery, we isolated a population of murine thymocytes enriched for rearranging pre-T cells. In the nuclear fraction of these cells, we detected a protein that specifically bound the recombination sequences that flank T-cell receptor and immunoglobulin genes and are required for their rearrangement. This protein recognized both heptamer and nonamer motifs of the recombination sequence, separated by either 12 or 23 bp. The protein complexed with the recombination sequence oligonucleotide had an apparent molecular mass of 30 kDa. The binding characteristics of the protein and its presence in rearranging thymocytes and cell lines suggest that it could serve as the recognition unit of a recombinase complex.
A Drosophila G-protein alpha subunit, Gf alpha, expressed in a spatially and temporally restricted pattern during Drosophila development.
Authors: Quan F , Wolfgang W J , Forte M
Published: May 2006

Heterotrimeric guanine nucleotide binding proteins (G proteins) couple receptors for extracellular signals to intracellular second messenger-generating systems. Previous studies have shown that G-protein alpha subunits (G alpha) are expressed in a spatially and temporally restricted manner during Drosophila embryogenesis and, thus, may be responsible for mediating developmental interactions. We have used the polymerase chain reaction to search for specific G alpha subunits that function primarily during development and not in the adult fly. Using poly(A)+ RNA isolated from early pupae (day 1), we have isolated a cDNA coding for a fly G alpha subunit, designated Gf alpha. This subunit is 30-38% identical to previously described vertebrate and Drosophila G alpha subunits and appears to define an additional family of G alpha proteins. Gf alpha transcripts are expressed primarily during embryonic, larval, and early pupal stages and only at low levels in adult flies. In situ hybridization studies indicate that Gf alpha transcripts are expressed maternally and later during embryogenesis primarily in the developing midgut and transiently in the amnioserosa. The Gf alpha gene has been characterized and mapped to position 73B of the Drosophila genome.
The redox and DNA-repair activities of Ref-1 are encoded by nonoverlapping domains.
Authors: Xanthoudakis S , Miao G G , Curran T
Published: May 2006

The DNA binding activity of transcription factor AP-1 is regulated in vitro by a posttranslational mechanism involving reduction/oxidation (redox). Redox regulation is mediated by a conserved cysteine residue in the DNA-binding domain of Fos and Jun. Previously, we demonstrated that a DNA repair protein, Ref-1, could stimulate the DNA binding activity of Fos-Jun dimers by reducing this cysteine residue. To examine the relationship between the redox and repair functions of Ref-1, we generated a series of deletion mutants. Analysis of the truncated proteins in vitro revealed that the redox and repair activities are encoded by distinct regions of Ref-1. Sequences in the N-terminal domain of Ref-1 that are not present in functionally related proteins from other organisms are required for the redox activity, whereas the DNA repair activity requires conserved C-terminal sequences. Chemical alkylation or oxidation of cysteine sulfhydryls inhibits the redox activity of Ref-1 without affecting its DNA repair activity. Crosslinking studies suggest that a direct cysteine-mediated interaction occurs between Ref-1 and Jun.
Nicotinic acid hydroxylase from Clostridium barkeri: electron paramagnetic resonance studies show that selenium is coordinated with molybdenum in the catalytically active selenium-dependent enzyme.
Authors: Gladyshev V N , Khangulov S V , Stadtman T C
Published: May 2006

Nicotinic acid hydroxylase from Clostridium barkeri contains selenium in an unidentified form that is dissociated as a low molecular weight compound upon denaturation of the enzyme. Other cofactors of this enzyme are molybdopterin, FAD, and iron-sulfur clusters. In the current study, we show that the enzyme, as isolated, exhibits a stable Mo(V) electron paramagnetic resonance (EPR) signal ("resting" signal) and that this signal is correlated with the selenium content and nicotinate hydroxylase activity of the enzyme. Substitution of 77Se for normal selenium isotope abundance results in splitting of the Mo(V) EPR signal of the native protein without affecting the iron signals of the FeS clusters. The Mo(V) EPR signal and nicotinic acid hydroxylase activity of enzyme isolated from cells grown in selenium-deficient medium are barely detectable. In contrast, the EPR signals of the FeS clusters, the electronic absorption spectrum, the NADPH oxidase activity, and the chromatographic behavior are changed little and are typical of active selenium-containing enzyme. An EPR signal indicative of the presence of molybdenum in the selenium-deficient enzyme also is exhibited. From these results, we conclude that a dissociable selenium moiety is coordinated directly with molybdenum in the molybdopterin cofactor and, moreover, this selenium is essential for nicotinic acid hydroxylase activity.
Pattern recognition, chaos, and multiplicity in neural networks of excitable systems.
Authors: Hjelmfelt A , Ross J
Published: May 2006

We study a neural network composed of excitable FitzHugh neurons that interact by diffusive type connections. Patterns of neural activity may be stored by a Hebbian rule. The stored patterns are recalled and given by the transient activity of the neurons after the network has been perturbed by related patterns and relaxes back to its steady state. Periodic perturbations of the network are repeated requests for computations and result in simple periodic, complex periodic, and chaotic responses and corresponding computational performances.
P-type Ca2+ channels mediate excitatory and inhibitory synaptic transmitter release in crayfish muscle.
Authors: Araque A , Clarac F , Buño W
Published: May 2006

The toxin fraction (FTX) and peptide omega-Aga-IVA from the venom of the funnel-web spider Agelenopsis aperta, as well as a synthetic analogue of FTX, specifically block the P-type voltage-dependent Ca2+ channel (VDCC). The effects of these toxins on synaptic transmission were studied in the neuromuscular synapses of the crayfish opener muscle, which has a single excitatory and a single inhibitory motoneuron. FTX selectively and reversibly blocked excitatory and inhibitory postsynaptic currents and potentials in a dose-dependent manner. FTX had no effect on (i) resting and postsynaptic membrane conductance, (ii) postsynaptic L-type VDCC, and (iii) both glutamate- and gamma-aminobutyric acid-induced postsynaptic responses. Mean amplitude and frequency of miniature postsynaptic potentials were unchanged by FTX. The postsynaptic VDCC was inhibited by nifedipine, a selective dihydropyridine antagonist of L-type VDCC, whereas synaptic transmission was unaffected. Transmission was also undisturbed by omega-conotoxin, suggesting that N-type VDCCs are not involved. The peptide omega-Aga-IVA blocked excitatory and inhibitory transmission without affecting postsynaptic VDCC. Synaptic transmission was also blocked by synthetic FTX. We conclude that presynaptic P-type VDCCs are involved in both evoked excitatory and inhibitory transmitter release in crayfish neuromuscular synapses.
Calcium regulates processing of the Alzheimer amyloid protein precursor in a protein kinase C-independent manner.
Authors: Buxbaum J D , Ruefli A A , Parker C A , Cypess A M , Greengard P
Published: May 2006

Various first messengers linked to phospholipase C, including acetylcholine and interleukin 1, regulate the production both of the secreted form of the amyloid protein precursor (APP) and of amyloid beta-protein. We have now identified intracellular signals which are responsible for mediating these effects. We show that activation of phospholipase C may affect APP processing by either of two pathways, one involving an increase in protein kinase C and the other an increase in cytoplasmic calcium levels. The effects of calcium on APP processing appear to be independent of protein kinase C activation. The observed effects of calcium on APP processing may be of therapeutic utility.
Direct determination of layer packing for a phospholipid solid solution at 0.32-nm resolution.
Authors: Dorset D L
Published: May 2006

Electron diffraction intensity data were collected from a 2:3 binary solid solution of two homologous phosphatidylethanolamines (1,2-dimyristoyl-sn-glycerophosphoethanolamine and 1,2-dipalmitoyl-sn-glycerophosphoethanolamine) epitaxially oriented by cocrystallization with naphthalene. The layer packing was determined directly by predicting the value of 12 of the 17 phases from sigma 1- and sigma 2-triplet invariants in space group P1. A reverse Fourier transform of the resulting potential maps provides estimates for three other phases and the two remaining ones were found by generating maps for the 2(2) = 4 possible phase combinations and then testing the smoothness of the potential profile of the hydrocarbon chain packing. The same phase solution can be found by translating a molecular model (based on the known x-ray crystal structure of a shorter homologue) past the unit cell origin. The solid solution is found to retain a stable polar group packing while the statistical occupancy of two terminal-chain carbons is expressed by a reduced potential profile at the nonpolar interface at the bilayer center.
Id proteins control growth induction in mammalian cells.
Authors: Barone M V , Pepperkok R , Peverali F A , Philipson L
Published: May 2006

Id1, Id2, and Id3 (HLH462) dimerize with members of the basic helix-loop-helix protein family, but due to the absence of the basic region, the resulting heterodimers cannot bind DNA. Therefore Id-type proteins negatively regulate DNA binding of the basic helix-loop-helix proteins. Here we report that Id1, Id2, and Id3 are induced shortly after serum stimulation in arrested NIH 3T3. Antisense oligonucleotides against the Id mRNAs delay the reentry of arrested cells into the cell cycle elicited by stimulation with serum or growth factors. Antisense oligonucleotides against all three Id mRNAs are more effective than individual ones. Combined, these results indicate that Id proteins are involved in the control of growth induction.
Phorbol ester-induced expression, phosphorylation, and translocation of protein-tyrosine-phosphatase 1C in HL-60 cells.
Authors: Zhao Z , Shen S H , Fischer E H
Published: May 2006

PTP1C, a protein-tyrosine-phosphatase (PTP) containing two Src homology 2 domains, is expressed at high levels in HL-60 human promyelocytic leukemia cells. It represents 0.15% of total protein in a postnuclear extract and corresponds to approximately 70% of phosphatase activity measured with p-nitrophenyl phosphate at pH 5.0. Upon differentiation of HL-60 cells to macrophages induced by phorbol 12-myristate 13-acetate (PMA), the activity and expression levels of PTP1C increase 2- to 3-fold. Furthermore, PTP1C is phosphorylated on serine residues upon PMA treatment. While the enzyme localizes entirely in the cytosolic fraction in untreated cells, 30-40% is found in a particulate fraction following differentiation. Immunofluorescent staining of differentiated cells before and after digitonin treatment indicates that the bound enzyme localizes on the plasma membrane. The time courses of induction and translocation of PTP1C correlate with the differentiation process. The PMA-induced differentiation is inhibited by sodium orthovanadate, suggesting the PTPs are required for this process.
Disulfide cross-linking in crude embryonic lysates reveals three complexes of the Drosophila morphogen dorsal and its inhibitor cactus.
Authors: Isoda K , Nüsslein-Volhard C
Published: May 2006

In Drosophila embryos dorsoventral polarity is determined by a concentration gradient of dorsal (dl) protein in the nuclei formed by the differential regulation of nuclear localization of dl protein. cactus (cact) represses the nuclear localization of dl protein. By introducing intermolecular disulfide bonds in homogenates of embryos, we detected three complexes of dl and/or cact proteins. Complex 1 (190 kDa) is a dl protein homodimer (dl2). Complex 2 (270 kDa) consists of one complex 1 and one cact molecule (dl2cact). Complex 3 (200 kDa) is a cact protein complex that does not contain dl protein. In wild-type embryos dl2cact was detected as the major form of dl protein, and dl2 was minor. With this assay virtually no dl monomer is detected. Analysis of the dl protein complexes in ventralized and dorsalized mutant embryos indicates that dl2cact is a cytoplasmic form, whereas dl2 is localized mainly in the nuclei. It seems that a small amount of dl2 is also present in the cytoplasm.
Island rescue PCR: a rapid and efficient method for isolating transcribed sequences from yeast artificial chromosomes and cosmids.
Authors: Valdes J M , Tagle D A , Collins F S
Published: May 2006

The identification of transcripts from large genomic regions cloned in yeast artificial chromosomes (YACs) or cosmids continues to be a critical and often rate-limiting step in positional cloning of human disease genes. We have developed a PCR-based method for rapid and efficient generation of probes from YACs or cosmids that can be used for cDNA library screening. The method, which we call island rescue PCR (IRP), is based upon the observation that the 5' ends of many genes are associated with (G+C)-rich regions called CpG islands. In IRP, the YAC of interest is digested with a restriction enzyme that recognizes sequences of high CpG content, and vectorette linkers are ligated to the cleaved ends. The PCR is used to amplify the region extending from the cleaved restriction enzyme site to the nearest SINE (Alu) repeat. In many cases this product contains sequences from the 5' end of the associated gene. cDNA clones isolated with these products are then verified by mapping them back to the original YAC. The method allows rapid screening of > 500 kb of human genomic insert in one experiment, is tolerant of contaminating yeast sequences, and can also be applied to cosmid pools. In a control experiment, the method was able to identify cDNA clones for the neurofibromatosis type 1 (NF1) gene using a probe generated from a YAC in the region. Application of IRP has yielded nine other genes from YACs isolated from chromosome locations 4p16.3 and 17q21.
Suppression of Myc, but not E1a, transformation activity by Max-associated proteins, Mad and Mxi1.
Authors: Lahoz E G , Xu L , Schreiber-Agus N , DePinho R A
Published: May 2006

Mad and Mxi1, two members of the Myc-related basic-region helix-loop-helix/leucine-zipper family of proteins, associate directly with Max to form sequence-specific DNA binding heterodimers that are transactivation-incompetent. Mad-Max complexes have been shown to exert a strong repressive effect on Myc-induced transactivation, perhaps through the competitive occupation of common promoter binding sites also recognized by active Myc-Max heterodimers. To place these recent biochemical observations in a biological context, mad and mxi1 expression vectors were tested for their ability to influence Myc transformation activity in the rat embryo fibroblast cooperation assay. Addition of an equimolar amount of mad or mxi1 expression vector to mouse c-myc/ras cotransfections resulted in a dramatic reduction in both the number of foci generated and the severity of the malignant phenotype. Myc-specific suppression by Mad and Mxi1 was demonstrated by their ability to affect c- and N-myc-, but not ela-, induced transformation. In contrast, mad and mxi1 expression constructs bearing deletions in the basic region exerted only mild repressive effects on Myc transformation activity, suggesting that occupation of common DNA binding sites by transactivation-incompetent Mad-Max or Mxi1-Max complexes appears to play a more dominant role in this suppression than titration of limited intracellular pools of Max away from active Myc-Max complexes. Thus, these biological data support a current model for regulation of Myc function in which relative intracellular levels of Mad and Mxi1 in comparison to those of Myc may determine the degree of activation of Myc-responsive growth pathways.
Stable DNA transformation in the obligate intracellular parasite Toxoplasma gondii by complementation of tryptophan auxotrophy.
Authors: Sibley L D , Messina M , Niesman I R
Published: May 2006

The protozoan parasite Toxoplasma gondii infects a wide range of vertebrate hosts and is an important opportunistic pathogen in immunocompromised humans. Although Toxoplasma is amenable to both biochemical and cellular experimental approaches, the molecular basis of its success as an intracellular parasite is poorly understood. To provide a system for molecular genetic analyses, we have developed a stable DNA transformation system for Toxoplasma based on complementation of its naturally occurring tryptophan auxotrophy. Complementation was accomplished by expressing the Escherichia coli trpB gene, encoding the beta subunit of tryptophan synthase (EC 4.2.1.20), the enzyme that catalyzes the formation of tryptophan from indole plus serine. Transformants were obtained by electroporation of a plasmid, called SAG1/trpB, containing the trpB gene flanked by Toxoplasma surface antigen 1 (SAG1) gene sequences and selection for growth on indole. Transformants were obtained with circular forms of the SAG1/trpB plasmid with efficiencies of 10(-4) per cell. Transformation with either circular or linear SAG1/trpB resulted in integration into the genome at distinct, nonhomologous sites. Trp+ transformants typically contained tandemly repeated copies of the SAG1/trpB plasmid and were stable in the absence of continued selection. The Trp phenotype provides a dominant selectable marker that should allow expression of foreign or altered genes in Toxoplasma and facilitate molecular analyses of genes important for intracellular survival.
Prion isolate specified allotypic interactions between the cellular and scrapie prion proteins in congenic and transgenic mice.
Authors: Carlson G A , Ebeling C , Yang S L , Telling G , Torchia M , Groth D , Westaway D , DeArmond S J , Prusiner S B
Published: May 2006

Different prion isolates, often referred to as "strains," present an enigma because considerable evidence argues that prions are devoid of nucleic acid. To investigate prion diversity, we inoculated three "strains" of prions into congenic and transgenic mice harboring variable numbers of two different alleles, designated a and b, of the prion protein (PrP) structural gene, Prn-p. The length of the incubation time was inversely related to the number of Prn-p(a) genes in mice inoculated with the Rocky Mountain Laboratory (RML) prion strain. Results with mice lacking this locus (Prn-p0/0) and transgenic mice argue that long incubation times are not a dominant trait as thought for many years, but rather they are due to reduced levels of the substrate PrPC-A (cellular isoform of PrP, allotype A) in (Prn-p(a) x Prn-pb)F1 mice. In contrast, the Prn-p(a) gene extended incubation times in mice inoculated with the 87V and 22A prion strains, whereas the Prn-pb gene was permissive. Experiments with the 87V isolate suggest that a genetic locus distinct from Prn-p controls deposition of the scrapie isoform of PrP (PrPSc) and attendant neuropathology. Each prion isolate produced distinguishable patterns of PrPSc accumulation in brain; of note, the patterns in Prn-p(a) and Prn-pb congenic mice inoculated with RML prions were more different than those in congenic Prn-pb mice with RML or 22A prions. Our results suggest that scrapie "strain-specific" incubation times can be explained by differences in the relative efficiency of allotypic interactions that lead to conversion of PrPC into PrPSc.
Loss of heterozygosity in cervical carcinoma: subchromosomal localization of a putative tumor-suppressor gene to chromosome 11q22-q24.
Authors: Hampton G M , Penny L A , Baergen R N , Larson A , Brewer C , Liao S , Busby-Earle R M , Williams A W , Steel C M , Bird C C
Published: May 2006

Infection of cervical epithelial cells with so-called "aggressive" subtypes of human papilloma virus (HPV) appears to be an important factor in the etiology of cervical carcinoma. However, mounting evidence suggests that additional genetic changes are required for progression to an invasive carcinoma. Functional studies have shown that human chromosome 11 contains a gene or genes capable of suppressing tumorigenicity in cell lines derived from different histopathological types of cervical carcinoma, suggesting that aberration of this gene(s) may represent at least one of the additional changes required for tumorigenic progression. To identify the likely chromosomal position of this gene(s), we have carried out a systematic genetic analysis of chromosome 11 in the primary tumors of 32 patients with cervical carcinoma. Sixteen highly polymorphic markers, 10 of which were based on simple sequence repeats typed by PCR, were used to compare matched DNA samples from noninvolved tissue and portions of tumor tissue highly enriched for neoplastic cells by the cryostat-sectioning technique. Of the 32 patients examined, 14 (44%) demonstrated clonal genetic alterations resulting in loss of heterozygosity for one or more markers. Seven of the clonal genetic alterations on chromosome 11 were specific to the long arm, and the overlap between these and other allelic deletions suggests that a suppressor gene(s) relevant to cervical carcinoma maps to chromosome 11q22-q24.
A scheme for sequencing large DNA molecules by identifying local nuclear-induced effects.
Authors: Kelson I , Nussinov S
Published: May 2006

An experimental scheme for sequencing large DNA molecules is proposed where DNA strands are replicated, with all nucleotides of a given kind marked with radioactive 32P. The marked strands are affixed to an appropriate substrate and are kept until most 32P atoms decay. The local damage caused by the decay is expected to allow the identification of the sites occupied by that particular nucleotide, using atomic scale microscopy (scanning tunneling or atomic force microscopy). Quantitative aspects and methodological considerations associated with the proposed scheme are discussed.
A 32P-postlabeling method for detecting unstable N-7-substituted deoxyguanosine adducts in DNA.
Authors: Yu D , Niu T Q , Austin-Ritchie P , Ludlum D B
Published: May 2006

Many antitumor agents, including the mustards, form N-7 deoxyguanosine adducts in DNA that are difficult to quantitate by the 32P-postlabeling procedure because of their instability. We have developed a method that is successful for the analysis of such adducts using, as a prototype mustard, 14C-labeled bis(2-chloroethyl)sulfide. This agent forms the unstable product 7-hydroxyethylthioethyldeoxyguanosine in DNA. By performing enzymatic digestions to 3'-deoxynucleotides at 10 degrees C, including a second N-7-substituted guanine deoxynucleotide as an internal standard, removing most of the unmodified nucleotides and [32P]ATP on disposable anion columns, and measuring the labeled products after separation on a C18 column, we are able to detect 1 unstable N-7 deoxyguanosine adduct in 10(7) normal nucleotides with good precision.
Assembly of synthetic cellulose I.
Authors: Lee J H , Brown R M , Kuga S , Shoda S , Kobayashi S
Published: May 2006

Cellulose microfibrils with an electron diffraction pattern characteristic of crystalline native cellulose I have been assembled abiotically by means of a cellulase-catalyzed polymerization of beta-cellobiosyl fluoride substrate monomer in acetonitrile/acetate buffer. Substantial purification of the Trichoderma viride cellulase enzyme was found to be essential for the formation of the synthetic cellulose I allomorph. Assembly of synthetic cellulose I appears to be a result of a micellar aggregation of the partially purified enzyme and the substrate in an organic/aqueous solvent system favoring the alignment of glucan chains with the same polarity and extended chain conformation, resulting in crystallization to form the metastable cellulose I allomorph.
Reduced Rho-dependent transcription termination permits NusA-independent growth of Escherichia coli.
Authors: Zheng C , Friedman D I
Published: May 2006

NusA and Rho are essential Escherichia coli proteins that influence transcription elongation and termination. We show that an E. coli derivative unable to express NusA, because its sole nusA gene contains a large deletion/substitution, is viable providing that the bacterium also carries a rho mutation that reduces transcription termination. This Rho-mediated suppression is not allele specific, since either a mutation changing amino acid 134 [rho(E134D)] or a mutation changing amino acid 352 (rho1) allows growth of a nusA-deleted E. coli. However, both rho mutations similarly decrease transcription termination 8- to 9-fold. We propose that the essential role of NusA is to enhance pausing of RNA polymerase at certain sites, permitting tight coupling of transcription and translation. This coupling interferes with Rho access to and/or movement on the nascent RNA and blocks premature termination of transcription. Thus, NusA-dependent coupling should be less important in a mutant with low Rho activity. The fact that E. coli grows without NusA argues that NusA should be considered an accessory factor rather than a subunit of RNA polymerase.
Expression of transcription factor HNF-4 in the extraembryonic endoderm, gut, and nephrogenic tissue of the developing mouse embryo: HNF-4 is a marker for primary endoderm in the implanting blastocyst.
Authors: Duncan S A , Manova K , Chen W S , Hoodless P , Weinstein D C , Bachvarova R F , Darnell J E
Published: May 2006

The expression of HNF-4 (hepatocyte nuclear factor 4) mRNA in postimplantation mouse embryos was analyzed by in situ hybridization. Expression was found in the primary endoderm at embryonic day 4.5 and was restricted to the columnar visceral endoderm cells of the yolk sac from day 5.5 to day 8.5. HNF-4 mRNA was first detected in embryonic tissues at day 8.5, in the liver diverticulum and the hindgut. At later times HNF-4 transcripts were observed in the mesonephric tubules, pancreas, stomach, and intestine and, still later, in the metanephric tubules of the developing kidney. This expression pattern suggests that HNF-4 has a role in the earliest stages of murine postimplantation development as well as in organogenesis.
Structure and function in rhodopsin: covalent crosslinking of the rhodopsin (metarhodopsin II)-transducin complex--the rhodopsin cytoplasmic face links to the transducin alpha subunit.
Authors: Resek J F , Farrens D , Khorana H G
Published: May 2006

We prepared rhodopsin mutants that contained a single reactive cysteine residue per rhodopsin molecule at position 65, 140, 240, or 316 on the cytoplasmic face. A carbene-generating photoactivatable group was linked by a disulfide bond to the cysteine sulfhydryl group of each of the rhodopsin mutants. The resulting derivative was then light-activated at lambda > 495 nm to form the metarhodopsin II intermediate, which bound transducin. Subsequent photoactivation (355 nm) of the carbene-generating group resulted in crosslinking of the rhodopsin mutant carrying a cysteine residue at position 240 to transducin. This crosslinking was determined to be specifically with the alpha subunit of transducin. An alternative reaction observed during photolysis of the rhodopsin mutants was intramolecular insertion of the carbene into rhodopsin.
Sequence-specific DNA binding of individual cut repeats of the human CCAAT displacement/cut homeodomain protein.
Authors: Aufiero B , Neufeld E J , Orkin S H
Published: May 2006

CCAAT displacement protein (CDP), a nuclear protein of 180-190 kDa, contains a triplicated motif, the cut domain, similar (80-90% conserved) to three repeats of 60-65 amino acids first identified in Drosophila cut, a homeo-domain protein involved in cell-fate decisions in development. Cut repeats bind DNA and exhibit subtle differences in target-site recognition. DNA sequences specifically bound by cut repeats were isolated by PCR-mediated DNA target-site selection. Sequences selected for cut repeat 2 and 3 (CR2 and CR3) binding are A+T-rich and favor an ATA motif with similar, but not identical, flanking base preferences. CR2 and CR3 discriminate among similar target sequences. CR1, which is more divergent from CR2 and CR3, displays the most restricted pattern of DNA sequence recognition. Methylation interference analysis demonstrates different protein-DNA contacts for CR1 and CR3 binding to a target sequence. Thus, CDP/cut is a complex protein whose DNA-binding properties reflect the combinatorial interaction of four domains (three cut repeats and one homeodomain) with target DNA sequences.