bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogeny of the Attine Ant Fungi Based on Analysis of Small Subunit Ribosomal RNA Gene Sequences
Authors: Hinkle Gregory , Wetterer James K. , Schultz Ted R. , Sogin Mitchell L.
Published: October 2006

Complete 16
S
-like ribosomal RNA coding regions were obtained from the fungal symbiont of five genera of attine (leaf-cutting) ants and two free-living fungi. Phylogenetic analyses with distance matrix, maximum likelihood, and parsimony methods revealed that the attine fungal symbionts are homobasidiomycetes in the order Agaricales. Comparison of the topology of the attine fungal symbiont phylogenetic tree with a tree based on attine ant morphology revealed a congruent branching pattern of the more derived attine ants and their fungal symbionts. The parallel branching pattern suggests a long-term coevolution of derived leaf-cutting attine ants and their fungal symbionts.
Naturally Occurring Variation in Bristle Number and DNA Polymorphisms at the
scabrous
Locus of
Drosophila melanogaster
Authors: Lai Chaoqiang , Lyman Richard F. , Long Anthony D. , Langley Charles H. , Mackay Trudy F. C.
Published: October 2006

The association between quantitative genetic variation in bristle number and molecular variation at a candidate neurogenic locus,
scabrous
, was examined in
Drosophila melanogaster
. Approximately 32 percent of the genetic variation in abdominal bristle number (21 percent for sternopleural bristle number) among 47 second chromosomes from a natural population was correlated with DNA sequence polymorphisms at this locus. Several polymorphic sites associated with large phenotypic effects occurred at intermediate frequency. Quantitative genetic variation in natural populations caused by alleles that have large effects at a few loci and that segregate at intermediate frequencies conflicts with the classical infinitesimal model of the genetic basis of quantitative variation.
Light-Regulated Translation of Chloroplast Messenger RNAs Through Redox Potential
Authors: Danon Avihai , Mayfield Stephen P.
Published: October 2006

Translation of key proteins in the chloroplast is regulated by light. Genetic and biochemical studies in the unicellular alga
Chlamydomonas reinhardtii
suggest that light may regulate translation by modulating the binding of activator proteins to the 5′ untranslated region of chloroplast messenger RNAs. In vitro binding of the activator proteins to psbA messenger RNA and in vivo translation of psbA messenger RNA is regulated by the redox state of these proteins, suggesting that the light stimulus is transduced by the photosynthesis-generated redox potential.
Subsets of HLA-DR1 Molecules Defined by SEB and TSST-1 Binding
Authors: Thibodeau Jacques , Cloutier Isabelle , Lavoie Pascal M. , Labrecque Nathalie , Mourad Walid , Jardetzky Theodore , Sékaly Rafick-Pierre
Published: October 2006

Superantigens bind to major histocompatibility complex class II molecules on antigen-presenting cells and stimulate T cells.
Staphylococcus aureus
enterotoxin B (SEB) and toxic shock syndrome toxin-1 (TSST-1) bind to the same region of human lymphocyte antigen (HLA)-DR1 but do not compete with each other, which indicates that they bind to different subsets of DR1 molecules. Here, a mutation in the peptide-binding groove disrupted the SEB and TSST-1 binding sites, which suggests that peptides can influence the interaction with bacterial toxins. In support of this, the expression of the DR1 molecule in various cell types differentially affected the binding of these toxins.
Specification of C/EBP Function During
Drosophila
Development by the bZIP Basic Region
Authors: Rørth Pernille
Published: October 2006

The biologically relevant interactions of a transcription factor are those that are important for function in the organism. Here, a transgenic rescue assay was used to determine which molecular functions of
Drosophila
CCAAT/enhancer binding protein (C/EBP), a basic region-leucine zipper transcription factor, are required for it to fulfill its essential role during development. Chimeric proteins that contain the
Drosophila
C/EBP (DmC/EBP) basic region, a heterologous zipper, and a heterologous activation domain could functionally substitute for DmC/EBP. Mammalian C/EBPs were also functional in
Drosophila
. In contrast, 9 of 25 single amino acid substitutions in the basic region disrupted biological function. Thus, the conserved basic region specifies DmC/EBP activity in the organism.
Malaria Pathogenesis
Authors: Miller Louis H. , Good Michael F. , Milon Geneviève
Published: October 2006

Malaria is a disease caused by repeated cycles of growth of the parasite
Plasmodium
in the erythrocyte. Various cellular and molecular strategies allow the parasite to evade the human immune response for many cycles of parasite multiplication. Under certain circumstances
Plasmodium
infection causes severe anemia or cerebral malaria; the expression of disease is influenced by both parasite and host factors, as exemplified by the exacerbation of disease during pregnancy. This article provides an overview of malaria pathogenesis, synthesizing the recent field, laboratory, and epidemiological data that will lead to the development of strategies to reduce mortality and morbidity.
African
Homo erectus
: Old Radiometric Ages and Young Oldowan Assemblages in the Middle Awash Valley, Ethiopia
Authors: Clark J. D. , de Heinzelin J. , Schick K. D. , Hart W. K. , White T. D. , WoldeGabriel G. , Walter R. C. , Suwa G. , Asfaw B. , Vrba E. , H.-Selassie Y.
Published: October 2006

Fossils and artifacts recovered from the middle Awash Valley of Ethiopia's Afar depression sample the Middle Pleistocene transition from
Homo erectus
to
Homo sapiens
. Ar/Ar ages, biostratigraphy, and tephrachronology from this area indicate that the Pleistocene Bodo hominid cranium and newer specimens are approximately 0.6 million years old. Only Oldowan chopper and flake assemblages are present in the lower stratigraphic units, but Acheulean bifacial artifacts are consistently prevalent and widespread in directly overlying deposits. This technological transition is related to a shift in sedimentary regime, supporting the hypothesis that Middle Pleistocene Oldowan assemblages represent a behavioral facies of the Acheulean industrial complex.
Structure of the RGD Protein Decorsin: Conserved Motif and Distinct Function in Leech Proteins That Affect Blood Clotting
Authors: Krezel Andrzej M. , Wagner Gerhard , Seymour-Ulmer Jana , Lazarus Robert A.
Published: October 2006

The structure of the leech protein decorsin, a potent 39-residue antagonist of glycoprotein IIb-IIIa and inhibitor of platelet aggregation, was determined by nuclear magnetic resonance. In contrast to other disintegrins, the Arg-Gly-Asp (RGD)-containing region of decorsin is well defined. The three-dimensional structure of decorsin is similar to that of hirudin, an anticoagulant leech protein that potently inhibits thrombin. Amino acid sequence comparisons suggest that ornatin, another glycoprotein IIb-IIIa antagonist, and antistasin, a potent Factor Xa inhibitor and anticoagulant found in leeches, share the same structural motif. Although decorsin, hirudin, and antistasin all affect the blood clotting process and appear similar in structure, their mechanisms of action and epitopes important for binding to their respective targets are distinct.
Deletion of a DNA Polymerase β Gene Segment in T Cells Using Cell Type-Specific Gene Targeting
Authors: Gu Hua , Marth Jamey D. , Orban Paul C. , Mossmann Horst , Rajewsky Klaus
Published: October 2006

Deletion of the promoter and the first exon of the DNA polymerase β gene (pol β) in the mouse germ line results in a lethal phenotype. With the use of the bacteriophage-derived, site-specific recombinase Cre in a transgenic approach, the same mutation can be selectively introduced into a particular cellular compartment-in this case, T cells. The impact of the mutation on those cells can then be analyzed because the mutant animals are viable.
Mediation of Epstein-Barr Virus EBNA2 Transactivation by Recombination Signal-Binding Protein J
κ
Authors: Henkel Thomas , Ling Paul D. , Hayward S. Diane , Peterson Michael Gregory
Published: October 2006

The Epstein-Barr virus (EBV) transactivator protein, termed Epstein-Barr virus nuclear antigen 2 (EBNA2), plays a critical role in the regulation of latent viral transcription and in the immortalization of EBV-infected B cells. Unlike most transcription factors, EBNA2 does not bind directly to its cis-responsive DNA element but requires a cellular factor, termed C-promoter binding factor 1 (CBF1). Here, CBF1 was purified and was found to directly interact with EBNA2. CBF1 is identical to a protein thought to be involved in immunoglobulin gene rearrangement, RBPJ
κ
. Contrary to previous reports, CBF1-RBPJ
κ
did not bind to the recombination signal sequences but instead bound to sites in the EBV C-promoter and in the CD23 promoter.
Peptide Synthesis Catalyzed by an Antibody Containing a Binding Site for Variable Amino Acids
Authors: Hirschmann Ralph , Smith Amos B. , Taylor Carol M. , Benkovic Patricia A. , Taylor Scott D. , Yager Kraig M. , Sprengeler Paul A. , Benkovic Stephen J.
Published: October 2006

Monoclonal antibodies, induced with a phosphonate diester hapten, catalyzed the coupling of
p
-nitrophenyl esters of
N
-acetyl valine, leucine, and phenylalanine with tryptophan amide to form the corresponding dipeptides. All possible stereoisomeric combinations of the ester and amide substrates were coupled at comparable rates. The antibodies did not catalyze the hydrolysis of the dipeptide product nor hydrolysis or racemization of the activated esters. The yields of the dipeptides ranged from 44 to 94 percent. The antibodies were capable of multiple turnovers at rates that exceeded the rate of spontaneous ester hydrolysis. This achievement suggests routes toward creating a small number of antibody catalysts for polypeptide syntheses.
Adaptive Reversion of a Frameshift Mutation in
Escherichia coli
by Simple Base Deletions in Homopolymeric Runs
Authors: Foster Patricia L. , Trimarchi Jeffrey M.
Published: October 2006

Spontaneous mutations are thought to occur primarily in growing cells. However, spontaneous mutations also arise in nutritionally deprived cells, and in some cases this process appears to be adaptive. Here it is reported that when a Lac- strain of
Escherichia coli
is under selection for lactose use, the spectrum of Lac+ mutations that arises is different, and simpler, than that arising without selection. Mutations appearing during selection were mainly one-base deletions in runs of iterated bases. Similar mutations occurring in repetitive DNA elements are associated with a variety of human hereditary diseases and are increased in cells that cannot correct heteroduplex DNA.
Growth-Promoting Effects of Glycine-Extended Progastrin
Authors: Seva Catherine , Dickinson Chris J. , Yamada Tadataka
Published: October 2006

Peptide α amidation is required to produce some hormones, such as gastrin, from their glycine-extended precursors. This terminal posttranslational processing reaction is thought to be essential for the biological activation of many peptide hormones; only amidated gastrin exerts a physiological effect that results in gastric acid secretion. However, both amidated gastrin and glycine-extended gastrin stimulate proliferation of exocrine pancreatic cell line AR4-2J through selective receptors for the substrate and the product, respectively, of peptide α amidation. Thus, the amidation reaction may function as a determinant of the specific biological actions of products derived from prohormones.
Fluctuations and Supercoiling of DNA
Authors: Marko John F. , Siggia Eric D.
Published: October 2006

Frequently, DNA in vivo is organized into loops that are partially underwound and consequently form interwound helical supercoils. Methods from polymer statistical mechanics are used to show how the competition between entropy (thermal fluctuations) and elastic energy determines supercoil radius and pitch, in good agreement with recent experiments and simulations. Supercoil reorganization by means of slithering (reptation) of the DNA along the supercoil is argued to be a slow process. Extension of supercoiled DNA by an applied force shows a number of unexpected features, including coexistence of interwound and helical states.
Contribution of Early Cells to the Fate Map of the Zebrafish Gastrula
Authors: Helde Kathryn Ann , Wilson Ellen T. , Cretekos Chris J. , Grunwald David Jonah
Published: October 2006

Previously, a tissue-specific fate map was compiled for the gastrula stage of the zebrafish embryo, indicating that development subsequent to this stage follows a reproducible pattern. Here it is shown that each early zebrafish blastomere normally contributes to a subset of the gastrula and thus gives rise to a limited array of tissues. However, the final contribution that any early blastomere makes to the fate map in the gastrula cannot be predicted because of variability in both the position of the future dorsoventral axis with respect to the early cleavage blastomeres and the scattering of daughter cells as the gastrula is formed. Therefore, early cell divisions of the zebrafish embryo cannot reproducibly segregate determinants of tissue fates.
Interaction of Rac with p67

phox

and Regulation pf Phagocytic NADPH Oxidase Activity
Authors: Diekmann Dagmar , Abo Arie , Johnston Caroline , Segal Anthony W. , Hall Alan
Published: October 2006

Rho and Rac, two members of the Ras superfamily of guanosine triphosphate (GTP)-binding proteins, regulate a variety of signal transduction pathways in eukaryotic cells. Upon stimulation of phagocytic cells, Rac enhances the activity of the enzyme nicotinamide adenine dinucleotide phosphate (reduced) (NADPH) oxidase, resulting in the production of superoxide radicals. Activation of the NADPH oxidase requires the assembly of a multimolecular complex at the plasma membrane consisting of two integral membrane proteins, gp91
phox
and p21
phox
, and two cytosolic proteins, p67
phox
and p47
phox
. Rac1 interacted directly with p67
phox
in a GTP-dependent manner. Modified forms of Rac with mutations in the effector site did not stimulate oxidase activity or bind to p67
phox
. Thus, p67
phox
appears to be the Rac effector protein in the NADPH oxidase complex.
Integration and Germ-Line Transmission of a Pseudotyped Retroviral Vector in Zebrafish
Authors: Lin Shuo , Gaiano Nicholas , Culp Patricia , Burns Jane C. , Friedmann Theodore , Yee Jiing-Kuan , Hopkins Nancy
Published: October 2006

The zebrafish is rapidly becoming a popular model system for the study of vertebrate development because it is ideal for both embryological studies and genetic analysis. To determine if a retroviral vector pseudotyped with the envelope glycoprotein of the vesicular stomatitis virus could infect zebrafish embryos, and in particular, the cells destined to become the germ line, a pseudotyped virus was injected into blastula-stage zebrafish embryos. Fifty-one embryos were allowed to develop and eight transmitted proviral DNA to their progeny. Founders were mosaic, but as expected, transgenic F
1
's transmitted proviral DNA in a Mendelian fashion to the F
2
progeny. Transgenic F
1
fish inherited a single integrated provirus, and a single founder could transmit more than one viral integration to its progeny. These results demonstrate that this pantropic pseudotyped vector, originally developed for human gene therapy, will make the use of retroviral vectors in zebrafish possible.
Orientation Selectivity of Cortical Neurons During Intracellular Blockade of Inhibition
Authors: Nelson Sacha , Toth Louis , Sheth Bhavin , Sur Mriganka
Published: October 2006

Neurons in the primary visual cortex of the cat are selectively activated by stimuli with particular orientations. This selectivity can be disrupted by the application of antagonists of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) to a local region of the cortex. In order to determine whether inhibitory inputs are necessary for a single cortical neuron to show orientation selectivity, GABA receptors were blocked intracellularly during whole cell recording. Although the membrane potential, spontaneous activity, subfield antagonism, and directional selectivity of neurons were altered after they were perfused internally with the blocking solution, 18 out of 18 neurons remained selective for stimulus orientation. These results indicate that excitatory inputs are sufficient to generate orientation selectivity.
Discontinuous Mechanism of Transcription Elongation
Authors: Nudler Evgeny , Goldfarb Alex , Kashlev Mikhail
Published: October 2006

During transcription elongation, three flexibly connected parts of RNA polymerase of
Escherichia coli
advance along the template so that the front-end domain is followed by the catalytic site which in turn is followed by the RNA product binding site. The advancing enzyme was found to maintain the same conformation throughout extended segments of the transcribed region. However, when the polymerase traveled across certain DNA sites that seemed to briefly anchor the front-end domain, cyclic shifting of the three parts, accompanied by buildup and relief of internal strain, was observed. Thus, elongation proceeded in alternating laps of monotonous and inchworm-like movement with the flexible RNA polymerase configuration being subject to direct sequence control.
Induction of Mesoderm in
Xenopus laevis
Embryos by Translation Initiation Factor 4E
Authors: Klein Peter S. , Melton Douglas A.
Published: October 2006

The microinjection of messenger RNA encoding the eukaryotic translation initiation factor 4E (eIF-4E) into early embryos of
Xenopus laevis
leads to the induction of mesoderm in ectodermal explants. This induction occurs without a stimulation of overall protein synthesis and is blocked by the co-expression of a dominant negative mutant of the proto-oncogene ras or a truncated activin type II receptor. Although other translation factors have been studied in vertebrate and invertebrate embryos, none have been shown to play a direct role in development. The results here suggest a mechanism for relaying and amplifying signals for mesoderm induction.
Kinetic Intermediates in RNA Folding
Authors: Zarrinkar Patrick P. , Williamson James R.
Published: October 2006

The folding pathways of large, highly structured RNA molecules are largely unexplored. Insight into both the kinetics of folding and the presence of intermediates was provided in a study of the Mg
2+
-induced folding of the
Tetrahymena
ribozyme by hybridization of complementary oligodeoxynucleotide probes. This RNA folds via a complex mechanism involving both Mg
2+
-dependent and Mg
2+
-independent steps. A hierarchical model for the folding pathway is proposed in which formation of one helical domain (P4-P6) precedes that of a second helical domain (P3-P7). The overall rate-limiting step is formation of P3-P7, and takes place with an observed rate constant of 0.72 ± 0.14 minute
-1
. The folding mechanism of large RNAs appears similar to that of many multidomain proteins in that formation of independently stable substructures precedes their association into the final conformation.
Bidirectional Replication from an Internal Origin in a Linear
Streptomyces
Plasmid
Authors: Chang Poa-Chun , Cohen Stanley N.
Published: October 2006

Commonly, linear replicons that have protein covalently attached to 5′ DNA termini replicate by protein-primed, strand-displacing, continuous synthesis of full-length strands. The synthesis of DNA in pSLA2, a 17-kilobase linear plasmid of
Streptomyces rochei
containing 5′ terminal protein, occurs bidirectionally from an internally located replication origin. The replication intermediates are linear duplex molecules that have recessed (∼280 nucleotides) 5′ ends rather than full-length single strands. The 3′ overhangs may serve as templates for the non-displacing synthesis of the lagging strand terminus primed by the covalently attached 5′ DNA binding protein.
High-Specificity DNA Cleavage Agent: Design and Application to Kilobase and Megabase DNA Substrates
Authors: Pendergrast P. Shannon , Ebright Yon W. , Ebright Richard H.
Published: October 2006

Strategies to cleave double-stranded DNA at specific DNA sites longer than those of restriction endonucleases (longer than 8 base pairs) have applications in chromosome mapping, chromosome cloning, and chromosome sequencing—provided that the strategies yield high DNA-cleavage efficiency and high DNA-cleavage specificity. In this report, the DNA-cleaving moiety copper:
o
-phenanthroline was attached to the sequence-specific DNA binding protein catabolite activator protein (CAP) at an amino acid that, because of a difference in DNA bending, is close to DNA in the specific CAP-DNA complex but is not close to DNA in the nonspecific CAP-DNA complex. The resulting CAP derivative, OP
26
CAP, cleaved kilobase and megabase DNA substrates at a 22-base pair consensus DNA site with high efficiency and exhibited no detectable nonspecific DNA-cleavage activity.
MLH1, PMS1, and MSH2 Interactions During the Initiation of DNA Mismatch Repair in Yeast
Authors: Prolla Tomas A. , Pang Qishen , Alani Eric , Kolodner Richard D. , Liskay R. Michael
Published: October 2006

The discovery that mutations in DNA mismatch repair genes can cause hereditary nonpolyposis colorectal cancer has stimulated interest in understanding the mechanism of DNA mismatch repair in eukaryotes. In the yeast
Saccharomyces cerevisiae
, DNA mismatch repair requires the MSH2, MLH1, and PMS1 proteins. Experiments revealed that the yeast MLH1 and PMS1 proteins physically associate, possibly forming a heterodimer, and that MLH1 and PMS1 act in concert to bind a MSH2-heteroduplex complex containing a G-T mismatch. Thus, MSH2, MLH1, and PMS1 are likely to form a ternary complex during the initiation of eukaryotic DNA mismatch repair.
Fc Receptors Initiate the Arthus Reaction: Redefining the Inflammatory Cascade
Authors: Sylvestre Diana L. , Ravetch Jeffrey V.
Published: October 2006

Antibody-antigen complexes initiate the inflammatory response and are central to the pathogenesis of tissue injury. The classical model for this immunopathological cascade, the Arthus reaction, was reinvestigated with a murine strain deficient in Fc receptor expression. Despite normal inflammatory responses to other stimuli, the inflammatory response to immune complexes was markedly attenuated. These results suggest that immune complex-triggered inflammation is initiated by cell bound Fc receptors and is then amplified by cellular mediators and activated complement. These results redefine the inflammatory cascade and may offer other approaches for the study and treatment of immunological injury.
Interaction of Dbf4, the Cdc7 Protein Kinase Regulatory Subunit, with Yeast Replication Origins in Vivo
Authors: Dowell Simon J. , Romanowski Piotr , Diffley John F. X.
Published: October 2006

DNA replication in the budding yeast
Saccharomyces cerevisiae
initiates from origins of specific DNA sequences during S phase. A screen based on two- and one-hybrid approaches demonstrates that the product of the
DBF4
gene interacts with yeast replication origins in vivo. The Dbf4 protein interacts with and positively regulates the activity of the Cdc7 protein kinase, which is required for entry into S phase in the yeast mitotic cell cycle. The analysis described here suggests a model in which one function of Dbf4 may be to recruit the Cdc7 protein kinase to initiation complexes.
Stern-Volmer in Reverse: 2:1 Stoichiometry of the Cytochrome c-Cytochrome c Peroxidase Electron-Transfer Complex
Authors: Zhou Jian S. , Hoffman Brian M.
Published: October 2006

A reverse protocol for measurements of molecular binding and reactivity by excited-state quenching has been developed in which the quencher, held at a fixed concentration, is titrated by a photoexcitable probe molecule whose decay is monitored. The binding stoichiometries, affinities, and reactivities of the electron-transfer complexes between cytochrome c (Cc) and cytochrome c peroxidase (CcP) were determined over a wide range of ionic strengths (4.5 to 118 millimolar) by the study of photoinduced electron-transfer quenching of the triplet excited state of zinc-substituted Cc (ZnCc) by Fe
3+
CcP. The 2:1 stoichiometry seen for the binding of Cc to CcP at low ionic strength persists at the physiologically relevant ionic strengths and likely has functional significance. Analysis of the stoichiometric binding and rate constants confirms that one surface domain of CcP binds Cc with a high affinity but with poor electron-transfer quenching of triplet-state ZnCc, whereas a second binds weakly but with a high rate of electron-transfer quenching.
RPS2 of
Arabidopsis thaliana
: a Leucine-Rich Repeat Class of Plant Disease Resistance Genes
Authors: Bent Andrew F. , Kunkel Barbara N. , Dahlbeck Douglas , Brown Kit L. , Schmidt Renate , Giraudat Jerome , Leung Jeffrey , Staskawicz Brian J.
Published: October 2006

Plant disease resistance genes function in highly specific pathogen recognition pathways.
RPS2
is a resistance gene of
Arabidopsis thaliana
that confers resistance against
Pseudomonas syringae
bacteria that express avirulence gene
avrRpt2
.
RPS2
was isolated by the use of a positional cloning strategy. The derived amino acid sequence of
RPS2
contains leucine-rich repeat, membrane-spanning, leucine zipper, and P loop domains. The function of the
RPS2
gene product in defense signal transduction is postulated to involve nucleotide triphosphate binding and protein-protein interactions and may also involve the reception of an elicitor produced by the avirulent pathogen.
Phosphorylation of the Transcription Factor PHO4 by a Cyclin-CDK Complex, PHO80-PHO85
Authors: Kaffman Arie , Herskowitz Ira , Tjian Robert , O'Shea Erin K.
Published: October 2006

Induction of the yeast gene
PHO5
is mediated by the transcription factors PHO2 and PHO4.
PHO5
transcription is not detectable in high phosphate; it is thought that the negative regulators PHO80 and PHO85 inactivate PHO2 and PHO4. Here it is reported that PHO80 has homology to yeast cyclins and interacts with PHO85, a p34
cdc2/CDC28
-related protein kinase. The PHO80-PHO85 complex phosphorylates PHO4; this phosphorylation is correlated with negative regulation of
PHO5
. These results demonstrate the existence of a cyclin-cdk complex that is used for a regulatory process other than cell-cycle control and identify a physiologically relevant substrate for this complex.
Encapsulation of Methane and Other Small Molecules in a Self-Assembling Superstructure
Authors: Branda N. , Wyler R. , Rebek J.
Published: October 2006

Physical inclusion of small molecules in larger structural lattices is well known in the crystalline state and is a common feature of the chemistry of zeolites. In the liquid state, a variety of synthetic macrocyclic molecules are available to complex and contain smaller guest species. An alternative strategy for binding is explored: assembly of cavity-forming structures from smaller subunits. Encapsulation of small guest molecules such as methane can be achieved with a synthetic structure that assembles reversibly through hydrogen bonding.
Open "Back Door" in a Molecular Dynamics Simulation of Acetylcholinesterase
Authors: Gilson M. K. , Straatsma T. P. , McCammon J. A. , Ripoll D. R. , Faerman C. H. , Axelsen P. H. , Silman I. , Sussman J. L.
Published: October 2006

The enzyme acetylcholinesterase generates a strong electrostatic field that can attract the cationic substrate acetylcholine to the active site. However, the long and narrow active site gorge seems inconsistent with the enzyme's high catalytic rate. A molecular dynamics simulation of acetylcholinesterase in water reveals the transient opening of a short channel, large enough to pass a water molecule, through a thin wall of the active site near tryptophan-84. This simulation suggests that substrate, products, or solvent could move through this "back door," in addition to the entrance revealed by the crystallographic structure. Electrostatic calculations show a strong field at the back door, oriented to attract the substrate and the reaction product choline and to repel the other reaction product, acetate. Analysis of the open back door conformation suggests a mutation that could seal the back door and thus test the hypothesis that thermal motion of this enzyme may open multiple routes of access to its active site.
Recombination Between Viral RNA and Transgenic Plant Transcripts
Authors: Greene Ann E. , Allison Richard F.
Published: October 2006

Transformed plants expressing the 3′ two-thirds of the cowpea chlorotic mottle virus (CCMV) capsid gene were inoculated with a CCMV deletion mutant lacking the 3′ one-third of the capsid gene. Although the deletion inoculum replicates in inoculated cells, systemic infections occur only if recombination restores a functional capsid gene. Four of 125 inoculated transgenic plants, representing three different transgenic lines, became systemically infected. Analysis of viral RNA confirmed that RNA recombination had united the transgenic messenger RNA and the challenging virus through aberrant homologous recombination.
Channel-Like Function of the Na,K Pump Probed at Microsecond Resolution in Giant Membrane Patches
Authors: Hilgemann Donald W.
Published: October 2006

Ion transporters can be thought of as ion channels that open and close only at one end at a time. As in real channels, ions may cross through an electrical field as they diffuse into and bind within the transporter pore, thereby generating electrical current. Extracellular sodium binding by the sodium potassium (Na,K) pump is associated with ultrafast charge movements in giant cardiac membrane patches. The charge movements are complete within 4 microseconds. They occur only when binding sites are open to the extracellular side, and they are abolished by ouabain and by the removal of extracellular sodium. Fast extracellular ion binding may be the exclusive source of Na,K pump electrogenicity.
Crystal Structures at 2.5 Angstrom Resolution of Seryl-tRNA Synthetase Complexed with Two Analogs of Seryl Adenylate
Authors: Belrhali Hassan , Yaremchuk Anna , Tukalo Michael , Larsen Kjeld , Berthet-Colominas Carmen , Leberman Reuben , Beijer Barbro , Sproat Brian , Als-Nielsen Jens , Grübel Gerhard , Legrand Jean-François , Lehmann Mogens , Cusack Stephen
Published: October 2006

Crystal structures of seryl-tRNA synthetase from
Thermus thermophilus
complexed with two different analogs of seryl adenylate have been determined at 2.5 Å resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically in the crystal from adenosine triphosphate (ATP) and serine hydroxamate, and the second is with a synthetic analog of seryl adenylate (5′-
O
-[
N
-(L-seryl)-sulfamoyl]adenosine), which is a strong inhibitor of the enzyme. Both molecules are bound in a similar fashion by a network of hydrogen bond interactions in a deep hydrophilic cleft formed by the antiparallel β sheet and surrounding loops of the synthetase catalytic domain. Four regions in the primary sequence are involved in the interactions, including the motif 2 and 3 regions of class 2 synthetases. Apart from the specific recognition of the serine side chain, the interactions are likely to be similar in all class 2 synthetases.
Slow Repair of Pyrimidine Dimers at
p53
Mutation Hotspots in Skin Cancer
Authors: Tornaletti Silvia , Pfeifer Gerd P.
Published: October 2006

Ultraviolet light has been linked with the development of human skin cancers. Such cancers often exhibit mutations in the
p53
tumor suppressor gene. Ligation-mediated polymerase chain reaction was used to analyze at nucleotide resolution the repair of cyclobutane pyrimidine dimers along the
p53
gene in ultraviolet-irradiated human fibroblasts. Repair rates at individual nucleotides were highly variable and sequence-dependent. Slow repair was seen at seven of eight positions frequently mutated in skin cancer, suggesting that repair efficiency may strongly contribute to the mutation spectrum in a cancer-associated gene.
Coding of Hemolysins Within the Ribosomal RNA Repeat on a Plasmid in
Entamoeba histolytica
Authors: Jansson Åslög , Gillin Frances , Kagardt Ulrika , Hagblom Per
Published: October 2006

The pathogenesis of amoebic dysentery is a result of cytolysis of the colonic mucosa by the parasitic protozoan
Entamoeba histolytica
. The cytolysis results in extensive local ulceration and allows the amoeba to penetrate and metastasize to distant sites. Factors involved in this process were defined with three clones that express hemolytic activities in
Escherichia coli
. These potential amoebic virulence determinants were also toxic to human colonic epithelial cells, the primary cellular targets in amoebal invasion of the large intestine. The coding sequences for the hemolysins were close to each other on a 2.6-kilobase segment of a 25-kilobase extrachromosomal DNA element. The structural genes for the hemolysins were within inverted repeats that encode ribosomal RNAs.
Functional Participation of the IL-2 Receptor γ Chain in IL-7 Receptor Complexes
Authors: Kondo Motonari , Takeshita Toshikazu , Higuchi Masaya , Nakamura Masataka , Sudo Tetsuo , Nishikawa Shin-lchi , Sugamura Kazuo
Published: October 2006

The γ chain of the interleukin-2 (IL-2) receptor is shared with the functional IL-4 receptor and is causatively related to X-linked severe combined immunodeficiency (XSCID), which is ascribed to a profound T cell defect. Studies with monoclonal antibodies specific for the IL-2 receptor γ chain showed that the γ chain participates in the functional high-affinity receptor complexes for IL-7 that are involved in the differentiation of T and B cells. Participation of the γ subunit in more than one receptor may enable the elucidation of the mechanisms of XSCID development and lymphocyte differentiation.
Long-Range Cis Preference in DNA Homology Search Over the Length of a
Drosophila
Chromosome
Authors: Engels William R. , Preston Christine R. , Johnson-Schlitz Dena M.
Published: October 2006

P element-induced chromosome breakage on the X chromosome of
Drosophila melanogaster
was repaired six times more frequently when a homologous template was located anywhere on the X chromosome rather than on an autosome. Cis-trans comparisons confirmed that recombinational repair was more frequent when the interacting sequences were physically connected. These results suggest that the search for homology between the broken ends and a matching template sequence occurs preferentially in the cis configuration. This cis advantage operates over more than 15 megabases of DNA.
Structure of an Electron Transfer Complex: Methylamine Dehydrogenase, Amicyanin, and Cytochrome c
551i
Authors: Chen Longyin , Durley Rosemary C. E. , Mathews F. Scott , Davidson Victor L.
Published: October 2006

The crystal structure of a ternary protein complex has been determined at 2.4 angstrom resolution. The complex is composed of three electron transfer proteins from
Paracoccus denitrificans
, the quinoprotein methylamine dehydrogenase, the blue copper protein amicyanin, and the cytochrome c
551i
. The central region of the c
551i
is folded similarly to several small bacterial c-type cytochromes; there is a 45-residue extension at the amino terminus and a 25-residue extension at the carboxyl terminus. The methylamine dehydrogenase-amicyanin interface is largely hydrophobic, whereas the amicyanin-cytochrome interface is more polar, with several charged groups present on each surface. Analysis of the simplest electron transfer pathways between the redox partners points out the importance of other factors such as energetics in determining the electron transfer rates.
Formation of Nascent Intercalated Disks Between Grafted Fetal Cardiomyocytes and Host Myocardium
Authors: Soonpaa Mark H. , Koh Gou Young , Klug Michael G. , Field Loren J.
Published: October 2006

Fetal cardiomyocytes isolated from transgenic mice carrying a fusion gene of the α-cardiac myosin heavy chain promoter with a β-galactosidase reporter were examined for their ability to form stable intracardiac grafts. Embryonic day 15 transgenic cardiomyocytes delivered directly into the myocardium of syngeneic hosts formed stable grafts, as identified by nuclear β-galactosidase activity. Grafted cardiomyocytes were observed as long as 2 months after implantation, the latest date assayed. Intracardiac graft formation did not induce overtly negative effects on the host myocardium and was not associated with chronic immune rejection. Electron microscopy revealed the presence of nascent intercalated disks connecting the engrafted fetal cardiomyocytes and the host myocardium. These results suggest that intracardiac grafting might provide a useful approach for myocardial repair, provided that the grafted cells can contribute to myocardial function.
Morphological Bifurcations Involving Reaction-Diffusion Processes During Microtubule Formation
Authors: Tabony James
Published: October 2006

Nonlinear chemically dissipative mechanisms have been proposed as providing a possible underlying process for some aspects of biological self-organization, pattern formation, and morphogenesis. Nonlinearities during the formation of microtubular solutions result in a chemical instability and bifurcation between pathways leading to macroscopically self-organized states of different morphology. The self-organizing process, which contains reactive and diffusive contributions, involves chemical waves and differences in microtubule concentration in the sample. Patterns of similar appearance are observed at different distance scales. This behavior is in agreement with theories of chemically dissipative systems.
Isolation of
S. cerevisiae
snRNPs: comparison of U1 and U4/U6.U5 to Their Human Counterparts
Authors: Fabrizio Patrizia , Esser Sybille , Kastner Berthold , Lührmann Reinhard
Published: October 2006

Small nuclear ribonucleoprotein (snRNP) particles are essential for pre-messenger RNA splicing. In human HeLa cells, 40 proteins associated with snRNPs have been identified. Yet, the function of many of these proteins remains unknown. Here, the immunoaffinity purification of the spliceosomal snRNPs U1, U2, U4/U6.U5, and several nucleolar snRNP species from the yeast
Saccharomyces cerevisiae
is presented. The U1 and U4/U6.U5 snRNPs were purified extensively and their protein composition and ultrastructure analyzed. The yeast U1 snRNP is larger and contains three times more specific proteins than its human counterpart. In contrast, the size, protein composition, and morphology of the yeast and the human U4/U6.U5 snRNPs are significantly similar. The preparative isolation of yeast snRNPs will allow the cloning as well as genetic and phylogenetic analysis of snRNP proteins which will accelerate our understanding of their function.
Soluble β-Amyloid Induction of Alzheimer's Phenotype for Human Fibroblast K
+
Channels
Authors: Etcheberrigaray René , Ito Etsuro , Kim Christopher S. , Alkon Daniel L.
Published: October 2006

Although β-amyloid is the main constituent of neurite plaques and may play a role in the pathophysiology of Alzheimer's disease, mechanisms by which soluble β-amyloid might produce early symptoms such as memory loss before diffuse plaque deposition have not been implicated. Treatment of fibroblasts with β-amyloid (10 nM) induced the same potassium channel dysfunction previously shown to occur specifically in fibroblasts from patients with Alzheimer's disease—namely, the absence of a 113-picosiemen potassium channel. A tetraethylammonium-induced increase of intracellular concentrations of calcium, [Ca
2+
]
i
, a response that depends on functional 113-picosiemen potassium channels, was also eliminated or markedly reduced by 10 nM β-amyloid. Increased [Ca
2+
]
i
induced by high concentrations of extracellular potassium and 166-picosiemen potassium channels were unaffected by 10 nM β-amyloid. In Alzheimer's disease, then, β-amyloid might alter potassium channels and thus impair neuronal function to produce symptoms such as memory loss by a means other than plaque formation.
Inactivation of Antibiotics and the Dissemination of Resistance Genes
Authors: Davies Julian
Published: October 2006

The emergence of multidrug-resistant bacteria is a phenomenon of concern to the clinician and the pharmaceutical industry, as it is the major cause of failure in the treatment of infectious diseases. The most common mechanism of resistance in pathogenic bacteria to antibiotics of the aminoglycoside, β-lactam (penicillins and cephalosporins), and chloramphenicol types involves the enzymic inactivation of the antibiotic by hydrolysis or by formation of inactive derivatives. Such resistance determinants most probably were acquired by pathogenic bacteria from a pool of resistance genes in other microbial genera, including antibiotic-producing organisms. The resistance gene sequences were subsequently integrated by site-specific recombination into several classes of naturally occurring gene expression cassettes (typically "integrons") and disseminated within the microbial population by a variety of gene transfer mechanisms. Although bacterial conjugation once was believed to be restricted in host range, it now appears that this mechanism of transfer permits genetic exchange between many different bacterial genera in nature.
Association of Intestinal Peptide Transport with a Protein Related to the Cadherin Superfamily
Authors: Dantzig Anne H. , Hoskins JoAnn , Tabas Linda B. , Bright Stuart , Shepard Robert L. , Jenkins Ivan L. , Duckworth Dale C. , Sportsman J. Richard , Mackensen Daniel , Rosteck Paul R. , Skatrud Paul L.
Published: October 2006

The first step in oral absorption of many medically important peptide-based drugs is mediated by an intestinal proton-dependent peptide transporter. This transporter facilitates the oral absorption of β-lactam antibiotics and angiotensin-converting enzyme inhibitors from the intestine into enterocytes lining the luminal wall. A monoclonal antibody that blocked uptake of cephalexin was used to identify and clone a gene that encodes an approximately 92-kilodalton membrane protein that was associated with the acquisition of peptide transport activity by transport-deficient cells. The amino acid sequence deduced from the complementary DNA sequence of the cloned gene indicated that this transport-associated protein shares several conserved structural elements with the cadherin superfamily of calcium-dependent, cell-cell adhesion proteins.
Loudness-Coding Mechanisms Inferred from Electric Stimulation of the Human Auditory System
Authors: Zeng Fan-Gang , Shannon Robert V.
Published: October 2006

Two distinct physiological mechanisms underlying loudness sensation were inferred from electric stimulation of the human auditory nerve and brainstem. In contrast to a power function relating loudness and stimulus intensity in acoustic hearing, loudness in electric stimulation of the auditory nerve depends on stimulus frequency. Loudness is an exponential function of electric amplitude for high frequencies and is a power function for low frequencies. A frequency-dependent, two-stage model is suggested to explain the loudness function, in which the first stage of processing is performed by a mechanical mechanism in the cochlea for high-frequency stimuli and by a neural mechanism in the cochlear nucleus for low-frequency stimuli.
Application and Accuracy of Molecular Phylogenies
Authors: Hillis David M. , Huelsenbeck John P. , Cunningham Clifford W.
Published: October 2006

Molecular investigations of evolutionary history are being used to study subjects as diverse as the epidemiology of acquired immune deficiency syndrome and the origin of life. These studies depend on accurate estimates of phylogeny. The performance of methods of phylogenetic analysis can be assessed by numerical simulation studies and by the experimental evolution of organisms in controlled laboratory situations. Both kinds of assessment indicate that existing methods are effective at estimating phylogenies over a wide range of evolutionary conditions, especially if information about substitution bias is used to provide differential weightings for character transformations.
Retention and 5′ Cap Trimethylation of U3 snRNA in the Nucleus
Authors: Terns Michael P. , Dahlberg James E.
Published: October 2006

It is shown here that maturation of the m
7
G-capped precursors of U3 small nuclear RNA (snRNA) occurs by a previously unknown pathway. In contrast to the 5′ m
7
G-capped precursors of other snRNAs, this RNA is not exported to the cytoplasm but is retained in the nuclei of
Xenopus laevis
oocytes, where it undergoes trimethylation of its 5′ cap. The m
7
G caps of most snRNA precursors are trimethylated only after transport of the RNAs to the cytoplasm. The nuclear retention and maturation of this nucleolar RNA raises the possibility that other m
7
G-capped RNAs are also retained and modified in the nucleus.
Cloning of a T Cell Growth Factor that Interacts with the β Chain of the Interleukin-2 Receptor
Authors: Grabstein Kenneth H. , Eisenman June , Shanebeck Kurt , Rauch Charles , Srinivasan Subhashini , Fung Victor , Beers Courtney , Richardson Jane , Schoenborn Michael A. , Ahdieh Minoo , Johnson Lisabeth , Alderson Mark R. , Watson James D. , Anderson, Dirk M. , Giri Judith G.
Published: October 2006

A cytokine was identified that stimulated the proliferation of T lymphocytes, and a complementary DNA clone encoding this new T cell growth factor was isolated. The cytokine, designated interleukin-15 (IL-15), is produced by a wide variety of cells and tissues and shares many biological properties with IL-2. Monoclonal antibodies to the β chain of the IL-2 receptor inhibited the biological activity of IL-15, and IL-15 competed for binding with IL-2, indicating that IL-15 uses components of the IL-2 receptor.
Cloning of a Grb2 Isoform with Apoptotic Properties
Authors: Fath Isabelle , Schweighoffer Fabien , Rey Isabelle , Multon Marie-Christine , Boiziau Janine , Duchesne Marc , Tocqué Bruno
Published: October 2006

Growth factor receptor-bound protein 2 (Grb2) links tyrosine-phosphorylated proteins to a guanine nucleotide releasing factor of the son of sevenless (Sos) class by attaching to the former by its Src homology 2 (SH2) moiety and to the latter by its SH3 domains. An isoform of
grb2
complementary DNA (cDNA) was cloned that has a deletion in the SH2 domain. The protein encoded by this cDNA, Grb3-3, did not bind to phosphorylated epidermal growth factor receptor (EGFR) but retained functional SH3 domains and inhibited EGF-induced transactivation of a Ras-responsive element. The messenger RNA encoding Grb3-3 was expressed in high amounts in the thymus of rats at an age when massive negative selection of thymocytes occurs. Microinjection of Grb3-3 into Swiss 3T3 fibroblasts induced apoptosis. These findings indicate that Grb3-3, by acting as a dominant negative protein over Grb2 and by suppressing proliferative signals, may trigger active programmed cell death.
Aberrant Neurites and Synaptic Vesicle Protein Deficiency in Synapsin II-Depleted Neurons
Authors: Ferreira Adriana , Kosik Kenneth S. , Greengard Paul , Han Hui-Quan
Published: October 2006

Synapsin I and synapsin II are neuron-specific phosphoproteins that have a role in the regulation of neurotransmitter release and in the formation of nerve terminals. After depletion of synapsin II by antisense oligonucleotides, rat hippocampal neurons in culture were unable to consolidate their minor processes and did not elongate axons. These aberrant morphological changes were accompanied by an abnormal distribution of intracellular filamentous actin (F-actin). In addition, synapsin II suppression resulted in a selective decrease in the amounts of several synaptic vesicle-associated proteins. These data suggest that synapsin II participates in cytoskeletal organization during the early stages of nerve cell development.