bluuebunny/crossref_metadata_2025 huggingface dataset:
Age and Paleogeographical Origin of Dominican Amber
Authors: Iturralde-Vinent Manuel A. , MacPhee R. D. E.
Published: October 2006

The age and depositional history of Dominican amber-bearing deposits have not been well constrained. Resinites of different ages exist in Hispaniola, but all of the main amberiferous deposits in the Dominican Republic (including those famous for yielding biological inclusions) were formed in a single sedimentary basin during the late Early Miocene through early Middle Miocene (15 to 20 million years ago), according to available biostratigraphic and paleogeographic data. There is little evidence for extensive reworking or redeposition, in either time or space. The brevity of the depositional interval (less than 5 million years) provides a temporal benchmark that can be used to calibrate rates of molecular evolution in amber taxa.
Requirement for CD40 Ligand in Costimulation Induction, T Cell Activation, and Experimental Allergic Encephalomyelitis
Authors: Grewal Iqbal S. , Foellmer Harald G. , Grewal Kate D. , Xu Jianchao , Hardardottir Fridrika , Baron Jody L. , Janeway Charles A. , Flavell Richard A.
Published: October 2006

The mechanism of CD40 ligand (CD40L)-mediated in vivo activation of CD4
+
T cells was examined by investigation of the development of experimental allergic encephalomyelitis (EAE) in CD40L-deficient mice that carried a transgenic T cell receptor specific for myelin basic protein. These mice failed to develop EAE after priming with antigen, and CD4
+
T cells remained quiescent and produced no interferon-γ (IFN-γ). T cells were primed to make IFN-γ and induce EAE by providing these mice with B7.1
+
antigen-presenting cells (APCs). Thus, CD40L is required to induce costimulatory activity on APCs for in vivo activation of CD4
+
T cells to produce IFN-γ and to evoke autoimmunity.
Dynamics of Ongoing Activity: Explanation of the Large Variability in Evoked Cortical Responses
Authors: Arieli Amos , Sterkin Alexander , Grinvald Amiram , Aertsen Ad
Published: October 2006

Evoked activity in the mammalian cortex and the resulting behavioral responses exhibit a large variability to repeated presentations of the same stimulus. This study examined whether the variability can be attributed to ongoing activity. Ongoing and evoked spatiotemporal activity patterns in the cat visual cortex were measured with real-time optical imaging; local field potentials and discharges of single neurons were recorded simultaneously, by electrophysiological techniques. The evoked activity appeared deterministic, and the variability resulted from the dynamics of ongoing activity, presumably reflecting the instantaneous state of cortical networks. In spite of the large variability, evoked responses in single trials could be predicted by linear summation of the deterministic response and the preceding ongoing activity. Ongoing activity must play an important role in cortical function and cannot be ignored in exploration of cognitive processes.
Temporal Hierarchical Control of Singing in Birds
Authors: Yu Albert C. , Margoliash Daniel
Published: October 2006

Songs of birds comprise hierarchical sets of vocal gestures. In zebra finches, songs include notes and syllables (groups of notes) delivered in fixed sequences. During singing, premotor neurons in the forebrain nucleus HVc exhibited reliable changes in activity rates whose patterns were uniquely associated with syllable identity. Neurons in the forebrain nucleus robustus archistriatalis, which receives input from the HVc, exhibited precisely timed and structured bursts of activity that were uniquely associated with note identity. Hence, units of vocal behavior are represented hierarchically in the avian forebrain. The representation of temporal sequences at each level of the hierarchy may be established by means of a decoding process involving interactions of higher level input with intrinsic local circuitry. Behavior is apparently represented by precise temporal patterning of spike trains at lower levels of the hierarchy.
Identification of Bases in 16
S
rRNA Essential for tRNA Binding at the 30
S
Ribosomal P Site
Authors: von Ahsen Uwe , Noller Harry F.
Published: October 2006

Previous studies suggest that the mechanism of action of the ribosome in translation involves crucial transfer RNA (tRNA)-ribosomal RNA (rRNA) interactions. Here, a selection scheme was developed to identify bases in 16S rRNA that are essential for tRNA binding to the P site of the small (30S) ribosomal subunit. Modification of the N-1 and N-2 positions of 2-methylguanine 966 and of the N-7 position of guanine 1401 interfered with messenger RNA (mRNA)-dependent binding of tRNA to the P site. Modification of the same positions as well as of the N-1 and N-2 positions of guanine 926 interfered with mRNA-independent binding of tRNA at high magnesium ion concentration. These results suggest that these three bases are involved in intermolecular contacts between ribosomes and tRNA.
Aminoacyl-RNA Synthesis Catalyzed by an RNA
Authors: Illangasekare Mali , Sanchez Giselle , Nickles Tim , Yarus Michael
Published: October 2006

An RNA has been selected that rapidly aminoacylates its 2′(3′) terminus when provided with phenylalanyl-adenosine monophosphate. That is, the RNA accelerates the same aminoacyl group transfer catalyzed by protein aminoacyl-transfer RNA synthetases. The best characterized RNA reaction requires both Mg
2+
and Ca
2+
. These results confirm a necessary prediction of the RNA world hypothesis and represent efficient RNA reaction (≥ 10
5
times accelerated) at a carbonyl carbon, exemplifying a little explored type of RNA catalysis.
Electronic States in Gallium Arsenide Quantum Wells Probed by Optically Pumped NMR
Authors: Tycko R. , Barrett S. E. , Dabbagh G. , Pfeiffer L. N. , West K. W.
Published: October 2006

An optical pumping technique was used to enhance and localize nuclear magnetic resonance (NMR) signals from an
n
-doped GaAs/Al
0.1
Ga
0.9
As multiple quantum well structure, permitting direct radio-frequency measurements of gallium-71 NMR spectra and nuclear spin-lattice relaxation rates (1/
T
1
) as functions of temperature (1.6 K <
T
< 4.2 K) and the Landau level filling factor (0.66 < ν < 1.76). The measurements reveal effects of electron-electron interactions on the energy levels and spin states of the two-dimensional electron system confined in the GaAs wells. Minima in 1/
T
1
at ν ≈ 1 and ν ≈ 2/3 indicate energy gaps for electronic excitations in both integer and fractional quantum Hall states. Rapid, temperature-independent relaxation at intermediate ν values indicates a manifold of low-lying electronic states with mixed spin polarizations.
Identification of a Graft Versus Host Disease-Associated Human Minor Histocompatibility Antigen
Authors: den Haan Joke M. M. , Sherman Nicholas E. , Blokland Els , Huczko Eric , Koning Frits , Drijfhout Jan Wouter , Skipper Jonathan , Shabanowitz Jeffrey , Hunt Donald F. , Engelhard Victor H. , Goulmy Els
Published: October 2006

Minor histocompatibility antigen disparities between human leukocyte antigen (HLA)-matched bone marrow donors and recipients are a major risk factor for graft versus host disease (GVHD). An HLA-A2.1-restricted cytotoxic T cell clone that recognized the minor histocompatibility antigen HA-2 was previously isolated from a patient with severe GVHD after HLA-identical bone marrow transplantation. The HLA-A2.1-bound peptide representing HA-2 has now been identified. This peptide appears to originate from a member of the non-filament-forming class I myosin family. Because HA-2 has a phenotype frequency of 95 percent in the HLA-A2.1-positive population, it is a candidate for immunotherapeutic intervention in bone marrow transplantation.
Natural Protection Against HIV-1 Infection Provided by HIV-2
Authors: Travers Karin , Mboup Souleymane , Marlink Richard , Guèye-Nidaye Aissatou , Siby Tidiane , Thior lbou , Traore Ibrahima , Dieng-Sarr Abdoulaye , Sankalé Jean-Louis , Mullins Christopher , Ndoye Ibrahima , Hsieh Chung-Cheng , Essex Max , Kanki Phyllis
Published: October 2006

Significant differences have been observed in the rates of transmission and disease development in human immunodeficiency virus (HIV) types 1 and 2. Because many HIV-2-infected people remain asymptomatic for prolonged periods, the hypothesis that HIV-2 might protect against subsequent infection by HIV-1 was considered. During a 9-year period in Dakar, Senegal, the seroincidence of both HIV types was measured in a cohort of commercial sex workers. Despite a higher incidence of other sexually transmitted diseases (STDs), HIV-2-infected women had a lower incidence of HIV-1 than did HIV-seronegative women, with a relative risk of 0.32 (
P
= 0.008). An understanding of the cross-protective mechanisms involved may be directly relevant to HIV-1 vaccine development.
Enhanced DNA-Binding Activity of a Stat3-Related Protein in Cells Transformed by the Src Oncoprotein
Authors: Yu Chao-Lan , Meyer Debra J. , Campbell George S. , Larner Andrew C. , Carter-Su Christin , Schwartz Jessica , Jove Richard
Published: October 2006

Cytokines and growth factors induce tyrosine phosphorylation of signal transducers and activators of transcription (STATs) that directly activate gene expression. Cells stably transformed by the Src oncogene tyrosine kinase were examined for STAT protein activation. Assays of electrophoretic mobility, DNA-binding specificity, and antigenicity indicated that Stat3 or a closely related STAT family member was constitutively activated by the Src oncoprotein. Induction of this DNA-binding activity was accompanied by tyrosine phosphorylation of Stat3 and correlated with Src transformation. These findings demonstrate that Src can activate STAT signaling pathways and raise the possibility that Stat3 contributes to oncogenesis by Src.
In Vivo Transfer of GPI-Linked Complement Restriction Factors from Erythrocytes to the Endothelium
Authors: Kooyman D. L. , Byrne G. W. , McClellan S. , Nielsen D. , Tone M. , Waldmann H. , Coffman T. M. , McCurry K. R. , Platt J. L. , Logan J. S.
Published: October 2006

Many proteins are associated with the outer layer of the cell membrane through a posttranslationally added glycosyl phosphatidylinositol (GPI) anchor. The functional significance of this type of protein linkage is unclear, although it results in increased lateral mobility, sorting to the apical surface of the cell, reinsertion into cell membranes, and possibly cell signaling. Here evidence is presented that GPI-linked proteins can undergo intermembrane transfer in vivo. GPI-linked proteins expressed on the surface of transgenic mouse red blood cells were transferred in a functional form to endothelial cells in vivo. This feature of GPI linkage may be potentially useful for the delivery of therapeutic proteins to vascular endothelium.
CFTR as a cAMP-Dependent Regulator of Sodium Channels
Authors: Stutts M. Jackson , Canessa Cecilia M. , Olsen John C. , Hamrick Maura , Cohn Jonathan A. , Rossier Bernard C. , Boucher Richard C.
Published: October 2006

Cystic fibrosis transmembrane regulator (CFTR), the gene product that is mutated in cystic fibrosis (CF) patients, has a well-recognized function as a cyclic adenosine 3′,5′-monophosphate (cAMP)-regulated chloride channel, but this property does not account for the abnormally high basal rate and cAMP sensitivity of sodium ion absorption in CF airway epithelia. Expression of complementary DNAs for rat epithelial Na
+
channel (rENaC) alone in Madin Darby canine kidney (MDCK) epithelial cells generated large amiloride-sensitive sodium currents that were stimulated by cAMP, whereas coexpression of human CFTR with rENaC generated smaller basal sodium currents that were inhibited by cAMP. Parallel studies that measured regulation of sodium permeability in fibroblasts showed similar results. In CF airway epithelia, the absence of this second function of CFTR as a cAMP-dependent regulator likely accounts for abnormal sodium transport.
TRAF2-Mediated Activation of NF-κB by TNF Receptor 2 and CD40
Authors: Rothe Mike , Sarma Vidya , Dixit Vishva M. , Goeddel David V.
Published: October 2006

TNF receptor-associated factor (TRAF) proteins are candidate signal transducers that associate with the cytoplasmic domains of members of the tumor necrosis factor (TNF) receptor superfamily. The role of TRAFs in the TNF-R2 and CD40 signal transduction pathways, which result in the activation of transcription factor NF-κB, was investigated. Overexpression of TRAF2, but not TRAF1 or TRAF3, was sufficient to induce NF-κB activation. A truncated derivative of TRAF2 lacking an amino-terminal RING finger domain was a dominant-negative inhibitor of NF-κB activation mediated by TNF-R2 and CD40. Thus, TRAF2 is a common mediator of TNF-R2 and CD40 signaling.
Requirement for Src Family Protein Tyrosine Kinases in G
2
for Fibroblast Cell Division
Authors: Roche Serge , Fumagalli Stefano , Courtneidge Sara A.
Published: October 2006

The protein tyrosine kinase c-Src is transiently activated at the transition from the G
2
phase to mitosis in the cell cycle of mammalian fibroblasts. Fyn and Yes, the other members of the Src family present in fibroblasts, were also found to be activated at mitosis. In cells microinjected with a neutralizing antibody specific for Src, Fyn, and Yes (anti-cst.1) during G
2
, cell division was inhibited by 75 percent. The block occurred before nuclear envelope breakdown. Antibodies specific for phosphatidylinositol-3 kinase α and phospholipase C-γ1 had no effect. Microinjection of the Src homology 2 (SH2) domain of Fyn was also inhibitory. Functional redundancy between members of the Src family was observed; a Src-specific antibody had no effect in NIH 3T3 cells but inhibited cell division in fibroblasts in which the only functional Src family kinase was Src itself. Thus, Src family kinases and proteins associating with their SH2 domains are required for entry into mitosis.
Mating Patterns in Malaria Parasite Populations of Papua New Guinea
Authors: Paul R. E. L. , Packer M. J. , Walmsley M. , Lagog M. , Ranford-Cartwright L. C. , Paru R. , Day K. P.
Published: October 2006

Description of the genetic structure of malaria parasite populations is central to an understanding of the spread of multiple-locus drug and vaccine resistance. The
Plasmodium falciparum
mating patterns from Madang, Papua New Guinea, where intense transmission of malaria occurs, are described here. A high degree of inbreeding occurs in the absence of detectable linkage disequilibrium. This contrasts with other studies, indicating that the genetic structure of malaria parasite populations is neither clonal nor panmictic but will vary according to the transmission characteristics of the region.
Activation of a G Protein Complex by Aggregation of β-1,4-Galactosyltransferase on the Surface of Sperm
Authors: Gong Xiaohai , Dubois Daniel H. , Miller David J. , Shur Barry D.
Published: October 2006

Fertilization is initiated by the species-specific binding of sperm to the extracellular coat of the egg. One sperm receptor for the mouse egg is β-1,4-galactosyltransferase (GalTase), which binds O-linked oligosaccharides on the egg coat glycoprotein ZP3. ZP3 binding induces acrosomal exocytosis through the activation of a pertussis toxin-sensitive heterotrimeric guanine nucleotide-binding protein (G protein). The cytoplasmic domain of sperm surface GalTase bound to and activated a heterotrimeric G protein complex that contained the G
iα
subunit. Aggregation of GalTase by multivalent ligands elicited G protein activation. Sperm from transgenic mice that overexpressed GalTase had higher rates of G protein activation than did wild-type sperm, which rendered transgenic sperm hypersensitive to their ZP3 ligand. Thus, the cytoplasmic domain of cell surface GalTase appears to enable it to function as a signal-transducing receptor for extracellular oligosaccharide ligands.
Requirement for MAP Kinase (ERK2) Activity in Interferon α- and Interferon β-Stimulated Gene Expression Through STAT Proteins
Authors: David Michael , Petricoin Emanuel , Benjamin Christopher , Pine Richard , Weber Michael J. , Larner Andrew C.
Published: October 2006

Activation of early response genes by interferons (IFNs) requires tyrosine phosphorylation of STAT (signal transducers and activators of transcription) proteins. It was found that the serine-threonine kinase mitogen-activated protein kinase (MAPK) [specifically, the 42-kilodalton MAPK or extracellular signal-regulated kinase 2 (ERK2)] interacted with the α subunit of IFN-α/β receptor in vitro and in vivo. Treatment of cells with IFN-β induced tyrosine phosphorylation and activation of MAPK and caused MAPK and Stat1α to coimmunoprecipitate. Furthermore, expression of dominant negative MAPK inhibited IFN-β-induced transcription. Therefore, MAPK appears to regulate IFN-α and IFN-β activation of early response genes by modifying the Jak-STAT signaling cascade.
Imaging Elementary Events of Calcium Release in Skeletal Muscle Cells
Authors: Tsugorka Alexander , Ríos Eduardo , Blatter Lothar A.
Published: October 2006

In skeletal muscle cells, calcium release to trigger contraction occurs at triads, specialized junctions where sarcoplasmic reticulum channels are opened by voltage sensors in the transverse tubule. Scanning confocal microscopy was used in cells under voltage clamp to measure the concentration of intracellular calcium, [Ca
2+
]
i
, at individual triads and [Ca
2+
]
i
gradients that were proportional to calcium release. In cells stimulated with small depolarizations, the [Ca
2+
]
i
gradients broke down into elementary events, corresponding to single-channel currents of about 0.1 picoampere. Because these events were one-tenth to one-fifth the size of calcium sparks (elementary release events of cardiac muscle), skeletal muscle control mechanisms appear to be fundamentally different.
From Molecular Diversity to Catalysis: Lessons from the Immune System
Authors: Schultz Peter G. , Lerner Richard A.
Published: October 2006

By combining the enormous molecular diversity of the immune system with basic mechanistic principles of chemistry, one can produce catalytic antibodies that allow control of reactions in ways heretofore not possible. Mechanistic and structural studies of these antibodies are also providing insights into important aspects of enzymatic catalysis and the evolution of catalytic function. Moreover, the ability to rationally direct the immune response to generate selective catalysts for reactions ranging from pericyclic and redox reactions to cationic rearrangement reactions underscores the chemical potential of this and other large combinatorial libraries.
Hemoglobin Allostery: Resonance Raman Spectroscopy of Kinetic Intermediates
Authors: Jayaraman Vasanthi , Rodgers Kenton R. , Mukerji Ishita , Spiro Thomas G.
Published: October 2006

The end states, R and T, of the allosteric transition in hemoglobin (Hb) are structurally well characterized, but there is little information on intermediate structures along the allosteric pathway. These intermediates were examined by means of time-resolved resonance Raman spectroscopy in the nanosecond-to-microsecond interval after HbCO photolysis. Complementary spectra of the heme group and of the tyrosine and tryptophan residues were recorded during laser excitation at 436 and 230 nanometers. These spectra reveal a sequence of interleaved tertiary and quaternary motions during the photocycle, motions involving the proximal and distal helices, and the α
1
β
2
subunit interface. This sequence leads to a modified form of the T state, in which the α
1
β
2
interface is deformed as a result of two carbon monoxide molecules binding to the same dimer within the tetramer.
Jak-STAT Signaling Induced by the v-
abl
oncogene
Authors: Danial Nika N. , Pernis Alessandra , Rothman Paul B.
Published: October 2006

The effect of the v-
abl
oncogene of the Abelson murine leukemia virus (A-MuLV) on the Jak-STAT pathway of cytokine signal transduction was investigated. In murine pre-B lymphocytes transformed with A-MuLV, the Janus kinases (Jaks) Jak1 and Jak3 exhibited constitutive tyrosine kinase activity, and the STAT proteins (signal transducers and activators of transcription) normally activated by interleukin-4 and interleukin-7 were tyrosine-phosphorylated in the absence of these cytokines. Coimmunoprecipitation experiments revealed that in these cells v-Abl was physically associated with Jak1 and Jak3. Inactivation of v-Abl tyrosine kinase in a pre-B cell line transformed with a temperature-sensitive mutant of v-
abl
resulted in abrogation of constitutive Jak-STAT signaling. A direct link may exist between transformation by v-
abl
and cytokine signal transduction.
Lateral Interactions in Primary Visual Cortex: A Model Bridging Physiology and Psychophysics
Authors: Stemmler Martin , Usher Marius , Niebur Ernst
Published: October 2006

Recent physiological studies show that the spatial context of visual stimuli enhances the response of cells in primary visual cortex to weak stimuli and suppresses the response to strong stimuli. A model of orientation-tuned neurons was constructed to explore the role of lateral cortical connections in this dual effect. The differential effect of excitatory and inhibitory current and noise conveyed by the lateral connections explains the physiological results as well as the psychophysics of pop-out and contour completion. Exploiting the model's property of stochastic resonance, the visual context changes the model's intrinsic input variability to enhance the detection of weak signals.
Crystal Structure of DNA Photolyase from
Escherichia coli
Authors: Park Hee-Won , Kim Sang-Tae , Sancar Aziz , Deisenhofer Johann
Published: October 2006

Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr <> Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 Å resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal α/βdomain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 Å. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr <> Pyr dinucleotide, suggesting that the Pyr <> Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr <> Pyr occurs over van der Waals contact distance.
Skulls and Anterior Teeth of
Catopithecus
(Primates:Anthropoidea) from the Eocene and Anthropoid Origins
Authors: Simons Elwyn L.
Published: October 2006

Recent finds of
Catopithecus browni
at an upper Eocene fossil site in the Fayum depression, Egypt, reveal features of the earliest higher primates. This basal anthropoidean shows a set of derived cranial and dental features that first occur in combination in this fossil. Old World Anthropoidea or Catarrhini can now be traced back to
Catopithecus
in Egypt. Size, shape, orientation of incisors and canines, and other features of the teeth and skull relate
Catopithecus
both to later Anthropoidea and to the early and middle Eocene cercamoniine adapoids. Most defining characteristics of higher primates cannot be documented earlier than the late Eocene of Africa.
Reversal of Raf-1 Activation by Purified and Membrane-Associated Protein Phosphatases
Authors: Dent Paul , Jelinek Tomas , Morrison Deborah K. , Weber Michael J. , Sturgill Thomas W.
Published: October 2006

The Raf-1 protein kinase participates in transduction of mitogenic signals, but its mechanisms of activation are incompletely understood. Treatment of human Raf-1 purified from insect Sf9 cells co-expressing c-H-Ras and Src(Y527F) (in which phenylalanine replaces tyrosine at residue 527) with either serine-threonine or tyrosine phosphatases resulted in enzymatic inactivation of Raf-1. Inactivation of purified Raf-1 was blocked by addition of either the 14-3-3ζ protein or heat shock protein 90. Loading of plasma membranes from transformed cells with guanosine triphosphate (GTP) resulted in inactivation of endogenous or exogenous Raf-1; inactivation was blocked by inclusion of protein phosphatase inhibitors. These results suggest the existence of protein phosphatases in the cell membrane that are regulated by GTP and are responsible for Raf-1 inactivation.
Isolation of an hMSH2-p160 Heterodimer That Restores DNA Mismatch Repair to Tumor Cells
Authors: Drummond James T. , Li Guo-Min , Longley Matthew J. , Modrich Paul
Published: October 2006

A mismatch-binding heterodimer of hMSH2 and a 160-kilodalton polypeptide has been isolated from HeLa cells by virtue of its ability to restore mismatch repair to nuclear extracts of hMSH2-deficient LoVo colorectal tumor cells. This heterodimer, designated hMutSα, also restores mismatch repair to extracts of alkylation-tolerant MT1 lymphoblastoid cells and HCT-15 colorectal tumor cells, which are selectively defective in the repair of base-base and single-nucleotide insertion-deletion mismatches. Because HCT-15 cells appear to be free of hMSH2 mutations, this selective repair defect is likely a result of a deficiency of the hMutSα 160-kilodalton subunit, and mutations in the corresponding gene may confer hypermutability and cancer predisposition.
GTBP, a 160-Kilodalton Protein Essential for Mismatch-binding Activity in Human Cells
Authors: Palombo Fabio , Gallinari Paola , Iaccarino Ingram , Lettieri Teresa , Hughes Melya , D'Arrigo Antonello , Truong Oanh , Hsuan J. Justin , Jiricny Josef
Published: October 2006

DNA mismatch recognition and binding in human cells has been thought to be mediated by the hMSH2 protein. Here it is shown that the mismatch-binding factor consists of two distinct proteins, the 100-kilodalton hMSH2 and a 160-kilodalton polypeptide, GTBP (for G/T binding protein). Sequence analysis identified GTBP as a new member of the MutS homolog family. Both proteins are required for mismatch-specific binding, a result consistent with the finding that tumor-derived cell lines devoid of either protein are also devoid of mismatch-binding activity.
Protein Folding Intermediates: Native-State Hydrogen Exchange
Authors: Bai Yawen , Sosnick Tobin R. , Mayne Leland , Englander S. Walter
Published: October 2006

The hydrogen exchange behavior of native cytochrome c in low concentrations of denaturant reveals a sequence of metastable, partially unfolded forms that occupy free energy levels reaching up to the fully unfolded state. The step from one form to another is accomplished by the unfolding of one or more cooperative units of structure. The cooperative units are entire omega loops or mutually stabilizing pairs of whole helices and loops. The partially unfolded forms detected by hydrogen exchange appear to represent the major intermediates in the reversible, dynamic unfolding reactions that occur even at native conditions and thus may define the major pathway for cytochrome c folding.
A Strategy for a Convergent Synthesis of N-Linked Glycopeptides on a Solid Support
Authors: Roberge Jacques Y. , Beebe Xenia , Danishefsky Samuel J.
Published: October 2006

Oligosaccharides and glycopeptides are of considerable importance in molecular biology and pharmacology. However, their synthesis is complicated by the large number of different linking sites between each saccharide unit, the need for stereochemical control, the chemical sensitivity of the glycopeptide bonds, and the need to harmonize diverse protecting groups. Here, an efficient solid-phase synthesis of three
N
-linked glycopeptides based on glycal assembly is presented. The peptide domain can be extended while the ensemble remains bound to the polymer. The glycopeptides synthesized here are among the largest
N
-linked glycopeptides ever accessed by either solution- or solid-phase synthesis.
Inhibitor-Enhanced Electron Transfer: Copper Cytochrome c as a Redox-Inert Probe of Ternary Complexes
Authors: Zhou Jian S. , Nocek Judith M. , DeVan Michael L. , Hoffman Brian M.
Published: October 2006

Copper-substituted cytochrome c (CuCc) has been used as a structurally faithful, redoxinert inhibitor to probe the mechanism of electron transfer (ET) between Cc molecules and cytochrome c peroxidase (CcP). This inhibitor enhances photoinduced ET quenching of the triplet excited state of a zinc-substituted protein (ZnCcP or ZnCc) by its iron(III) partner (Fe
3+
Cc or Fe
3+
CcP). These results show that CcP and Cc form a ternary complex in which one Cc molecule binds tightly at a surface domain of CcP having low ET reactivity, whereas the second Cc molecule binds weakly to the 1:1 complex at a second domain with markedly greater (∼10
3
) reactivity. These results also rule out the possibility that Cc bound at the second domain cooperatively enhances ET to Cc at the first domain. The multiphasic kinetics observed for the photoproduced ET intermediate do not reflect electron self-exchange between two Cc molecules within the ternary complex.
Age-Related Reductions in Human Recognition Memory Due to Impaired Encoding
Authors: Grady Cheryl L. , McIntosh Anthony R. , Horwitz Barry , Maisog Jose Ma. , Ungerleider Leslie G. , Mentis Marc J. , Pietrini Pietro , Schapiro Mark B. , Haxby James V.
Published: October 2006

The participation of the medial temporal cortex and other cerebral structures in the memory impairment that accompanies aging was examined by means of positron emission tomography. Cerebral blood flow (rCBF) was measured during encoding and recognition of faces. Young people showed increased rCBF in the right hippocampus and the left prefrontal and temporal cortices during encoding and in the right prefrontal and parietal cortex during recognition. Old people showed no significant activation in areas activated during encoding in young people but did show right prefrontal activation during recognition. Age-related impairments of memory may be due to a failure to encode the stimuli adequately, which is reflected in the lack of cortical and hippocampal activation during encoding.
First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle Protein
Authors: Boczko Erik M. , Brooks Charles L.
Published: October 2006

The folding and unfolding of a three-helix bundle protein were explored with molecular-dynamics simulations, cluster analysis, and weighted-histogram techniques. The folding-unfolding process occurs by means of a "folding funnel," in which a uniform and broad distribution of conformational states is accessible outside of the native manifold. This distribution narrows near a transition region and becomes compact within the native manifold. Key thermodynamic steps in folding include initial interactions around the amino-terminal helix-turn-helix motif, interactions between helices I and II, and, finally, the docking of helix III onto the helix I-II subdomain. A metastable minimum in the calculated free-energy surface is observed at approximately 1.5 times the native volume. Folding-unfolding thermodynamics are dominated by the opposing influences of protein-solvent energy, which favors unfolding, and the overall entropy, which favors folding by means of the hydrophobic effect.
Importance of Historical Contingency in the Stereochemistry of Hydratase-Dehydratase Enzymes
Authors: Mohrig Jerry R. , Moerke Katherine A. , Cloutier David L. , Lane Brian D. , Person Eric C. , Onasch Timothy B.
Published: October 2006

There are two stereochemical classes of hydratase-dehydratase enzymes. Those that catalyze the addition of water to α,β-unsaturated thioesters give
syn
addition-elimination stereochemistry, whereas those that catalyze the addition of water to conjugated carboxylate substrates give
anti
stereochemistry. This dichotomy could reflect different adaptive advantages or contingencies of separate evolutionary histories. Determination of the nonenzymatic stereochemistry of deuterium oxide addition to fumarate and to S-crotonyl
N
-acetylcysteamine has provided direct evidence for the importance of the contingencies of evolutionary history, rather than chemical efficiency, in the pathways of these hydratase-dehydratase enzymes.
Unimpaired Thymic and Peripheral T Cell Death in Mice Lacking the Nuclear Receptor NGFI-B (Nur77)
Authors: Lee Stephen L. , Wesselschmidt Robin L. , Linette Gerald P. , Kanagawa Osami , Russell John H. , Milbrandt Jeffrey
Published: October 2006

T cell hybridomas require the immediate-early gene NGFI-B (
nur77
) for T cell receptor (TCR)-mediated apoptosis, a model for negative selection of self-reactive T cells. TCR-mediated death was examined in mice bearing an NGFI-B loss-of-function mutation, either by administration of antibodies to CD3 (anti-CD3) or in two well-characterized transgenic models expressing self-reactive TCRs. Both the extent and the rate of thymocyte death were unimpaired. Anti-CD3-induced death was normal in CD4
+
peripheral T cells, in which death is mediated predominantly by the Fas signaling pathway. Thus, no unique requirement for NGFI-B is observed for thymic or peripheral T cell death.
Motor Cortical Activity in a Context-Recall Task
Authors: Pellizzer Giuseppe , Sargent Patricia , Georgopoulos Apostolos P.
Published: October 2006

A monkey was trained to respond on the basis of the serial position of a test stimulus in a sequence. First, three stimuli were presented successively on a circle. Then one of them (except the last) changed color (test stimulus) and served as the go signal: The monkey was required to produce a motor response in the direction of the stimulus that followed the test stimulus. When the test stimulus was the second in the sequence, there was a change in motor cortical activity from a pattern reflecting the direction of this stimulus to the pattern associated with the direction of the motor response. This change was abrupt, occurred 100 to 150 milliseconds after the go signal, and was evident both in the activity of single cells and in the time-varying neuronal population vector. These findings identify the neural correlates of a switching process that is different from a mental rotation described previously.
Lower Pleistocene Hominids and Artifacts from Atapuerca-TD6 (Spain)
Authors: Carbonell E. , Bermúdez de Castro J. M. , Arsuaga J. L. , Díez J. C. , Rosas A. , Cuenca-Bescós G. , Sala R. , Mosquera M. , Rodriguez X. P.
Published: October 2006

Human remains dating to more than 780,000 years ago are associated with a rich faunal and lithic assemblage in the Pleistocene cave site of Gran Dolina (TD), Sierra de Atapuerca, Burgos, Spain. The micromammal species represent the late Biharian (
Mimomys savini
zone), and the lithic objects represent pre-Acheulean technology (Mode 1) and comes from the TD6 level below the Matuyama-Brunhes boundary. The Gran Dolina hominid fossils cannot be comfortably accommodated in any of the defined
Homo
species. They could be considered a primitive form of
Homo heidelbergensis
, but a new species might be named in the future if the sample is enlarged. The new human fossil evidence demonstrates that Western Europe was settled at least since the late early Pleistocene.
Asymmetrical Interaction of GroEL and GroES in the ATPase Cycle of Assisted Protein Folding
Authors: Hayer-Hartl Manajit K. , Martin Jörg , Hartl F. Ulrich
Published: October 2006

The chaperonins GroEL and GroES of
Escherichia coli
facilitate protein folding in an adenosine triphosphate (ATP)-dependent reaction cycle. The kinetic parameters for the formation and dissociation of GroEL-GroES complexes were analyzed by surface plasmon resonance. Association of GroES and subsequent ATP hydrolysis in the interacting GroEL toroid resulted in the formation of a stable GroEL:ADP:GroES complex. The complex dissociated as a result of ATP hydrolysis in the opposite GroEL toroid, without formation of a symmetrical GroEL:(GroES)
2
intermediate. Dissociation was accelerated by the addition of unfolded polypeptide. Thus, the functional chaperonin unit is an asymmetrical GroEL:GroES complex, and substrate protein plays an active role in modulating the chaperonin reaction cycle.
Structure of the
Arabidopsis RPM1
Gene Enabling Dual Specificity Disease Resistance
Authors: Grant Murray R. , Godiard Laurence , Straube Esther , Ashfield Tom , Lewald Jürgen , Sattler Airlie , Innes Roger W. , Dangl Jeffery L.
Published: October 2006

Plants can recognize pathogens through the action of disease resistance (
R
) genes, which confer resistance to pathogens expressing unique corresponding avirulence (
avr
) genes. The molecular basis of this gene-for-gene specificity is unknown. The
Arabidopsis thaliana
RPM1
gene enables dual specificity to pathogens expressing either of two unrelated
Pseudomonas syringae
avr
genes. Despite this function,
RPM1
encodes a protein sharing molecular features with recently described single-specificity R genes. Surprisingly,
RPM1
is lacking from naturally occurring, disease-susceptible
Arabidopsis
accessions.
Ultrasound-Mediated Transdermal Protein Delivery
Authors: Mitragotri Samir , Blankschtein Daniel , Langer Robert
Published: October 2006

Transdermal drug delivery offers a potential method of drug administration. However, its application has been limited to a few low molecular weight compounds because of the extremely low permeability of human skin. Low-frequency ultrasound was shown to increase the permeability of human skin to many drugs, including high molecular weight proteins, by several orders of magnitude, thus making transdermal administration of these molecules potentially feasible. It was possible to deliver and control therapeutic doses of proteins such as insulin, interferon γ, and erythropoeitin across human skin. Low-frequency ultrasound is thus a potential noninvasive substitute for traditional methods of drug delivery, such as injections.
Control of Electron Transfer Between the L- and M-sides of Photosynthetic Reaction Centers
Authors: Heller Barbara A. , Holten Dewey , Kirmaier Christine
Published: October 2006

An aspartic acid residue has been introduced near ring V of the L-side accessory bacteriochlorophyll (BChl
L
) of the photosynthetic reaction center in a
Rhodobacter capsulatus
mutant in which a His also replaces Leu 212 on the M-polypeptide. The initial stage of charge separation in the G(M201)D/L(M212)H double mutant yields ∼70 percent electron transfer to the L-side cofactors, ∼15 percent rapid deactivation to the ground state, and ∼15 percent electron transfer to the so-called inactive M-side bacteriopheophytin (BPh
M
). It is suggested here that the Asp introduced at M201 modulates the reduction potential of BChl
L
, thereby changing the energetics of charge separation. The results demonstrate that an individual amino acid residue can, through its influence on the free energies of the charge-separated states, effectively dictate the balance between the forward electron transfer reactions on the L-side of the RC, the charge-recombination processes, and electron transfer to the M-side chromophores.
Crystal Structure of a Conserved Protease That Binds DNA: the Bleomycin Hydrolase, Gal6
Authors: Joshua-Tor Leemor , Xu H. Eric , Johnston Stephen Albert , Rees Douglas C.
Published: October 2006

Bleomycin hydrolase is a cysteine protease that hydrolyzes the anticancer drug bleomycin. The homolog in yeast, Gal6, has recently been identified and found to bind DNA and to act as a repressor in the Gal4 regulatory system. The crystal structure of Gal6 at 2.2 Å resolution reveals a hexameric structure with a prominent central channel. The papain-like active sites are situated within the central channel, in a manner resembling the organization of active sites in the proteasome. The Gal6 channel is lined with 60 lysine residues from the six subunits, suggesting a role in DNA binding. The carboxyl-terminal arm of Gal6 extends into the active site cleft and may serve a regulatory function. Rather than each residing in distinct, separable domains, the protease and DNA-binding activities appear structurally intertwined in the hexamer, implying a coupling of these two activities.
A Familial Alzheimer's Disease Locus on Chromosome 1
Authors: Levy-Lahad Ephrat , Wijsman Ellen M. , Nemens Ellen , Anderson Leojean , Goddard Katrina A. B. , Weber James L. , Bird Thomas D. , Schellenberg Gerard D.
Published: October 2006

The Volga German kindreds are a group of seven related families with autosomal dominant early-onset Alzheimer's disease (AD). Linkage to known AD-related loci on chromosomes 21 and 14 has been excluded. Significant evidence for linkage to AD in these families was obtained with D1S479 and there was also positive evidence for linkage with other markers in the region. A 112-base pair allele of D1S479 co-segregated with the disease in five of seven families, which is consistent with a common genetic founder. This study demonstrates the presence of an AD locus on chromosome 1q31-42.
Ionic Mechanisms of Neuronal Excitation by Inhibitory GABA
A
Receptors
Authors: Staley Kevin J. , Soldo Brandi L. , Proctor William R.
Published: October 2006

Gamma-aminobutyric acid A (GABA
A
) receptors are the principal mediators of synaptic inhibition, and yet when intensely activated, dendritic GABA
A
receptors excite rather than inhibit neurons. The membrane depolarization mediated by GABA
A
receptors is a result of the differential, activity-dependent collapse of the opposing concentration gradients of chloride and bicarbonate, the anions that permeate the GABA
A
ionophore. Because this depolarization diminishes the voltage-dependent block of the
N
-methyl-D-aspartate (NMDA) receptor by magnesium, the activity-dependent depolarization mediated by GABA is sufficient to account for frequency modulation of synaptic NMDA receptor activation. Anionic gradient shifts may represent a mechanism whereby the rate and coherence of synaptic activity determine whether dendritic GABA
A
receptor activation is excitatory or inhibitory.
Recurrent Excitation in Neocortical Circuits
Authors: Douglas Rodney J. , Koch Christof , Mahowald Misha , Martin Kevan A. C. , Suarez Humbert H.
Published: October 2006

The majority of synapses in the mammalian cortex originate from cortical neurons. Indeed, the largest input to cortical cells comes from neighboring excitatory cells. However, most models of cortical development and processing do not reflect the anatomy and physiology of feedback excitation and are restricted to serial feedforward excitation. This report describes how populations of neurons in cat visual cortex can use excitatory feedback, characterized as an effective "network conductance", to amplify their feedforward input signals and demonstrates how neuronal discharge can be kept proportional to stimulus strength despite strong, recurrent connections that threaten to cause runaway excitation. These principles are incorporated into models of cortical direction and orientation selectivity that emphasize the basic design principles of cortical architectures.
Structures of Metal Sites of Oxidized Bovine Heart Cytochrome c Oxidase at 2.8 Å
Authors: Tsukihara Tomitake , Aoyama Hiroshi , Yamashita Eiki , Tomizaki Takashi , Yamaguchi Hiroshi , Shinzawa-Itoh Kyoko , Nakashima Ryosuke , Yaono Rieko , Yoshikawa Shinya
Published: October 2006

The high resolution three-dimensional x-ray structure of the metal sites of bovine heart cytochrome c oxidase is reported. Cytochrome c oxidase is the largest membrane protein yet crystallized and analyzed at atomic resolution. Electron density distribution of the oxidized bovine cytochrome c oxidase at 2.8 Å resolution indicates a dinuclear copper center with an unexpected structure similar to a [2Fe-2S]-type iron-sulfur center. Previously predicted zinc and magnesium sites have been located, the former bound by a nuclear encoded subunit on the matrix side of the membrane, and the latter situated between heme a
3
and Cu
A
, at the interface of subunits I and II. The O
2
binding site contains heme a
3
iron and copper atoms (Cu
B
) with an interatomic distance of 4.5 Å; there is no detectable bridging ligand between iron and copper atoms in spite of a strong antiferromagnetic coupling between them. A hydrogen bond is present between a hydroxyl group of the hydroxyfarnesylethyl side chain of heme a
3
and an OH of a tyrosine. The tyrosine phenol plane is immediately adjacent and perpendicular to an imidazole group bonded to Cu
B
, suggesting a possible role in intramolecular electron transfer or conformational control, the latter of which could induce the redox-coupled proton pumping. A phenyl group located halfway between a pyrrole plane of the heme a
3
and an imidazole plane liganded to the other heme (heme a) could also influence electron transfer or conformational control.
Adaptive Evolution of Color Vision Genes in Higher Primates
Authors: Shyue Song-Kun , Hewett-Emmett David , Sperling Harry G. , Hunt David M. , Bowmaker James K. , Mollon John D. , Li Wen-Hsiung
Published: October 2006

The intron 4 sequences of the three polymorphic alleles at the X-linked color photo-pigment locus in the squirrel monkey and the marmoset reveal that the alleles in each species are exceptionally divergent. The data further suggest either that each triallelic system has arisen independently in these two New World monkey lineages, or that in each species at least seven deletions and insertions (14 in the two species) in intron 4 have been transferred and homogenized among the alleles by gene conversion or recombination. In either case, the alleles in each species apparently have persisted more than 5 million years and probably have been maintained by overdominant selection.
An Essential Role for Rho, Rac, and Cdc42 GTPases in Cell Cycle Progression Through G
1
Authors: Olson Michael F. , Ashworth Alan , Hall Alan
Published: October 2006

Members of the Rho family of small guanosine triphosphatases (GTPases) regulate the organization of the actin cytoskeleton; Rho controls the assembly of actin stress fibers and focal adhesion complexes, Rac regulates actin filament accumulation at the plasma membrane to produce lamellipodia and membrane ruffles, and Cdc42 stimulates the formation of filopodia. When microinjected into quiescent fibroblasts, Rho, Rac, and Cdc42 stimulated cell cycle progression through G1 and subsequent DNA synthesis. Furthermore, microinjection of dominant negative forms of Rac and Cdc42 or of the Rho inhibitor C3 transferase blocked serum-induced DNA synthesis. Unlike Ras, none of the Rho GTPases activated the mitogen-activated protein kinase (MAPK) cascade that contains the protein kinases c-Raf1, MEK (MAPK or ERK kinase), and ERK (extracellular signal-regulated kinase). Instead, Rac and Cdc42, but not Rho, stimulated a distinct MAP kinase, the c-Jun kinase JNK/SAPK (Jun NH
2
-terminal kinase or stress-activated protein kinase). Rho, Rac, and Cdc42 control signal transduction pathways that are essential for cell growth.
A p16
INK4a
-Insensitive CDK4 Mutant Targeted by Cytolytic T Lymphocytes in a Human Melanoma
Authors: Wölfel Thomas , Hauer Martina , Schneider Jörg , Serrano Manuel , Wölfel Catherine , Klehmann-Hieb Eva , De Plaen Etienne , Hankeln Thomas , Meyer zum Büschenfelde Karl-Hermann , Beach David
Published: October 2006

A mutated cyclin-dependent kinase 4 (CDK4) was identified as a tumor-specific antigen recognized by HLA-A2. 1-restricted autologous cytolytic T lymphocytes (CTLs) in a human melanoma. The mutated CDK4 allele was present in autologous cultured melanoma cells and metastasis tissue, but not in the patient's lymphocytes. The mutation, an arginine-to-cysteine exchange at residue 24, was part of the CDK4 peptide recognized by CTLs and prevented binding of the CDK4 inhibitor p16
INK4a
, but not of p21 or of p27
KIP1
. The same mutation was found in one additional melanoma among 28 melanomas analyzed. These results suggest that mutation of CDK4 can create a tumor-specific antigen and can disrupt the cell-cycle regulation exerted by the tumor suppressor p16
INK4a
.