bluuebunny/crossref_metadata_2025 huggingface dataset:
Visual- and saccade-related signals in the primate inferior colliculus
Authors: Porter Kristin Kelly , Metzger Ryan R. , Groh Jennifer M.
Published: November 2007

The inferior colliculus (IC) is normally thought of as a predominantly auditory structure because of its early position in the ascending auditory pathway just before the auditory thalamus. Here, we show that a majority of IC neurons (64% of 180 neurons) in awake monkeys carry visual- and/or saccade-related signals in addition to their auditory responses (
P
< 0.05). The response patterns involve primarily excitatory visual responses, but also increased activity time-locked to the saccade, slow rises in activity time-locked to the onset of the visual stimulus, and inhibitory responses. The presence of these visual-related signals suggests that the IC plays a role in integrating visual and auditory information. More broadly, our results show that interactions between sensory pathways can occur at very early points in sensory processing streams, which implies that multisensory integration may be a low-level rather than an exclusively high-level process.
Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin
Authors: Zhang Bin W. , Jasnow David , Zuckerman Daniel M.
Published: November 2007

The computational sampling of rare, large-scale, conformational transitions in proteins is a well appreciated challenge—for which a number of potentially efficient path-sampling methodologies have been proposed. Here, we study a large-scale transition in a united-residue model of calmodulin using the “weighted ensemble” (WE) approach of Huber and Kim. Because of the model's relative simplicity, we are able to compare our results with brute-force simulations. The comparison indicates that the WE approach quantitatively reproduces the brute-force results, as assessed by considering (
i
) the reaction rate, (
ii
) the distribution of event durations, and (
iii
) structural distributions describing the heterogeneity of the paths. Importantly, the WE method is readily applied to more chemically accurate models, and by studying a series of lower temperatures, our results suggest that the WE method can increase efficiency by orders of magnitude in more challenging systems.
JY-1
, an oocyte-specific gene, regulates granulosa cell function and early embryonic development in cattle
Authors: Bettegowda Anilkumar , Yao Jianbo , Sen Aritro , Li Qinglei , Lee Kyung-Bon , Kobayashi Yasuhiro , Patel Osman V. , Coussens Paul M. , Ireland James J. , Smith George W.
Published: November 2007

Oocyte-specific gene products play a key role in regulation of fertility in mammals. Here, we describe the discovery, molecular characterization, and function of
JY-1
, a bovine oocyte-expressed gene shown to regulate both function of ovarian granulosa cells and early embryogenesis in cattle and characteristics of
JY-1
loci in other species. The
JY-1
gene encodes for a secreted protein with multiple mRNA transcripts containing an identical ORF but differing lengths of 3′ UTR. JY-1 mRNA and protein are oocyte-specific and detectable throughout folliculogenesis. Recombinant JY-1 protein regulates function of follicle-stimulating hormone-treated ovarian granulosa cells, resulting in enhanced progesterone synthesis accompanied by reduced cell numbers and estradiol production. JY-1 mRNA of maternal origin is also present in early bovine embryos, temporally regulated during the window from meiotic maturation through embryonic genome activation, and is required for blastocyst development. The
JY-1
gene has three exons and is located on bovine chromosome 29.
JY-1
-like sequences are present on syntenic chromosomes of other vertebrate species, but lack exons 1 and 2, including the protein-coding region, suggestive of species specificity in evolution and function of this oocyte-specific gene.
Loss of luminal Ca
2+
activation in the cardiac ryanodine receptor is associated with ventricular fibrillation and sudden death
Authors: Jiang Dawei , Chen Wenqian , Wang Ruiwu , Zhang Lin , Chen S. R. Wayne
Published: November 2007

Different forms of ventricular arrhythmias have been linked to mutations in the cardiac ryanodine receptor (RyR)2, but the molecular basis for this phenotypic heterogeneity is unknown. We have recently demonstrated that an enhanced sensitivity to luminal Ca
2+
and an increased propensity for spontaneous Ca
2+
release or store-overload-induced Ca
2+
release (SOICR) are common defects of RyR2 mutations associated with catecholaminergic polymorphic or bidirectional ventricular tachycardia. Here, we investigated the properties of a unique RyR2 mutation associated with catecholaminergic idiopathic ventricular fibrillation, A4860G. Single-channel analyses revealed that, unlike all other disease-linked RyR2 mutations characterized previously, the A4860G mutation diminished the response of RyR2 to activation by luminal Ca
2+
, but had little effect on the sensitivity of the channel to activation by cytosolic Ca
2+
. This specific impact of the A4860G mutation indicates that the luminal Ca
2+
activation of RyR2 is distinct from its cytosolic Ca
2+
activation. Stable, inducible HEK293 cells expressing the A4860G mutant showed caffeine-induced Ca
2+
release but exhibited no SOICR. Importantly, HL-1 cardiac cells transfected with the A4860G mutant displayed attenuated SOICR activity compared with cells transfected with RyR2 WT. These observations provide the first evidence that a loss of luminal Ca
2+
activation and SOICR activity can cause ventricular fibrillation and sudden death. These findings also indicate that although suppressing enhanced SOICR is a promising antiarrhythmic strategy, its oversuppression can also lead to arrhythmias.
Bio-foam enhances larval retention in a free-spawning marine tunicate
Authors: Castilla Juan Carlos , Manríquez Patricio H. , Delgado Alejandro P. , Gargallo Ligia , Leiva Angel , Radic Deodato
Published: November 2007

Here we report a mechanism that reduces dispersal of early developing stages and larvae in a free-spawning intertidal and shallow subtidal tunicate,
Pyura praeputialis
(Heller 1878), in the Bay of Antofagasta, Chile. The spawning of gametes by the tunicate into the naturally turbulent aerated seawater decreases their surface tension and induces the formation of a bio-foam. Water collected from foamy intertidal pools and tide channels showed a high concentration of
P. praeputialis
early developing stages and tadpole larvae in the foam. Because gametes are synchronically spawned for external fertilization and larvae settle near adults, our results suggest that this bio-foam increases fertilization success and effective settlement of their short-lived larvae in the vicinity of the adults spawning the gametes. This mechanism reinforces published evidence suggesting that local retention of intertidal and inshore marine invertebrate larvae may be more common than previously thought, offering, for instance, new perspectives for the design and networking of marine protected and management areas.
Designer enediynes generate DNA breaks, interstrand cross-links, or both, with concomitant changes in the regulation of DNA damage responses
Authors: Kennedy Daniel R. , Ju Jianhua , Shen Ben , Beerman Terry A.
Published: November 2007

The ability of the radiomimetic anticancer enediyne C-1027 to induce ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR)-independent damage responses was discovered to reside in its unique ability to concurrently generate robust amounts of double-strand breaks (DSBs) and interstrand cross-links (ICLs) in cellular DNA. Furthermore, a single substitution to the chromophore's benzoxazolinate moiety shifted DNA damage to primarily ICLs and an ATR- but not ATM-dependent damage response. In contrast, single substitutions of the chromophore's β-amino acid component shifted DNA damage to primarily DSBs, consistent with its induction of conventional ATM-dependent damage responses of the type generated by ionizing radiation and other radiomimetics. Thus, phosphatidylinositol 3-kinase-like protein kinase regulation of DNA damage responses is dictated by the relative proportions of DSBs and ICLs.
Statistical evaluation of alternative models of human evolution
Authors: Fagundes Nelson J. R. , Ray Nicolas , Beaumont Mark , Neuenschwander Samuel , Salzano Francisco M. , Bonatto Sandro L. , Excoffier Laurent
Published: November 2007

An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the
Homo
genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species ≈141 thousand years ago (Kya), an exit out-of-Africa ≈51 Kya, and a recent colonization of the Americas ≈10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with
Homo erectus
.
Identification of teosinte, maize, and
Tripsacum
in Mesoamerica by using pollen, starch grains, and phytoliths
Authors: Holst Irene , Moreno J. Enrique , Piperno Dolores R.
Published: November 2007

We examined pollen grains and starch granules from a large number of modern populations of teosinte (wild
Zea
spp.), maize (
Zea
mays L.), and closely related grasses in the genus
Tripsacum
to assess their strengths and weaknesses in studying the origins and early dispersals of maize in its Mesoamerican cradle of origin. We report new diagnostic criteria and question the accuracy of others used previously by investigators to identify ancient maize where its wild ancestor, teosinte, is native. Pollen grains from teosinte overlap in size with those of maize to a much greater degree than previously reported, making the differentiation of wild and domesticated maize in palynological studies difficult. There is presently no valid method for separating maize and teosinte pollen on a morphological basis. Starch grain analysis, a recently developed tool of archaeobotany, appears to be of significant utility in distinguishing the seeds of teosinte from maize. We propose that the differences in starch grain morphology and size between wild and domesticated maize defined in this study may be associated with domestication genes in
Zea
that have been documented in the starch biosynthesis pathway. As previously reported, phytoliths effectively discriminate the female reproductive structures of
Tripsacum
, teosinte, and maize. Multiproxy microfossil studies of archaeological and paleoecological contexts appear to be effective tools for investigating the earliest stages of maize domestication and dispersals.
Duplication and segregation of the actin (MreB) cytoskeleton during the prokaryotic cell cycle
Authors: Vats Purva , Rothfield Lawrence
Published: November 2007

The bacterial actin homolog MreB exists as a single-copy helical cytoskeletal structure that extends between the two poles of rod-shaped bacteria. In this study, we show that equipartition of the MreB cytoskeleton into daughter cells is accomplished by division and segregation of the helical MreB array into two equivalent structures located in opposite halves of the predivisional cell. This process ensures that each daughter cell inherits one copy of the MreB cytoskeleton. The process is triggered by the membrane association of the FtsZ cell division protein. The cytoskeletal division and segregation events occur before and independently of cytokinesis and involve specialized MreB structures that appear to be intermediates in this process.
Human capping enzyme promotes formation of transcriptional R loops
in vitro
Authors: Kaneko Syuzo , Chu Chun , Shatkin Aaron J. , Manley James L.
Published: November 2007

Cap formation is the first step of pre-mRNA processing in eukaryotic cells. Immediately after transcription initiation, capping enzyme (CE) is recruited to RNA polymerase II (Pol II) by the phosphorylated carboxyl-terminal domain of the Pol II largest subunit (CTD), allowing cotranscriptional capping of the nascent pre-mRNA. Recent studies have indicated that CE affects transcription elongation and have suggested a checkpoint model in which cotranscriptional capping is a necessary step for the early phase of transcription. To investigate further the role of the CTD in linking transcription and processing, we generated a fusion protein of the mouse CTD with T7 RNA polymerase (CTD-T7 RNAP). Unexpectedly,
in vitro
transcription assays with CTD-T7 RNAP showed that CE promotes formation of DNA·RNA hybrids or R loops. Significantly, phosphorylation of the CTD was required for CE-dependent R-loop formation (RLF), consistent with a critical role for the CTD in CE recruitment to the transcription complex. The guanylyltransferase domain was necessary and sufficient for RLF, but catalytic activity was not required.
In vitro
assays with appropriate synthetic substrates indicate that CE can promote RLF independent of transcription. ASF/SF2, a splicing factor known to prevent RLF, and GTP, which affects CE conformation, antagonized CE-dependent RLF. Our findings suggest that CE can play a direct role in transcription by modulating displacement of nascent RNA during transcription.
Symmetry breaking and quantum correlations in finite systems: studies of quantum dots and ultracold Bose gases and related nuclear and chemical methods
Authors: Yannouleas Constantine , Landman Uzi
Published: November 2007

Investigations of emergent symmetry breaking phenomena occurring in small finite-size systems are reviewed, with a focus on the strongly correlated regime of electrons in two-dimensional semiconductor quantum dots and trapped ultracold bosonic atoms in harmonic traps. Throughout the review we emphasize universal aspects and similarities of symmetry breaking found in these systems, as well as in more traditional fields like nuclear physics and quantum chemistry, which are characterized by very different interparticle forces. A unified description of strongly correlated phenomena in finite systems of repelling particles (whether fermions or bosons) is presented through the development of a two-step method of symmetry breaking at the unrestricted Hartree–Fock level and of subsequent symmetry restoration via post Hartree–Fock projection techniques. Quantitative and qualitative aspects of the two-step method are treated and validated by exact diagonalization calculations.

Strongly-correlated phenomena emerging from symmetry breaking include the following.

Chemical bonding, dissociation and entanglement (at zero and finite magnetic fields) in quantum dot molecules and in pinned electron molecular dimers formed within a single anisotropic quantum dot, with potential technological applications to solid-state quantum-computing devices.

Electron crystallization, with particle localization on the vertices of concentric polygonal rings, and formation of rotating electron molecules (REMs) in circular quantum dots. Such electron molecules exhibit ro-vibrational excitation spectra, in analogy with natural molecules.

At high magnetic fields, the REMs are described by parameter-free analytic wave functions, which are an alternative to the Laughlin and composite-fermion approaches, offering a new point of view of the fractional quantum Hall regime in quantum dots (with possible implications for the thermodynamic limit).

Crystalline phases of strongly repelling bosons. In rotating traps and in analogy with the REMs, such repelling bosons form rotating boson molecules (RBMs). For a small number of bosons, the RBMs are energetically favored compared with the Gross–Pitaevskii solutions describing vortex formation.

We discuss the present status concerning experimental signatures of such strongly correlated states, in view of the promising outlook created by the latest experimental improvements that are achieving unprecedented control over the range and strength of interparticle interactions.
Cholecystokinin Activates Pancreatic Calcineurin-NFAT Signaling In Vitro and In Vivo
Authors: Gurda Grzegorz T. , Guo LiLi , Lee Sae-Hong , Molkentin Jeffery D. , Williams John A.
Published: November 2007

Elevated endogenous cholecystokinin (CCK) release induced by protease inhibitors leads to pancreatic growth. This response has been shown to be mediated by the phosphatase calcineurin, but its downstream effectors are unknown. Here we examined activation of calcineurin-regulated nuclear factor of activated T-cells (NFATs) in isolated acinar cells, as well as in an in vivo model of pancreatic growth. Western blotting of endogenous NFATs and confocal imaging of NFATc1-GFP in pancreatic acini showed that CCK dose-dependently stimulated NFAT translocation from the cytoplasm to the nucleus within 0.5–1 h. This shift in localization correlated with CCK-induced activation of NFAT-driven luciferase reporter and was similar to that induced by a calcium ionophore and constitutively active calcineurin. The effect of CCK was dependent on calcineurin, as these changes were blocked by immunosuppressants FK506 and CsA and by overexpression of the endogenous protein inhibitor CAIN. Parallel NFAT activation took place in vivo. Pancreatic growth was accompanied by an increase in nuclear NFATs and subsequent elevation in expression of NFAT-luciferase in the pancreas, but not in organs unresponsive to CCK. The changes also required calcineurin, as they were blocked by FK506. We conclude that CCK activates NFATs in a calcineurin-dependent manner, both in vitro and in vivo.
S100A11, an Dual Mediator for Growth Regulation of Human Keratinocytes
Authors: Sakaguchi Masakiyo , Sonegawa Hiroyuki , Murata Hitoshi , Kitazoe Midori , Futami Jun-ichiro , Kataoka Ken , Yamada Hidenori , Huh Nam-ho
Published: November 2007

We previously revealed a novel signal pathway involving S100A11 for inhibition of the growth of normal human keratinocytes (NHK) caused by high Ca++or transforming growth factor β. Exposure to either agent resulted in transfer of S100A11 to nuclei, where it induced p21WAF1. In contrast, S100A11 has been shown to be overexpressed in many human cancers. To address this apparent discrepancy, we analyzed possible new functions of S100A11, and we provide herein evidence that 1) S100A11 is actively secreted by NHK; 2) extracellular S100A11 acts on NHK to enhance the production of epidermal growth factor family proteins, resulting in growth stimulation; 3) receptor for advanced glycation end products, nuclear factor-κB, Akt, and cAMP response element-binding protein are involved in the S100A11-triggered signal transduction; and 4) production and secretion of S100A11 are markedly enhanced in human squamous cancer cells. These findings indicate that S100A11 plays a dual role in growth regulation of epithelial cells.
The Peripheral Membrane Subunits of the SAM Complex Function Codependently in Mitochondrial Outer Membrane Biogenesis
Authors: Chan Nickie C. , Lithgow Trevor
Published: November 2007

The sorting and assembly machinery (SAM) complex functions in the assembly of β-barrel proteins into the mitochondrial outer membrane. It is related to the Omp85/YaeT machinery in bacterial outer membranes, but the eukaryotic SAM complex is distinguished by two peripheral subunits, Sam37 and Sam35, that sit on the cytosolic face of the complex. The function of these subunits in β-barrel protein assembly is currently unclear. By screening a library of sam35 mutants, we show that 13 distinct alleles were each specifically suppressed by overexpression of SAM37. Two of these mutants, sam35-409 and sam35-424, show distinct phenotypes that enable us to distinguish the function of Sam35 from that of Sam37. Sam35 is required for the SAM complex to bind outer membrane substrate proteins: destabilization of Sam35 inhibits substrate binding by Sam50. Sam37 acts later than Sam35, apparently to assist release of substrates from the SAM complex. Very different environments surround bacteria and mitochondria, and we discuss the role of Sam35 and Sam37 in terms of the problems peculiar to mitochondrial protein substrates.
A Motif in the Clathrin Heavy Chain Required for the Hsc70/Auxilin Uncoating Reaction
Authors: Rapoport Iris , Boll Werner , Yu Anan , Böcking Till , Kirchhausen Tom
Published: November 2007

The 70-kDa heat-shock cognate protein (Hsc70) chaperone is an ATP-dependent “disassembly enzyme” for many subcellular structures, including clathrin-coated vesicles where it functions as an uncoating ATPase. Hsc70, and its cochaperone auxilin together catalyze coat disassembly. Like other members of the Hsp70 chaperone family, it is thought that ATP-bound Hsc70 recognizes the clathrin triskelion through an unfolded exposed hydrophobic segment. The best candidate is the unstructured C terminus (residues 1631–1675) of the heavy chain at the foot of the tripod below the hub, containing the sequence motif QLMLT, closely related to the sequence bound preferentially by the substrate groove of Hsc70 ( Fotin et al., 2004b ). To test this hypothesis, we generated in insect cells recombinant mammalian triskelions that in vitro form clathrin cages and clathrin/AP-2 coats exactly like those assembled from native clathrin. We show that coats assembled from recombinant clathrin are good substrates for ATP- and auxilin-dependent, Hsc70-catalyzed uncoating. Finally, we show that this uncoating reaction proceeds normally when the coats contain recombinant heavy chains truncated C-terminal to the QLMLT motif, but very inefficiently when the motif is absent. Thus, the QLMLT motif is required for Hsc-70–facilitated uncoating, consistent with the proposal that this sequence is a specific target of the chaperone.
The Structure of the γ-Tubulin Small Complex: Implications of Its Architecture and Flexibility for Microtubule Nucleation
Authors: Kollman Justin M. , Zelter Alex , Muller Eric G.D. , Fox Bethany , Rice Luke M. , Davis Trisha N. , Agard David A.
Published: November 2007

The γ-tubulin small complex (γ-TuSC) is an evolutionarily conserved heterotetramer essential for microtubule nucleation. We have determined the structure of the Saccharomyces cerevisiae γ-TuSC at 25-Å resolution by electron microscopy. γ-TuSC is Y-shaped, with an elongated body connected to two arms. Gold labeling showed that the two γ-tubulins are located in lobes at the ends of the arms, and the relative orientations of the other γ-TuSC components were determined by in vivo FRET. The structures of different subpopulations of γ-TuSC indicate flexibility in the connection between a mobile arm and the rest of the complex, resulting in variation of the relative positions and orientations of the γ-tubulins. In all of the structures, the γ-tubulins are distinctly separated, a configuration incompatible with the microtubule lattice. The separation of the γ-tubulins in isolated γ-TuSC likely plays a role in suppressing its intrinsic microtubule-nucleating activity, which is relatively weak until the γ-TuSC is incorporated into higher order complexes or localized to microtubule-organizing centers. We propose that further movement of the mobile arm is required to bring the γ-tubulins together in microtubule-like interactions, and provide a template for microtubule growth.
Regulation of Rtt107 Recruitment to Stalled DNA Replication Forks by the Cullin Rtt101 and the Rtt109 Acetyltransferase
Authors: Roberts Tania M. , Zaidi Iram Waris , Vaisica Jessica A. , Peter Matthias , Brown Grant W.
Published: November 2007

RTT107 (ESC4, YHR154W) encodes a BRCA1 C-terminal domain protein that is important for recovery from DNA damage during S phase. Rtt107 is a substrate of the checkpoint kinase Mec1, and it forms complexes with DNA repair enzymes, including the nuclease subunit Slx4, but the role of Rtt107 in the DNA damage response remains unclear. We find that Rtt107 interacts with chromatin when cells are treated with compounds that cause replication forks to arrest. This damage-dependent chromatin binding requires the acetyltransferase Rtt109, but it does not require acetylation of the known Rtt109 target, histone H3-K56. Chromatin binding of Rtt107 also requires the cullin Rtt101, which seems to play a direct role in Rtt107 recruitment, because the two proteins are found in complex with each other. Finally, we provide evidence that Rtt107 is bound at or near stalled replication forks in vivo. Together, these results indicate that Rtt109, Rtt101, and Rtt107, which genetic evidence suggests are functionally related, form a DNA damage response pathway that recruits Rtt107 complexes to damaged or stalled replication forks.
Pepitope: epitope mapping from affinity-selected peptides
Authors: Mayrose Itay , Penn Osnat , Erez Elana , Rubinstein Nimrod D. , Shlomi Tomer , Freund Natalia Tarnovitski , Bublil Erez M. , Ruppin Eytan , Sharan Roded , Gershoni Jonathan M. , Martz Eric , Pupko Tal
Published: November 2007

Identifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein–protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure.

Availability:  http://pepitope.tau.ac.il/

Contact:  talp@post.tau.ac.il
Accurate prediction of enzyme mutant activity based on a multibody statistical potential
Authors: Masso Majid , Vaisman Iosif I.
Published: November 2007

Motivation: An important area of research in biochemistry and molecular biology focuses on characterization of enzyme mutants. However, synthesis and analysis of experimental mutants is time consuming and expensive. We describe a machine-learning approach for inferring the activity levels of all unexplored single point mutants of an enzyme, based on a training set of such mutants with experimentally measured activity.

Results: Based on a Delaunay tessellation-derived four-body statistical potential function, a perturbation vector measuring environmental changes relative to wild type (wt) at every residue position uniquely characterizes each enzyme mutant for model development and prediction. First, a measure of model performance utilizing area (AUC) under the receiver operating characteristic (ROC) curve surpasses 0.83 and 0.77 for data sets of experimental HIV-1 protease and T4 lysozyme mutants, respectively. Additionally, a novel method is introduced for evaluating statistical significance associated with the number of correct test set predictions obtained from a trained model. Third, 100 stratified random splits of the protease and T4 lysozyme mutant data sets into training and test sets achieve 77.0% and 80.8% mean accuracy, respectively. Next, protease and T4 lysozyme models trained with experimental mutants are used to predict activity levels for all remaining mutants; a subsequent search for publications reporting on dozens of these test mutants reveals that experimental results are matched by 79% and 86% of predictions, respectively. Finally, learning curves for each mutant enzyme system indicate the influence of training set size on model performance.

Availability: Prediction databases at http://proteins.gmu.edu/automute/

Contact:  ivaisman@gmu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Graph sharpening plus graph integration: a synergy that improves protein functional classification
Authors: Shin Hyunjung , Lisewski Andreas Martin , Lichtarge Olivier
Published: November 2007

Motivation: Predicting protein function is a central problem in bioinformatics, and many approaches use partially or fully automated methods based on various combination of sequence, structure and other information on proteins or genes. Such information establishes relationships between proteins that can be modelled most naturally as edges in graphs. A priori, however, it is often unclear which edges from which graph may contribute most to accurate predictions. For that reason, one established strategy is to integrate all available sources, or graphs as in graph integration, in the hope that the positive signals will add to each other. However, in the problem of functional prediction, noise, i.e. the presence of inaccurate or false edges, can still be large enough that integration alone has little effect on prediction accuracy. In order to reduce noise levels and to improve integration efficiency, we present here a recent method in graph-based learning, graph sharpening, which provides a theoretically firm yet intuitive and practical approach for disconnecting undesirable edges from protein similarity graphs. This approach has several attractive features: it is quick, scalable in the number of proteins, robust with respect to errors and tolerant of very diverse types of protein similarity measures.

Results: We tested the classification accuracy in a test set of 599 proteins with remote sequence homology spread over 20 Gene Ontology (GO) functional classes. When compared to integration alone, graph sharpening plus integration of four vastly different molecular similarity measures improved the overall classification by nearly 30% [0.17 average increase in the area under the ROC curve (AUC)]. Moreover, and partially through the increased sparsity of the graphs induced by sharpening, this gain in accuracy came at negligible computational cost: sharpening and integration took on average 4.66 (±4.44) CPU seconds.

Availability: Software and Supplementary data will be available on http://mammoth.bcm.tmc.edu/

Contact:  shin@ajou.ac.kr or lisewski@bcm.edu

Supplementary information: Supplementary materials are available at Bioinformatics online.
Ensemble learning of genetic networks from time-series expression data
Authors: Nam Dougu , Yoon Sung Ho , Kim Jihyun F.
Published: November 2007

Motivation: Inferring genetic networks from time-series expression data has been a great deal of interest. In most cases, however, the number of genes exceeds that of data points which, in principle, makes it impossible to recover the underlying networks. To address the dimensionality problem, we apply the subset selection method to a linear system of difference equations. Previous approaches assign the single most likely combination of regulators to each target gene, which often causes over-fitting of the small number of data.

Results: Here, we propose a new algorithm, named LEARNe, which merges the predictions from all the combinations of regulators that have a certain level of likelihood. LEARNe provides more accurate and robust predictions than previous methods for the structure of genetic networks under the linear system model. We tested LEARNe for reconstructing the SOS regulatory network of Escherichia coli and the cell cycle regulatory network of yeast from real experimental data, where LEARNe also exhibited better performances than previous methods.

Availability: The MATLAB codes are available upon request from the authors.

Contact:  dunam@nims.re.kr or jfk@kribb.re.kr
A computational strategy for the prediction of functional linear peptide motifs in proteins
Authors: Dinkel Holger , Sticht Heinrich
Published: November 2007

Motivation: Short linear peptide motifs mediate protein–protein interaction, cell compartment targeting and represent the sites of post-translational modification. The identification of functional motifs by conventional sequence searches, however, is hampered by the short length of the motifs resulting in a large number of hits of which only a small portion is functional.

Results: We have developed a procedure for the identification of functional motifs, which scores pattern conservation in homologous sequences by taking explicitly into account the sequence similarity to the query sequence. For a further improvement of this method, sequence filters have been optimized to mask those sequence regions containing little or no linear motifs. The performance of this approach was verified by measuring its ability to identify 576 experimentally validated motifs among a total of 15 563 instances in a set of 415 protein sequences. Compared to a random selection procedure, the joint application of sequence filters and the novel scoring scheme resulted in a 9-fold enrichment of validated functional motifs on the first rank. In addition, only half as many hits need to be investigated to recover 75% of the functional instances in our dataset. Therefore, this motif-scoring approach should be helpful to guide experiments because it allows focusing on those short linear peptide motifs that have a high probability to be functional.

Contact:  h.sticht@biochem.uni-erlangen.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Precisely wrong or vaguely right: simulations of noisy discard data and trends in fishing effort being included in the stock assessment of North Sea plaice
Authors: Dickey-Collas Mark , Pastoors Martin A. , van Keeken Olvin A.
Published: November 2007

Dickey-Collas, M., Pastoors, M. A, and van Keeken, O. A. 2007. Precisely wrong or vaguely right: simulations of noisy discard data and trends in fishing effort being included in the stock assessment of North Sea plaice. – ICES Journal of Marine Science, 64: 000–000. ICES stock assessments of North Sea plaice are routinely carried out with eXtended Survivors Analysis (XSA), based on landings and survey data. Recently, the assessments included data on discarded young fish, sampled with high variance. Fishing effort has been declining since the mid-1990s, so conditioning the estimated fishing mortality (F) on the recent past could introduce bias into the perceived stock size. Simulated populations with North Sea plaice-like characteristics are used to explore the dependence of the perceived stock dynamics on the inclusion of discards data at different sampling noise, using the same methods and XSA settings as ICES. The sensitivities of the results were tested against different trends in fishing effort and recruitment, and different scenarios for “shrinkage” (i.e. the way in which the past is used to estimate the most recent fishing mortality). Within the bounds of the simulation assumptions, the perception of population trends from an XSA stock assessment can be biased when there are trends in fishing effort: decreasing effort leads to underestimating SSB and overestimating F. When discards are not included, bias in SSB is greatest when effort decreases, and bias in F is greatest when effort increases. Bias in SSB and F were removed by including discard data, but at substantial loss of precision. If effort shows a clear trend and discards are substantial and estimated noisily, the recent trend in the target population may be hard to track with an XSA-type assessment methodology.
Focusing the view on nature's water-splitting catalyst
Authors: Zein Samir , Kulik Leonid V , Yano Junko , Kern Jan , Pushkar Yulia , Zouni Athina , Yachandra Vittal K , Lubitz Wolfgang , Neese Frank , Messinger Johannes
Published: November 2007

Nature invented a catalyst about 3 Gyr ago, which splits water with high efficiency into molecular oxygen and hydrogen equivalents (protons and electrons). This reaction is energetically driven by sunlight and the active centre contains relatively cheap and abundant metals: manganese and calcium. This biological system therefore forms the paradigm for all man-made attempts for direct solar fuel production, and several studies are underway to determine the electronic and geometric structures of this catalyst. In this report we briefly summarize the problems and the current status of these efforts and propose a density functional theory-based strategy for obtaining a reliable high-resolution structure of this unique catalyst that includes both the inorganic core and the first ligand sphere.
On the structure of the manganese complex of photosystem II: extended-range EXAFS data and specific atomic-resolution models for four S-states
Authors: Dau Holger , Grundmeier Alexander , Loja Paola , Haumann Michael
Published: November 2007

The water-oxidizing manganese complex bound to the proteins of photosystem II (PSII) was studied by X-ray absorption spectroscopy on PSII membrane particles. An extended range for collection of extended X-ray absorption fine-structure (EXAFS) data was used (up to 16.6 Å
−1
). The EXAFS suggests the presence of two Mn–Mn distances close to 2.7 Å (per Mn
4
Ca complex); the existence of a third Mn–Mn distance below 2.9 Å is at least uncertain. Interestingly, a distance of 3.7 Å is clearly resolved in the extended-range data and tentatively assigned to a Mn–Mn distance. Taking into account the above EXAFS results (inter alia), we present a model for the structure of the PSII manganese complex, which differs from previous atomic-resolution models. Emphasizing the hypothetical character, we propose for all semi-stable S-states: (i) a structure of the Mn
4
Ca(μ-O)

n

core, (ii) a model of the amino acid environment, and (iii) assignments of distinct Mn oxidation states to all the individual Mn ions. This specific working model may permit discussion, verification and invalidation of its various features in comparison with experimental and theoretical findings.
The functional interplay between EGFR overexpression, hTERT activation, and p53 mutation in esophageal epithelial cells with activation of stromal fibroblasts induces tumor development, invasion, and differentiation
Authors: Okawa Takaomi , Michaylira Carmen Z. , Kalabis Jiri , Stairs Douglas B. , Nakagawa Hiroshi , Andl Claudia , Johnstone Cameron N. , Klein-Szanto Andres J. , El-Deiry Wafik S. , Cukierman Edna , Herlyn Meenhard , Rustgi Anil K.
Published: November 2007

Esophageal cancer is a prototypic squamous cell cancer that carries a poor prognosis, primarily due to presentation at advanced stages. We used human esophageal epithelial cells as a platform to recapitulate esophageal squamous cell cancer, thereby providing insights into the molecular pathogenesis of squamous cell cancers in general. This was achieved through the retroviral-mediated transduction into normal, primary human esophageal epithelial cells of epidermal growth factor receptor (EGFR), the catalytic subunit of human telomerase (hTERT), and p53R175H, genes that are frequently altered in human esophageal squamous cell cancer. These cells demonstrated increased migration and invasion when compared with control cells. When these genetically altered cells were placed within the in vivo-like context of an organotypic three-dimensional (3D) culture system, the cells formed a high-grade dysplastic epithelium with malignant cells invading into the stromal extracellular matrix (ECM). The invasive phenotype was in part modulated by the activation of matrix metalloproteinase-9 (MMP-9). Using pharmacological and genetic approaches to decrease MMP-9, invasion into the underlying ECM could be suppressed partially. In addition, tumor differentiation was influenced by the type of fibroblasts within the stromal ECM. To that end, fetal esophageal fibroblasts fostered a microenvironment conducive to poorly differentiated invading tumor cells, whereas fetal skin fibroblasts supported a well-differentiated tumor as illustrated by keratin “pearl” formation, a hallmark feature of well-differentiated squamous cell cancers. When inducible AKT was introduced into fetal skin esophageal fibroblasts, a more invasive, less-differentiated esophageal cancer phenotype was achieved. Invasion into the stromal ECM was attenuated by genetic knockdown of AKT1 as well as AKT2. Taken together, alterations in key oncogenes and tumor suppressor genes in esophageal epithelial cells, the composition and activation of fibroblasts, and the components of the ECM conspire to regulate the physical and biological properties of the stroma.
The TR2 and TR4 orphan nuclear receptors repress Gata1 transcription
Authors: Tanabe Osamu , Shen Yannan , Liu Qinghui , Campbell Andrew D. , Kuroha Takashi , Yamamoto Masayuki , Engel James Douglas
Published: November 2007

When the orphan nuclear receptors TR2 and TR4, the DNA-binding subunits of the DRED repressor complex, are forcibly expressed in erythroid cells of transgenic mice, embryos exhibit a transient mid-gestational anemia as a consequence of a reduction in the number of primitive erythroid cells. GATA-1 mRNA is specifically diminished in the erythroid cells of these TR2/TR4 transgenic embryos as it is in human CD34+ progenitor cells transfected with forcibly expressed TR2/TR4. In contrast, in loss-of-function studies analyzing either Tr2- or Tr4-germline-null mutant mice or human CD34+ progenitor cells transfected with force-expressed TR2 and TR4 short hairpin RNAs (shRNAs), GATA-1 mRNA is induced. An evolutionarily conserved direct repeat (DR) element, a canonical binding site for nuclear receptors, was identified in the GATA1 hematopoietic enhancer (G1HE), and TR2/TR4 binds to that site in vitro and in vivo. Mutation of that DR element led to elevated Gata1 promoter activity, and reduced promoter responsiveness to cotransfected TR2/TR4. Thus, TR2/TR4 directly represses Gata1/GATA1 transcription in murine and human erythroid progenitor cells through an evolutionarily conserved binding site within a well-characterized, tissue-specific Gata1 enhancer, thereby providing a mechanism by which Gata1 can be directly silenced during terminal erythroid maturation.
Malignant astrocytic glioma: genetics, biology, and paths to treatment
Authors: Furnari Frank B. , Fenton Tim , Bachoo Robert M. , Mukasa Akitake , Stommel Jayne M. , Stegh Alexander , Hahn William C. , Ligon Keith L. , Louis David N. , Brennan Cameron , Chin Lynda , DePinho Ronald A. , Cavenee Webster K.
Published: November 2007

Malignant astrocytic gliomas such as glioblastoma are the most common and lethal intracranial tumors. These cancers exhibit a relentless malignant progression characterized by widespread invasion throughout the brain, resistance to traditional and newer targeted therapeutic approaches, destruction of normal brain tissue, and certain death. The recent confluence of advances in stem cell biology, cell signaling, genome and computational science and genetic model systems have revolutionized our understanding of the mechanisms underlying the genetics, biology and clinical behavior of glioblastoma. This progress is fueling new opportunities for understanding the fundamental basis for development of this devastating disease and also novel therapies that, for the first time, portend meaningful clinical responses.
Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb–MuvB/dREAM complex in proliferating cells
Authors: Georlette Daphne , Ahn Soyeon , MacAlpine David M. , Cheung Evelyn , Lewis Peter W. , Beall Eileen L. , Bell Stephen P. , Speed Terry , Manak J. Robert , Botchan Michael R.
Published: November 2007

Myb–MuvB (MMB)/dREAM is a nine-subunit complex first described in Drosophila as a repressor of transcription, dependent on E2F2 and the RBFs. Myb, an integral member of MMB, curiously plays no role in the silencing of the test genes previously analyzed. Moreover, Myb plays an activating role in DNA replication in Drosophila egg chamber follicle cells. The essential functions for Myb are executed as part of MMB. This duality of function lead to the hypothesis that MMB, which contains both known activator and repressor proteins, might function as part of a switching mechanism that is dependent on DNA sites and developmental context. Here, we used proliferating Drosophila Kc tissue culture cells to explore both the network of genes regulated by MMB (employing RNA interference and microarray expression analysis) and the genomic locations of MMB following chromatin immunoprecipitation (ChIP) and tiling array analysis. MMB occupied 3538 chromosomal sites and was promoter-proximal to 32% of Drosophila genes. MMB contains multiple DNA-binding factors, and the data highlighted the combinatorial way by which the complex was targeted and utilized for regulation. Interestingly, only a subset of chromatin-bound complexes repressed genes normally expressed in a wide range of developmental pathways. At many of these sites, E2F2 was critical for repression, whereas at other nonoverlapping sites, Myb was critical for repression. We also found sites where MMB was a positive regulator of transcript levels that included genes required for mitotic functions (G2/M), which may explain some of the chromosome instability phenotypes attributed to loss of Myb function in myb mutants.
Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control
Authors: Zhao Bin , Wei Xiaomu , Li Weiquan , Udan Ryan S. , Yang Qian , Kim Joungmok , Xie Joe , Ikenoue Tsuneo , Yu Jindan , Li Li , Zheng Pan , Ye Keqiang , Chinnaiyan Arul , Halder Georg , Lai Zhi-Chun , Guan Kun-Liang
Published: November 2007

The Hippo pathway plays a key role in organ size control by regulating cell proliferation and apoptosis in Drosophila. Although recent genetic studies have shown that the Hippo pathway is regulated by the NF2 and Fat tumor suppressors, the physiological regulations of this pathway are unknown. Here we show that in mammalian cells, the transcription coactivator YAP (Yes-associated protein), is inhibited by cell density via the Hippo pathway. Phosphorylation by the Lats tumor suppressor kinase leads to cytoplasmic translocation and inactivation of the YAP oncoprotein. Furthermore, attenuation of this phosphorylation of YAP or Yorkie (Yki), the Drosophila homolog of YAP, potentiates their growth-promoting function in vivo. Moreover, YAP overexpression regulates gene expression in a manner opposite to cell density, and is able to overcome cell contact inhibition. Inhibition of YAP function restores contact inhibition in a human cancer cell line bearing deletion of Salvador (Sav), a Hippo pathway component. Interestingly, we observed that YAP protein is elevated and nuclear localized in some human liver and prostate cancers. Our observations demonstrate that YAP plays a key role in the Hippo pathway to control cell proliferation in response to cell contact.