bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular basis for the inhibition of the carboxyltransferase domain of acetyl-coenzyme-A carboxylase by haloxyfop and diclofop
Authors: Zhang Hailong , Tweel Benjamin , Tong Liang
Published: April 2004

Acetyl-CoA carboxylases (ACCs) are crucial for the metabolism of fatty acids, making these enzymes important targets for the development of therapeutics against obesity, diabetes, and other diseases. The carboxyltransferase (CT) domain of ACC is the site of action of commercial herbicides, such as haloxyfop, diclofop, and sethoxydim. We have determined the crystal structures at up to 2.5-Å resolution of the CT domain of yeast ACC in complex with the herbicide haloxyfop or diclofop. The inhibitors are bound in the active site, at the interface of the dimer of the CT domain. Unexpectedly, inhibitor binding requires large conformational changes for several residues in this interface, which create a highly conserved hydrophobic pocket that extends deeply into the core of the dimer. Two residues that affect herbicide sensitivity are located in this binding site, and mutation of these residues disrupts the structure of the domain. Other residues in the binding site are strictly conserved among the CT domains.
A domain for editing by an archaebacterial tRNA synthetase
Authors: Beebe Kirk , Merriman Eve , de Pouplana Lluis Ribas , Schimmel Paul
Published: April 2004

The rules of the genetic code are established by aminoacylations of transfer RNAs by aminoacyl tRNA synthetases. New codon assignments, and the introduction of new kinds of amino acids, are blocked by vigorous tRNA-dependent editing reactions occurring at hydrolytic sites embedded within specialized domains in the synthetases. For some synthetases, these domains were present at the time of the last common ancestor and were fixed in evolution through all three of the kingdoms of life. Significantly, a well characterized domain for editing found in bacterial and eukaryotic threonyl– and all alanyl–tRNA synthetases is missing from archaebacterial threonine enzymes. Here we show that the archaebacterial
Methanosarcina mazei
ThrRS efficiently misactivates serine, but does not fuse serine to tRNA. Consistent with this observation, the enzyme cleared serine that was linked to threonine-specific tRNAs
. M. mazei
and most other archaebacterial ThrRSs have a domain, N2
A
, fused to the N terminus and not found in bacterial or eukaryotic orthologs. Mutations at conserved residues in this domain led to an inability to clear threonine-specific tRNA mischarged with serine. Thus, these results demonstrate a domain for editing that is distinct from all others, is restricted to just one branch of the tree of life, and was most likely added to archaebacterial ThrRSs after the eukaryote/archaebacteria split.
Regulation of
spalt
expression in the
Drosophila
wing blade in response to the Decapentaplegic signaling pathway
Authors: Barrio Rosa , de Celis Jose F.
Published: April 2004

Pattern formation depends on the acquisition of precise cellular identities due to the differential expression of transcription factors. Enhancers within regulatory regions integrate the positive and negative regulatory signals directing gene transcription. Here, we analyze the enhancer that drives expression of the
Drosophila
gene
spalt
in the wing blade. This enhancer integrates positive signals, mediated by the Decapentaplegic signaling effector protein Medea, with the repressor activity of Brinker. The enhancer functions in the absence of binding sites for the wing-specific factor Scalloped. The molecular analysis of this enhancer indicates that there are additional factors yet unknown involved in the activation of
spalt
in the wing blade and that the mechanism of repression by Brinker does not rely on competition with Mad–Medea overlapping sites. The comparisons with other enhancers that respond to Decapentaplegic suggest that there are different possibilities to integrate the positive and negative inputs triggered by this signaling pathway.
c-FLIP Mediates Resistance of Hodgkin/Reed-Sternberg Cells to Death Receptor–induced Apoptosis
Authors: Mathas Stephan , Lietz Andreas , Anagnostopoulos Ioannis , Hummel Franziska , Wiesner Burkhard , Janz Martin , Jundt Franziska , Hirsch Burkhard , Jöhrens-Leder Korinna , Vornlocher Hans-Peter , Bommert Kurt , Stein Harald , Dörken Bernd
Published: April 2004

Resistance to death receptor–mediated apoptosis is supposed to be important for the deregulated growth of B cell lymphoma. Hodgkin/Reed-Sternberg (HRS) cells, the malignant cells of classical Hodgkin's lymphoma (cHL), resist CD95-induced apoptosis. Therefore, we analyzed death receptor signaling, in particular the CD95 pathway, in these cells. High level CD95 expression allowed a rapid formation of the death-inducing signaling complex (DISC) containing Fas-associated death domain–containing protein (FADD), caspase-8, caspase-10, and most importantly, cellular FADD-like interleukin 1β–converting enzyme-inhibitory protein (c-FLIP). The immunohistochemical analysis of the DISC members revealed a strong expression of CD95 and c-FLIP overexpression in 55 out of 59 cases of cHL. FADD overexpression was detectable in several cases. Triggering of the CD95 pathway in HRS cells is indicated by the presence of CD95L in cells surrounding them as well as confocal microscopy showing c-FLIP predominantly localized at the cell membrane. Elevated c-FLIP expression in HRS cells depends on nuclear factor (NF)-κB. Despite expression of other NF-κB–dependent antiapoptotic proteins, the selective down-regulation of c-FLIP by small interfering RNA oligoribonucleotides was sufficient to sensitize HRS cells to CD95 and tumor necrosis factor–related apoptosis-inducing ligand–induced apoptosis. Therefore, c-FLIP is a key regulator of death receptor resistance in HRS cells.
TOX Provides a Link Between Calcineurin Activation and CD8 Lineage Commitment
Authors: Aliahmad Parinaz , O'Flaherty Emmett , Han Peggy , Goularte Olivia D. , Wilkinson Beverley , Satake Masanobu , Molkentin Jeffery D. , Kaye Jonathan
Published: April 2004

T cell development is dependent on the integration of multiple signaling pathways, although few links between signaling cascades and downstream nuclear factors that play a role in thymocyte differentiation have been identified. We show here that expression of the HMG box protein TOX is sufficient to induce changes in coreceptor gene expression associated with β-selection, including CD8 gene demethylation. TOX expression is also sufficient to initiate positive selection to the CD8 lineage in the absence of MHC–TCR interactions. TOX-mediated positive selection is associated with up-regulation of Runx3, implicating CD4 silencing in the process. Interestingly, a strong T cell receptor–mediated signal can modify this cell fate. We further demonstrate that up-regulation of TOX in double positive thymocytes is calcineurin dependent, linking this critical signaling pathway to nuclear changes during positive selection.
NH2-terminal Inactivation Peptide Binding to C-type–inactivated Kv Channels
Authors: Kurata Harley T. , Wang Zhuren , Fedida David
Published: April 2004

In many voltage-gated K+ channels, N-type inactivation significantly accelerates the onset of C-type inactivation, but effects on recovery from inactivation are small or absent. We have exploited the Na+ permeability of C-type–inactivated K+ channels to characterize a strong interaction between the inactivation peptide of Kv1.4 and the C-type–inactivated state of Kv1.4 and Kv1.5. The presence of the Kv1.4 inactivation peptide results in a slower decay of the Na+ tail currents normally observed through C-type–inactivated channels, an effective blockade of the peak Na+ tail current, and also a delay of the peak tail current. These effects are mimicked by addition of quaternary ammonium ions to the pipette-filling solution. These observations support a common mechanism of action of the inactivation peptide and intracellular quaternary ammonium ions, and also demonstrate that the Kv channel inner vestibule is cytosolically exposed before and after the onset of C-type inactivation. We have also examined the process of N-type inactivation under conditions where C-type inactivation is removed, to compare the interaction of the inactivation peptide with open and C-type–inactivated channels. In C-type–deficient forms of Kv1.4 or Kv1.5 channels, the Kv1.4 inactivation ball behaves like an open channel blocker, and the resultant slowing of deactivation tail currents is considerably weaker than observed in C-type–inactivated channels. We present a kinetic model that duplicates the effects of the inactivation peptide on the slow Na+ tail of C-type–inactivated channels. Stable binding between the inactivation peptide and the C-type–inactivated state results in slower current decay, and a reduction of the Na+ tail current magnitude, due to slower transition of channels through the Na+-permeable states traversed during recovery from inactivation.
All-trans-retinal Is a Closed-state Inhibitor of Rod Cyclic Nucleotide–gated Ion Channels
Authors: McCabe Sarah L. , Pelosi Diana M. , Tetreault Michelle , Miri Andrew , Nguitragool Wang , Kovithvathanaphong Pranisa , Mahajan Rahul , Zimmerman Anita L.
Published: April 2004

Rod vision begins when 11-cis-retinal absorbs a photon and isomerizes to all-trans-retinal (ATR) within the photopigment, rhodopsin. Photoactivated rhodopsin triggers an enzyme cascade that lowers the concentration of cGMP, thereby closing cyclic nucleotide–gated (CNG) ion channels. After isomerization, ATR dissociates from rhodopsin, and after a bright light, this release is expected to produce a large surge of ATR near the CNG channels. Using excised patches from Xenopus oocytes, we recently showed that ATR shuts down cloned rod CNG channels, and that this inhibition occurs in the nanomolar range (aqueous concentration) at near-physiological concentrations of cGMP. Here we further characterize the ATR effect and present mechanistic information. ATR was found to decrease the apparent cGMP affinity, as well as the maximum current at saturating cGMP. When ATR was applied to outside-out patches, inhibition was much slower and less effective than when it was applied to inside-out patches, suggesting that ATR requires access to the intracellular surface of the channel or membrane. The apparent ATR affinity and maximal inhibition of heteromeric (CNGA1/CNGB1) channels was similar to that of homomeric (CNGA1) channels. Single-channel and multichannel data suggest that channel inhibition by ATR is reversible. Inhibition by ATR was not voltage dependent, and the form of its dose–response relation suggested multiple ATR molecules interacting per channel. Modeling of the data obtained with cAMP and cGMP suggests that ATR acts by interfering with the allosteric opening transition of the channel and that it prefers closed, unliganded channels. It remains to be determined whether ATR acts directly on the channel protein or instead alters channel–bilayer interactions.
Caspase-dependent Regulation of Histone Deacetylase 4 Nuclear-Cytoplasmic Shuttling Promotes Apoptosis
Authors: Paroni Gabriela , Mizzau Michela , Henderson Clare , Del Sal Giannino , Schneider Claudio , Brancolini Claudio
Published: April 2004

Histone deacetylases (HDACs) are important regulators of gene expression as part of transcriptional corepressor complexes. Here, we demonstrate that caspases can repress the activity of the myocyte enhancer factor (MEF)2C transcription factor by regulating HDAC4 processing. Cleavage of HDAC4 occurs at Asp 289 and disjoins the carboxy-terminal fragment, localized into the cytoplasm, from the amino-terminal fragment, which accumulates into the nucleus. In the nucleus, the caspase-generated fragment of HDAC4 is able to trigger cytochrome c release from mitochondria and cell death in a caspase-9–dependent manner. The caspase-cleaved amino-terminal fragment of HDAC4 acts as a strong repressor of the transcription factor MEF2C, independently from the HDAC domain. Removal of amino acids 166–289 from the caspase-cleaved fragment of HDAC4 abrogates its ability to repress MEF2 transcription and to induce cell death. Caspase-2 and caspase-3 cleave HDAC4 in vitro and caspase-3 is critical for HDAC4 cleavage in vivo during UV-induced apoptosis. After UV irradiation, GFP-HDAC4 translocates into the nucleus coincidentally/immediately before the retraction response, but clearly before nuclear fragmentation. Together, our data indicate that caspases could specifically modulate gene repression and apoptosis through the proteolyic processing of HDAC4.
Role of Cytoplasmic Domain Serines in Intracellular Trafficking of Furin
Authors: Schapiro Florencia B. , Soe Thwe Thwe , Mallet William G. , Maxfield Frederick R.
Published: April 2004

Furin is a transmembrane protein that cycles between the plasma membrane, endosomes, and the trans-Golgi network, maintaining a predominant distribution in the latter. It has been shown previously that Tac-furin, a chimeric protein expressing the extracellular and transmembrane domains of the interleukin-2 receptor α chain (Tac) and the cytoplasmic domain of furin, is delivered from the plasma membrane to the TGN through late endosomes, bypassing the endocytic recycling compartment. Tac-furin also recycles in a loop between the TGN and late endosomes. Localization of furin to the TGN is modulated by a six-amino acid acidic cluster that contains two phosphorylatable serines (SDSEED). We investigated the role of these serines in the trafficking of Tac-furin by using a mutant chimera in which the SDS sequence was replaced by the nonphosphorylatable sequence ADA (Tac-furin/ADA). Although the mutant construct is internalized and delivered to the TGN, both the postendocytic trafficking and the steady-state distribution were found to differ from the wild-type. In contrast with Tac-furin, Tac-furin/ADA does not enter late endosomes after being internalized. Instead, it traffics with transferrin to the endocytic recycling compartment, and from there it is delivered to the TGN. As with Tac-furin, Tac-furin/ADA is sorted from the TGN into late endosomes at steady state, but its retrieval from the late endosomes to the TGN is inhibited. These results suggest that serine phosphorylation plays an important role in at least two steps of Tac-furin trafficking, acting as an active sorting signal that mediates the selective sorting of Tac-furin into late endosomes after internalization, as well as its retrieval from late endosomes back to the TGN.
Role of the Midbody Matrix in Cytokinesis: RNAi and Genetic Rescue Analysis of the Mammalian Motor Protein CHO1
Authors: Matuliene Jurgita , Kuriyama Ryoko
Published: April 2004

CHO1 is a kinesin-like motor protein essential for cytokinesis in mammalian cells. To analyze how CHO1 functions, we established RNAi and genetic rescue assays. CHO1-depleted cells reached a late stage of cytokinesis but fused back to form binucleate cells because of the absence of the midbody matrix in the middle of the intercellular bridge. Expression of exogenous CHO1 restored the formation of the midbody matrix and rescued cytokinesis in siRNA-treated cells. By analyzing phenotypes rescued with different constructs, it was shown that both motor and stalk domains function in midbody formation, whereas the tail is essential for completion of cytokinesis after the midbody matrix has formed. During the terminal stage of cytokinesis, different subregions of the tail play distinctive roles in stabilizing the midbody matrix and maintaining an association between the midbody and cell cortex. These results demonstrate that CHO1 consists of functionally differentiated subregions that act in concert to ensure complete cell separation.
Deficiencies in the Endoplasmic Reticulum (ER)-Membrane Protein Gab1p Perturb Transfer of Glycosylphosphatidylinositol to Proteins and Cause Perinuclear ER-associated Actin Bar Formation
Authors: Grimme Stephen J. , Gao Xiang-Dong , Martin Paul S. , Tu Kim , Tcheperegine Serguei E. , Corrado Kathleen , Farewell Anne E. , Orlean Peter , Bi Erfei
Published: April 2004

The essential GAB1 gene, which encodes an endoplasmic reticulum (ER)-membrane protein, was identified in a screen for mutants defective in cellular morphogenesis. A temperature-sensitive gab1 mutant accumulates complete glycosylphosphatidylinositol (GPI) precursors, and its temperature sensitivity is suppressed differentially by overexpression of different subunits of the GPI transamidase, from strong suppression by Gpi8p and Gpi17p, to weak suppression by Gaa1p, and to no suppression by Gpi16p. In addition, both Gab1p and Gpi17p localize to the ER and are in the same protein complex in vivo. These findings suggest that Gab1p is a subunit of the GPI transamidase with distinct relationships to other subunits in the same complex. We also show that depletion of Gab1p or Gpi8p, but not Gpi17p, Gpi16p, or Gaa1p causes accumulation of cofilin-decorated actin bars that are closely associated with the perinuclear ER, which highlights a functional interaction between the ER network and the actin cytoskeleton.
Excessive Myosin Activity inMbsMutants Causes Photoreceptor Movement Out of theDrosophilaEye Disc Epithelium
Authors: Lee Arnold , Treisman Jessica E.
Published: April 2004

Neuronal cells must extend a motile growth cone while maintaining the cell body in its original position. In migrating cells, myosin contraction provides the driving force that pulls the rear of the cell toward the leading edge. We have characterized the function of myosin light chain phosphatase, which down-regulates myosin activity, in Drosophila photoreceptor neurons. Mutations in the gene encoding the myosin binding subunit of this enzyme cause photoreceptors to drop out of the eye disc epithelium and move toward and through the optic stalk. We show that this phenotype is due to excessive phosphorylation of the myosin regulatory light chain Spaghetti squash rather than another potential substrate, Moesin, and that it requires the nonmuscle myosin II heavy chain Zipper. Myosin binding subunit mutant cells continue to express apical epithelial markers and do not undergo ectopic apical constriction. In addition, mutant cells in the wing disc remain within the epithelium and differentiate abnormal wing hairs. We suggest that excessive myosin activity in photoreceptor neurons may pull the cell bodies toward the growth cones in a process resembling normal cell migration.
An Lsm2–Lsm7 Complex inSaccharomyces cerevisiaeAssociates with the Small Nucleolar RNA snR5
Authors: Fernandez Cesar F. , Pannone Barbara K. , Chen Xinguo , Fuchs Gabriele , Wolin Sandra L.
Published: April 2004

Sm-like (Lsm) proteins function in a variety of RNA-processing events. In yeast, the Lsm2–Lsm8 complex binds and stabilizes the spliceosomal U6 snRNA, whereas the Lsm1–Lsm7 complex functions in mRNA decay. Here we report that a third Lsm complex, consisting of Lsm2–Lsm7 proteins, associates with snR5, a box H/ACA snoRNA that functions to guide site-specific pseudouridylation of rRNA. Experiments in which the binding of Lsm proteins to snR5 was reconstituted in vitro reveal that the 3′ end of snR5 is critical for Lsm protein recognition. Glycerol gradient sedimentation and sequential immunoprecipitation experiments suggest that the Lsm protein-snR5 complex is partly distinct from the complex formed by snR5 RNA with the box H/ACA proteins Gar1p and Nhp2p. Consistent with a separate complex, Lsm proteins are not required for the function of snR5 in pseudouridylation of rRNA. We demonstrate that in addition to their known nuclear and cytoplasmic locations, Lsm proteins are present in nucleoli. Taken together with previous findings that a small fraction of pre-RNase P RNA associates with Lsm2–Lsm7, our experiments suggest that an Lsm2–Lsm7 protein complex resides in nucleoli, contributing to the biogenesis or function of specific snoRNAs.
STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces
Authors: Mancini A. L. , Higa R. H. , Oliveira A. , Dominiquini F. , Kuser P. R. , Yamagishi M. E. B. , Togawa R. C. , Neshich G.
Published: April 2004

Amino acid contacts in terms of atomic interactions are essential factors to be considered in the analysis of the structure of a protein and its complexes. Consequently, molecular biologists do require specific tools for the identification and visualization of all such contacts. Graphical contacts (GC) and interface forming residue graphical contacts (IFRgc) presented here, calculate atomic contacts among amino acids based on a table of predefined pairs of the atom types and their distances, and then display them using number of different forms. The inventory of currently listed contact types by GC and IFRgc include hydrogen bonds (in nine different flavors), hydrophobic interactions, charge–charge interactions, aromatic stacking and disulfide bonds. Such extensive catalog of the interactions, representing the forces that govern protein folding, stability and binding, is the key feature of these two applications. GC and IFRgc are part of STING Millennium Suite.

Availability:  http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org//SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS (Options: Graphical Contacts and IFR Graphical Contacts).
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
Authors: Huber Thomas , Faulkner Geoffrey , Hugenholtz Philip
Published: April 2004

Summary: Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

Availability: Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl
MedPost: a part-of-speech tagger for bioMedical text
Authors: Smith L. , Rindflesch T. , Wilbur W. J.
Published: April 2004

Summary: We present a part-of-speech tagger that achieves over 97% accuracy on MEDLINE citations.

Availability: Software, documentation and a corpus of 5700 manually tagged sentences are available at ftp://ftp.ncbi.nlm.nih.gov/pub/lsmith/MedPost/medpost.tar.gz
Alignment of RNA base pairing probability matrices
Authors: Hofacker Ivo L. , Bernhart Stephan H. F. , Stadler Peter F.
Published: April 2004

Motivation: Many classes of functional RNA molecules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore be constructed only when the shared structural features are taken into account. Since multiple alignments are used as input for many subsequent methods of data analysis, structure-based alignments are an indispensable necessity in RNA bioinformatics.

Results: We present here a method to compute pairwise and progressive multiple alignments from the direct comparison of base pairing probability matrices. Instead of attempting to solve the folding and the alignment problem simultaneously as in the classical Sankoff's algorithm, we use McCaskill's approach to compute base pairing probability matrices which effectively incorporate the information on the energetics of each sequences. A novel, simplified variant of Sankoff's algorithms can then be employed to extract the maximum-weight common secondary structure and an associated alignment.

Availability: The programs pmcomp and pmmulti described in this contribution are implemented in Perl and can be downloaded together with the example datasets from http://www.tbi.univie.ac.at/RNA/PMcomp/. A web server is available at http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl
Proteins associated with diseases show enhanced sequence correlation between charged residues
Authors: Dima Ruxandra I. , Thirumalai D.
Published: April 2004

Motivation: Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation. Bioinformatic and structural analysis methods have been introduced to infer residues that are correlated. Recently, increasing attention has been paid to obtain the sequence properties that determine the tendency of disease-related proteins (Aβ peptides, prion proteins, transthyretin, etc.) to aggregate and form fibrils. Motivated in part by the need to identify sequence characteristics that indicate a tendency to aggregate, we introduce a general method that probes covariations in charged residues along the sequence in a given protein family. The method, which involves computing the sequence correlation entropy (SCE) using the quenched probability Psk(i,j) of finding a residue pair at a given sequence separation, sk, allows us to classify protein families in terms of their SCE. Our general approach may be a useful way in obtaining evolutionary covariations of amino acid residues on a genome wide level.

Results: We use a combination of SCE and clustering based on the principle component analysis to classify the protein families. From an analysis of 839 families, covering ∼500 000 sequences, we find that proteins with relatively low values of SCE are predominantly associated with various diseases. In several families, residues that give rise to peaks in Psk(i,j) are clustered in the three-dimensional structure. For the class of proteins with low SCE values, there are significant numbers of mixed charged-hydrophobic (CH) and charged-polar (CP) runs. Our findings suggest that the low values of SCE and the presence of (CH) and/or (CP) may be indicative of disease association or tendency to aggregate. Our results led to the hypothesis that functions of proteins with similar SCE values may be linked. The hypothesis is validated with a few anecdotal examples. The present results also lead to the prediction that the overall charge correlations in proteins affect the kinetics of amyloid formation—a feature that is common to all proteins implicated in neurodegenerative diseases.
Supertree algorithms for ancestral divergence dates and nested taxa
Authors: Semple Charles , Daniel Philip , Hordijk Wim , Page Roderic D.M. , Steel Mike
Published: April 2004

Motivation: Supertree methods have been often identified as a possible approach to the reconstruction of the ‘Tree of Life’. However, a limitation of such methods is that, typically, they use just leaf-labelled phylogenetic trees to infer the resulting supertree.

Results: In this paper, we describe several new supertree algorithms that extend the allowable information that can be used for phylogenetic inference. These algorithms have been recently implemented and we describe here two illustrative applications.

Availability: These new algorithms are freely available for application at http://darwin.zoology.gla.ac.uk/cgi-bin/build.pl
BAPS 2: enhanced possibilities for the analysis of genetic population structure
Authors: Corander Jukka , Waldmann Patrik , Marttinen Pekka , Sillanpää Mikko J.
Published: April 2004

Summary: Bayesian statistical methods based on simulation techniques have recently been shown to provide powerful tools for the analysis of genetic population structure. We have previously developed a Markov chain Monte Carlo (MCMC) algorithm for characterizing genetically divergent groups based on molecular markers and geographical sampling design of the dataset. However, for large-scale datasets such algorithms may get stuck to local maxima in the parameter space. Therefore, we have modified our earlier algorithm to support multiple parallel MCMC chains, with enhanced features that enable considerably faster and more reliable estimation compared to the earlier version of the algorithm. We consider also a hierarchical tree representation, from which a Bayesian model-averaged structure estimate can be extracted. The algorithm is implemented in a computer program that features a user-friendly interface and built-in graphics. The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset.

Availability: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html
Data mining in bioinformatics using Weka
Authors: Frank Eibe , Hall Mark , Trigg Len , Holmes Geoffrey , Witten Ian H.
Published: April 2004

Summary: The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection—common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data pre-processing methods complemented by graphical user interfaces for data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it.

Availability:  http://www.cs.waikato.ac.nz/ml/weka
Wnt-1 signal induces phosphorylation and degradation of c-Myb protein via TAK1, HIPK2, and NLK
Authors: Kanei-Ishii Chie , Ninomiya-Tsuji Jun , Tanikawa Jun , Nomura Teruaki , Ishitani Tohru , Kishida Satoshi , Kokura Kenji , Kurahashi Toshihiro , Ichikawa-Iwata Emi , Kim Yongsok , Matsumoto Kunihiro , Ishii Shunsuke
Published: April 2004

The c-myb proto-oncogene product (c-Myb) regulates both the proliferation and apoptosis of hematopoietic cells by inducing the transcription of a group of target genes. However, the biologically relevant molecular mechanisms that regulate c-Myb activity remain unclear. Here we report that c-Myb protein is phosphorylated and degraded by Wnt-1 signal via the pathway involving TAK1 (TGF-β-activated kinase), HIPK2 (homeodomain-interacting protein kinase 2), and NLK (Nemo-like kinase). Wnt-1 signal causes the nuclear entry of TAK1, which then activates HIPK2 and the mitogen-activated protein (MAP) kinase-like kinase NLK. NLK binds directly to c-Myb together with HIPK2, which results in the phosphorylation of c-Myb at multiple sites, followed by its ubiquitination and proteasome-dependent degradation. Furthermore, overexpression of NLK in M1 cells abrogates the ability of c-Myb to maintain the undifferentiated state of these cells. The down-regulation of Myb by Wnt-1 signal may play an important role in a variety of developmental steps.
Nucleosomal histone kinase-1 phosphorylates H2A Thr 119 during mitosis in the early Drosophila embryo
Authors: Aihara Hitoshi , Nakagawa Takeya , Yasui Kiyoshi , Ohta Tsutomu , Hirose Susumu , Dhomae Naoshi , Takio Koji , Kaneko Mayumi , Takeshima Yukio , Muramatsu Masami , Ito Takashi
Published: April 2004

Posttranslational histone modifications are important for the regulation of many biological phenomena. Here, we show the purification and characterization of nucleosomal histone kinase-1 (NHK-1). NHK-1 has a high affinity for chromatin and phosphorylates a novel site, Thr 119, at the C terminus of H2A. Notably, NHK-1 specifically phosphorylates nucleosomal H2A, but not free H2A in solution. In Drosophila embryos, phosphorylated H2A Thr 119 is found in chromatin, but not in the soluble core histone pool. Immunostaining of NHK-1 revealed that it goes to chromatin during mitosis and is excluded from chromatin during S phase. Consistent with the shuttling of NHK-1 between chromatin and cytoplasm, H2A Thr 119 is phosphorylated during mitosis but not in S phase. These studies reveal that NHK-1-catalyzed phosphorylation of a conserved serine/threonine residue in H2A is a new component of the histone code that might be related to cell cycle progression.
p27Kip1 modulates cell migration through the regulation of RhoA activation
Authors: Besson Arnaud , Gurian-West Mark , Schmidt Anja , Hall Alan , Roberts James M.
Published: April 2004

The tumor suppressor p27Kip1 is an inhibitor of cyclin/cyclin-dependent kinase (CDK) complexes and plays a crucial role in cell cycle regulation. However, p27Kip1 also has cell cycle-independent functions. Indeed, we find that p27Kip1 regulates cell migration, as p27Kip1-null fibroblasts exhibit a dramatic decrease in motility compared with wild-type cells. The regulation of motility by p27Kip1 is independent of its cell-cycle regulatory functions, as re-expression of both wild-type p27Kip1 and a mutant p27Kip1 (p27CK–) that cannot bind to cyclins and CDKs rescues migration of p27–/– cells. p27–/– cells have increased numbers of actin stress fibers and focal adhesions. This is reminiscent of cells in which the Rho pathway is activated. Indeed, active RhoA levels were increased in cells lacking p27Kip1. Moreover, inhibition of ROCK, a downstream effector of Rho, was able to rescue the migration defect of p27–/– cells in response to growth factors. Finally, we found that p27Kip1 binds to RhoA, thereby inhibiting RhoA activation by interfering with the interaction between RhoA and its activators, the guanine–nucleotide exchange factors (GEFs). Together, the data suggest a novel role for p27Kip1 in regulating cell migration via modulation of the Rho pathway.
BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis
Authors: Takeda Shin , Tadele Zerihun , Hofmann Ingo , Probst Aline V. , Angelis Karel J. , Kaya Hidetaka , Araki Takashi , Mengiste Tesfaye , Scheid Ortrun Mittelsten , Shibahara Kei-ichi , Scheel Dierk , Paszkowski Jerzy
Published: April 2004

DNA repair associated with DNA replication is important for the conservation of genomic sequence information, whereas reconstitution of chromatin after replication sustains epigenetic information. We have isolated and characterized mutations in the BRU1 gene of Arabidopsis that suggest a novel link between these underlying maintenance mechanisms. Bru1 plants are highly sensitive to genotoxic stress and show stochastic release of transcriptional gene silencing. They also show increased intrachromosomal homologous recombination and constitutively activated expression of poly (ADP-ribose) polymerase-2 (AtPARP-2), the induction of which is associated with elevated DNA damage. Bru1 mutations affect the stability of heterochromatin organization but do not interfere with genome-wide DNA methylation. BRU1 encodes a novel nuclear protein with two predicted protein–protein interaction domains. The developmental abnormalities characteristic of bru1 mutant plants resemble those triggered by mutations in genes encoding subunits of chromatin assembly factor (CAF-1), the condensin complex, or MRE11. Comparison of bru1 with these mutants indicates cooperative roles in the replication and stabilization of chromatin structure, providing a novel link between chromatin replication, epigenetic inheritance, S-phase DNA damage checkpoints, and the regulation of meristem development.
An Overview of Ensembl
Authors: Birney Ewan , Andrews T. Daniel , Bevan Paul , Caccamo Mario , Chen Yuan , Clarke Laura , Coates Guy , Cuff James , Curwen Val , Cutts Tim , Down Thomas , Eyras Eduardo , Fernandez-Suarez Xose M. , Gane Paul , Gibbins Brian , Gilbert James , Hammond Martin , Hotz Hans-Rudolf , Iyer Vivek , Jekosch Kerstin , Kahari Andreas , Kasprzyk Arek , Keefe Damian , Keenan Stephen , Lehvaslaiho Heikki , McVicker Graham , Melsopp Craig , Meidl Patrick , Mongin Emmanuel , Pettett Roger , Potter Simon , Proctor Glenn , Rae Mark , Searle Steve , Slater Guy , Smedley Damian , Smith James , Spooner Will , Stabenau Arne , Stalker James , Storey Roy , Ureta-Vidal Abel , Woodwark K. Cara , Cameron Graham , Durbin Richard , Cox Anthony , Hubbard Tim , Clamp Michele
Published: April 2004

Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them. It is also a framework for integration of any biological data that can be mapped onto features derived from the genomic sequence. Ensembl is available as an interactive Web site, a set of flat files, and as a complete, portable open source software system for handling genomes. All data are provided without restriction, and code is freely available. Ensembl's aims are to continue to “widen” this biological integration to include other model organisms relevant to understanding human biology as they become available; to “deepen” this integration to provide an ever more seamless linkage between equivalent components in different species; and to provide further classification of functional elements in the genome that have been previously elusive.
Computational Analysis of Plasmodium falciparum Metabolism: Organizing Genomic Information to Facilitate Drug Discovery
Authors: Yeh Iwei , Hanekamp Theodor , Tsoka Sophia , Karp Peter D. , Altman Russ B.
Published: April 2004

Identification of novel targets for the development of more effective antimalarial drugs and vaccines is a primary goal of the Plasmodium genome project. However, deciding which gene products are ideal drug/vaccine targets remains a difficult task. Currently, a systematic disruption of every single gene in Plasmodium is technically challenging. Hence, we have developed a computational approach to prioritize potential targets. A pathway/genome database (PGDB) integrates pathway information with information about the complete genome of an organism. We have constructed PlasmoCyc, a PGDB for Plasmodium falciparum 3D7, using its annotated genomic sequence. In addition to the annotations provided in the genome database, we add 956 additional annotations to proteins annotated as “hypothetical” using the GeneQuiz annotation system. We apply a novel computational algorithm to PlasmoCyc to identify 216 “chokepoint enzymes.” All three clinically validated drug targets are chokepoint enzymes. A total of 87.5% of proposed drug targets with biological evidence in the literature are chokepoint reactions. Therefore, identifying chokepoint enzymes represents one systematic way to identify potential metabolic drug targets.
Direct measurement of protein osmotic second virial cross coefficients by cross‐interaction chromatography
Authors: Tessier Peter M. , Sandler Stanley I. , Lenhoff Abraham M.
Published: April 2004

The importance of weak protein interactions, such as protein self‐association, is widely recognized in a variety of biological and technological processes. Although protein self‐association has been studied extensively, much less attention has been devoted to weak protein cross‐association, mainly due to the difficulties in measuring weak interactions between different proteins in solution. Here a framework is presented for quantifying the osmotic second virial cross coefficient directly using a modified form of self‐interaction chromatography called cross‐interaction chromatography. A theoretical relationship is developed between the virial cross coefficient and the chromatographic retention using statistical mechanics. Measurements of bovine serum albumin (BSA)/lysozyme cross‐association using cross‐interaction chromatography agree well with the few osmometry measurements available in the literature. Lysozyme/α‐chymotrypsinogen interactions were also measured over a wide range of solution conditions, and some counterintuitive trends were observed that may provide new insight into the molecular origins of weak protein interactions. The virial cross coefficients presented in this work may also provide insight into separation processes that are influenced by protein cross‐interactions, such as crystallization, precipitation, and ultrafiltration.
Conformational analysis of HAMLET, the folding variant of human α‐lactalbumin associated with apoptosis
Authors: Casbarra Annarita , Birolo Leila , Infusini Giuseppe , Dal Piaz Fabrizio , Svensson Malin , Pucci Piero , Svanborg Catharina , Marino Gennaro
Published: April 2004

A combination of hydrogen/deuterium (H/D) exchange and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the conformation in solution of HAMLET, the folding variant of human α‐lactalbumin, complexed to oleic acid, that induces apoptosis in tumor and immature cells. Although near‐ and far‐UV CD and fluorescence spectroscopy were not able to discriminate between HAMLET and apo‐α‐lactalbumin, H/D exchange experiments clearly showed that they correspond to two distinct conformational states, with HAMLET incorporating a greater number of deuterium atoms than the apo and holo forms. Complementary proteolysis experiments revealed that HAMLET and apo are both accessible to proteases in the β‐domain but showed substantial differences in accessibility to proteases at specific sites. The overall results indicated that the conformational changes associated with the release of Ca2+ are not sufficient to induce the HAMLET conformation. Metal depletion might represent the first event to produce a partial unfolding in the β‐domain of α‐lactalbumin, but some more unfolding is needed to generate the active conformation HAMLET, very likely allowing the protein to bind the C18:1 fatty acid moiety. On the basis of these data, a putative binding site of the oleic acid, which stabilizes the HAMLET conformation, is proposed.
Identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium Microbulbifer degradans
Authors: Howard Michael B. , Ekborg Nathan A. , Taylor Larry E. , Hutcheson Steven W. , Weiner Ronald M.
Published: April 2004

Polyserine linkers (PSLs) are interdomain, serine‐rich sequences found in modular proteins. Though common among eukaryotes, their presence in prokaryotic enzymes is limited. We identified 46 extracellular proteins involved in complex carbohydrate degradation from Microbulbifer degradans that contain PSLs that separate carbohydrate‐binding domains or catalytic domains from other binding domains. In nine M. degradans proteins, PSLs also separated amino‐terminal lipoprotein acylation sites from the remainder of the polypeptide. Furthermore, among the 76 PSL proteins identified in sequence repositories, 65 are annotated as proteins involved in complex carbohydrate degradation. We discuss the notion that PSLs are flexible, disordered spacer regions that enhance substrate accessibility.
Structure of fosfomycin resistance protein FosA from transposon Tn2921
Authors: Pakhomova Svetlana , Rife Chris L. , Armstrong Richard N. , Newcomer Marcia E.
Published: April 2004

The crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been established at a resolution of 2.5 Å. The protein crystallized without bound Mn(II) and K+, ions crucial for efficient catalysis, providing a structure of the apo enzyme. The protein maintains the three‐dimensional domain‐swapped arrangement of the paired βαβββ‐motifs observed in the genomically encoded homologous enzyme from Pseudomonas aeruginosa (PA1129). The basic architecture of the active site is also maintained, despite the absence of the catalytically essential Mn(II). However, the absence of K+, which has been shown to enhance enzymatic activity, appears to contribute to conformational heterogeneity in the K+‐binding loops.
Mistletoe viscotoxins induce membrane permeabilization and spore death in phytopathogenic fungi
Authors: Giudici Ana Marcela , Regente Mariana Clelia , Villalaín José , Pfüller Karola , Pfüller Uwe , De La Canal Laura
Published: April 2004

Viscotoxins (Vts) are basic peptides expressed in mistletoe leaves, seeds and stems which have been shown to be cytotoxic to mammalian cells. The aim of this study was to analyse whether Vts were able to control and/or inhibit the growth of phytopathogenic fungi to obtain a clue to their biological function. Incubation of two Vt isoforms, VtA3 and VtB, at a final concentration of 10 µM resulted in a complete blockage of the germination of spores from three different pathogenic fungi. It was also shown that lower concentrations than 10 µM of VtA3 and VtB inhibit their mycelial growth in a dose‐dependent manner. The protein dose required to inhibit the growth of Fusarium solani and Sclerotinia sclerotiorum to a 50% was between 1.5 and 3.75 µM , which represents a potent activity. No significant differences in the antifungal potency for each Vt isoform, either VtA3 and VtB, were observed, although they have been shown to exert differential cytotoxicity on mammalian cells. It was also demonstrated that Vts act as fungicidal compounds. To explore the basis of the antifungal activity the ability of VtA3 to induce changes in membrane permeability and on the oxidative status of F. solani spores was analysed. By using a specific fluorescent probe on intact spores, it was demonstrated that VtA3 produces rapid changes in fungal membrane permeability. It also induces H2O2 production verified by a histochemical staining. The data presented in this study support a direct role of Vts in the plant defence determined by their lethal effect on fungal pathogens.
A highly conserved gene for vitamin B6 biosynthesis may have consequences for stress and hormone responses in plants
Authors: Graham Cindy M. , Ehrenshaft Marilyn , Hausner Georg , Reid David M.
Published: April 2004

Pyridoxine (vitamin B6) is not only an essential cofactor in amino acid biosynthesis but has recently been added to the list of potent antioxidants found in plants (Bilski et al., 71: 129–134, 2000). Herein the cloning of a gene (pvPDX1) from Phaseolus vulgaris that has a high degree of similarity to PDX1 from Cercospora nicotianae is reported. In C. nicotianae, PDX1 is involved in the biosynthesis of pyridoxine as null mutants exhibit pyridoxine auxotrophy (Ehrenshaft et al., Proc Natl Acad Sci USA 96: 9374–9378, 1999). Expression of pvPDX1 in PDX1 mutants of C. nicotianae partially complements pyridoxine auxotrophy suggesting that a similar biosynthetic pathway for pyridoxine exists in both plants and fungi. In P. vulgaris, expression of pvPDX1 was induced by mechanical wounding via a mechanism that is independent of the production of AOS (active oxygen species). Furthermore, whereas the expression of pvPDX1 in P. vulgaris was up‐regulated by treatment with 1‐aminocyclopropane‐1‐ carboxylic acid (ACC) treatment in a time course similar to that observed with wounding, expression was not consistently regulated by other treatments that caused a similar increase in ethylene production suggesting a more complicated regulatory pathway.
Characterization of NADPH‐dependent oxidoreductase induced by auxin in rice
Authors: Oguchi Keiko , Tanaka Naoki , Komatsu Setsuko , Akao Shoichiro
Published: April 2004

An NADPH‐dependent oxidoreductase (NADPH‐DO) with an isoelectric point of 5.2 and a molecular mass of 35 kDa was isolated from suspension‐cultured rice cells. NADPH‐DO was inducible by auxin and gibberellin. NADPH‐DO mRNA was expressed in roots and leaf sheaths of rice seedlings, but not in leaf blades. The levels of NADPH‐DO mRNA and protein in suspension‐cultured cells were increased by auxin; they were further raised by the application of zinc. In contrast, NADPH‐DO mRNA and protein accumulation in intact roots was stimulated by auxin, but in this case the stimulation was inhibited by zinc. Auxin‐induced callus growth and root formation in intact rice plants were further enhanced by zinc. These results indicate that high levels of NADPH‐DO are necessary for auxin‐ and zinc‐induced callus formation, and imply that zinc plays a role in the regulation of NADPH‐DO induction by auxin.