bluuebunny/crossref_metadata_2025 huggingface dataset:
Chasing Duhem
Authors: Stanford P. Kyle
Published: June 2006

Nearly a century ago, French physicist Pierre Duhem offered a characteristically lucid and provocative articulation of the challenge to the power of scientific methods to uncover theoretical truths about the natural world. What seems to have worried Duhem is the eliminative character of many important scientific inferences: often in science, perhaps even typically, we arrive at a decision to accept or believe a given theory because we take ourselves to have convincingly eliminated or discredited any and all of its proposed rivals or competing explanations of the available evidence. But as Duhem saw, such an eliminative inferential procedure will only guide us to the truth about nature if the truth is among these competitors in the first place. It is argued that eliminative inferences are only reliable when we can be reasonably sure that we have considered all of the most likely, plausible, or reasonable alternatives before we proceed to eliminate all but one of them (or, in the limiting case, simply rest content with the lone contender). But the history of science shows that we have repeatedly failed to conceive of (and therefore consider) alternatives to our best theories that were both well confirmed by the evidence available at the time and sufficiently plausible as to be later accepted by actual scientific communities. The historical record suggests that in science we are typically unable to exhaust the space of likely, plausible, or reasonable candidate theoretical explanations for a given set of phenomena before proceeding to eliminate all but a single contender, but this is just what would be required for such eliminative inferences to be reliable.
Galton and the Stirp Theory
Authors: Stanford P. Kyle
Published: June 2006

This chapter begins with a discussion of Galton's transfusion experiments and his development of the “stirp” theory of inheritance. It then discusses Galton's understanding of “correlation” and “ variable influences” in development. It is argued that just as Darwin failed to conceive of the very possibility of any common-cause mechanism for inheritance, after surmounting this conceptual obstacle Galton failed in turn to conceive of any alternatives to the maturational and invariant aspects of his own account of particulate inheritance.
August Weismann's Theory of the Germ‐Plasm
Authors: Stanford P. Kyle
Published: June 2006

This chapter focuses on August Weismann's theory of the germ-plasm. It is argued that both Weismann's failure to conceive of any alternative to the disintegration of the idioplasm as the mechanism of ontogenetic differentiation and nuclear control, and his failure to conceive of any genuinely facultative capacity on the part of the germ-plasm suggest that Weismann never conceived of the quite general possibility that the germ-plasm could itself serve as what we might call a productive rather than an expendable resource for the cell and/or the organism.
History Revisited
Authors: Stanford P. Kyle
Published: June 2006

This chapter examines the most influential recent efforts by scientific realists to blunt or block the pessimistic induction by engaging the details of the history of science itself, including the first serious efforts to recruit those details to the realist cause. It argues that the most promising and influential realist replies to the historical challenge (including those of Clyde Hardin and Alexander Rosenberg, Philip Kitcher, Stathis Psillos, Jarrett Leplin, and John Worrall) ultimately manage to achieve only Pyrrhic victories for realism, that is, “defences” of scientific realism that are forced to concede to the realist's opponent either just the substantive points that were in dispute between them or everything he/she needs for a convincing historical case against realism itself. Both the problem of unconceived alternatives and the pessimistic induction itself survive even the best recent efforts to defend realism from the specter of the historical record.
Selective Confirmation and the Historical Record
Authors: Stanford P. Kyle
Published: June 2006

The preceding chapter showed that the best remaining hope for defending realism from the challenges of history seems to lie with the strategy of “selective confirmation.” On this strategy, we defend only some parts or components of past theories as responsible for (and therefore confirmed by) their successes, while abandoning others as idle, merely presuppositional, or otherwise not involved in the empirical successes those theories managed to achieve, and therefore never genuinely confirmed by those successes in the first place. This chapter argues that without some prospectively applicable and historically reliable criterion for distinguishing idle and/or genuinely confirmed parts of our theories from others, the strategy of selective confirmation offers no refuge for the scientific realist. Without such a criterion, we can have no confidence in our ability to pick out the parts of theories needed for (and thus selectively confirmed by) their successes while those theories are live contenders. We will therefore not be in a position to identify those parts or features of our own theories we may safely regard as accurate descriptions of the natural world (even though we know that not all are), and thus the realist's opponent will again be entitled to the conclusion that was wanted all along. Such criteria are just what existing appeals to selective confirmation do not (and perhaps cannot) provide.
Science without Realism?
Authors: Stanford P. Kyle
Published: June 2006

This chapter addresses the question of whether there is any sense to be made of science without scientific realism. That is, it will try to identify whether there is any coherent positive view we might take of our successful scientific theories if we abandon the presumption that they must be approximately true descriptions of nature's innermost recesses and secret domains. A long and distinguished minority tradition has embraced a view entitled “instrumentalism,” which instead regards even our best scientific theories merely as effective tools or instruments for achieving our practical goals. It is argued that the problem of unconceived alternatives promises to breathe new life into this instrumentalist tradition: not into its discredited semantic theses, but into its positive conception of the status of scientific theories.
caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid
Authors: Saltz Joel , Oster Scott , Hastings Shannon , Langella Stephen , Kurc Tahsin , Sanchez William , Kher Manav , Manisundaram Arumani , Shanbhag Krishnakant , Covitz Peter
Published: June 2006

Motivation: The complexity of cancer is prompting researchers to find new ways to synthesize information from diverse data sources and to carry out coordinated research efforts that span multiple institutions. There is a need for standard applications, common data models, and software infrastructure to enable more efficient access to and sharing of distributed computational resources in cancer research. To address this need the National Cancer Institute (NCI) has initiated a national-scale effort, called the cancer Biomedical Informatics Grid (caBIG™), to develop a federation of interoperable research information systems.

Results: At the heart of the caBIG approach to federated interoperability effort is a Grid middleware infrastructure, called caGrid. In this paper we describe the caGrid framework and its current implementation, caGrid version 0.5. caGrid is a model-driven and service-oriented architecture that synthesizes and extends a number of technologies to provide a standardized framework for the advertising, discovery, and invocation of data and analytical resources. We expect caGrid to greatly facilitate the launch and ongoing management of coordinated cancer research studies involving multiple institutions, to provide the ability to manage and securely share information and analytic resources, and to spur a new generation of research applications that empower researchers to take a more integrative, trans-domain approach to data mining and analysis.

Availability: The caGrid version 0.5 release can be downloaded from . The operational test bed Grid can be accessed through the client included in the release, or through the caGrid-browser web application .

Contact:  joel.saltz@osumc.edu
Intramolecular surface contacts contain information about protein–protein interface regions
Authors: de Vries Sjoerd J. , Bonvin Alexandre M. J. J.
Published: June 2006

Motivation: Some amino acids clearly show preferences over others in protein–protein interfaces. These preferences, or so-called interface propensities can be used for a priori interface prediction. We investigated whether the prediction accuracy could be improved by considering not single but pairs of residues in an interface. Here we present the first systematic analysis of intramolecular surface contacts in interface prediction.

Results: We show that preferences do exist for contacts within and around an interface region within one molecule: specific pairs of amino acids are more often occurring than others. Using intramolecular contact propensities in a blind test, higher average scores were assigned to interface residues than to non-interface residues. This effect persisted as small but significant when the contact propensities were corrected to eliminate the influence of single amino acid interface propensity. This indicates that intramolecular contact propensities may replace interface propensities in protein–protein interface prediction.

Availability: The source code is available on request from the authors.

Contact:  a.m.j.j.bonvin@chem.uu.nl

Supplementary Information: Supplementary data are available at Bioinformatics online.
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
Authors: Bellew Matthew , Coram Marc , Fitzgibbon Matthew , Igra Mark , Randolph Tim , Wang Pei , May Damon , Eng Jimmy , Fang Ruihua , Lin ChenWei , Chen Jinzhi , Goodlett David , Whiteaker Jeffrey , Paulovich Amanda , McIntosh Martin
Published: June 2006

Motivation: Comparing two or more complex protein mixtures using liquid chromatography mass spectrometry (LC-MS) requires multiple analysis steps to locate and quantitate natural peptides within a single experiment and to align and normalize findings across multiple experiments.

Results: We describe msInspect, an open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental measurements. The platform integrates novel algorithms for detecting signatures of natural peptides within a single LC-MS measurement and combines multiple experimental measurements into a peptide array, which may then be mined using analysis tools traditionally applied to genomic array analysis. The platform supports quantitation by both label-free and isotopic labeling approaches. The software implementation has been designed so that many key components may be easily replaced, making it useful as a workbench for integrating other novel algorithms developed by a growing research community.

Availability: The msInspect software is distributed freely under an Apache 2.0 license. The software as well as a Zip file with all peptide feature files and scripts needed to generate the tables and figures in this article are available at

Contact:  mmcintos@fhcrc.org

Supplementary Information: Supplementary materials are available at (select ‘Published Experiments’ from the list of Projects and then ‘msInspect Paper’).
JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation
Authors: Li J.-L. , Li M.-X. , Guo Y.-F. , Deng H.-Y. , Deng H.-W.
Published: June 2006

Summary: The characterization of deleterious genomic mutation (DGM) is of central significance for evolutionary biology and genetic studies. Fitness moment method has been developed to efficiently characterize DGM from natural population directly. In order to enable researchers to employ this method for theoretical and empirical research on characterizing DGM, we here present a distributed Java Application for DGM Estimation (JADE).

Availability:  

Contact:  Jinlong.Li@sbri.org
Transcriptome network component analysis with limited microarray data
Authors: Galbraith Simon J. , Tran Linh M. , Liao James C.
Published: June 2006

Summary: Network component analysis (NCA) is a method to deduce transcription factor (TF) activities and TF-gene regulation control strengths from gene expression data and a TF-gene binding connectivity network. Previously, this method could analyze a maximum number of regulators equal to the total sample size because of the identifiability limit in data decomposition. As such, the total number of source signal components was limited to the total number of experiments rather than the total number of biological regulators. However, networks that have less transcriptome data points than the number of regulators are of interest. Thus it is imperative to develop a theoretical basis that allows realistic source signal extraction based on relatively few data points. On the other hand, such methods would inherently increase numerical challenges leading to multiple solutions. Therefore, solutions to both the problems are needed.

Results: We have improved NCA for transcription factor activity (TFA) estimation, based on the observation that most genes are regulated by only a few TFs. This observation leads to the derivation of a new identifiability criterion which is tested during numerical iteration that allows us to decompose data when the number of TFs is greater than the number of experiments. To show that our method works with real microarray data and has biological utility, we analyze Saccharomyces cerevisiae cell cycle microarray data (73 experiments) using a TF-gene connectivity network (96 TFs) derived from ChIP-chip binding data. We compare the results of NCA analysis with the results obtained from ChIP-chip regression methods, and we show that NCA and regression produce TFAs that are qualitatively similar, but the NCA TFAs outperform regression in statistical tests. We also show that NCA can extract subtle TFA signals that correlate with known cell cycle TF function and cell cycle phase. Overall we determined that 31 TFs have statistically periodic TFAs in one or more experiments, 75% of which are known cell cycle regulators. In addition, we find that the 12 TFAs that are periodic in two or more experiments correspond to well-known cell cycle regulators. We also investigated TFA sensitivity to the choice of connectivity network we constructed two networks using different ChIP-chip p-value cut-offs.

Availability: The NCA Toolbox for MATLAB is available at

Contact:  liaoj@seas.ucla.edu
Evolutionary simulations to detect functional lineage-specific genes
Authors: Dupanloup Isabelle , Kaessmann Henrik
Published: June 2006

Motivation: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference.

Results: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (∼1400 bp), restricted to hominoids, can be predicted to be functional in ∼94–100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale.

Availability: ReEVOLVER is available at .

Contact:  Henrik.Kaessmann@unil.ch

Supplementary Data: Supplementary Data are available at Bioinformatics online.
Combination of text-mining algorithms increases the performance
Authors: Malik Rainer , Franke Lude , Siebes Arno
Published: June 2006

Motivation: Recently, several information extraction systems have been developed to retrieve relevant information out of biomedical text. However, these methods represent individual efforts. In this paper, we show that by combining different algorithms and their outcome, the results improve significantly. For this reason, CONAN has been created, a system which combines different programs and their outcome. Its methods include tagging of gene/protein names, finding interaction and mutation data, tagging of biological concepts and linking to MeSH and Gene Ontology terms.

Results: In this paper, we will present data that show that combining different text-mining algorithms significantly improves the results. Not only is CONAN a full-scale approach that will ultimately cover all of PubMed/MEDLINE, we also show that this universality has no effect on quality: our system performs as well as or better than existing systems.

Availability: The LDD corpus presented is available by request to the author. The system will be available shortly. For information and updates on CONAN please visit

Contact:  rainer@cs.uu.nl

Supplementary information: Supplementary data are available at Bioinformatics online.
Application of the multiensemble sampling to the equilibrium folding of proteins
Authors: Son Hyeon S. , Kim Seung-Yeon , Lee Jooyoung , Han Kyu-Kwang
Published: June 2006

Motivation: Conventional Monte Carlo and molecular dynamics simulations of proteins in the canonical ensemble are of little use, because they tend to get trapped in states of energy local minima at low temperatures. One way to surmount this difficulty is to use a non-Boltzmann sampling method in which conformations are sampled upon a general weighting function instead of the conventional Boltzmann weighting function. The multiensemble sampling (MES) method is a non-Boltzmann sampling method that was originally developed to estimate free energy differences between systems with different potential energies and/or at different thermodynamic states. The method has not yet been applied to studies of complex molecular systems such as proteins.

Results: MES Monte Carlo simulations of small proteins have been carried out using a united-residue force field. The proteins at several temperatures from the unfolded to the folded states were simulated in a single MC run at a time and their equilibrium thermodynamic properties were calculated correctly. The distributions of sampled conformations clearly indicate that, when going through states of energy local minima, the MES simulation did not get trapped in them but escaped from them so quickly that all the relevant parts of conformation space could be sampled properly. A two-step folding process consisting of a collapse transition followed by a folding transition is observed. This study demonstrates that the use of MES alleviates the multiple-minima problem greatly.

Availability: Available on request from the authors

Contact:  khan@pcu.ac.kr

Supplementary information: A FORTRAN90 code of MES algorithm for MC simulation and its sample input have been deposited as Supplementary data available at Bioinformatics online.
Clustering microarray gene expression data using weighted Chinese restaurant process
Authors: Qin Zhaohui S.
Published: June 2006

Motivation: Clustering microarray gene expression data is a powerful tool for elucidating co-regulatory relationships among genes. Many different clustering techniques have been successfully applied and the results are promising. However, substantial fluctuation contained in microarray data, lack of knowledge on the number of clusters and complex regulatory mechanisms underlying biological systems make the clustering problems tremendously challenging.

Results: We devised an improved model-based Bayesian approach to cluster microarray gene expression data. Cluster assignment is carried out by an iterative weighted Chinese restaurant seating scheme such that the optimal number of clusters can be determined simultaneously with cluster assignment. The predictive updating technique was applied to improve the efficiency of the Gibbs sampler. An additional step is added during reassignment to allow genes that display complex correlation relationships such as time-shifted and/or inverted to be clustered together. Analysis done on a real dataset showed that as much as 30% of significant genes clustered in the same group display complex relationships with the consensus pattern of the cluster. Other notable features including automatic handling of missing data, quantitative measures of cluster strength and assignment confidence. Synthetic and real microarray gene expression datasets were analyzed to demonstrate its performance.

Availability: A computer program named Chinese restaurant cluster (CRC) has been developed based on this algorithm. The program can be downloaded at

Contact:  qin@umich.edu

Supplementary information:
NetAlign: a web-based tool for comparison of protein interaction networks
Authors: Liang Zhi , Xu Meng , Teng Maikun , Niu Liwen
Published: June 2006

Summary: NetAlign is a web-based tool designed to enable comparative analysis of protein interaction networks (PINs). NetAlign compares a query PIN with a target PIN by combining interaction topology and sequence similarity to identify conserved network substructures (CoNSs), which may derive from a common ancestor and disclose conserved topological organization of interactions in evolution. To exemplify the application of NetAlign, we perform two genome-scale comparisons with (1) the Escherichia coli PIN against the Helicobacter pylori PIN and (2) the Saccharomyces cerevisiae PIN against the Caenorrhabditis elegans PIN. Many of the identified CoNSs correspond to known complexes; therefore, cross-species PIN comparison provides a way for discovery of conserved modules. In addition, based on the species-to-species differences in CoNSs, we reformulate the problems of protein–protein interaction (PPI) prediction and species divergence from a network perspective.

Availability:  

Supplementary Data: Supplementary data are available at Bioinformatics online.

Contact:  mkteng@ustc.edu.cn, lwniu@ustc.edu.cn
THE PRIVATE SECTOR IMPACT OF STATE AND LOCAL GOVERNMENT: HAS MORE BECOME BAD?
Authors: TAYLOR LORI L. , BROWN STEPHEN P. A.
Published: June 2006

Early research suggests some increases in state and local government spending more than offset the negative effects of the tax increases needed to fund them. More recent research finds the growth of state and local government generally discourages private sector growth. Using panel data on private employment, capital and output for the 48 contiguous states, the authors find that government size influences whether additional government helps or hinders private sector growth. The rapid growth of state and local government in the late 1980s likely outstripped the willingness to pay. With government growth moderating in the 1990s, however, the private sector response has become more favorable. (JEL H3, H4, R5)
Imitating the neighbours: vocal dialect matching in a mimic–model system
Authors: Putland David A , Nicholls James A , Noad Michael J , Goldizen Anne W
Published: June 2006

Vocal mimicry provides a unique system for investigating song learning and cultural evolution in birds. Male lyrebirds produce complex vocal displays that include extensive and accurate mimicry of many other bird species. We recorded and analysed the songs of the Albert's lyrebird (
Menura alberti
) and its most commonly imitated model species, the satin bowerbird (
Ptilonorhynchus violaceus
), at six sites in southeast Queensland, Australia. We show that each population of lyrebirds faithfully reproduces the song of the local population of bowerbirds. Within a population, lyrebirds show less variation in song structure than the available variation in the songs of the models. These results provide the first quantitative evidence for dialect matching in the songs of two species that have no direct ecological relationship.
Dislocations in gradient elasticity revisited
Authors: Lazar Markus , Maugin Gérard A
Published: June 2006

In this paper, we consider dislocations in the framework of first as well as second gradient theory of elasticity. Using the Fourier transform, rigorous analytical solutions of the two-dimensional bi-Helmholtz and Helmholtz equations are derived in closed form for the displacement, elastic distortion, plastic distortion and dislocation density of screw and edge dislocations. In our framework, it was not necessary to use boundary conditions to fix constants of the solutions. The discontinuous parts of the displacement and plastic distortion are expressed in terms of two-dimensional as well as one-dimensional Fourier-type integrals. All other fields can be written in terms of modified Bessel functions.
Turbulent boundary-layer effects on transient wave propagation in shallow water
Authors: Liu Philip L.-F
Published: June 2006

The depth-integrated continuity and momentum equations developed by Liu & Orfila are extended to include the effects of turbulent bottom boundary layer. The eddy viscosity model is employed in the boundary layer, in which the eddy viscosity is assumed to be a power function of the vertical elevation from the bottom. The leading-order effects of the turbulent boundary layer appear as a convolution integral in the depth-integrated continuity equation because of the boundary-layer displacement. The bottom stress is also expressed as a convolution integral of the depth-averaged horizontal velocity. For simple harmonic progressive waves, the analytical expression for the phase shift between the bottom stress and the depth-averaged velocity is obtained. The analytical solutions for the solitary wave damping rate due to a turbulent boundary layer are also derived. Prandtl's one-seventh power law is described in detail as an example.
Crossing the impassable: genetic connections in 20 reef fishes across the eastern Pacific barrier
Authors: Lessios H.A , Robertson D.R
Published: June 2006

The ‘impassable’ Eastern Pacific Barrier (EPB),ca5000 km of deep water separating the eastern from the central Pacific, is the World's widest marine biogeographic barrier. Sequencing of mitochondrial DNA in 20 reef fish morphospecies encountered on both sides of the barrier revealed cryptic speciation in two. Among the other 18 species only two showed significant differentiation (as revealed by haplotype networks andFSTstatistics) between the eastern and the central Pacific. Coalescence analyses indicated that genetic similarity in the 18 truly transpacific species resulted from different combinations of ages of most recent invasion and of levels of recurrent gene flow, with estimated times of initial separation ranging from approximately 30 000 to 1 Myr (ago). There is no suggestion of simultaneous interruptions of gene flow among the species. Migration across the EPB was previously thought to be exclusively eastward, but our evidence showed two invasions from east to west and eight cases in which subsequent gene flow possibly proceeded in the same direction. Thus, the EPB is sporadically permeable to propagules originating on either side.
Pheromone-sensitive glomeruli in the primary olfactory centre of ants
Authors: Yamagata Nobuhiro , Nishino Hiroshi , Mizunami Makoto
Published: June 2006

Tremendous evolutional success and the ecological dominance of social insects, including ants, termites and social bees, are due to their efficient social organizations and their underlying communication systems. Functional division into reproductive and sterile castes, cooperation in defending the nest, rearing the young and gathering food are all regulated by communication by means of various kinds of pheromones. No brain structures specifically involved in the processing of non-sexual pheromone have been physiologically identified in any social insects. By use of intracellular recording and staining techniques, we studied responses of projection neurons of the antennal lobe (primary olfactory centre) of ants to alarm pheromone, which plays predominant roles in colony defence. Among 23 alarm pheromone-sensitive projection neurons recorded and stained in this study, eight were uniglomerular projection neurons with dendrites in one glomerulus, a structural unit of the antennal lobe, and the remaining 15 were multiglomerular projection neurons with dendrites in multiple glomeruli. Notably, all alarm pheromone-sensitive uniglomerular projection neurons had dendrites in one of five ‘alarm pheromone-sensitive (AS)’ glomeruli that form a cluster in the dorsalmost part of the antennal lobe. All alarm pheromone-sensitive multiglomerular projection neurons had dendrites in some of the AS glomeruli as well as in glomeruli in the anterodorsal area of the antennal lobe. The results suggest that components of alarm pheromone are processed in a specific cluster of glomeruli in the antennal lobe of ants.
Vervet monkeys and humans show brain asymmetries for processing conspecific vocalizations, but with opposite patterns of laterality
Authors: Gil-da-Costa Ricardo , Hauser Marc D
Published: June 2006

A robust finding in the human neurosciences is the observation of a left hemisphere specialization for processing spoken language. Previous studies suggest that this auditory specialization and brain asymmetry derive from a primate ancestor. Most of these studies focus on the genusMacacaand all demonstrate a left hemisphere bias. Due to the narrow taxonomic scope, however, we lack a sense of the distribution of this asymmetry among primates. Further, although the left hemisphere bias appears mediated by conspecific calls, other possibilities exist including familiarity, emotional relevance and more general acoustic properties of the signal. To broaden the taxonomic scope and test the specificity of the apparent hemisphere bias, we conducted an experiment on vervets (Cercopithecus aethiops)—a different genus of old world monkeys and implemented the relevant acoustic controls. Using the same head orienting procedure tested with macaques, results show a strong left ear/right hemisphere bias for conspecific vocalizations (both familiar and unfamiliar), but no asymmetry for other primate vocalizations or non-biological sounds. These results suggest that although auditory asymmetries for processing species-specific vocalizations are a common feature of the primate brain, the direction of this asymmetry may be relatively plastic. This finding raises significant questions for how ontogenetic and evolutionary forces have impacted on primate brain evolution.
RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humans
Authors: Shen Haihong , Green Michael R.
Published: June 2006

Serine–arginine (SR) proteins are general metazoan splicing factors that contain an essential arginine–serine-rich (RS) domain. We have previously found that mammalian spliceosome assembly involves a series of sequential interactions between RS domains and two splicing signals: the branchpoint and the 5′ splice site. Here we study how RS domains are directed to specifically contact splicing signals, and how this interaction promotes splicing. The yeast Saccharomyces cerevisiae lacks SR proteins. However, we show that tethering a mammalian RS domain to a yeast actin pre-mRNA rescues splicing of certain branchpoint or 5′ splice site mutants in which U snRNA base-pairing has been decreased. Conversely, on a mammalian pre-mRNA, a normally essential SR protein becomes dispensable when the complementarity of a splicing signal to a U snRNA is increased. We find that in the absence of other splicing factors an RS domain tethered to a pre-mRNA selectively contacts a double-stranded RNA region and enhances RNA–RNA base-pairing. Significantly, all of these activities require phosphorylation of the RS domain. Based on these results, we propose that RS domains selectively contact splicing signals because, due to transient U snRNA base-pairing, they are partially double-stranded. The RS domain–splicing signal interaction, in turn, promotes (or stabilizes) base-pairing between the U snRNA and pre-mRNA substrate, thereby enhancing splicing. Our results reveal a common mechanism of RS domain function in yeast through humans.
Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes
Authors: Watanabe Toshiaki , Takeda Atsushi , Tsukiyama Tomoyuki , Mise Kazuyuki , Okuno Tetsuro , Sasaki Hiroyuki , Minami Naojiro , Imai Hiroshi
Published: June 2006

Small RNAs ranging in size between 18 and 30 nucleotides (nt) are found in many organisms including yeasts, plants, and animals. Small RNAs are involved in the regulation of gene expression through translational repression, mRNA degradation, and chromatin modification. In mammals, microRNAs (miRNAs) are the only small RNAs that have been well characterized. Here, we have identified two novel classes of small RNAs in the mouse germline. One class consists of ∼20- to 24-nt small interfering RNAs (siRNAs) from mouse oocytes, which are derived from retroelements including LINE, SINE, and LTR retrotransposons. Addition of retrotransposon-derived sequences to the 3′ untranslated region (UTR) of a reporter mRNA destabilizes the mRNA significantly when injected into full-grown oocytes. These results suggest that retrotransposons are suppressed through the RNAi pathway in mouse oocytes. The other novel class of small RNAs is 26- to 30-nt germline small RNAs (gsRNAs) from testes. gsRNAs are expressed during spermatogenesis in a developmentally regulated manner, are mapped to the genome in clusters, and have strong strand bias. These features are reminiscent of Tetrahymena ∼23- to 24-nt small RNAs and Caenorhabditis elegans X-cluster small RNAs. A conserved novel small RNA pathway may be present in diverse animals.
A novel class of small RNAs in mouse spermatogenic cells
Authors: Grivna Shane T. , Beyret Ergin , Wang Zhong , Lin Haifan
Published: June 2006

Small noncoding RNAs, including small interfering RNAs (siRNAs) and micro RNAs (miRNAs) of ∼21 nucleotides (nt) in length, have emerged as potent regulators of gene expression at both transcriptional and post-transcriptional levels in diverse organisms. Here we report the identification of a novel class of small RNAs in the mouse male germline termed piwi-interacting RNAs (piRNAs). piRNAs are ∼30 nt in length. They are expressed during spermatogenesis, mostly in spermatids. piRNAs are associated with MIWI, a spermatogenesis-specific PIWI subfamily member of the Argonaute protein family, and depend on MIWI for their biogenesis and/or stability. Furthermore, a subpopulation of piRNAs are associated with polysomes, suggesting their potential role in translational regulation.
Identification of Features Regulating OST1 Kinase Activity and OST1 Function in Guard Cells
Authors: Belin Christophe , de Franco Pierre-Olivier , Bourbousse Clara , Chaignepain Stéphane , Schmitter Jean-Marie , Vavasseur Alain , Giraudat Jérôme , Barbier-Brygoo Hélène , Thomine Sébastien
Published: June 2006

The phytohormone abscisic acid (ABA) mediates drought responses in plants and, in particular, triggers stomatal closure. Snf1-related kinase 2 (SnRK2) proteins from several plant species have been implicated in ABA-signaling pathways. In Arabidopsis (Arabidopsis thaliana) guard cells, OPEN STOMATA 1 (OST1)/SRK2E/SnRK2-6 is a critical positive regulator of ABA signal transduction. A better understanding of the mechanisms responsible for SnRK2 protein kinase activation is thus a major goal toward understanding ABA signal transduction. Here, we report successful purification of OST1 produced in Escherichia coli: The protein is active and autophosphorylates. Using mass spectrometry, we identified five target residues of autophosphorylation in recombinant OST1. Sequence analysis delineates two conserved boxes located in the carboxy-terminal moiety of OST1 after the catalytic domain: the SnRK2-specific box (glutamine-303 to proline-318) and the ABA-specific box (leucine-333 to methionine-362). Site-directed mutagenesis and serial deletions reveal that serine (Ser)-175 in the activation loop and the SnRK2-specific box are critical for the activity of recombinant OST1 kinase. Targeted expression of variants of OST1 kinase in guard cells uncovered additional features that are critical for OST1 function in ABA signaling, although not required for OST1 kinase activity: Ser-7, Ser-18, and Ser-29 and the ABA-specific box. Ser-7, Ser-18, Ser-29, and Ser-43 represent putative targets for regulatory phosphorylation and the ABA-specific box may be a target for the binding of signaling partners in guard cells.
Induction of Abscisic Acid-Regulated Gene Expression by Diacylglycerol Pyrophosphate Involves Ca2+ and Anion Currents in Arabidopsis Suspension Cells
Authors: Zalejski Christine , Paradis Sophie , Maldiney Régis , Habricot Yvette , Miginiac Emile , Rona Jean-Pierre , Jeannette Emmanuelle
Published: June 2006

Diacylglycerol pyrophosphate (DGPP) was recently shown to be a possible intermediate in abscisic acid (ABA) signaling. In this study, reverse transcription-PCR of ABA up-regulated genes was used to evaluate the ability of DGPP to trigger gene expression in Arabidopsis (Arabidopsis thaliana) suspension cells. At5g06760, LTI30, RD29A, and RAB18 were stimulated by ABA and also specifically expressed in DGPP-treated cells. Use of the Ca2+ channel blockers fluspirilene and pimozide and the Ca2+ chelator EGTA showed that Ca2+ was required for ABA induction of DGPP formation. In addition, Ca2+ participated in DGPP induction of gene expression via stimulation of anion currents. Hence, a sequence of Ca2+, DGPP, and anion currents, constituting a core of early ABA-signaling events necessary for gene expression, is proposed.
Analysis of the Subcellular Localization, Function, and Proteolytic Control of the Arabidopsis Cyclin-Dependent Kinase Inhibitor ICK1/KRP1
Authors: Jakoby Marc J. , Weinl Christina , Pusch Stefan , Kuijt Suzanne J.H. , Merkle Thomas , Dissmeyer Nico , Schnittger Arp
Published: June 2006

Recent studies have shown that cyclin-dependent kinase (CDK) inhibitors can have a tremendous impact on cell cycle progression in plants. In animals, CDK inhibitors are tightly regulated, especially by posttranslational mechanisms of which control of nuclear access and regulation of protein turnover are particularly important. Here we address the posttranslational regulation of INHIBITOR/INTERACTOR OF CDK 1 (ICK1)/KIP RELATED PROTEIN 1 (KRP1), an Arabidopsis (Arabidopsis thaliana) CDK inhibitor. We show that ICK1/KRP1 exerts its function in the nucleus and its presence in the nucleus is controlled by multiple nuclear localization signals as well as by nuclear export. In addition, we show that ICK1/KRP1 localizes to different subnuclear domains, i.e. in the nucleoplasm and to the chromocenters, hinting at specific actions within the nuclear compartment. Localization to the chromocenters is mediated by an N-terminal domain, in addition we find that this domain may be involved in cyclin binding. Further we demonstrate that ICK1/KRP1 is an unstable protein and degraded by the 26S proteasome in the nucleus. This degradation is mediated by at least two domains indicating the presence of at least two different pathways impinging on ICK1/KRP1 protein stability.
Biosynthesis of Ascorbic Acid in Legume Root Nodules
Authors: Matamoros Manuel A. , Loscos Jorge , Coronado Maria J. , Ramos Javier , Sato Shusei , Testillano Pilar S. , Tabata Satoshi , Becana Manuel
Published: June 2006

Ascorbic acid (vitamin C) is a major antioxidant and redox buffer, but is also involved in other critical processes of plants. Recently, the hypothesis has been proposed that legume nodules are unable to synthesize ascorbate and have to import it from the shoot or root, thus providing a means by which the plant regulates nodule senescence. The last step of ascorbate biosynthesis in plants is catalyzed by l-galactono-1,4-lactone dehydrogenase (GalLDH). The mRNAs encoding GalLDH and three other enzymes involved in ascorbate biosynthesis are clearly detectable in nodules. Furthermore, an active membrane-bound GalLDH enzyme is present in nodule mitochondria. Biochemical assays on dissected nodules reveal that GalLDH activity and ascorbate are correlated in nodule tissues and predominantly localized in the infected zone, with lower levels of both parameters (relative to the infected tissues) in the apex (87%) and senescent region (43%) of indeterminate nodules and in the peripheral tissues (65%) of determinate nodules. In situ RNA hybridization showed that the GalLDH mRNA is particularly abundant in the infected zone of indeterminate and determinate nodules. Thus, our results refute the hypothesis that ascorbate is not synthesized in nodules and lend support to a previous conclusion that ascorbate in the infected zone is primarily involved in the protection of host cells against peroxide damage. Likewise, the high ascorbate and GalLDH activity levels found in the apex of indeterminate nodules strongly suggest a participation of ascorbate in additional functions during symbiosis, possibly related to cell growth and division and to molecular signaling.
Glyphosate-Induced Anther Indehiscence in Cotton Is Partially Temperature Dependent and Involves Cytoskeleton and Secondary Wall Modifications and Auxin Accumulation
Authors: Yasuor Hagai , Abu-Abied Mohamad , Belausov Eduard , Madmony Anat , Sadot Einat , Riov Joseph , Rubin Baruch
Published: June 2006

Yield reduction caused by late application of glyphosate to glyphosate-resistant cotton (Gossypium hirsutum; GRC) expressing CP4 5-enol-pyruvylshikmate-3-P synthase under the cauliflower mosaic virus-35S promoter has been attributed to male sterility. This study was aimed to elucidate the factors and mechanisms involved in this phenomenon. Western and tissue-print blots demonstrated a reduced expression of the transgene in anthers of GRC compared to ovules of the same plants. Glyphosate application to GRC grown at a high temperature regime after the initiation of flower buds caused a complete loss of pollen viability and inhibition of anther dehiscence, while at a moderate temperature regime only 50% of the pollen grains were disrupted and anther dehiscence was normal. Glyphosate-damaged anthers exhibited a change in the deposition of the secondary cell wall thickenings (SWT) in the endothecium cells, from the normal longitudinal orientation to a transverse orientation, and hindered septum disintegration. These changes occurred only at the high temperature regime. The reorientation of SWT in GRC was accompanied by a similar change in microtubule orientation. A similar reorientation of microtubules was also observed in Arabidopsis (Arabidopsis thaliana) seedlings expressing green fluorescent protein tubulin (tubulin α 6) following glyphosate treatment. Glyphosate treatment induced the accumulation of high levels of indole-3-acetic acid in GRC anthers. Cotton plants treated with 2,4-dichlorophenoxyacetic acid had male sterile flowers, with SWT abnormalities in the endothecium layer similar to those observed in glyphosate-treated plants. Our data demonstrate that glyphosate inhibits anther dehiscence by inducing changes in the microtubule and cell wall organization in the endothecium cells, which are mediated by auxin.
CYP71B15 (PAD3) Catalyzes the Final Step in Camalexin Biosynthesis
Authors: Schuhegger Regina , Nafisi Majse , Mansourova Madina , Petersen Bent Larsen , Olsen Carl Erik , Svatoš Aleš , Halkier Barbara Ann , Glawischnig Erich
Published: June 2006

Camalexin represents the main phytoalexin in Arabidopsis (Arabidopsis thaliana). The camalexin-deficient phytoalexin deficient 3 (pad3) mutant has been widely used to assess the biological role of camalexin, although the exact substrate of the cytochrome P450 enzyme 71B15 encoded by PAD3 remained elusive. 2-(Indol-3-yl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid (dihydrocamalexic acid) was identified as likely intermediate in camalexin biosynthesis downstream of indole-3-acetaldoxime, as it accumulated in leaves of silver nitrate-induced pad3 mutant plants and it complemented the camalexin-deficient phenotype of a cyp79b2/cyp79b3 double-knockout mutant. Recombinant CYP71B15 heterologously expressed in yeast catalyzed the conversion of dihydrocamalexic acid to camalexin with preference of the (S)-enantiomer. Arabidopsis microsomes isolated from leaves of CYP71B15-overexpressing and induced wild-type plants were capable of the same reaction but not microsomes from induced leaves of pad3 mutants. In conclusion, CYP71B15 catalyzes the final step in camalexin biosynthesis.
New Construct Approaches for Efficient Gene Silencing in Plants
Authors: Yan Hua , Chretien Robert , Ye Jingsong , Rommens Caius M.
Published: June 2006

An important component of conventional sense, antisense, and double-strand RNA-based gene silencing constructs is the transcriptional terminator. Here, we show that this regulatory element becomes obsolete when gene fragments are positioned between two oppositely oriented and functionally active promoters. The resulting convergent transcription triggers gene silencing that is at least as effective as unidirectional promoter-to-terminator transcription. In addition to short, variably sized, and nonpolyadenylated RNAs, terminator-free cassette produced rare, longer transcripts that reach into the flanking promoter. These read-through products did not influence the efficacy and expression levels of the neighboring hygromycin phosphotransferase gene. Replacement of gene fragments by promoter-derived sequences further increased the extent of gene silencing. This finding indicates that genomic DNA may be a more efficient target for gene silencing than gene transcripts.
Long-Term Submergence-Induced Elongation in Rumex palustris Requires Abscisic Acid-Dependent Biosynthesis of Gibberellin1
Authors: Benschop Joris J. , Bou Jordi , Peeters Anton J.M. , Wagemaker Niels , Gühl Kerstin , Ward Dennis , Hedden Peter , Moritz Thomas , Voesenek Laurentius A.C.J.
Published: June 2006

Rumex palustris (polygonceae) responds to complete submergence with enhanced elongation of its youngest petioles. This process requires the presence of gibberellin (GA) and is associated with an increase in the concentration of GA1 in elongating petioles. We have examined how GA biosynthesis was regulated in submerged plants. Therefore, cDNAs encoding GA-biosynthetic enzymes GA 20-oxidase and GA 3-oxidase, and the GA-deactivating enzyme GA 2-oxidase were cloned from R. palustris and the kinetics of transcription of the corresponding genes was determined during a 24 h submergence period. The submergence-induced elongation response could be separated into several phases: (1) during the first phase of 4 h, petiole elongation was insensitive to GA; (2) from 4 to 6 h onward growth was limited by GA; and (3) from 15 h onward underwater elongation was dependent, but not limited by GA. Submergence induced an increase of GA1 concentration, as well as enhanced transcript levels of RpGA3ox1. Exogenous abscisic acid repressed the transcript levels of RpGA20ox1 and RpGA3ox1 and thus inhibited the submergence-induced increase in GA1. Abscisic acid had no effect on the tissue responsiveness to GA.