bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local RNA structure alignment with incomplete sequence
Authors: Kolbe Diana L. , Eddy Sean R. 
Published: March 2009

Abstract
Motivation: Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing.
Results: We present a local RNA structural alignment algorithm, trCYK, for aligning and scoring incomplete sequences under a model using primary sequence conservation and secondary structure information when possible. The trCYK algorithm improves alignment accuracy and coverage of sequence fragments of structural RNAs in simulated metagenomic shotgun datasets.
Availability: The source code for Infernal 1.0, which includes trCYK, is available at http://infernal.janelia.org
Contact: kolbed@janelia.hhmi.org; eddys@janelia.hhmi.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated diagnosis of LC-MS/MS performance
Authors: Xu Hua , Freitas Michael A. 
Published: March 2009

Abstract
Summary: We report a software scheme for automated diagnosis of liquid chromatography tandem mass spectrometry (LC-MS/MS) system performance. The proposed software scheme provides a robust framework for establishing automated diagnosis of LC-MS/MS system performance for a variety of instruments and experiments. This schematic consists of four main software components: (i) data conversion, (ii) peptide identification, (iii) LC retention time analysis and (iv) system performance evaluation. The implementation of a standard approach for assessing LC-MS/MS system performance enables researchers to apply reliable metrics to assess their workflows performance over different batch experiments. Furthermore, the results from system diagnosis can provide feedback to the workflow to stop batch analysis if system performance falls below prescribed thresholds. A basic implementation of the approach based on the MassMatrix database search and LC retention time analysis programs is presented.
Availability: An open source implementation of the LC-MS/MS system diagnosis software based on the MassMatrix database search program is freely available to non-commercial users and can be downloaded at www.massmatrix.net.
Contact: huaxu@uic.edu; freitas.5@osu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models
Authors: Bois Frédéric Y. 
Published: March 2009

Abstract
Summary: Statistical inference about the parameter values of complex models, such as the ones routinely developed in systems biology, is efficiently performed through Bayesian numerical techniques. In that framework, prior information and multiple levels of uncertainty can be seamlessly integrated. GNU MCSim was precisely developed to achieve those aims, in a general non-linear differential context. Starting with version 5.3.0, GNU MCSim reads in and simulates Systems Biology Markup Language models. Markov chain Monte Carlo simulations can be used to generate samples from the joint posterior distribution of the model parameters, given a dataset and prior distributions. Hierarchical statistical models can be used. Optimal design of experiments can also be investigated.
Availability and Implementation: The GNU GPL source is available at http://savannah.gnu.org/projects/mcsim. A distribution package is at http://www.gnu.org/software/mcsim. GNU MCSim is written in standard C and runs on any platform supporting a C compiler. Supplementary Material is available online at http://www.gnu.org/software/mcsim.
Contact: frederic.bois@ineris.fr
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Authors: Cock Peter J. A. , Antao Tiago , Chang Jeffrey T. , Chapman Brad A. , Cox Cymon J. , Dalke Andrew , Friedberg Iddo , Hamelryck Thomas , Kauff Frank , Wilczynski Bartek , de Hoon Michiel J. L. 
Published: March 2009

Abstract
Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license.
Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk.
BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server
Authors: Geeleher Paul , Morris Dermot , Hinde John P. , Golden Aaron 
Published: March 2009

Abstract
Summary: BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets.
Availability: BioconductorBuntu is available for download under a creative commons license along with additional documentation and a tutorial from http://bioinf.nuigalway.ie
Contact: paul.geeleher@nuigalway.ie
Investigating and mitigating uncertainties in the assessment of Scottish Nephrops norvegicus populations using simulated underwater television data
Authors: Campbell N. , Dobby H. , Bailey N. 
Published: March 2009

AbstractCampbell, N., Dobby, H., and Bailey, N. 2009. Investigating and mitigating uncertainties in the assessment of Scottish Nephrops norvegicus populations using simulated underwater television data. – ICES Journal of Marine Science, 66: 646–655. Nephrops norvegicus is a commercially significant decapod crustacean that excavates and inhabits burrows in muddy sediments throughout the Northeast Atlantic and Mediterranean Sea. Because of its variable emergence behaviour, traditional surveys are considered a poor indicator of the status of its populations, and underwater television (TV) survey methods have been developed. The approach involves towing a TV camera over patches of muddy sediment and counting the number of Nephrops burrow complexes within a known area. Assuming a 1:1 rate of occupancy, the average population density can be estimated. This is raised to the known area of suitable sediment to give a measure of population size. Recently, underwater TV surveys have been used to provide absolute measures of abundance for a number of Nephrops stocks in the North Sea and Northeast Atlantic. It is therefore imperative to identify, quantify, and control for uncertainties in this process. Previous workers have suggested that visual recognition of Nephrops burrows and “edge effects”, where single openings of burrow complexes at the sides of the viewed transect are counted, are important sources of uncertainty. This study shows edge effects to be responsible for an overestimation of population size of between 4 and 55%, depending on the width of the field of view and the mean size of the burrow complex. This overestimation is countered to some extent by variability in burrow entrance structure, which leads to Nephrops burrows going unrecognized. The scales of these errors are discussed in relation to observed sediment softness, sediment distribution, and burrow dimensions from sites around Scotland.
Phospholipase D Activation Is an Early Component of the Salicylic Acid Signaling Pathway in Arabidopsis Cell Suspensions
Authors: Krinke Ondřej , Flemr Matyáš , Vergnolle Chantal , Collin Sylvie , Renou Jean-Pierre , Taconnat Ludivine , Yu Agnès , Burketová Lenka , Valentová Olga , Zachowski Alain , Ruelland Eric 
Published: March 2009

Abstract
Salicylic acid (SA) plays a central role in defense against pathogen attack, as well as in germination, flowering, senescence, and the acquisition of thermotolerance. In this report we investigate the involvement of phospholipase D (PLD) in the SA signaling pathway. In presence of exogenous primary alcohols, the production of phosphatidic acid by PLD is diverted toward the formation of phosphatidylalcohols through a reaction called transphosphatidylation. By in vivo metabolic phospholipid labeling with 33Pi, PLD activity was found to be induced 45 min after addition of SA. We show that incubation of Arabidopsis (Arabidopsis thaliana) cell suspensions with primary alcohols inhibited the induction of two SA-responsive genes, PATHOGENESIS-RELATED1 and WRKY38, in a dose-dependent manner. This inhibitory effect was more pronounced when the primary alcohols were more hydrophobic. Secondary or tertiary alcohols had no inhibitory effect. These results provide compelling arguments for PLD activity being upstream of the induction of these genes by SA. A subsequent study of n-butanol effects on the SA-responsive transcriptome identified 1,327 genes differentially expressed upon SA treatment. Strikingly, the SA response of 380 of these genes was inhibited by n-butanol but not by tert-butanol. A detailed analysis of the regulation of these genes showed that PLD could act both positively and negatively, either on gene induction or gene repression. The overlap with the previously described phosphatidylinositol-4-kinase pathway is discussed.
The Synthetic Elicitor 3,5-Dichloroanthranilic Acid InducesNPR1-Dependent andNPR1-Independent Mechanisms of Disease Resistance in Arabidopsis
Authors: Knoth Colleen , Salus Melinda S. , Girke Thomas , Eulgem Thomas 
Published: March 2009

AbstractImmune responses of Arabidopsis (Arabidopsis thaliana) are at least partially mediated by coordinated transcriptional up-regulation of plant defense genes, such as the Late/sustained Up-regulation in Response to Hyaloperonospora parasitica (LURP) cluster. We found a defined region in the promoter of the LURP member CaBP22 to be important for this response. Using a CaBP22 promoter-reporter fusion, we have established a robust and specific high-throughput screening system for synthetic defense elicitors that can be used to trigger defined subsets of plant immune responses. Screening a collection of 42,000 diversity-oriented molecules, we identified 114 candidate LURP inducers. One representative, 3,5-dichloroanthranilic acid (DCA), efficiently induced defense reactions to the phytopathogens H. parasitica and Pseudomonas syringae. In contrast to known salicylic acid analogs, such as 2,6-dichloroisonicotinic acid (INA), which exhibit a long-lasting defense-inducing activity and are fully dependent on the transcriptional cofactor NPR1 (for Nonexpresser of Pathogenesis-Related genes1), DCA acts transiently and is only partially dependent on NPR1. Microarray analyses revealed a cluster of 142 DCA- and INA-responsive genes that show a pattern of differential expression coinciding with the kinetics of DCA-mediated disease resistance. These ACID genes (for Associated with Chemically Induced Defense) constitute a core gene set associated with chemically induced disease resistance, many of which appear to encode components of the natural immune system of Arabidopsis.
The Analysis of Arabidopsis Nicotianamine Synthase Mutants Reveals Functions for Nicotianamine in Seed Iron Loading and Iron Deficiency Responses
Authors: Klatte Marco , Schuler Mara , Wirtz Markus , Fink-Straube Claudia , Hell Rüdiger , Bauer Petra 
Published: March 2009

Abstract
Nicotianamine chelates and transports micronutrient metal ions in plants. It has been speculated that nicotianamine is involved in seed loading with micronutrients. A tomato (Solanum lycopersicum) mutant (chloronerva) and a tobacco (Nicotiana tabacum) transgenic line have been utilized to analyze the effects of nicotianamine loss. These mutants showed early leaf chlorosis and had sterile flowers. Arabidopsis (Arabidopsis thaliana) has four NICOTIANAMINE SYNTHASE (NAS) genes. We constructed two quadruple nas mutants: one had full loss of NAS function, was sterile, and showed a chloronerva-like phenotype (nas4x-2); another mutant, with intermediate phenotype (nas4x-1), developed chlorotic leaves, which became severe upon transition from the vegetative to the reproductive phase and upon iron (Fe) deficiency. Residual nicotianamine levels were sufficient to sustain the life cycle. Therefore, the nas4x-1 mutant enabled us to study late nicotianamine functions. This mutant had no detectable nicotianamine in rosette leaves of the reproductive stage but low nicotianamine levels in vegetative rosette leaves and seeds. Fe accumulated in the rosette leaves, while less Fe was present in flowers and seeds. Leaves, roots, and flowers showed symptoms of Fe deficiency, whereas leaves also showed signs of sufficient Fe supply, as revealed by molecular-physiological analysis. The mutant was not able to fully mobilize Fe to sustain Fe supply of flowers and seeds in the normal way. Thus, nicotianamine is needed for correct supply of seeds with Fe. These results are fundamental for plant manipulation approaches to modify Fe homeostasis regulation through alterations of NAS genes.
SHALLOT-LIKE1 Is a KANADI Transcription Factor That Modulates Rice Leaf Rolling by Regulating Leaf Abaxial Cell Development
Authors: Zhang Guang-Heng , Xu Qian , Zhu Xu-Dong , Qian Qian , Xue Hong-Wei 
Published: March 2009

AbstractAs an important agronomic trait, rice (Oryza sativa L.) leaf rolling has attracted much attention from plant biologists and breeders. Moderate leaf rolling increases the photosynthesis of cultivars and hence raises grain yield. However, the relevant molecular mechanism remains unclear. Here, we show the isolation and functional characterization of SHALLOT-LIKE1 (SLL1), a key gene controlling rice leaf rolling. sll1 mutant plants have extremely incurved leaves due to the defective development of sclerenchymatous cells on the abaxial side. Defective development can be functionally rescued by expression of SLL1. SLL1 is transcribed in various tissues and accumulates in the abaxial epidermis throughout leaf development. SLL1 encodes a SHAQKYF class MYB family transcription factor belonging to the KANADI family. SLL1 deficiency leads to defective programmed cell death of abaxial mesophyll cells and suppresses the development of abaxial features. By contrast, enhanced SLL1 expression stimulates phloem development on the abaxial side and suppresses bulliform cell and sclerenchyma development on the adaxial side. Additionally, SLL1 deficiency results in increased chlorophyll and photosynthesis. Our findings identify the role of SLL1 in the modulation of leaf abaxial cell development and in sustaining abaxial characteristics during leaf development. These results should facilitate attempts to use molecular breeding to increase the photosynthetic capacity of rice, as well as other crops, by modulating leaf development and rolling.
A Single Vegetative Actin Isovariant Overexpressed under the Control of Multiple Regulatory Sequences Is Sufficient for NormalArabidopsisDevelopment
Authors: Kandasamy Muthugapatti K. , McKinney Elizabeth C. , Meagher Richard B. 
Published: March 2009

AbstractThe relative significance of gene regulation and protein isovariant differences remains unexplored for most gene families, particularly those participating in multicellular development. Arabidopsis thaliana encodes three vegetative actins, ACT2, ACT7, and ACT8, in two ancient and highly divergent subclasses. Mutations in any of these differentially expressed actins revealed only mild phenotypes. However, double mutants were extremely dwarfed, with altered cell and organ morphology and an aberrant F-actin cytoskeleton (e.g., act2-1 act7-4 and act8-2 act7-4) or totally root-hairless (e.g., act2-1 act8-2). Our studies suggest that the three vegetative actin genes and protein isovariants play distinct subclass-specific roles during plant morphogenesis. For example, during root development, ACT7 was involved in root growth, epidermal cell specification, cell division, and root architecture, and ACT2 and ACT8 were essential for root hair tip growth. Also, genetic complementation revealed that the ACT2 and ACT8 isovariants, but not ACT7, fully rescued the root hair growth defects of single and double mutants. Moreover, we synthesized fully normal plants overexpressing the ACT8 isovariant from multiple actin regulatory sequences as the only vegetative actin in the act2-1 act7-4 background. In summary, it is evident that differences in vegetative actin gene regulation and the diversity in actin isovariant sequences are essential for normal plant development.
Pheophytin Pheophorbide Hydrolase (Pheophytinase) Is Involved in Chlorophyll Breakdown during Leaf Senescence in Arabidopsis
Authors: Schelbert Silvia , Aubry Sylvain , Burla Bo , Agne Birgit , Kessler Felix , Krupinska Karin , Hörtensteiner Stefan 
Published: March 2009

Abstract
During leaf senescence, chlorophyll is removed from thylakoid membranes and converted in a multistep pathway to colorless breakdown products that are stored in vacuoles. Dephytylation, an early step of this pathway, increases water solubility of the breakdown products. It is widely accepted that chlorophyll is converted into pheophorbide via chlorophyllide. However, chlorophyllase, which converts chlorophyll to chlorophyllide, was found not to be essential for dephytylation in Arabidopsis thaliana. Here, we identify pheophytinase (PPH), a chloroplast-located and senescence-induced hydrolase widely distributed in algae and land plants. In vitro, Arabidopsis PPH specifically dephytylates the Mg-free chlorophyll pigment, pheophytin (phein), yielding pheophorbide. An Arabidopsis mutant deficient in PPH (pph-1) is unable to degrade chlorophyll during senescence and therefore exhibits a stay-green phenotype. Furthermore, pph-1 accumulates phein during senescence. Therefore, PPH is an important component of the chlorophyll breakdown machinery of senescent leaves, and we propose that the sequence of early chlorophyll catabolic reactions be revised. Removal of Mg most likely precedes dephytylation, resulting in the following order of early breakdown intermediates: chlorophyll → pheophytin → pheophorbide. Chlorophyllide, the last precursor of chlorophyll biosynthesis, is most likely not an intermediate of breakdown. Thus, chlorophyll anabolic and catabolic reactions are metabolically separated.
The ESCRT-Related CHMP1A and B Proteins Mediate Multivesicular Body Sorting of Auxin Carriers inArabidopsisand Are Required for Plant Development
Authors: Spitzer Christoph , Reyes Francisca C. , Buono Rafael , Sliwinski Marek K. , Haas Thomas J. , Otegui Marisa S. 
Published: March 2009

AbstractPlasma membrane proteins internalized by endocytosis and targeted for degradation are sorted into lumenal vesicles of multivesicular bodies (MVBs) by the endosomal sorting complexes required for transport (ESCRT) machinery. Here, we show that the Arabidopsis thaliana ESCRT-related CHARGED MULTIVESICULAR BODY PROTEIN/CHROMATIN MODIFYING PROTEIN1A (CHMP1A) and CHMP1B proteins are essential for embryo and seedling development. Double homozygous chmp1a chmp1b mutant embryos showed limited polar differentiation and failed to establish bilateral symmetry. Mutant seedlings show disorganized apical meristems and rudimentary true leaves with clustered stomata and abnormal vein patterns. Mutant embryos failed to establish normal auxin gradients. Three proteins involved in auxin transport, PINFORMED1 (PIN1), PIN2, and AUXIN-RESISTANT1 (AUX1) mislocalized to the vacuolar membrane of the mutant. PIN1 was detected in MVB lumenal vesicles of control cells but remained in the limiting membrane of chmp1a chmp1b MVBs. The chmp1a chmp1b mutant forms significantly fewer MVB lumenal vesicles than the wild type. Furthermore, CHMP1A interacts in vitro with the ESCRT-related proteins At SKD1 and At LIP5. Thus, Arabidopsis CHMP1A and B are ESCRT-related proteins with conserved endosomal functions, and the auxin carriers PIN1, PIN2, and AUX1 are ESCRT cargo proteins in the MVB sorting pathway.
Disruption of Adenosine-5′-Phosphosulfate Kinase inArabidopsisReduces Levels of Sulfated Secondary Metabolites
Authors: Mugford Sarah G. , Yoshimoto Naoko , Reichelt Michael , Wirtz Markus , Hill Lionel , Mugford Sam T. , Nakazato Yoshimi , Noji Masaaki , Takahashi Hideki , Kramell Robert , Gigolashvili Tamara , Flügge Ulf-Ingo , Wasternack Claus , Gershenzon Jonathan , Hell Rüdiger , Saito Kazuki , Kopriva Stanislav 
Published: March 2009

AbstractPlants can metabolize sulfate by two pathways, which branch at the level of adenosine 5′-phosphosulfate (APS). APS can be reduced to sulfide and incorporated into Cys in the primary sulfate assimilation pathway or phosphorylated by APS kinase to 3′-phosphoadenosine 5′-phosphosulfate, which is the activated sulfate form for sulfation reactions. To assess to what extent APS kinase regulates accumulation of sulfated compounds, we analyzed the corresponding gene family in Arabidopsis thaliana. Analysis of T-DNA insertion knockout lines for each of the four isoforms did not reveal any phenotypical alterations. However, when all six combinations of double mutants were compared, the apk1 apk2 plants were significantly smaller than wild-type plants. The levels of glucosinolates, a major class of sulfated secondary metabolites, and the sulfated 12-hydroxyjasmonate were reduced approximately fivefold in apk1 apk2 plants. Although auxin levels were increased in the apk1 apk2 mutants, as is the case for most plants with compromised glucosinolate synthesis, typical high auxin phenotypes were not observed. The reduction in glucosinolates resulted in increased transcript levels for genes involved in glucosinolate biosynthesis and accumulation of desulfated precursors. It also led to great alterations in sulfur metabolism: the levels of sulfate and thiols increased in the apk1 apk2 plants. The data indicate that the APK1 and APK2 isoforms of APS kinase play a major role in the synthesis of secondary sulfated metabolites and are required for normal growth rates.