bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pepitope: epitope mapping from affinity-selected peptides
Authors: Mayrose Itay , Penn Osnat , Erez Elana , Rubinstein Nimrod D. , Shlomi Tomer , Freund Natalia Tarnovitski , Bublil Erez M. , Ruppin Eytan , Sharan Roded , Gershoni Jonathan M. , Martz Eric , Pupko Tal 
Published: November 2007

AbstractIdentifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein–protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure.Availability: http://pepitope.tau.ac.il/Contact: talp@post.tau.ac.il
Accurate prediction of enzyme mutant activity based on a multibody statistical potential
Authors: Masso Majid , Vaisman Iosif I. 
Published: November 2007

AbstractMotivation: An important area of research in biochemistry and molecular biology focuses on characterization of enzyme mutants. However, synthesis and analysis of experimental mutants is time consuming and expensive. We describe a machine-learning approach for inferring the activity levels of all unexplored single point mutants of an enzyme, based on a training set of such mutants with experimentally measured activity.Results: Based on a Delaunay tessellation-derived four-body statistical potential function, a perturbation vector measuring environmental changes relative to wild type (wt) at every residue position uniquely characterizes each enzyme mutant for model development and prediction. First, a measure of model performance utilizing area (AUC) under the receiver operating characteristic (ROC) curve surpasses 0.83 and 0.77 for data sets of experimental HIV-1 protease and T4 lysozyme mutants, respectively. Additionally, a novel method is introduced for evaluating statistical significance associated with the number of correct test set predictions obtained from a trained model. Third, 100 stratified random splits of the protease and T4 lysozyme mutant data sets into training and test sets achieve 77.0% and 80.8% mean accuracy, respectively. Next, protease and T4 lysozyme models trained with experimental mutants are used to predict activity levels for all remaining mutants; a subsequent search for publications reporting on dozens of these test mutants reveals that experimental results are matched by 79% and 86% of predictions, respectively. Finally, learning curves for each mutant enzyme system indicate the influence of training set size on model performance.Availability: Prediction databases at http://proteins.gmu.edu/automute/Contact: ivaisman@gmu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Graph sharpening plus graph integration: a synergy that improves protein functional classification
Authors: Shin Hyunjung , Lisewski Andreas Martin , Lichtarge Olivier 
Published: November 2007

AbstractMotivation: Predicting protein function is a central problem in bioinformatics, and many approaches use partially or fully automated methods based on various combination of sequence, structure and other information on proteins or genes. Such information establishes relationships between proteins that can be modelled most naturally as edges in graphs. A priori, however, it is often unclear which edges from which graph may contribute most to accurate predictions. For that reason, one established strategy is to integrate all available sources, or graphs as in graph integration, in the hope that the positive signals will add to each other. However, in the problem of functional prediction, noise, i.e. the presence of inaccurate or false edges, can still be large enough that integration alone has little effect on prediction accuracy. In order to reduce noise levels and to improve integration efficiency, we present here a recent method in graph-based learning, graph sharpening, which provides a theoretically firm yet intuitive and practical approach for disconnecting undesirable edges from protein similarity graphs. This approach has several attractive features: it is quick, scalable in the number of proteins, robust with respect to errors and tolerant of very diverse types of protein similarity measures.Results: We tested the classification accuracy in a test set of 599 proteins with remote sequence homology spread over 20 Gene Ontology (GO) functional classes. When compared to integration alone, graph sharpening plus integration of four vastly different molecular similarity measures improved the overall classification by nearly 30% [0.17 average increase in the area under the ROC curve (AUC)]. Moreover, and partially through the increased sparsity of the graphs induced by sharpening, this gain in accuracy came at negligible computational cost: sharpening and integration took on average 4.66 (±4.44) CPU seconds.Availability: Software and Supplementary data will be available on http://mammoth.bcm.tmc.edu/Contact: shin@ajou.ac.kr or lisewski@bcm.eduSupplementary information: Supplementary materials are available at Bioinformatics online.
Ensemble learning of genetic networks from time-series expression data
Authors: Nam Dougu , Yoon Sung Ho , Kim Jihyun F. 
Published: November 2007

AbstractMotivation: Inferring genetic networks from time-series expression data has been a great deal of interest. In most cases, however, the number of genes exceeds that of data points which, in principle, makes it impossible to recover the underlying networks. To address the dimensionality problem, we apply the subset selection method to a linear system of difference equations. Previous approaches assign the single most likely combination of regulators to each target gene, which often causes over-fitting of the small number of data.Results: Here, we propose a new algorithm, named LEARNe, which merges the predictions from all the combinations of regulators that have a certain level of likelihood. LEARNe provides more accurate and robust predictions than previous methods for the structure of genetic networks under the linear system model. We tested LEARNe for reconstructing the SOS regulatory network of Escherichia coli and the cell cycle regulatory network of yeast from real experimental data, where LEARNe also exhibited better performances than previous methods.Availability: The MATLAB codes are available upon request from the authors.Contact: dunam@nims.re.kr or jfk@kribb.re.kr
A computational strategy for the prediction of functional linear peptide motifs in proteins
Authors: Dinkel Holger , Sticht Heinrich 
Published: November 2007

AbstractMotivation: Short linear peptide motifs mediate protein–protein interaction, cell compartment targeting and represent the sites of post-translational modification. The identification of functional motifs by conventional sequence searches, however, is hampered by the short length of the motifs resulting in a large number of hits of which only a small portion is functional.Results: We have developed a procedure for the identification of functional motifs, which scores pattern conservation in homologous sequences by taking explicitly into account the sequence similarity to the query sequence. For a further improvement of this method, sequence filters have been optimized to mask those sequence regions containing little or no linear motifs. The performance of this approach was verified by measuring its ability to identify 576 experimentally validated motifs among a total of 15 563 instances in a set of 415 protein sequences. Compared to a random selection procedure, the joint application of sequence filters and the novel scoring scheme resulted in a 9-fold enrichment of validated functional motifs on the first rank. In addition, only half as many hits need to be investigated to recover 75% of the functional instances in our dataset. Therefore, this motif-scoring approach should be helpful to guide experiments because it allows focusing on those short linear peptide motifs that have a high probability to be functional.Contact: h.sticht@biochem.uni-erlangen.deSupplementary information: Supplementary data are available at Bioinformatics online.
Precisely wrong or vaguely right: simulations of noisy discard data and trends in fishing effort being included in the stock assessment of North Sea plaice
Authors: Dickey-Collas Mark , Pastoors Martin A. , van Keeken Olvin A. 
Published: November 2007

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

INTRODUCTIONThere are several ways to quantitate solutions of nucleic acids. If the solution is pure, one can use a spectrophotometer to measure the amount of ultraviolet radiation absorbed by the bases. DNA can also be quantified by measuring the UV-induced emission of fluorescence from intercalated ethidium bromide. This method is useful if there is not enough DNA to quantify with a spectrophotometer, or if the DNA solution is contaminated. Strategies for accurately quantifying nucleic acids using these approaches are discussed here.
Preparation of Reversed-Phase Microcolumns: Figure 1.
Authors: Larsen Martin R. 
Published: November 2007

INTRODUCTIONOne versatile strategy for sample cleanup prior to MALDI-MS analysis uses microscale columns designed for direct sample elution onto the MALDI target plate. This protocol describes the fabrication of a reversed-phase microcolumn designed for this purpose. The microcolumns are prepared from GELoader tips. This protocol has been optimized for sample cleanup prior to MALDI-MS. However, with slight modifications, it works equally well with samples destined for ESI-MS.
Phosphopeptide Purification by IMAC with Fe(III) and Ga(III)
Authors: Steen Hanno , Stensballe Allan , Jensen Ole N. 
Published: November 2007

INTRODUCTIONImmobilized metal ion affinity chromatography (IMAC) makes use of matrix-bound metals to affinity-purify phosphoproteins and phosphopeptides. Commonly used metals in early studies such as Ni2+, Co2+, Zn2+, and Mn2+ were shown to bind strongly to proteins with a high density of histidines. More recently, immobilized Fe3+, Ga3+, and Al3+ metal ions have been used for the selective enrichment of phosphopeptides from complex proteolytic digest mixtures containing both phosphorylated and nonphosphorylated components. The use of a nitrilotriacetic acid (NTA) matrix over iminodiacetic-acid-modified matrices has been reported to provide an advantage in selectivity. The development of elution conditions that are directly compatible with MS analysis of the enriched phosphopeptide samples provides the option to interface IMAC and MS online. This protocol describes the enrichment of phosphopeptides by IMAC using Fe3+- and Ga3+-NTA resin.
Offline Micro-IMAC Enrichment of Phosphoproteins
Authors: Corthals Garry L. , Wasinger Valerie C. , Goodlett David R. 
Published: November 2007

INTRODUCTIONImmobilized metal affinity chromatography (IMAC) can be performed offline or online with μLC-ESI-MS/MS. The online configuration has been used successfully despite suboptimal low-level analysis due to the relative disparity between IMAC and μLC flow rates. With IMAC performed offline from μLC-ESI-MS, sample volumes from 1 to 100 μL can be loaded using a sample pressure vessel or an autosampling system equipped with a sample-trapping cartridge. This protocol describes the construction and use of a micro-IMAC column for the enrichment of phosphoproteins.
Imaging Mouse Embryos after Whole-Mount In Situ Hybridization
Authors: Wakamiya Maki 
Published: November 2007

INTRODUCTIONEmbryos that are processed for whole-mount in situ hybridization can be photodocumented after the staining procedure depending on the region of the embryo of interest. The embryos can be photodocumented immediately after the color reaction or after clearing in glycerol solutions. This protocol describes methods for embryo clearing and imaging.
Handling Mouse Blastocysts for Fixation
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard 
Published: November 2007

INTRODUCTIONWhole blastocysts or sections of blastocysts can be fixed and used for histological studies, including in situ hybridization and immunohistochemistry. As described in this protocol, different handling techniques are required for whole versus sectioned embryos. For sectioning, it is more convenient to transfer blastocysts into the ampulla of an oviduct prior to fixation. The oviduct serves as a carrier that is easy to handle during subsequent processing for histology.
Embedding Mouse Embryos and Tissues in Wax
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard 
Published: November 2007

INTRODUCTIONThis protocol describes how to embed mouse tissues and embryos (large and small) in wax. The specimens must be dehydrated prior to embedding. Embedded samples are subsequently sectioned and used for in situ hybridization and immunohistochemistry experiments.
Preparing Glass Slides and Coverslips for In Situ Hybridization
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard 
Published: November 2007

INTRODUCTIONPrecleaned glass slides are of high enough quality for both in situ and immunohistochemical techniques. However, for in situ hybridization, the slides need to be treated with diethyl pyrocarbonate (DEPC) so that any RNase attached to them is destroyed. The slides also need to be coated with 3-triethoxysilylpropylamine (TESPA) or poly-L-lysine so that the sections adhere tightly and do not detach during subsequent extensive washing procedures. This protocol describes techniques for coating slides with TESPA and poly-L-lysine. There are advantages and disadvantages to each coating method. TESPA-treated slides can be stored for a long time, but the sections do not adhere tightly until after drying. Poly-L-lysine-coated slides need to be made fresh, but the sections adhere immediately on contact with the surface. This protocol also describes how to prepare coverslips for in situ hybrization by coating them in a siliconizing solution.
In Situ Hybridization of Mouse Embryo and Tissue Sections with Radiolabeled RNA Probes
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard 
Published: November 2007

INTRODUCTIONThis protocol describes in situ hybridization of embryo and tissue sections with 35S-labeled, single-stranded, antisense RNA probes (riboprobes). Protocols have also been developed for in situ hybridization to tissue sections using nonradiolabeled RNA probes that can be detected with antibodies coupled to alkaline phosphatase and a chromogenic substrate. Nonradioactive methods have the advantage that the results can be obtained relatively quickly, but the sensitivity is probably lower than with radioactive probes. In addition, care must be taken to optimize the amount of each probe used in the hybridization reaction.
In Situ Hybridization of Whole-Mount Mouse Embryos with RNA Probes: Preparation of Embryos and Probes
Authors: Lufkin Thomas 
Published: November 2007

INTRODUCTIONThis is the first of two protocols describing how to perform in situ hybridization on whole mouse embryos. Here we describe how to fix and permeabilize embryos with detergent and how to synthesize single-stranded RNA probes (riboprobes) in vitro using UTP labeled with the plant steroid digoxigenin (DIG-11-UTP). Antisense digoxigenin-labeled riboprobes are synthesized as run-off transcripts from linearized plasmid templates using bacteriophage RNA polymerases (T3, T7, SP6) under standard conditions. The probe is precipitated with ethanol in the presence of NaCl, and after resuspension in DEPC-treated H2O is stable at −20°C for many months. Probes ranging from 250 to 1500 bp have been used successfully. The optimal probe concentration is in the 100 ng to 1 μg/mL range and should be determined empirically.
In Situ Hybridization of Whole-Mount Mouse Embryos with RNA Probes: Hybridization, Washes, and Histochemistry
Authors: Lufkin Thomas 
Published: November 2007

INTRODUCTIONThis is the second of two protocols describing how to perform in situ hybridization on whole mouse embryos. Here we describe the hybridization procedure, and the localization of the DIG-labeled RNA using a conjugate of anti-DIG Fab antibody and calf intestinal alkaline phosphatase. Enzyme activity of the reporter is detected by a color reaction, resulting in the formation of a water-insoluble purple/blue precipitate.
Imaging Real-Time Gene Expression in Living Yeast
Authors: Zenklusen Daniel , Wells Amber L , Condeelis John S. , Singer Robert H. 
Published: November 2007

INTRODUCTIONThis protocol describes the application of the MS2 system to the yeast Saccharomyces cerevisiae. ASH1 mRNA tagged with six MS2 repeats (6MBSs) is used to follow the localization of the ASH1 mRNA particles to the bud tip of a haploid yeast cell. W303 yeast cells transformed with pG14-MS2-GFP and pGAL-lacZ-MS2-ASH1 are grown on select medium lacking tryptophan and leucine. RNA expression is induced by the addition of galactose, and a time-lapse movie is then acquired.
Imaging Real-Time Gene Expression in Living Systems with Single-Transcript Resolution: Image Analysis of Single mRNA Transcripts
Authors: Wells Amber L. , Condeelis John S. , Singer Robert H. , Zenklusen Daniel 
Published: November 2007

INTRODUCTIONThis protocol describes a method for establishing a green fluorescent protein (GFP) calibration curve using dilutions of recombinant GFP and blue fluorescent beads. The total fluorescence intensity (TFI) per mRNA molecule is first calculated by imaging serial dilutions of purified enhanced GFP (eGFP) to determine the TFI within a specific volume. A calibration curve of fluorescence intensity in a given voxel per molecule of GFP is then used to determine the number of GFP molecules in the sample of formaldehyde fixed cells to be imaged. This is followed by a method for detection of single molecules in formaldehyde-fixed and live cells. These cells have been cotransfected with mRNA reporter and MCP-xFP plasmids, where MCP-xFP refers to a fluorescent protein fused to the MS2 capsid protein. It is important to collect micrographs and establish the calibration curve on the same day that the cells are imaged, using the same equipment configuration, camera settings, and image acquisition parameters.
Micrococcal Nuclease-Southern Blot Assay: I. MNase and Restriction Digestions: Figure 1.
Authors: Carey Michael , Smale Stephen T. 
Published: November 2007

INTRODUCTIONThis is the first phase of a two-part assay for exploring whether an endogenous control region of interest is assembled into nucleosomes or is devoid of nucleosomes. This assay can also be used to determine if nucleosomes are similarly positioned at the locus in every cell within a population. Micrococcal nuclease (MNase) is unique among nucleases in its relative ability to induce double-strand breaks within nucleosomal linker regions, but only single-stranded nicks within the nucleosome itself. Because of this property, micrococcal nuclease can be used to determine whether a DNA fragment of interest is nucleosomal. In this phase of the assay, the cells are lysed and nuclei are isolated. Limiting concentrations of micrococcal nuclease are added to the nuclei, resulting in cleavage at nucleosome linker regions (preferably cleavage at two sites per DNA molecule). The cleavage reactions are stopped, and then the genomic DNA is purified and digested with restriction enzymes.
Micrococcal Nuclease-Southern Blot Assay: II. Capillary Transfer and Hybridization: Figure 1.
Authors: Carey Michael , Smale Stephen T. 
Published: November 2007

INTRODUCTIONThis is the second phase of a two-part assay for exploring whether an endogenous control region of interest is assembled into nucleosomes or is devoid of nucleosomes. This assay can also be used to determine if nucleosomes are similarly positioned at the locus in every cell within a population. In this second part of the assay, the restricted genomic DNA is separated by agarose gel electrophoresis and stained with ethidium bromide, resulting in a ladder of bands corresponding in size to multiples of the nucleosome core plus linker (~200 bp). To determine whether a DNA fragment of interest is nucleosomal, the genomic DNA is subjected to Southern blot analysis. If a probe derived from the DNA fragment hybridizes to the ladder of nucleosomal bands, the fragment may indeed be assembled into nucleosomes.