bluuebunny/crossref_metadata_2025_split huggingface dataset:
MapQuant: Open‐source software for large‐scale protein quantification
Authors: Leptos Kyriacos C. , Sarracino David A. , Jaffe Jacob D. , Krastins Bryan , Church George M. 
Published: February 2006

AbstractWhole‐cell protein quantification using MS has proven to be a challenging task. Detection efficiency varies significantly from peptide to peptide, molecular identities are not evident a priori, and peptides are dispersed unevenly throughout the multidimensional data space. To overcome these challenges we developed an open‐source software package, MapQuant, to quantify comprehensively organic species detected in large MS datasets. MapQuant treats an LC/MS experiment as an image and utilizes standard image processing techniques to perform noise filtering, watershed segmentation, peak finding, peak fitting, peak clustering, charge‐state determination and carbon‐content estimation. MapQuant reports abundance values that respond linearly with the amount of sample analyzed on both low‐ and high‐resolution instruments (over a 1000‐fold dynamic range). Background noise added to a sample, either as a medium‐complexity peptide mixture or as a high‐complexity trypsinized proteome, exerts negligible effects on the abundance values reported by MapQuant and with coefficients of variance comparable to other methods. Finally, MapQuant's ability to define accurate mass and retention time features of isotopic clusters on a high‐resolution mass spectrometer can increase protein sequence coverage by assigning sequence identities to observed isotopic clusters without corresponding MS/MS data.
Proteomic profiling of cell envelope‐associated proteins from Staphylococcus aureus
Authors: Gatlin Christine L. , Pieper Rembert , Huang Shih‐Ting , Mongodin Emmanuel , Gebregeorgis Elizabeth , Parmar Prashanth P. , Clark David J. , Alami Hamid , Papazisi Leka , Fleischmann Robert D. , Gill Steven R. , Peterson Scott N. 
Published: February 2006

AbstractThe emergence of highly virulent community acquired Staphylococcus aureus and continued progression of resistance to multiple antimicrobials, including methicillin and vancomycin, marks the reemergence of S. aureus as a serious health care threat. Investigation of proteins localized to the cell surface could help to elucidate mechanisms of virulence and antibiotic resistance in S. aureus. In this study, proteomic profiling methods were developed to solubilize, display, and evaluate abundance levels of proteins present in the supernatants of the lysostaphin‐digested cell envelope from cultured vancomycin‐intermediate S. aureus (VISA) cells. Combining approaches of 2‐DE or chromatographic separation of proteins with MS analyses resulted in the identification of 144 proteins of particular interest. Of these proteins, 48 contained predicted cell wall localization or export signal motifs, including 14 with distinct covalent peptidoglycan‐anchor sites, four of which are uncharacterized to date. One of the two most abundant cell envelope proteins, which showed remarkably high variations in MW and pI in the 2‐DE gel display, was the S. aureus surface protein G. The display of numerous secreted proteins that are not covalently cell wall‐anchored, suggests that, in the exponential growth phase, secreted proteins can be retained physiologically in the cell envelope and may interact with cell wall‐anchored proteins and carbohydrate structures in a manner yet to be determined. The remaining 96 proteins, devoid of recognizable motifs, were repeatedly profiled in the VISA cell envelope fractions. We describe a novel semiquantitative method to determine abundance factors of such proteins in 2‐DE gels of cell envelope fractions relative to whole cell lysates and discuss these data in the context of true cell envelope localization versus experimentally caused cell lysis.
The identification and characterization of xenoantigenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney
Authors: Kim Yun‐Gon , Kim Sun‐Young , Hur Young‐Mi , Joo Hwang‐Soo , Chung Junho , Lee Dong‐Sup , Royle Louise , Rudd Pauline M. , Dwek Raymond A. , Harvey David J. , Kim Byung‐Gee 
Published: February 2006

AbstractThe immunogenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney were identified and characterized using MALDI‐TOF MS and ESI‐QTOF‐MS. The MALDI profile, investigated by incubation with exoglycosidases, showed a series of about 40 carbohydrates that were identified as high mannose glycans (Man3–9GlcNAc2) and complex bi‐, tri‐, and tetra‐antennary glycans with and without core fucose. The antennae of many of the complex glycans were terminated with α‐galactose residues, with the numbers of these residues ranging from one up to the number of antennae. Negative ion ESI‐MS/MS spectra confirmed the location of the α‐galactose residues on the ends of the antennae. This total glycan profile of the membrane proteins from porcine kidney will thus provide important information for the study of molecular interactions between antigenic carbohydrates and proteins in xenotransplantation.
Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2‐DE/MS and cleavable isotope‐coded affinity tag analysis
Authors: Kim Young Hwan , Cho Kun , Yun Sung‐Ho , Kim Jin Young , Kwon Kyung‐Hoon , Yoo Jong Shin , Kim Seung Il 
Published: February 2006

AbstractProteomic analysis of Pseudomonas putida KT2440 cultured in monocyclic aromatic compounds was performed using 2‐DE/MS and cleavable isotope‐coded affinity tag (ICAT) to determine whether proteins involved in aromatic compound degradation pathways were altered as predicted by genomic analysis (Jiménez et al., Environ Microbiol. 2002, 4, 824–841). Eighty unique proteins were identified by 2‐DE/MS or MS/MS analysis from P. putida KT2440 cultured in the presence of six different organic compounds. Benzoate dioxygenase (BenA, BenD) and catechol 1,2‐dioxygenase (CatA) were induced by benzoate. Protocatechuate 3,4‐dixoygenase (PcaGH) was induced by p‐hydroxybenzoate and vanilline. β‐Ketoadipyl CoA thiolase (PcaF) and 3‐oxoadipate enol‐lactone hydrolase (PcaD) were induced by benzoate, p‐hydroxybenzoate and vanilline, suggesting that benzoate, p‐hydroxybenzoate and vanilline were degraded by different dioxygenases and then converged in the same β‐ketoadipate degradation pathway. An additional 110 proteins, including 19 proteins from 2‐DE analysis, were identified by cleavable ICAT analysis for benzoate‐induced proteomes, which complemented the 2‐DE results. Phenylethylamine exposure induced β‐ketoacyl CoA thiolase (PhaD) and ring‐opening enzyme (PhaL), both enzymes of the phenylacetate (pha) biodegradation pathway. Phenylalanine induced 4‐hydroxyphenyl‐pyruvate dioxygenase (Hpd) and homogentisate 1,2‐dioxygenase (HmgA), key enzymes in the homogentisate degradation pathway. Alkyl hydroperoxide reductase (AphC) was induced under all aromatic compounds conditions. These results suggest that proteome analysis complements and supports predictive information obtained by genomic sequence analysis.
Analysis of the wheat and Puccinia triticina (leaf rust) proteomes during a susceptible host‐pathogen interaction
Authors: Rampitsch Christof , Bykova Natalia V. , McCallum Brent , Beimcik Eva , Ens Werner 
Published: February 2006

AbstractWheat leaf rust is caused by the fungus Puccinia triticina. The genetics of resistance follows the gene‐for‐gene hypothesis, and thus the presence or absence of a single host resistance gene renders a plant resistant or susceptible to a leaf rust race bearing the corresponding avirulence gene. To investigate some of the changes in the proteomes of both host and pathogen during disease development, a susceptible line of wheat infected with a virulent race of leaf rust were compared to mock‐inoculated wheat using 2‐DE (with IEF pH 4–8) and MS. Up‐regulated protein spots were excised and analyzed by MALDI‐QqTOF MS/MS, followed by cross‐species protein identification. Where possible MS/MS spectra were matched to homologous proteins in the NCBI database or to fungal ESTs encoding putative proteins. Searching was done using the MASCOT search engine. Remaining unmatched spectra were then sequenced de novo and queried against the NCBInr database using the BLAST and MS BLAST tools. A total of 32 consistently up‐regulated proteins were examined from the gels representing the 9‐day post‐infection proteome in susceptible plants. Of these 7 are host proteins, 22 are fungal proteins of known or hypothetical function and 3 are unknown proteins of putative fungal origin.
Proteases and chaperones are the most abundant proteins in the parasitophorous vacuole of Plasmodium falciparum‐infected erythrocytes
Authors: Nyalwidhe Julius , Lingelbach Klaus 
Published: February 2006

AbstractAfter invasion of erythrocytes, the human malaria parasite Plasmodium falciparum resides within a parasitophorous vacuole (PV) which forms an interface between the host cell cytosol and the parasite surface. This vacuole protects the parasite from potentially harmful substances, but allows access of essential nutrients to the parasite. Furthermore, the vacuole acts as a transit compartment for parasite proteins en route to the host cell cytoplasm. Recently we developed a strategy to biotin label soluble proteins of the PV. Here, we have paired this strategy with a high‐throughput MALDI‐TOF‐MS analysis to identify 27 vacuolar proteins. These proteins fall into the following main classes: chaperones, proteases, and metabolic enzymes, consistent with the expected functions of the vacuole. These proteins are likely to be involved in several processes including nutrient acquisition from the host cytosol, protein sorting within the vacuole, and release of parasites at the end of the intraerythrocytic cycle.
Analysis of the interacting partners of the neuronal calcium‐binding proteins L‐CaBP1, hippocalcin, NCS‐1 and neurocalcin δ
Authors: Haynes Lee P. , Fitzgerald Daniel J. , Wareing Brian , O'Callaghan Dermott W. , Morgan Alan , Burgoyne Robert D. 
Published: February 2006

AbstractIntracellular Ca2+signals are transduced by the binding of Ca2+ to sensor proteins, which subsequently modify the activity of their target proteins. Identification of these target proteins is, therefore, important for an understanding of cellular signalling processes. We have investigated the binding partners of four EF‐hand Ca2+‐binding proteins. Three proteins of the neuronal calcium sensor (NCS) family, hippocalcin, NCS‐1 and neurocalcin δ were prepared as N‐terminally tagged GST fusion proteins, and the less closely related protein L‐CaBP1 was prepared in both N‐ and C‐terminally tagged forms, the latter requiring generation of a new vector. Immobilised fusion proteins were used to purify binding partners from bovine brain cytosol and membrane extracts in the presence of 1 μM free Ca2+. Bound proteins were eluted with Ca2+‐free and high‐salt buffers and eluted proteins were identified by MALDI‐MS and Western blotting. New protein targets detected included ARF1, Ca2+‐dependent activator protein for secretion 1, cyclic nucleotide 3', 5'‐phosphodiesterase, the vacuolar ATPase, AP1 and AP2 complexes and the type I TGF‐β receptor. While certain of these interactions occurred with more than one of the Ca2+‐binding proteins, others were found to be specific targets for particular Ca2+ sensors, and many of these did not overlap with known calmodulin‐binding proteins. These findings provide new clues to the functional roles of the neuronal calcium sensor proteins.
PRISM: A data management system for high‐throughput proteomics
Authors: Kiebel Gary R. , Auberry Ken J. , Jaitly Navdeep , Clark David A. , Monroe Matthew E. , Peterson Elena S. , Tolić Nikola , Anderson Gordon A. , Smith Richard D. 
Published: February 2006

AbstractAdvanced proteomic research efforts involving areas such as systems biology or biomarker discovery are enabled by the use of high level informatics tools that allow the effective analysis of large quantities of differing types of data originating from various studies. Performing such analyses on a large scale is not feasible without a computational platform that performs data processing and management tasks. Such a platform must be able to provide high‐throughput operation while having sufficient flexibility to accommodate evolving data analysis tools and methodologies. The Proteomics Research Information Storage and Management system (PRISM) provides a platform that serves the needs of the accurate mass and time tag approach developed at Pacific Northwest National Laboratory. PRISM incorporates a diverse set of analysis tools and allows a wide range of operations to be incorporated by using a state machine that is accessible to independent, distributed computational nodes. The system has scaled well as data volume has increased over several years, while allowing adaptability for incorporating new and improved data analysis tools for more effective proteomics research.
Quantitation of protein phosphorylation in pregnant rat uteri using stable isotope dimethyl labeling coupled with IMAC
Authors: Huang Sheng‐Yu , Tsai Mei‐Ling , Wu Chin‐Jen , Hsu Jue‐Liang , Ho Shih‐Hsin , Chen Shu‐Hui 
Published: February 2006

AbstractQuantitative analysis of protein phosphorylation provides important insights into molecular signaling mechanisms and a better understanding of many cellular processes. In this study, we coupled stable isotope dimethyl labeling with immobilized metal affinity chromatography (IMAC) enrichment to quantify protein phosphorylation at MS‐determined phosphorylation sites. The proposed method was first characterized using α‐ and β‐casein as two model phosphoproteins, and further applied to the analysis of pregnant rat uteri with and without treatment with 8‐bromo‐cGMP. Dimethyl labeling has several significant advantages: global, fast (within 5 min) and complete (near 100%). Our results indicate that the labeling has no adverse effect on the IMAC enrichment for tryptic peptides having single and multiple phosphorylation sites. Moreover, the enhanced a1 signal and the complete reaction by dimethyl labeling provide unequivocal identification of both the N‐terminal amino acid and the number of the labeling site. Using these two criteria in data validation, which is particularly important for identifying phosphoproteins, we found that the confidence in interpreting dimethyl‐labeled peptides had greatly increased. In the analysis of late gestation rat uteri, the abundance ratio between treated and un‐treated phosphopeptide signals ranged from 0.51 to 1.69 with an average of around 1.01 ± 0.25. The obtained ratio of the phosphorylation levels at Ser 15 of HSP27 was further confirmed by the consistent results obtained from Western blot analyses. Based on the analysis of the results, it is interesting to note that the activated cGMP dependentt protein kinase G (PKG) seems to affect the phosphorylation of proteins associated with the inhibition of cell migration and proliferation, redistribution of actin‐associated proteins, and the increase of protein synthesis in late‐gestation uteri. These observations provide important evidence suggesting that activated PKG may play a critical role in the shift of pregnant uteri from proliferative to hypertrophic states.
Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling
Authors: Resch Alexandra , Leicht Stefan , Saric Marc , Pásztor Linda , Jakob Andreas , Götz Friedrich , Nordheim Alfred 
Published: February 2006

AbstractPathogenic staphylococci can form biofilms in which they show a higher resistance to antibiotics and the immune defense system than their planktonic counterparts, which suggests that the cells in a biofilm have an altered metabolic activity. Here, 2‐D PAGE was used to identify secreted, cell wall‐associated and cytoplasmic proteins expressed in Staphylococcus aureus after 8 and 48 h of growth. The proteins were separated at pH ranges of 4–7 or 6–11. The protein patterns revealed significant differences in 427 protein spots; from these, 258 non‐redundant proteins were identified using ESI‐MS/MS. Biofilm cells expressed higher levels of proteins associated with cell attachment and peptidoglycan synthesis, and in particular fibrinogen‐binding proteins. Enzymes involved in pyruvate and formate metabolism were upregulated. Furthermore, biofilm cells expressed more staphylococcal accessory regulator A protein (SarA), which corroborates the positive effect of SarA on the expression of the intercellular adhesion operon ica and biofilm growth. In contrast, proteins, such as proteases and particularly immunodominant antigen A (IsaA) and staphylococcal secretory antigen (SsaA), were found in lower amounts. The RNA expression profiling largely supports the proteomic data. The results were mapped onto KEGG pathways.
A proteomic analysis of 14‐3‐3 binding proteins from developing barley grains
Authors: Alexander Ross D. , Morris Peter C. 
Published: February 2006

Abstract14‐3‐3 proteins are important eukaryotic regulatory proteins. Barley (Hordeum vulgare L.) 14‐3‐3A was over‐expressed, immobilised and used to affinity purify 14‐3‐3 binding proteins from developing barley grains. Binding was shown to be phosphorylation‐dependent. These proteins were fractionated by PAGE and identified by MALDI‐TOF MS. In total, 54 14‐3‐3 binding proteins were identified, 49 of these interactions are novel to plants. These proteins fell into a number of functional categories. The largest category was for carbohydrate metabolism, including plastidic enzymes for starch synthesis and modification. 14‐3‐3 was shown to be present in isolated plastids. Four of five enzymes involved in sucrose biosynthesis from triose phosphates were identified, suggesting co‐ordinated regulation of this pathway. Invertase and sucrose synthase, which break down sucrose to hexoses, were found. Sucrose synthase activity was shown to be inhibited by exogenous 14‐3‐3 in a dosage‐dependent manner. The second‐largest functional group was for proteins involved in stress and defence responses; for example, RGH2A, closely related to the MLA powdery mildew resistance protein, was found. This work illustrates the broad range of processes in which 14‐3‐3 may be involved, and augments previous data demonstrating key roles in carbohydrate metabolism and plant defence.
Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large‐scale organization and robustness
Authors: Li Dong , Li Jianqi , Ouyang Shuguang , Wang Jian , Wu Songfeng , Wan Ping , Zhu Yunping , Xu Xiaojie , He Fuchu 
Published: February 2006

AbstractNo abstracts.
Acrylic polymer/silica hybrid for electron‐beam resists
Authors: Tamai Toshiyuki , Matsuura Yukihito , Watanabe Mitsuru , Matsukawa Kimihiro 
Published: February 2006

AbstractAn acrylic polymer/silica hybrid resist film was investigated for fabricating a microstructure by electron‐beam (EB) lithography. EB lithography on the hybrid thin film afforded a positive pattern whose depth corresponded to the EB exposure dose; this indicated that the hybrid was an analog resist and could fabricate a three‐dimensional microstructure. The resist film had high heat resistance and compatibility with the underlying quartz plate, probably because of the silica component. The acrylic polymer/(RSiO1.5)n hybrid film showed higher EB sensitivity than a film of the crosslinked acrylic polymer and an acrylic polymer/(SiO2)n hybrid. Atomic force microscopy observation of the hybrid film surface showed the homogeneous dispersion of the acrylic polymer and the silica components in the hybrid film. The acrylic polymer component was EB‐sensitive, whereas dispersing the acrylic polymer and silica components homogeneously also played an important role in increasing the EB sensitivity. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2107–2116, 2006
Synthesis and characterization of macrocyclic vinyl aromatic polymers
Authors: Hogen‐Esch Thieo E. 
Published: February 2006

AbstractThe synthesis and characterization by size exclusion chromatography, liquid chromatography, NMR, matrix‐assisted laser desorption/ionization, thermal analysis, and other techniques of well‐defined and narrow molecular weight distribution macrocyclic polystyrene (PS), poly(2‐vinylpyridine), poly(α‐methylstyrene), poly (2‐vinyl‐naphthalene) (P2VN), and poly(9,9‐dimethyl‐2‐vinylfluorene) (PDMVF) containing a single 1,4‐benzylidene, methylidene, or 9,10‐anthracenylidene unit are reviewed. The absorption and emission spectroscopy of PS, P2VN, and PDMVF is also discussed. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2139–2155, 2006
Demographic and clinical predictors of preparatory grief in a sample of advanced cancer patients
Authors: Mystakidou Kyriaki , Tsilika Eleni , Parpa Efi , Katsouda Emmanuela , Sakkas Palvos , Galanos Antonis , Vlahos Lambros 
Published: February 2006

AbstractBackground: Preparatory grief encompasses grief for losses that have already occurred, are currently being experienced, and losses that will or might ensue in the future after the death, as a consequence of it.Aim: To examine the relative contribution of demographic and clinical variables in predicting cancer patients' preparatory grief as recorded from the Preparatory Grief in Advanced Cancer Patients (PGAC) scale. Moreover, researchers were interested in determining whether these dimensions were independently and uniquely associated with preparatory grief.Methods: Two hundred advanced cancer patients treated in a Pain Relief and Palliative Care Unit completed the PGAC scale, while researchers recorded data on demographic characteristics, disease status and treatment regimen.Results: The analyses showed that the most significant correlations were found between preparatory grief and age (r=−0.227, p=0.001), gender (p=0.006), family status (p=0.019), performance status (p=0.010), surgery (p=0.029), opioids (p=0.019), and diagnosis (p=0.038). In the prediction of preparatory grief, the contribution of age, performance status, history of other surgery, gender and opioids is high.Conclusions: Awareness of the specific patients' demographic and medical characteristics, such as old age, poor performance status, history of other surgery, female gender, and strong opioids, contribute to the prediction of patients' preparatory grief. Copyright © 2006 John Wiley & Sons, Ltd.