bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics for Human Proteomics: Current State and Future Status
Authors: Bairoch Amos 
Published: October 2010

AbstractWe are entering a new era in the exploration of the human proteome.Advances in technologies are allowing researchers to map with a much better resolution and improved accuracy this very complex universe. Such an exploration also requires a compendium of adequate bioinformatics tools, data repositories and knowledge resources. We are going to describe what are the state of the art in term of data and knowledge resources for human proteins: from repositories of proteomics data such as PRIDE,PeptideAtlas or Peptidome, databases such as SRMAtlas and HPA and knowledgebase such as UniProtKB/Swiss-Prot.In September 2008, the UniProt/Swiss-Prot group achieved a major milestone: the first complete manual annotation of what is believed to be the full set of human proteins (derived from about 20'000 genes). This corpus of data is already quite rich in information pertinent to modern biomolecular medical research, but made us realize how large is the gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions,subcellular locations, etc).This gap resides not only in the available experimental information, but also in the way this information has been stored, which is far from being sufficient to help researchers making sense of what all these human proteins do in our bodies! Therefore, in the framework of CALIPHO, a new interdisciplinary group created jointly by the University of Geneva and the Swiss Institute of Bioinformatics (SIB), we are developing neXtProt, a new human-centric protein knowledge resource.neXtProt is developed with the aim to help researchers answer pertinent questions relevant to human proteins. This requires answering 3 different challenges:1) Add to the corpus of data on human proteins that is already in Swiss-Prot, a lot of additional information. We will import in neXtProt data originating from a variety of high-throughput approaches such as microarray, antibodies, proteomics, siRNAs, interactomics, etc. All of these data sets must be carefully selected so as to only provide high-quality data as we want to avoid creating a noisy and dirty compendium.2) Organize the data in such a way that it is possible to make powerful queries in the most user-friendly environment. Here also, it is necessary to be able to capture the complexity and the heterogeneity of the data that will be available in neXtProt, yet make it easy for the user to forget this complexity!3) Build a software platform that will allows tools ranging from sequence analysis to text and data mining to be integrated in various research environments so as to answer specific needs of academic and industrial users.
Expression of the cannabinoid system in muscle: effects of a high-fat diet and CB1 receptor blockade
Authors: Crespillo Ana , Suárez Juan , Bermúdez-Silva Francisco J. , Rivera Patricia , Vida Margarita , Alonso Monica , Palomino Ana , Lucena Miguel A. , Serrano Antonia , Pérez-Martín Margarita , Macias Manuel , Fernández-Llébrez Pedro , Rodríguez de Fonseca Fernando 
Published: October 2010

The ECS (endocannabinoid system) plays an important role in the onset of obesity and metabolic disorders, implicating central and peripheral mechanisms predominantly via CB1 (cannabinoid type 1) receptors. CB1 receptor antagonist/inverse agonist treatment improves cardiometabolic risk factors and insulin resistance. However, the relative contribution of peripheral organs to the net beneficial metabolic effects remains unclear. In the present study, we have identified the presence of the endocannabinoid signalling machinery in skeletal muscle and also investigated the impact of an HFD (high-fat diet) on lipid-metabolism-related genes and endocannabinoid-related proteins. Finally, we tested whether administration of the CB1 inverse agonist AM251 restored the alterations induced by the HFD. Rats were fed on either an STD (standard/low-fat diet) or an HFD for 10 weeks and then treated with AM251 (3 mg/kg of body weight per day) for 14 days. The accumulated caloric intake was progressively higher in rats fed on the HFD than the STD, resulting in a divergence in body weight gain. AM251 treatment reduced accumulated food/caloric intake and body weight gain, being more marked in rats fed on the HFD. CB2 (cannabinoid type 2) receptor and PPARα (peroxisome-proliferator-activated receptor α) gene expression was decreased in HFD-fed rats, whereas MAGL (monoglyceride lipase) gene expression was up-regulated. These data suggest an altered endocannabinoid signalling as a result of the HFD. AM251 treatment reduced CB2 receptor, PPARγ and AdipoR1 (adiponectin receptor 1) gene expression in STD-fed rats, but only partially normalized the CB2 receptor in HFD-fed rats. Protein levels corroborated gene expression results, but also showed a decrease in DAGL (diacylglycerol) β and DAGLα after AM251 treatment in STD- and HFD-fed rats respectively. In conclusion, the results of the present study indicate a diet-sensitive ECS in skeletal muscle, suggesting that blockade of CB1 receptors could work towards restoration of the metabolic adaption imposed by diet.
Eotaxin and CCR3 are up‐regulated in exacerbations of chronic bronchitis
Authors: Bocchino V. , Bertorelli G. , Bertrand C.P. , Ponath P.D. , Newman W. , Franco C. , Marruchella A. , Merlini S. , Del Donno M. , Zhuo X. , Olivieri D. 
Published: October 2010

Background: Eosinophils and T lymphocytes represent constant features in the airways of subjects with exacerbated chronic bronchitis. Eotaxin is the most potent and selective eosinophil chemoattractant which can also attracts lymphocytes. The aim of the study was to evaluate the expression of eotaxin and its receptor, CCR3, in bronchial airways during exacerbation of chronic bronchitis. Methods: By immunohistochemistry we studied eotaxin and CCR3 expression in the lamina propria of 14 subjects with acute exacerbation of chronic bronchitis, 20 asthmatics, and 8 healthy subjects. We determined the cell types expressing the CCR3 receptor by colocalization experiments. We finally studied the relationship between eotaxin and CCR3 and eosinophils and T lymphocytes. Results: The number of eotaxin+ and CCR3+ cells was significantly higher in exacerbated chronic bronchitis (P < 0.003 and P < 0.002) and asthma (P < 0.002 and P < 0.0001) when compared to healthy subjects. CCR3 was mainly expressed by eosinophils and to a lesser extent by CD4+ and CD8+ lymphocytes. In exacerbated chronic bronchitis the number of CCR3+ cells was strongly correlated to the number of eosinophils (P < 0.0002, r = 0.85) and to the number of CD4+ lymphocytes (P < 0.05, r = 0.57). Conclusion: Our study suggests that eotaxin and CCR3 are up‐regulated and could be involved in the eosinophil and CD4+ lymphocyte recruitment into the airways which occur during acute exacerbations of chronic bronchitis.
Major changes in volcano behaviour after a sector collapse: insights from Stromboli, Italy
Authors: Tibaldi Alessandro 
Published: October 2010

AbstractIn recent years, increasing numbers of volcanoes are being recognized as having undergone large sector collapses. How far such events can change the succeeding behaviour of the volcano is poorly known, despite the importance for natural hazards and economic applications. By analysing the last 100‐kyr geological history of Stromboli (Italy), which has involved multiple collapses, this paper illuminates the feedback effect between sector collapse and magma upwelling and emplacement. The collapsed zone of Stromboli is episodically unbuttressed, draining magma preferentially with formation of eruptive centres in the collapse amphitheatre and dyking along the collapse shoulders. After a collapse, there were no further linear eruptions across the cone on opposing middle–lower slopes, but these occurred again after rebuilding of the cone. The time‐averaged eruption rate increased immediately before the first collapse and remained higher during the succeeding period of frequent collapses.
Structural controls on sulphide deposition at the dyke–lava boundary, slow‐spreading ocean crust, Macquarie Island
Authors: Davidson Garry J. , Varne Rick , Brown Anthony V. , Connell Robert 
Published: October 2010

AbstractOcean Drilling Program hole 504B revealed an ocean crust hydrothermal sulphur anomaly on the dyke–lava transition, with implications for global sulphur sinks. Here we confirm the presence of the anomaly sporadically along 7.5 km of dyke–basalt contact on the Macquarie Ridge at Macquarie Island, a 39–9.7 Ma slow‐spreading setting. Background contact‐zone pyrite S contents average 1845 p.p.m. across ∼50 m. However, zones of small‐scale brittle faulting that commonly occur on and above the dyke–basalt contact average between 5000 and 11 000 p.p.m. S (20–30 m widths). These consist of steep ridge‐parallel faults and fault splays on the contact, overlain by up to 50 m of linked pyritic fault trellis. The contact zone faults are haloed by disseminated pyrite–chlorite, cross‐cut by quartz–chlorite–sphalerite and epidote‐cemented breccias, containing evidence of turbulent flow. The structural control on sulphur deposition is attributed to the active extensional slow spreading setting. With increasing extension, diffuse mixing across the contact was replaced by channellized flow and dynamic mixing in fault arrays. The magnitude of the dyke–lava transition sulphur sink must be reassessed to take account of this heterogeneity.
Buoyancy‐controlled eruption of magmas at Mt Etna
Authors: Corsaro Rosa Anna , Pompilio Massimo 
Published: October 2010

AbstractBuoyancy controls the ability of magma to rise, its ascent rate and the style of the eruptions. Geophysical, geological and petrological data have been integrated to evaluate the buoyancy of magmas at Mt Etna. The density difference between host rocks and magmas is mainly related to the amount of H2O dissolved in the magma and to the bubble‐liquid separation processes. In the depth interval 22–2 km b.s.l. highly hydrated (H2O ∼ 3%) basaltic magmas or mixtures of bubbles + liquid have positive buoyancy and rise rapidly. Conversely, bubble‐depleted liquids, with an intermediate H2O content (∼ 1.5%), having neutral buoyancy, will spread out and form magmatic reservoirs at different depths until cooling/crystallization further modify composition and density. These different processes account for the magma compositions, location of magmatic reservoirs as determined by geophysical methods, and the complex eruptive cycles (slow effusions, fire fountains and Plinian eruptions) that have been observed in the history of the volcano.
Isotope fractionation of neon during stepheating extraction?: a comment on ‘Re‐interpretation of the existence of a primitive plume under Australia based on neon isotope fractionation during step heating’ by Gautheron and Moreira (2003)
Authors: Matsumoto Takuya , Honda Masahiko , McDougall Ian , Yatsevich Igor , O'Reilly Suzanne Y. 
Published: October 2010

AbstractUsing a Rayleigh distillation fractionation model, we calculate that the maximum isotope fractionation potentially achievable is less than 5% during the early stages of gas release from a sample. Our calculation corrects the erroneous conclusions of Gautheron and Moreira (2003), who re‐interpreted the plume‐like neon isotopic compositions found in metasomatic apatite from a south‐eastern Australian xenolith (Matsumotoet al., 1997) to be the result of Rayleigh‐type isotope fractionation of originally MORB‐type neon during stepheating gas extraction. We stress that the modelling of neon isotopic fractionation by Gautheron and Moreira (2003) is incorrect, and that the finding of a plume‐like neon isotopic composition in the apatite by Matsumotoet al. (1997) remains a quite valid and robust conclusion.
Active extension of the Shanxi rift, north China: does it result from anticlockwise block rotations?
Authors: He Jiankun , Cai Dongsheng , Li Yanxing , Gong Zaisheng 
Published: October 2010

AbstractThe Shanxi rift is an intraplate extensional zone in the North China Block. Active extension has previously been considered to result from anticlockwise block rotation, with successive indentation of the Indian plate toward the Eurasian plate. However, GPS data show that the entire North China Block is moving coherently from WNW to ESE, indicating that no significant block rotations presently exist along the two sides of the rift. We use a viscoelastic model to predict that its active extension might be caused by intraplate deformation localization with lateral changes of the crustal rheological structures. A model result shows that for the ESE movement of the North China Block, the existing topographical loading and crustal weakness could have resulted in the obvious long‐term extension of the Shanxi rift even without different block rotations. The surface extension rate approximated from lateral inhomogeneous crustal models is ∼ 0.5–1.4 mm yr−1, consistent with observed geological and seismological extension rates.
Conditions for Infection of Apple by Phytophthora syringae
Authors: Harris D. C. , Xu X.‐M. 
Published: October 2010

AbstractThe processes leading to Phytophthora fruit rot were divided into two main stages for the purposes of investigating the effects of temperature and duration of wet periods on pathogen development: oospore germination and infection of fruit by zoospores. It was found that the first stage was markedly affected by temperature over the range 10–20°C and required a wet period of 4–7 days. At 18 and 20°C, activation was low regardless of the length of the wet period. Once oospore germination (first stage) had occurred, free water was necessary for only a few hours for fruit infection (second stage) to occur, but the incidence of infection rose rapidly over the first 48 h, regardless of temperature over the range 10–20°C. From the data obtained, mathematical models were produced relating the incidence of Phytophthora fruit rot to the two weather variables. These models can be used to develop a weather‐based risk assessment system for the disease.
Biological and Molecular Categorization of Strains of Banana bunchy top virus
Authors: Su H.‐J. , Tsao L.‐Y. , Wu M.‐L. , Hung T.‐H. 
Published: October 2010

Abstract Banana bunchy top virus (BBTV), a complex circular single‐stranded DNA virus with multiple genomic components, is a destructive pathogen in banana‐cultivating areas worldwide. Based on symptoms (such as vein clearing, green streak on pseudostem, leaf atrophy, bunchy top and stunting) as well as polymerase chain reaction (PCR) amplification patterns with different primer pairs, all BBTV isolates collected from Taiwan and other countries can be divided into five distinctive strains. Three primer pairs, C1, stem‐loop common region (CR‐SL) and TS were used for PCR amplifications. Strain 1, which induces conspicuous symptoms, is a common severe strain; it reacted positively with C1 and CR‐SL but negatively with TS in the PCR assays, so its PCR pattern was indicated as ‘+/+/−’ for C1, CR‐SL and TS primer pairs, respectively. Strain 2 seemed to be a Taiwan‐specific severe strain which induced severe symptoms, and its PCR pattern was ‘+/+/+’ as it showed positive reactions with all three primer pairs. Strain 3, causing the most severe symptoms, is a Malaysia‐specific severe strain whose PCR pattern is ‘−/+/−’. Strain 4 induced moderately severe symptoms and is an intermediate strain whose PCR pattern is ‘−/+/−’. Strain 5 is a mild strain; it did not induce symptoms in banana and it reacted positively with C1, CR‐SL and TS primer pairs. Interestingly, an additional 537‐bp fragment was amplified from Strain 5 with the CR‐SL primer pair. The PCR pattern of Strain 5 is therefore indicated as ‘+/++/+’. This study demonstrates that various BBTV strains exist in nature and they differ biologically and also molecularly.
Improvement of RT‐PCR Based Detection of Two Closteroviruses Associated with Little Cherry Disease in Sweet Cherries
Authors: Rybak M. , Kountrias A. , Eppler A. , Jelkmann W. , Heinze C. , Adam G. 
Published: October 2010

AbstractThe increasing availability of nucleotide sequence data from plant pathogenic fruit tree viruses led recently to the development of nucleic‐acid‐based detection methods as a routine tool for diagnosis. We present a simplification and modification of the previously described test procedure for the two closteroviruses Little cherry virus 1 and 2 (LChV‐1, LChV‐2). For LChV‐1, a single tube reaction reduced unspecific amplification that led to false positive results. For the detection of LChV‐2, a primer set was developed for the local isolates of the area ‘Altes Land’ in the northern part of Germany. To determine the optimal sampling conditions for a reliable detection of both viruses different types of tissue (bark, bud, leaves) were tested in monthly intervals.
Viruses Associated with Cassava Mosaic Disease in Senegal and Guinea Conakry
Authors: Okao‐Okuja G. , Legg J. P. , Traore L. , Jorge M. Alexandra 
Published: October 2010

AbstractA survey in Senegal and Guinea Conakry established the presence and incidence of cassava mosaic virus disease (CMD) in both countries. CMD occurred in all the fields surveyed, although its incidence was higher in Senegal (83%) than in Guinea (64%). Populations of the whitefly vector, Bemisia tabaci, were low in both countries averaging 1.7 adults per shoot in Guinea and 3.2 in Senegal. Most infections were attributed to the use of infected cuttings, 86 and 83% in Senegal and Guinea, respectively, and there was no evidence of rapid current‐season, whitefly‐borne infection at any of the sampled locations. Disease severity was generally low in the two countries and averaged 2.5 in Guinea and 2.3 in Senegal. No plants with unusually severe CMD symptoms characteristic of the CMD pandemic in East and Central Africa were observed. Restriction fragment length polymorphism (RFLP)‐based diagnostics revealed that African cassava mosaic virus (ACMV) is exclusively associated with CMD in both the countries. Neither East African cassava mosaic virus (EACMV), nor the recombinant Uganda variant (EACMV‐UG2) was detected in any sample. These survey data indicate that CMD could be effectively controlled in both countries by phytosanitation, involving the use of CMD‐free planting material and the removal of diseased plants.
Model-free unsupervised gene set screening based on information enrichment in expression profiles
Authors: Niida Atushi , Imoto Seiya , Yamaguchi Rui , Nagasaki Masao , Fujita André , Shimamura Teppei , Miyano Satoru 
Published: October 2010

Abstract
Motivation: A number of unsupervised gene set screening methods have recently been developed for search of putative functional gene sets based on their expression profiles. Most of the methods statistically evaluate whether the expression profiles of each gene set are fit to assumed models: e.g. co-expression across all samples or a subgroup of samples. However, it is possible that they fail to capture informative gene sets whose expression profiles are not fit to the assumed models.
Results: To overcome this limitation, we propose a model-free unsupervised gene set screening method, Matrix Information Enrichment Analysis (MIEA). Without assuming any specific models, MIEA screens gene sets based on information richness of their expression profiles. We extensively compared the performance of MIEA to those of other unsupervised gene set screening methods, using various types of simulated and real data. The benchmark tests demonstrated that MIEA can detect singular expression profiles that the other methods fail to find, and performs broadly well for various types of input data. Taken together, this study introduces MIEA as a broadly applicable gene set screening tool for mining regulatory programs from transcriptome data.
Contact: aniida@ims.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Characterization of δ-Guaiene Synthases from Cultured Cells of Aquilaria, Responsible for the Formation of the Sesquiterpenes in Agarwood
Authors: Kumeta Yukie , Ito Michiho 
Published: October 2010

Abstract
The resinous portions of Aquilaria plants, called agarwood, have been used as medicines and incenses. Agarwood contains a great variety of sesquiterpenes, and a study using cultured cells of Aquilaria showed the production of sesquiterpenes (α-guaiene, α-humulene, and δ-guaiene) to be induced by treatment with methyl jasmonate (MJ). In this study, the accumulation and production of sesquiterpenes were quantified. The amounts accumulated and produced reached a maximum at 12 h, and the most abundant product was α-humulene at 6 h and δ-guaiene after 12 h. However, a headspace analysis of the cells revealed that α-humulene is likely to be volatilized; so overall, the most abundant sesquiterpene in the cells was δ-guaiene. A cDNA library from RNA isolated from MJ-treated cells was screened using PCR methodologies to isolate five clones with very similar amino acid sequences. These clones were expressed in Escherichia coli, and enzymatic reactions using farnesyl pyrophosphate revealed that three of the clones yielded the same compounds as extracted from MJ-treated cells, the major product being δ-guaiene. These genes and their encoded enzymes are the first sesquiterpene synthases yielding guaiane-type sesquiterpenes as their major products to be reported. Expression of a fourth terpene synthase gene in bacteria resulted in the accumulation of the protein in insoluble forms. Site-directed mutagenesis of the inactive clone and three-dimensional homology modeling suggested that the structure of the N-terminal domain was important in facilitating proper folding of the protein to form a catalytically active structure.
Protein arginine methylation modulates light‐harvesting antenna translation in Chlamydomonas reinhardtii
Authors: Blifernez Olga , Wobbe Lutz , Niehaus Karsten , Kruse Olaf 
Published: October 2010

SummaryMethylation of protein arginines represents an important post‐translational modification mechanism, which has so far primarily been characterized in mammalian cells. In this work, we successfully identified and characterized arginine methylation as a crucial type of post‐translational modification in the activity regulation of the cytosolic translation repressor protein NAB1 in the plant model organism Chlamydomonas reinhardtii. NAB1 represses the cytosolic translation of light‐harvesting protein encoding mRNAs by sequestration into translationally silent messenger ribonucleoprotein complexes (mRNPs). Protein arginine methylation of NAB1 could be demonstrated by PRMT1 catalyzed methylation of recombinant NAB1 in vitro, and by immunodetection of methylated NAB1 arginines in vivo. Mass spectrometric analyses of NAB1 purified from C. reinhardtii revealed the asymmetric dimethylation of Arg90 and Arg92 within GAR motif I. Inhibition of arginine methylation by either adenosine‐2′‐3′‐dialdehyde (AdOx) or 7,7′‐carbonylbis(azanediyl)bis(4‐hydroxynaphthalene‐2‐sulfonic acid) sodium salt hydrate (AMI‐1) caused a dark‐green phenotype characterized by the increased accumulation of light‐harvesting complex proteins, and indicating a reduced translation repressor activity of NAB1. The extent of NAB1 arginine methylation depends on the growth conditions, with phototrophic growth causing a high methylation state and heterotrophic growth resulting in lowered methylation of the protein. In addition, we could show that NAB1 activity regulation by arginine methylation operates independently from cysteine‐based redox control, which has previously been shown to control the activity of NAB1.