bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neglected markers: Altered serum proteome in murine models of disease
Authors: Gianazza Elisabetta , Vegeto Elisabetta , Eberini Ivano , Sensi Cristina , Miller Ingrid 
Published: January 2012

AbstractMore than a decade ago our groups pioneered the analysis of serum proteins of laboratory animals with up‐to‐date proteomic techniques. We were, and still are, convinced that conforming animal procedures to the minimally invasive approaches typical of clinical biochemistry focuses attention on the actual conditions under which any finding arrived at on animal models of disease may eventually be applied to human patients for screening/diagnosis. We are also convinced that, besides the proteins present in trace level as a result of tissue leakage during disorders affecting specific peripheral organs, changes in the concentration of some of the major serum proteins as part of an acute‐phase response may be taken as biological end‐points during a number of experimental procedures. When reviewing literature data about proteomic investigations on plasma or serum of mice, we realized that not much work has been done in the direction we favor. In addition, we noticed that sometimes information about serum proteome has been coarsely treated and in a few cases even misunderstood/misused. In the following, we present current findings on serum/plasma proteome of the laboratory mouse not only under control conditions and during an experimentally induced acute‐phase reaction, but also in a number of models of disease, mainly related to cancer and to metabolic disorders.
To label or not to label: Applications of quantitative proteomics in neuroscience research
Authors: Filiou Michaela D. , Martins‐de‐Souza Daniel , Guest Paul C. , Bahn Sabine , Turck Christoph W. 
Published: January 2012

AbstractProteomics has provided researchers with a sophisticated toolbox of labeling‐based and label‐free quantitative methods. These are now being applied in neuroscience research where they have already contributed to the elucidation of fundamental mechanisms and the discovery of candidate biomarkers. In this review, we evaluate and compare labeling‐based and label‐free quantitative proteomic techniques for applications in neuroscience research. We discuss the considerations required for the analysis of brain and central nervous system specimens, the experimental design of quantitative proteomic workflows as well as the feasibility, advantages, and disadvantages of the available techniques for neuroscience‐oriented questions. Furthermore, we assess the use of labeled standards as internal controls for comparative studies in humans and review applications of labeling‐based and label‐free mass spectrometry approaches in relevant model organisms and human subjects. Providing a comprehensive guide of feasible and meaningful quantitative proteomic methodologies for neuroscience research is crucial not only for overcoming current limitations but also for gaining useful insights into brain function and translating proteomics from bench to bedside.
Proteomic characterization of adipose tissue constituents, a necessary step for understanding adipose tissue complexity
Authors: Peinado Juan R. , Pardo María , de la Rosa Olga , Malagón Maria M. 
Published: January 2012

AbstractThe original concept of adipose tissue as an inert storage depot for the excess of energy has evolved over the last years and it is now considered as one of the most important organs regulating body homeostasis. This conceptual change has been supported by the demonstration that adipose tissue serves as a major endocrine organ, producing a wide variety of bioactive molecules, collectively termed adipokines, with endocrine, paracrine and autocrine activities. Adipose tissue is indeed a complex organ wherein mature adipocytes coexist with the various cell types comprising the stromal‐vascular fraction (SVF), including preadipocytes, adipose‐derived stem cells, perivascular cells, and blood cells. It is known that not only mature adipocytes but also the components of SVF produce adipokines. Furthermore, adipokine production, proliferative and metabolic activities and response to regulatory signals (i.e. insulin, catecholamines) differ between the different fat depots, which have been proposed to underlie their distinct association to specific diseases. Herein, we discuss the recent proteomic studies on adipose tissue focused on the analysis of the separate cellular components and their secretory products, with the aim of identifying the basic features and the contribution of each component to different adipose tissue‐associated pathologies.
Post‐genomics of bone metabolic dysfunctions and neoplasias
Authors: Bernardini Giulia , Braconi Daniela , Spreafico Adriano , Santucci Annalisa 
Published: January 2012

AbstractPost‐genomic research on osteoblastic and osteoclastic cells, in contrast to that on many other cell types, has only been undertaken recently. Nevertheless, important information has been gained from these investigations on the mechanisms involved in osteoblast differentiation and on markers relevant for tissue regeneration and therapeutic validation of drugs, hormones and growth factors. These protein indicators may also have a diagnostic and prognostic value for bone dysfunctions and tumors. Some reviews have already focused on the application of transcriptomics and/or proteomics for exploring skeletal biology and related disorders. The main goal of the present review is to systematically summarize the most relevant post‐genomic studies on various metabolic bone diseases (osteoporosis, Paget's disease and osteonecrosis), neoplasias (osteosarcoma) and metabolic conditions that indirectly affect bone tissue, such as alkaptonuria.
Affinity‐based proteomic profiling: Problems and achievements
Authors: Medvedev Alexei , Kopylov Arthur , Buneeva Olga , Zgoda Victor , Archakov Alexander 
Published: January 2012

AbstractAffinity chromatography becomes a more and more popular method used in proteomic studies for separation of various groups of proteins (subproteomes). The review highlights the role of affinity chromatography fractionation for proteomic profiling of the most of intensively studied groups of proteins including cyclic nucleotide‐binding proteins, protein kinases (kinomes), phosphoproteins, glycoproteins, ubiquitinated proteins. Special attention is paid to the use of affinity chromatography for the characterization of small‐molecule protein targets. The latter is especially important for the elucidation of direct protein targets of potential drug substances for evaluation of their possible side‐effects or additional pharmacological application.
Mass spectrometry‐based proteomics strategies for protease cleavage site identification
Authors: van den Berg Bart H. J. , Tholey Andreas 
Published: January 2012

AbstractProtease‐catalyzed hydrolysis of peptide bonds is one of the most pivotal post‐translational modifications fulfilling manifold functions in the regulation of cellular processes. Therefore, dysregulation of proteolytic reactions plays a central role in many pathophysiological events. For this reason, understanding the molecular mechanisms in proteolytic reactions, in particular the knowledge of proteases involved in complex processes, expression levels and activity of protease and knowledge of the targeted substrates are an indispensable prerequisite for targeted drug development. The present review focuses on mass spectrometry‐based proteomic methods for the analysis of protease cleavage sites, including the identification of the hydrolyzed bonds as well as of the surrounding sequence. Peptide‐ and protein‐centric approaches and bioinformatic tools for experimental data interpretation will be presented and the major advantages and drawbacks of the different approaches will be addressed. The recent applications of these approaches for the analysis of biological function of different protease classes and potential future directions will be discussed.
Resolving confusion of tongues in statistics and machine learning: A primer for biologists and bioinformaticians
Authors: van Iterson Maarten , van Haagen Herman H. H. B. M. , Goeman Jelle J. 
Published: January 2012

AbstractBioinformatics is the field where computational methods from various domains have come together for analysis of biological data. Each domain has introduced its own specific jargon. However, in closely related domains, e.g. machine learning and statistics, concordant and discordant terminology occurs, the later can lead to confusion. This article aims to help solve the confusion of tongues arising from these two closely related domains, which are frequently used in bioinformatics. We provide a short summary of the most commonly applied machine learning and statistical approaches to data analysis in bioinformatics, i.e. classification and statistical hypothesis testing. We explain differences and similarities in common terminology used in various domains, such as precision, recall, sensitivity and true positive rate. This primer can serve as a guide to the terminology used in these fields.
The methylproteome and the intracellular methylation network
Authors: Erce Melissa A. , Pang Chi N. I. , Hart‐Smith Gene , Wilkins Marc R. 
Published: January 2012

AbstractSince its discovery more than 50 years ago, post‐translational modification (PTM) of proteins via methylation has grown in prominence, its involvement having been recognised in a number of central processes in the cell. Of these, the best characterised is its role in the epigenetic code. However, there is increasing evidence that its role extends far beyond this and we propose that it is a key regulator in interactome dynamics. In this review, we focus on the role of methylation in regulating protein‐protein interactions and illustrate, by providing a broad‐scale summary of our current knowledge of methylation and its impact on systems biology, how this can ultimately affect interactome dynamics. We describe the variety of analytical techniques available for the study of the methylproteome, comment on their advantages and limitations, and consider how these tools can help elucidate how methylation regulates the dynamics of the interactome. The insights gained from methyltransferase‐substrate networks will be summarised and the ability of protein methylation to facilitate or block protein‐protein interactions as well as their interplay with other post‐translational modifications, in particular phosphorylation, is highlighted. Finally, the importance of methylation in pathology‐associated protein interaction networks will be discussed using examples involving human diseases and the p53 protein.
Using SILAC and quantitative proteomics to investigate the interactions between viral and host proteomes
Authors: Munday Diane C. , Surtees Rebecca , Emmott Edward , Dove Brian K. , Digard Paul , Barr John N. , Whitehouse Adrian , Matthews David , Hiscox Julian A. 
Published: January 2012

AbstractViruses continue to pose some of the greatest threats to human and animal health, and food security worldwide. Therefore, new approaches are required to increase our understanding of virus‐host cell interactions and subsequently design more effective therapeutic countermeasures. Quantitative proteomics based on stable isotope labeling by amino acids in cell culture (SILAC), coupled to LC‐MS/MS and bioinformatic analysis, is providing an excellent resource for studying host cell proteomes and can readily be applied for the study of virus infection. Here, we review this approach and discuss how virus‐host cell interactions can best be studied, what is realistically feasible, and the potential limitations. For example, sub‐cellular fractionation can reduce sample complexity for LC‐MS/MS, increase data return and provide information regarding protein trafficking between different cellular compartments. The key to successful quantitative proteomics combines good experimental design and appropriate sample preparation with statistical analysis and validation of the MS data through the use of independent techniques and functional analysis. The annotation of the human genome and the increasing availability of biological reagents such as antibodies, provide the optimum parameters for studying viruses that infect humans, in human cell lines. SILAC‐based quantitative proteomics can also be used to study the interactome of viral proteins with the host cell. Coupling proteomic studies with global transcriptomic and RNA depletion experiments will provide great insights into the complexity of the infection process, and potentially reveal new antiviral targets.
β‐Tubulins in Gibberella zeae: their characterization and contribution to carbendazim resistance
Authors: Qiu JianBo , Huang TingTing , Xu JianQiang , Bi ChaoWei , Chen ChangJun , Zhou MingGuo 
Published: January 2012

AbstractBACKGROUND: Fusarium head blight caused by Gibberella zeae is an important disease of wheat and barley because it reduces grain yield and quality and results in the contamination of grain with mycotoxins. Recent studies have shown that carbendazim resistance in field strains of G. zeae is not caused by mutation of the β‐tubulin gene (β1tub), which is the case with other filamentous fungi, but that fungicide resistance is greatly increased by deletion of β1tub. The aim of the present study was to clarify the function of β1tub and its role in carbendazim resistance in G. zeae by artificial gene operation.RESULTS: Deletion of β1tub reduced vegetative growth and pathogenicity but increased asexual reproduction in G. zeae. All the mutants were more resistant to carbendazim than parent strains. A three‐dimensional model of β1tub was constructed, and the possible carbendazim binding site was analysed.CONCLUSION: β1tub is not an essential gene in G. zeae, but it affects the sensitivity of the fungus to carbendazim. Copyright © 2012 Society of Chemical Industry
AZO/Au/AZO multilayer as a transparent conductive electrode
Authors: Lee Seungjun , Bang Seokhwan , Park Joohyun , Park Soyeon , Ko Youngbin , Jeon Hyeongtag 
Published: January 2012

AbstractA multilayer of Al doped ZnO/gold/Al doped ZnO (AZO/Au/AZO) was deposited by atomic layer deposition (ALD), and its structural, electrical, and optical properties were investigated. The thin Au interlayer was deposited by e‐beam evaporator and showed a series of islands. As the Au interlayer thickness increased, the Au islands coalesced resulting in a continuous Au film at 12 nm or thicker. As the Au interlayer thickness increased to 12 nm, the carrier concentration increased from 1.3 × 1020 to 4.2 × 1021 cm−3, the Hall mobility increased from 13.4 to 22.4 cm2/Vs, and the resistivity decreased from 2.6 × 10−3 to 1.2 × 10−4 Ωcm. However, the transmittance decreased from 80 to 48%. Additionally, the AZO/Au/AZO multilayer was less crystalline than a single AZO layer.
Does female representation in top management improve firm performance? A panel data investigation
Authors: Dezsö Cristian L. , Ross David Gaddis 
Published: January 2012

AbstractWe argue that female representation in top management brings informational and social diversity benefits to the top management team, enriches the behaviors exhibited by managers throughout the firm, and motivates women in middle management. The result should be improved managerial task performance and thus better firm performance. We test our theory using 15 years of panel data on the top management teams of the S&P 1,500 firms. We find that female representation in top management improves firm performance but only to the extent that a firm's strategy is focused on innovation, in which context the informational and social benefits of gender diversity and the behaviors associated with women in management are likely to be especially important for managerial task performance. Copyright © 2012 John Wiley & Sons, Ltd.
Enrichment of Fe‐Containing Phases and Recovery of Iron and Its Oxides by Magnetic Separation from BOF Slags
Authors: Wang Deyong , Jiang Maofa , Liu Chengjun , Min Yi , Cui Yuyuan , Liu Jian , Zhang Yongcang 
Published: January 2012

AbstractSteel slag normally contains a large amount of iron and its oxides. Therefore, it is a potential renewable resource in case of inadequate iron ore supply. To recover the metals from steel slag, two types of BOF slags were remelted at 1873 K. The liquid slags were cooled using four types of cooling conditions, namely, water granulation, splashing, air cooling, and furnace cooling, to investigate the influence of cooling rate on mineral components, especially the enrichment behavior of Fe‐containing minerals. Subsequently, wet magnetic separation was conducted to examine the relations between iron recovery ratio and cooling conditions. The results show that the slags under the four cooling conditions mainly contained dicalcium silicate, RO phase, FetO, 2CaO(Fe,Al)2O3, and calcium ferrite. However, tricalcium silicate, 12CaO·7Al2O3, M‐A spinel, and free CaO and MgO were occasionally observed. The amount of glass matrix decreased, the Fe‐containing minerals increased, and the minerals more fully crystallized when the cooling rate of the liquid slag was decreased. From granulation to furnace cooling of the slags, the iron content in the recovered concentrate and the iron recovery ratio both increased. This result is in agreement with the findings on phase transformation through SEM analysis.
Effect of TiO2 on the Viscosity and Slag Structure in Blast Furnace Type Slags
Authors: Park Hyunsik , Park Jun‐Young , Kim Gi Hyun , Sohn Il 
Published: January 2012

AbstractTiO2 additions up to 10 mass% behaved as a basic oxide and lowered the viscosity in the CaO–SiO2–17 mass% Al2O3–10 mass% MgO‐based slags by depolymerizing the silicate network structure. Raman spectroscopy revealed the sum of NBO/Si 1 and 3 decreased while the sum of NBO/Si 2 and 4 increased with TiO2 content. Unlike the silicate structures, the aluminate structures seems to be relatively unaffected by TiO2 additions according to the FTIR results. 5 mass% TiO2 significantly decreased the viscosity compared to the TiO2 free slags, but beyond 5 mass% TiO2 meaningful changes in the viscosity was not observed. From the comparison of the viscosity at constant TiO2 of 5 and 10 mass% and varying CaO/SiO2 ratio, increasing the CaO/SiO2 ratio was more effective in decreasing the viscosity than TiO2 additions.
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
Authors: Soergel David A W , Dey Neelendu , Knight Rob , Brenner Steven E 
Published: January 2012

Abstract
Microbial community profiling using 16S rRNA gene sequences requires accurate taxonomy assignments. ‘Universal’ primers target conserved sequences and amplify sequences from many taxa, but they provide variable coverage of different environments, and regions of the rRNA gene differ in taxonomic informativeness—especially when high-throughput short-read sequencing technologies (for example, 454 and Illumina) are used. We introduce a new evaluation procedure that provides an improved measure of expected taxonomic precision when classifying environmental sequence reads from a given primer. Applying this measure to thousands of combinations of primers and read lengths, simulating single-ended and paired-end sequencing, reveals that these choices greatly affect taxonomic informativeness. The most informative sequence region may differ by environment, partly due to variable coverage of different environments in reference databases. Using our Rtax method of classifying paired-end reads, we found that paired-end sequencing provides substantial benefit in some environments including human gut, but not in others. Optimal primer choice for short reads totaling 96 nt provides 82–100% of the confident genus classifications available from longer reads.
Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin
Authors: Westfall Patrick J. , Pitera Douglas J. , Lenihan Jacob R. , Eng Diana , Woolard Frank X. , Regentin Rika , Horning Tizita , Tsuruta Hiroko , Melis David J. , Owens Andrew , Fickes Scott , Diola Don , Benjamin Kirsten R. , Keasling Jay D. , Leavell Michael D. , McPhee Derek J. , Renninger Neil S. , Newman Jack D. , Paddon Chris J. 
Published: January 2012

Malaria, caused by
Plasmodium sp
, results in almost one million deaths and over 200 million new infections annually. The World Health Organization has recommended that artemisinin-based combination therapies be used for treatment of malaria. Artemisinin is a sesquiterpene lactone isolated from the plant
Artemisia annua
. However, the supply and price of artemisinin fluctuate greatly, and an alternative production method would be valuable to increase availability. We describe progress toward the goal of developing a supply of semisynthetic artemisinin based on production of the artemisinin precursor amorpha-4,11-diene by fermentation from engineered
Saccharomyces cerevisiae
, and its chemical conversion to dihydroartemisinic acid, which can be subsequently converted to artemisinin. Previous efforts to produce artemisinin precursors used
S. cerevisiae
S288C overexpressing selected genes of the mevalonate pathway [Ro et al. (2006)
Nature
440:940–943]. We have now overexpressed every enzyme of the mevalonate pathway to
ERG20
in
S. cerevisiae
CEN.PK2, and compared production to CEN.PK2 engineered identically to the previously engineered S288C strain. Overexpressing every enzyme of the mevalonate pathway doubled artemisinic acid production, however, amorpha-4,11-diene production was 10-fold higher than artemisinic acid. We therefore focused on amorpha-4,11-diene production. Development of fermentation processes for the reengineered CEN.PK2 amorpha-4,11-diene strain led to production of > 40 g/L product. A chemical process was developed to convert amorpha-4,11-diene to dihydroartemisinic acid, which could subsequently be converted to artemisinin. The strains and procedures described represent a complete process for production of semisynthetic artemisinin.
METALLICITY DISTRIBUTION FUNCTIONS OF THE OLD POPULATIONS OF THE MAGELLANIC CLOUDS FROM RR Lyrae STARS
Authors: Haschke Raoul , Grebel Eva K. , Duffau Sonia , Jin Shoko 
Published: January 2012

ABSTRACT
We present the first metallicity distribution functions of the old field populations in the Magellanic Clouds (MCs). Our metallicities are based on the Fourier decomposition of Type ab RR Lyrae light curves from the Optical Gravitational Lensing Experiment. On the metallicity scale of Zinn & West, we find a mean metallicity of [Fe/H] = −1.50 ± 0.24 dex based on 16,776 RR Lyrae stars in the Large Magellanic Cloud (LMC). For the Small Magellanic Cloud (SMC) we obtain −1.70 ± 0.27 dex based on 1831 RR Lyrae stars. These uncertainties represent the intrinsic spread in the population rather than the standard deviation of the mean. Our results are in good agreement with the few existing spectroscopic metallicity determinations for LMC RR Lyrae stars from the literature. For both the LMC and the SMC the metallicity spread exceeds 1 dex in [Fe/H]. The distribution of metallicities in both Clouds is very uniform, and no significant metallicity gradient is detectable. We also do not find any pronounced populations of extremely metal-poor RR Lyrae candidates with metallicities well below −2 dex, although we need to caution that the photometric method used may overestimate the metallicities of metal-deficient stars. Moreover, because of stellar evolutionary effects one does not expect to observe many RR Lyrae stars among very metal-poor horizontal branch stars. We suggest that the MCs experienced fairly rapid and efficient early enrichment involving pre-enriched gas as well as possibly gas infall, while metal loss through outflows does not seem to have played a significant role. Moreover, we suggest that the differences in the metallicities of the old population of LMC and SMC make an origin from a single, common progenitor unlikely, unless the separation happened very early on.