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991.
992.
Detecting biomarkers at pg/ml concentrations or below is, in many situations, critical for quantifying levels in healthy individuals as well as the changes that can occur in the progression of disease states. The ability to detect multiple biomarkers from the same sample allows for better diagnoses, more efficient testing, and lower volumes of sample required. Based on single molecule counting technology, a multiplex instrument was designed and built that is capable of detecting cytokines and other low-abundance proteins at sub-pg/ml quantities in human plasma samples. The multiplex single molecule counting instrument was used to generate 95% reference limits for interleukin 4 (IL-4, <0.61 pg/ml), interleukin 6 (IL-6, <6.53 pg/ml), and interleukin 10 (IL-10, <1.08 pg/ml) from 100 healthy human donor plasma samples, with more than 90% of IL-4 concentrations and 100% of IL-6 and IL-10 concentrations above the limit of detection. 相似文献
993.
Michele Paleari Monica Lavagna Andrea Campioli 《The International Journal of Life Cycle Assessment》2016,21(12):1667-1690
Purpose
Since the construction sector is a considerable energy consumer and greenhouse gas (GHG) producer, the EU rules strive to build nearly zero-energy buildings, by reducing the operative energy and yearning for on-site energy production. This article underlines the necessity to go beyond the energy evaluations and move towards the environmental assessment in a life cycle perspective, by comparing the impacts due to building materials and energy production devices.Methods
We compared the operational energy impacts and those of technologies and materials carrying out a life cycle assessment (LCA; ISO 14040, ISO 14044, EN 15643–2, EN 15978) on a nearly zero-energy building (ZEB), a residential complex with 61 apartments in four buildings, situated near Milan (Italy). We consider all life cycle phases, including production, transport, building site activities, use and maintenance; the materials inventory was filled out collecting data from invoices paid, building site reports, construction drawings and product data sheets. To make the assessment results comparable, we set a functional unit of 1 m2 of net floor area in 1 year (1 m2y), upon a lifespan of 100 years. The environmental data were acquired from Ecoinvent 2.2.Results and discussion
The results highlight the important role of the pre-use and maintenance phases in building life so that in a nearly ZEB, the environmental impacts linked to the use are no longer the major proportion: the pre-use phase accounts for 56 %, while the operative energy is only 31 % of the total. For this reason, if the environmental assessment of the case study was shrunk to the operational consumption, only one third of the impacts would be considered. The consumption of non-renewable resources after 100 years are 193,950 GJ (133.5 kWh/m2y); the GHG emissions are 15,300 t (37.8 kg of CO2?eq/m2y). In the pre-use phase, structures have the major impacts (50 %) and the load of system components is unexpectedly high (12 %) due to the ambition of on-site energy production.Conclusions
Paying attention to the operative energy consumption seems to address to only one third of the environmental impacts of buildings: the adoption of LCA as a tool to guide the design choices could help to identify the solution which ensures the lowest overall impact on the whole life, balancing the options of reducing the energy requirements, the on-site production from renewable sources and the limitation of the impacts due to building components (simpler and more durable).994.
Franco Baldi Michele Gallo Dario Battistel Elena Barbaro Andrea Gambaro Salvatore Daniele 《Biometals》2016,29(6):1097-1106
The Pseudomonas putida FB1, known as a broad-spectrum mercury resistant strain, becomes yellow-green due to the secretion of pyoverdine (PVDs) under limited iron conditions and high mercury concentrations. Different modified Nelson’s media were obtained by adding mercury, iron, and the complexing agent nitrilotriacetic acid to demonstrate that the strain produces only the highest concentrations of PVDs due to the induction with 25 µM Hg2+. An amount of 250 mg PVDs was purified from the supernatant of 1 litre culture. The various forms of PVDs were characterized using different techniques such as fluorescence spectroscopy, high performance liquid chromatography coupled with high resolution mass spectrometry, and scanning electron microscope equipped with energy dispersive X-ray analyser. A set of “in vivo” experiments demonstrated that additions of Hg2+ to the cultures from 10 to 25 µM Hg2+ stimulate an over secretion of PVDs suggesting that the toxic cation strongly reduces the availability of apo-PVDs, because the complex mercuric-pyoverdine is very stable at neutral pH, and hinder the formation of PVDs-Fe(III). 相似文献
995.
Kerstin U. Ludwig Syeda Tasnim Ahmed Anne C. B?hmer Nasim Bahram Sangani Sheryil Varghese Johanna Klamt Hannah Schuenke Pinar Gültepe Andrea Hofmann Michele Rubini Khalid Ahmed Aldhorae Regine P. Steegers-Theunissen Augusto Rojas-Martinez Rudolf Reiter Guntram Borck Michael Knapp Mitsushiro Nakatomi Daniel Graf Elisabeth Mangold Heiko Peters 《PLoS genetics》2016,12(3)
Nonsyndromic orofacial clefts are common birth defects with multifactorial etiology. The most common type is cleft lip, which occurs with or without cleft palate (nsCLP and nsCLO, respectively). Although genetic components play an important role in nsCLP, the genetic factors that predispose to palate involvement are largely unknown. In this study, we carried out a meta-analysis on genetic and clinical data from three large cohorts and identified strong association between a region on chromosome 15q13 and nsCLP (P = 8.13×10−14 for rs1258763; relative risk (RR): 1.46, 95% confidence interval (CI): 1.32–1.61)) but not nsCLO (P = 0.27; RR: 1.09 (0.94–1.27)). The 5 kb region of strongest association maps downstream of Gremlin-1 (GREM1), which encodes a secreted antagonist of the BMP4 pathway. We show during mouse embryogenesis, Grem1 is expressed in the developing lip and soft palate but not in the hard palate. This is consistent with genotype-phenotype correlations between rs1258763 and a specific nsCLP subphenotype, since a more than two-fold increase in risk was observed in patients displaying clefts of both the lip and soft palate but who had an intact hard palate (RR: 3.76, CI: 1.47–9.61, Pdiff<0.05). While we did not find lip or palate defects in Grem1-deficient mice, wild type embryonic palatal shelves developed divergent shapes when cultured in the presence of ectopic Grem1 protein (P = 0.0014). The present study identified a non-coding region at 15q13 as the second, genome-wide significant locus specific for nsCLP, after 13q31. Moreover, our data suggest that the closely located GREM1 gene contributes to a rare clinical nsCLP entity. This entity specifically involves abnormalities of the lip and soft palate, which develop at different time-points and in separate anatomical regions. 相似文献
996.
Katarina Truvé Peter Dickinson Anqi Xiong Daniel York Kartika Jayashankar Gerli Pielberg Michele Koltookian Eva Murén Hans-Henrik Fuxelius Holger Weishaupt Fredrik J. Swartling G?ran Andersson ?ke Hedhammar Erik Bongcam-Rudloff Karin Forsberg-Nilsson Danika Bannasch Kerstin Lindblad-Toh 《PLoS genetics》2016,12(5)
Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS) was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA) 26 (p = 2.8 x 10−8). Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate genes that were highly associated with glioma susceptibility: CAMKK2, P2RX7 and DENR. CAMKK2 showed reduced expression in both canine and human brain tumors, and a non-synonymous variant in P2RX7, previously demonstrated to have a 50% decrease in receptor function, was also associated with disease. Thus, one or more of these genes appear to affect glioma susceptibility. 相似文献
997.
Mark Larance Kathryn J. Kirkwood Michele Tinti Alejandro Brenes Murillo Michael A. J. Ferguson Angus I. Lamond 《Molecular & cellular proteomics : MCP》2016,15(7):2476-2490
We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754).Proteins rarely work as monomers to carry out all the biological processes needed for cells to function. An estimate of the total number of protein-protein interactions within the human proteome, based on currently available data sets, is ∼650,000 (1). This is likely an underestimate, given that many proteins form either transient, or weak interactions within intact cells that may not yet have been detected. This suggests that the majority of human proteins can participate in protein complex formation, at least under some conditions. This includes the many well-studied soluble protein complexes in the cytoplasm, exemplified by the proteasome, ribosomes and cytoskeletal network. It also includes many membrane-associated complexes, for example receptor tyrosine kinase signaling complexes, integrin networks and transmembrane transporters (2). To characterize the many roles of multi-protein complexes in biological regulatory mechanisms, it is important to have convenient methods for the rapid and efficient analysis of their composition and dynamics (3). Ideally, such methods should be applicable to system-wide studies and allow the analysis of endogenous proteins, rather than exclusively use tagged and/or over-expressed baits.The methods available for the proteome-wide analysis of protein interactions have developed swiftly over the last ten years. This field is dominated by affinity-enrichment based approaches, using either tagged constructs, or antibodies specific for endogenous proteins. Another approach is in vivo proximity labeling, based, for example, on the exogenous expression of a protein of interest, fused either to a promiscuous biotin-ligase (BioID) (4), or to a peroxidase enzyme that activates biotin-phenol (APEX) (5). While these data sets have proved very useful, there are some downsides. For example, a large expense in terms of both time and money to generate the thousands of individual “bait” proteins required for global interaction analyses. In addition, each of these affinity enrichments will be performed in only one type of buffer system, which is unlikely to be compatible with the maintenance of all protein-protein interactions. Another dimension to the analytical problem is that many proteins are expressed as different sized isoforms and/or in different post-translationally modified forms, resulting in formation of multiple, related, but functionally distinct complexes, with different combinations of interaction partners (6). Using affinity-enrichment/pull-down methods alone makes it difficult to resolve such mixtures of different forms of related protein complexes, complicating a detailed understanding of biological response mechanisms.An alternative strategy involves protein correlation profiling-MS, i.e. correlating similarities in the fractionation profiles of proteins detected by mass spectrometry, assuming that proteins in a common complex will cofractionate. This approach was previously applied to the analysis of subcellular organelle proteomes (7, 8), and subsequently extended to analyze soluble protein complexes. Thus, recent studies have shown that chromatography-based separation of soluble protein complexes, combined with fraction collection and high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS)1, facilitates analysis of many hundreds of soluble complexes from a single experiment (6, 9–11). A limitation of all of these studies, however, is that the native extraction conditions used to preserve protein-protein interactions isolates predominantly stable, soluble complexes. For example, many proteins that are integral to membranes are not recovered (12). Similarly, soluble protein complexes that have weakly bound protein subunits can dissociate upon cell lysis and the inevitable dilution associated with extraction. Thus, the potential value of this approach for the system-wide analysis of protein complexes is limited without a covalent tether to hold protein-protein interactions intact during extraction and subsequent chromatographic separation (13).Covalent protein crosslinking has been used extensively to stabilize protein complexes, cultured cells and tissues for subsequent analysis, either by microscopy, nucleotide sequencing or mass spectrometry. The agents employed to crosslink proteins to each other include various chemical groups able to react with the side-chains of either amino acids, nucleotides, carbohydrates or lipids (14). These crosslinking agents vary in the efficiency with which they perfuse into unbroken cells/tissues and the speed of their reaction when in proximity to a suitable chemical group. One of the most widely used crosslinkers is formaldehyde, which can reversibly form a covalent crosslink to stabilize both protein-protein and protein-nucleotide interactions (15–21). One of the main benefits of using formaldehyde is that because of its small size, it readily permeates intact cells and tissues. Another benefit of using formaldehyde is the easy reversal of the crosslinks by heating and subsequent compatibility with mass spectrometry-based proteome analysis.Here, we describe a mass spectrometry-based proteomic approach for the efficient global analysis of protein complexes, including membrane proteins, using in vivo protein crosslinking combined with denaturing extraction. Using high-resolution, size-exclusion chromatography (SEC) to separate crosslinked complexes under denaturing conditions and MS analysis of fractionated proteins, we could identify membrane bound and membrane associated complexes not accessible in native extracts. We present a detailed comparison of the sets of protein complexes that can be identified using protein correlation profiling MS analysis in conjunction with both formaldehyde crosslinked and native extracts from U2OS cells. We provide access to the entire proteome-wide data sets of both in vivo crosslinked and native U2OScell protein complexes via a searchable online database (http://www.peptracker.com/epd/). 相似文献
998.
Francesca Bianchi Michele Sommariva Loris De Cecco Tiziana Triulzi Sandra Romero-Cordoba Elda Tagliabue 《Cell cycle (Georgetown, Tex.)》2016,15(23):3220-3229
The autoimmune regulator gene (AIRE) plays a fundamental role in tolerance by promoting the expression of tissue-specific antigens in medullary thymic epithelial cells (mTECs). Recently, AIRE expression was detected also in human keratinocytes and in tumors originating in stratified epithelia. Here, we tested whether AIRE is expressed in cancer cells. We analyzed AIRE expression in cancer cases from The Cancer Genome Atlas (TCGA) RNA-seq dataset and we found association with better outcome. AIRE protein expression was verified by immunohistochemistry in a cohort of 39 human breast cancer specimens and its prognostic relevance was confirmed in microarray-based gene expression data set NKI-295 and KM-Plotter. Both in the RNA-seq and gene expression datasets analyzed, AIRE expression was an independent strong prognostic factor for relapse-free survival (RFS), particularly in estrogen receptor-positive tumors. Enrichment of translation-related pathways was observed in AIRE-expressing tumors by Ingenuity Pathway Analysis and a significant increase of cells in G1 phase and activation of caspase cascades was induced by AIRE transfection in breast cancer luminal cell lines, suggesting that AIRE-induced over-translation of proteins lead to cycle arrest and apoptosis. These data are the first to identify AIRE expression in breast cancer and an association with prognosis. 相似文献
999.
1000.
Plant hydraulics as a central hub integrating plant and ecosystem function: meeting report for ‘Emerging Frontiers in Plant Hydraulics’ (Washington,DC, May 2015)
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Lawren Sack Marilyn C. Ball Craig Brodersen Stephen D. Davis David L. Des Marais Lisa A. Donovan Thomas J. Givnish Uwe G. Hacke Travis Huxman Steven Jansen Anna L. Jacobsen Daniel M. Johnson George W. Koch Christophe Maurel Katherine A. McCulloh Nate G. McDowell Andrew McElrone Frederick C. Meinzer Peter J. Melcher Gretchen North Matteo Pellegrini William T. Pockman R. Brandon Pratt Anna Sala Louis S. Santiago Jessica A. Savage Christine Scoffoni Sanna Sevanto John Sperry Stephen D. Tyerman Danielle Way N. Michele Holbrook 《Plant, cell & environment》2016,39(9):2085-2094
Water plays a central role in plant biology and the efficiency of water transport throughout the plant affects both photosynthetic rate and growth, an influence that scales up deterministically to the productivity of terrestrial ecosystems. Moreover, hydraulic traits mediate the ways in which plants interact with their abiotic and biotic environment. At landscape to global scale, plant hydraulic traits are important in describing the function of ecological communities and ecosystems. Plant hydraulics is increasingly recognized as a central hub within a network by which plant biology is connected to palaeobiology, agronomy, climatology, forestry, community and ecosystem ecology and earth‐system science. Such grand challenges as anticipating and mitigating the impacts of climate change, and improving the security and sustainability of our food supply rely on our fundamental knowledge of how water behaves in the cells, tissues, organs, bodies and diverse communities of plants. A workshop, ‘Emerging Frontiers in Plant Hydraulics’ supported by the National Science Foundation, was held in Washington DC, 2015 to promote open discussion of new ideas, controversies regarding measurements and analyses, and especially, the potential for expansion of up‐scaled and down‐scaled inter‐disciplinary research, and the strengthening of connections between plant hydraulic research, allied fields and global modelling efforts. 相似文献