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31.
Gold L Ayers D Bertino J Bock C Bock A Brody EN Carter J Dalby AB Eaton BE Fitzwater T Flather D Forbes A Foreman T Fowler C Gawande B Goss M Gunn M Gupta S Halladay D Heil J Heilig J Hicke B Husar G Janjic N Jarvis T Jennings S Katilius E Keeney TR Kim N Koch TH Kraemer S Kroiss L Le N Levine D Lindsey W Lollo B Mayfield W Mehan M Mehler R Nelson SK Nelson M Nieuwlandt D Nikrad M Ochsner U Ostroff RM Otis M Parker T Pietrasiewicz S Resnicow DI Rohloff J Sanders G Sattin S Schneider D Singer B 《PloS one》2010,5(12):e15004
Background
The interrogation of proteomes (“proteomics”) in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine.Methodology/Principal Findings
We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 µL of serum or plasma). Our current assay measures 813 proteins with low limits of detection (1 pM median), 7 logs of overall dynamic range (∼100 fM–1 µM), and 5% median coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding signature of DNA aptamer concentrations, which is quantified on a DNA microarray. Our assay takes advantage of the dual nature of aptamers as both folded protein-binding entities with defined shapes and unique nucleotide sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to rapidly discover unique protein signatures characteristic of various disease states.Conclusions/Significance
We describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine. 相似文献32.
Active form of Notch imposes T cell fate in human progenitor cells 总被引:14,自引:0,他引:14
De Smedt M Reynvoet K Kerre T Taghon T Verhasselt B Vandekerckhove B Leclercq G Plum J 《Journal of immunology (Baltimore, Md. : 1950)》2002,169(6):3021-3029
The crucial role of Notch signaling in cell fate decisions in hematopoietic lineage and T lymphocyte development has been well established in mice. Overexpression of the intracellular domain of Notch mediates signal transduction of the protein. By retroviral transduction of this constitutively active truncated intracellular domain in human CD34+ umbilical cord blood progenitor cells, we were able to show that, in coculture with the stromal MS-5 cell line, depending on the cytokines added, the differentiation toward CD19+ B lymphocytes was blocked, the differentiation toward CD14+ monocytes was inhibited, and the differentiation toward CD56+ NK cells was favored. The number of CD7+cyCD3+ cells, a phenotype similar to T/NK progenitor cells, was also markedly increased. In fetal thymus organ culture, transduced CD34+ progenitor cells from umbilical cord blood cells or from thymus consistently generated more TCR-gammadelta T cells, whereas the other T cell subpopulations were largely unaffected. Interestingly, when injected in vivo in SCID-nonobese diabetic mice, the transduced cells generated ectopically human CD4+CD8+ TCR-alphabeta cells in the bone marrow, cells that are normally only present in the thymus, and lacked B cell differentiation potential. Our results show unequivocally that, in human, Notch signaling inhibits the monocyte and B cell fate, promotes the T cell fate, and alters the normal T cell differentiation pathway compatible with a pretumoral state. 相似文献
33.
Inhibitory effect of sulfur dioxide and other stress compounds in wine on the ATPase activity of Oenococcus oeni 总被引:5,自引:0,他引:5
Malolactic fermentation (MLF) is carried out by Oenococcus oeni under very harsh conditions. This paper shows that stress compounds in wine such as SO(2), fatty acids and copper have an inhibitory effect on cell growth and MLF duration, and relates this effect to an inhibition of ATPase activity. Of the stress compounds, SO(2) and dodecanoic acid had the strongest effect, decreasing the ATPase specific activity to 37% and 58%, respectively. It can be concluded that ATPase is a good indicator of the physiological state of the cells and their ability to lead MLF. 相似文献
34.
BackgroundFour biopesticide prototypes formulated as dispersible granules and dry powders based on 2 Colombian isolates of Trichoderma koningiopsis (Th003) and T. asperellum (Th034) were developed. These microorganisms have antagonist activity against Fusarium oxysporum f. sp. lycopersici and Rhizoctonia solani with a reduction in incidence of between 70 and 100% in tomato crops and potato crops, respectively.AimTo determine the effect of the formulation on the shelf-life of 4 biopesticides based on T. koningiopsis Th003 and Trichoderma asperellum Th034 at 3 different temperatures.MethodsThe formulation effect was determined by evaluating the germination of unformulated and formulated conidia (dispersible granules and dry powder) stored at 8, 18 and 28 °C for 18 months. Germination kinetics were used to estimate the shelf-life by using different mathematical models (zero order, first order, second order, Higuchi model, Korsmeyer-Peppas model and polynomial model).ResultsThe products showed high stability of the conidia germination when they were stored at 8 and 18° C, with shelf-lives of 14.4 and 13.9 months for dry powder based on Th003, and 12.0 and 10.8 months for dry powder based on Th034, respectively. Prototypes formulated as dispersible granules stored at the same temperatures (8 and 18 °C) showed lower shelf-lives, with values of 11.6 and 10.9 months for the Th003 product, and 10.7 and 7.2 months for the dispersible granules based on Th034. Significant reductions in germination were observed on unformulated conidia at all storage temperatures evaluated.ConclusionsThe formulation type affected the conidia stability of the 2 Trichoderma spp. Colombian isolates. Dry powder was the prototype with the highest stability and shelf-life at all temperatures evaluated. 相似文献
35.
The Synura petersenii species complex represents a common, cosmopolitan and highly diverse taxon of autotrophic freshwater flagellates. In this paper, we describe and characterize four new species (S. borealis, S. heteropora, S. hibernica and S. laticarina) that have been identified during our extensive sampling of freshwater habitats in 15 European countries. Morphometric analyses of siliceous scales led to the significant phenotypic differentiation of all four newly described species, and their separation from other related species of the S. petersenii complex. Two of these newly described species (S. hibernica and S. borealis) can be clearly distinguished by characteristic large colonies consisting of elongated, lanceolate-shaped cells. Development of strongly elongated, narrow cells in S. hibernica could be explained by the adaptation of this species to oligotrophic conditions. Though morphologically distinct, S. borealis possesses an exceptionally high degree of genetic diversity, possibly indicating recent speciation and evolutionary diversification within this taxon. Three of the four newly described species exhibit restricted biogeographic distribution. The evolutionarily related S. borealis and S. laticarina occur only in Northern Europe, and seem to be adapted to colder areas. The most remarkable distribution pattern was observed for S. hibernica, which has a geographic distribution that is restricted to western Ireland. 相似文献
36.
Alfonso Benítez-Páez Magda Villarroya Stephen Douthwaite Toni Gabaldón M.-Eugenia Armengod 《RNA (New York, N.Y.)》2010,16(11):2131-2143
Transfer RNAs are the most densely modified nucleic acid molecules in living cells. In Escherichia coli, more than 30 nucleoside modifications have been characterized, ranging from methylations and pseudouridylations to more complex additions that require multiple enzymatic steps. Most of the modifying enzymes have been identified, although a few notable exceptions include the 2′-O-methyltransferase(s) that methylate the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNALeuCmAA and tRNALeucmnm5UmAA. Here, we have used a comparative genomics approach to uncover candidate E. coli genes for the missing enzyme(s). Transfer RNAs from null mutants for candidate genes were analyzed by mass spectrometry and revealed that inactivation of yibK leads to loss of 2′-O-methylation at position 34 in both tRNALeuCmAA and tRNALeucmnm5UmAA. Loss of YibK methylation reduces the efficiency of codon–wobble base interaction, as demonstrated in an amber suppressor supP system. Inactivation of yibK had no detectable effect on steady-state growth rate, although a distinct disadvantage was noted in multiple-round, mixed-population growth experiments, suggesting that the ability to recover from the stationary phase was impaired. Methylation is restored in vivo by complementing with a recombinant copy of yibK. Despite being one of the smallest characterized α/β knot proteins, YibK independently catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2′-OH of the wobble nucleotide; YibK recognition of this target requires a pyridine at position 34 and N6-(isopentenyl)-2-methylthioadenosine at position 37. YibK is one of the last remaining E. coli tRNA modification enzymes to be identified and is now renamed TrmL. 相似文献
37.
Héctor Flores-Villase?or Adrian Canizalez-Román Magda Reyes-Lopez Kamram Nazmi Mireya de la Garza Jorge Zazueta-Beltrán Nidia León-Sicairos Jan G. M. Bolscher 《Biometals》2010,23(3):569-578
Increased prevalence of antibiotic-resistant bacteria has become a major threat to the health sector worldwide due to their
virulence, limited therapeutic options and distribution in both hospital and community settings. Discovery and development
of new agents to combat antibiotic-resistant bacteria is thus needed. This study therefore aimed to evaluate the ability of
bovine lactoferrin (LF), peptides from two antimicrobial domains lactoferricin B (LFcin17-30) and lactoferrampin (LFampin265-284)
and a chimeric construct (LFchimera) containing both peptides, as potential bactericidal agents against clinical isolates
of antibiotic-resistant Staphylococcus aureus and Escherichia coli. Results in kinetics of growth show that LF chimera and peptides inhibited the growth of both bacterial species. By confocal
microscopy and flow cytometry it was observed that LF and FITC-labeled peptides are able to interact with these bacteria and
cause membrane permeabilization, as monitored by propidium iodide staining, these effects were decreased by preincubation
with lipopolysaccharide in E. coli. By electron microscopy, a clear cellular damage was observed in bacteria after treatments with LFchimera and peptides, suggesting
that interaction and membrane disruption are probably involved as a mechanism of action. In conclusion, results show that
LFchimera, LF and peptides have potential as bactericidal agents in the antibiotic-resistant strains of S.
aureus and E. coli and also the work strongly suggest that LFcin17-30 and LFampin265-284 acts synergistically with antibiotics against multidrug
resistant EPEC and MRSA in vitro. 相似文献
38.
TERMINAL FLOWER1 is a breeding target for a novel everbearing trait and tailored flowering responses in cultivated strawberry (Fragaria × ananassa Duch.) 下载免费PDF全文
39.
Domínguez-Machín ME Hernández-Vergara MP Jiménez-García I Simá-Alvarez R Rodríguez-Canul R 《Diseases of aquatic organisms》2011,96(2):97-103
We surveyed protozoan and metazoan parasites as well as white spot syndrome virus (WSSV) and infectious hypodermal hematopoietic necrosis virus (IHHNV) in white shrimp Litopenaeus setiferus and the palaemonid prawn Macrobrachium acanthurus native to the lower Jamapa River region of Veracruz, Mexico. The presence of parasites and the infection parameters were evaluated in 113 palaemonid prawns collected during the northwind (n = 45), rainy (n = 38) and dry seasons (n = 30) between October 2007 and July 2008, and in 91 shrimp collected in the rainy season between May and June 2008. In L. setiferus, ciliates of the subclass Apostomatia (Ascophrys sp.) were evident in gills, and third-stage larvae of the nematode Physocephalus sexalatus were evident in the stomach. Cestodes of the genus Prochristianella were evident in the hepatopancreas, while some gregarines of the genus Nematopsis, as well as unidentified larval cestodes, were observed in the intestine. Histology identified Ascophrys sp. in association with gill necrosis and tissue melanization. Slight inflammation was observed in intestinal epithelium near cestode larvae. In M. acanthurus, epibionts of the protozoans Epistylis sp., Acineta sp. and Lagenophrys sp. were observed under uropods, periopods and pleopods. An unidentified ciliate of the Apostomatia was also found in the gills, and Nematopsis was identified in the intestine. No histopathology was observed in association with these parasites. Moreover, neither WSSV nor IHHNV were detected by the polymerase chain reaction (PCR) in any of the L. setiferus or M. acanthurus analysed. 相似文献
40.
Gomez L Hack MD McClure K Sehon C Huang L Morton M Li L Barrett TD Shankley N Breitenbucher JG 《Bioorganic & medicinal chemistry letters》2007,17(23):6493-6498
A high throughput screening campaign revealed compound 1 as a potent antagonist of the human CCK(1) receptor. Here, we report the syntheses and SAR studies of 1,5-diarylpyrazole analogs with various structural modifications of the alkane side chain of the molecule. The difference in affinity between the two enantiomers for the CCK(1) receptor and the flexible nature of the linker led to the design of constrained analogs with increased potency. 相似文献