Significant Enrichment (significant + enrichment)

Distribution by Scientific Domains

Selected Abstracts

Sample complexity reduction for two-dimensional electrophoresis using solution isoelectric focusing prefractionation

Matthew R. Richardson
Abstract Despite its excellent resolving power, 2-DE is of limited use when analyzing cellular proteomes, especially in differential expression studies. Frequently, fewer than 2000 protein spots are detected on a single 2-D gel (a fraction of the total proteome) regardless of the gel platform, sample, or detection method used. This is due to the vast number of proteins expressed and their equally vast dynamic range. To exploit 2-DE unique ability as both an analytical and a preparative tool, the significant sample prefractionation is necessary. We have used solution isoelectric focusing (sIEF) via the ZOOM® IEF Fractionator (Invitrogen) to generate sample fractions from complex bacterial lysates, followed by parallel 2-DE, using narrow-range IPG strips that bracket the sIEF fractions. The net result of this process is a significant enrichment of the bacterial proteome resolved on multiple 2-D gels. After prefractionation, we detected 5525 spots, an approximate 3.5-fold increase over the 1577 spots detected in an unfractionated gel. We concluded that sIEF is an effective means of prefractionation to increase depth of field and improve the analysis of low-abundance proteins. [source]

Strain- and region-specific gene expression profiles in mouse brain in response to chronic nicotine treatment

J. Wang
A pathway-focused complementary DNA microarray and gene ontology analysis were used to investigate gene expression profiles in the amygdala, hippocampus, nucleus accumbens, prefrontal cortex (PFC) and ventral tegmental area of C3H/HeJ and C57BL/6J mice receiving nicotine in drinking water (100 ,g/ml in 2% saccharin for 2 weeks). A balanced experimental design and rigorous statistical analysis have led to the identification of 3.5,22.1% and 4.1,14.3% of the 638 sequence-verified genes as significantly modulated in the aforementioned brain regions of the C3H/HeJ and C57BL/6J strains, respectively. Comparisons of differential expression among brain tissues showed that only a small number of genes were altered in multiple brain regions, suggesting presence of a brain region-specific transcriptional response to nicotine. Subsequent principal component analysis and Expression Analysis Systematic Explorer analysis showed significant enrichment of biological processes both in C3H/HeJ and C57BL/6J mice, i.e. cell cycle/proliferation, organogenesis and transmission of nerve impulse. Finally, we verified the observed changes in expression using real-time reverse transcriptase polymerase chain reaction for six representative genes in the PFC region, providing an independent replication of our microarray results. Together, this report represents the first comprehensive gene expression profiling investigation of the changes caused by nicotine in brain tissues of the two mouse strains known to exhibit differential behavioral and physiological responses to nicotine. [source]

Analysis of two common ,1 -antitrypsin deficiency alleles (PI*Z and PI*S) in subjects with periodontitis

D. A. Scott
Abstract Background: ,,1 -Antitrypsin deficiency is a genetically determined condition resulting in predisposition to certain inflammatory diseases due to a protease: antiprotease imbalance that is exacerbated by tobacco smoking. Limited evidence suggests that there may be a significant enrichment of mild ,1 -antitrypsin deficiency phenotypes in subjects with chronic inflammatory periodontal disease. Objective: To examine the prevalence of two common ,1 -antitrypsin deficiency alleles (PI*Z and PI*S) in a UK population of subjects with periodontitis. Subjects and methods: The prevalence of PI*M, PI*S and PI*Z allele combinations was determined in 31 subjects with periodontitis and compared with 31 healthy control subjects matched for smoking status, ethnicity, age and gender. ,1 -Antitrypsin genotyping was performed by multiplex real-time fluorescence polymerase chain reaction (PCR) using DNA extracted from whole blood. Results: There was no difference in the proportion of any ,1 -antitrypsin genotype found in the diseased and control populations. Conclusions: We did not find evidence to support an association between mutant PI* alleles and periodontitis in a small, controlled study. Larger studies will be required to clarify the relationship between ,1 -antitrypsin genotype and susceptibility to inflammatory periodontal disease. [source]

Short-term dietary restriction and fasting precondition against ischemia reperfusion injury in mice

AGING CELL, Issue 1 2010
James R. Mitchell
Summary Dietary restriction (DR) extends lifespan and increases resistance to multiple forms of stress, including ischemia reperfusion injury to the brain and heart in rodents. While maximal effects on lifespan require long-term restriction, the kinetics of onset of benefits against acute stress is not known. Here, we show that 2,4 weeks of 30% DR improved survival and kidney function following renal ischemia reperfusion injury in mice. Brief periods of water-only fasting were similarly effective at protecting against ischemic damage. Significant protection occurred within 1 day, persisted for several days beyond the fasting period and extended to another organ, the liver. Protection by both short-term DR and fasting correlated with improved insulin sensitivity, increased expression of markers of antioxidant defense and reduced expression of markers of inflammation and insulin/insulin-like growth factor-1 signaling. Unbiased transcriptional profiling of kidneys from mice subject to short-term DR or fasting revealed a significant enrichment of signature genes of long-term DR. These data demonstrate that brief periods of reduced food intake, including short-term daily restriction and fasting, can increase resistance to ischemia reperfusion injury in rodents and suggest a rapid onset of benefits of DR in mammals. [source]

Cyclic acetal hydroxyapatite composites and endogenous osteogenic gene expression of rat marrow stromal cells

Minal Patel
Abstract In this study, bone marrow stromal cells (BMSCs) were differentiated on cyclic acetal composites containing hydroxyapatite (HA) particles (110 or 550 nm). These composites were evaluated for their role in influencing osteogenic signalling by encapsulated BMSCs. While a number of factors exert influence on osteogenic signalling during the production of an osteogenic matrix, we hypothesize that HA particles may upregulate bone growth factor expression due to enhanced BMSC adhesion. To this end, fluorescence-activated cell sorting (FACS) analysis was performed for the evaluation of BMSC surface marker expression after culture on two-dimensional (2D) cyclic acetal/HA composites. Three-dimensional (3D) composites were then fabricated by incorporating 110 or 550 nm HA particles at 5, 10 and 50 ng/ml concentrations. Bone growth factor molecules (TGF,1, FGF-2 and PDGFa), bone biomarker molecules (ALP, OC, OPN and OCN) and extracellular matrix-related molecules (FN, MMP-13, Dmp1 and aggrecan) were selected for evaluation of osteogenic signalling mechanisms when in presence of these composites. FACS results at day 0 demonstrated that BMSCs were a heterogeneous population with a small percentage of cells staining positive for CD29, CD90 and CD51/61, while staining negative for CD34 and CD45. At day 3, a significant enrichment of cells staining strongly for CD29, CD90 and CD51/61 was achieved. Gene expression patterns for bone growth factors and extracellular matrix molecules were found to be largely dependent upon the size of HA particles. Bone marker molecules, except OCN, had unaltered expression patterns in response to the varied size of HA particles. Overall, the results indicate that larger-sized HA particles upregulate PDGF and these groups were also associated with the most significant increase in osteodifferentiation markers, particularly ALP. Our results suggest that endogenous signalling is dependent upon material properties. Furthermore, we propose that studying gene expression patterns induced by the surrounding biomaterials environment is a fundamental step in the creation of engineered tissues. Copyright © 2010 John Wiley & Sons, Ltd. [source]

Control of Nitrate Uptake by Phloem-Translocated Glutamine in Zea mays L. Seedlings

PLANT BIOLOGY, Issue 4 2002
P. Pal'ove-Balang
Abstract: The putative role of glutamine, exported from leaves to roots, as a negative feedback signal for nitrate uptake was investigated in Zea mays L. seedlings. Glutamine (Gln) was supplied by immersion of the tip-cut leaves in a concentrated solution. Nitrate (NO3,) uptake was measured by its depletion in amino acid-free medium. The treatment with Gln resulted in a strong inhibition of nitrate uptake rate, accompanied by a significant enrichment of amino compounds in root tissue. The effect of N-availability on NO3, uptake was determined in split-root cultures. The plants were subjected to complete or localized N supply. Inducible NO3, uptake systems were also induced in N-deprived roots when the opposite side of the root system was supplied with KNO3. The inhibitory effect of Gln was unaffected by localized N supply on one side of the split-root. The potential role of Gln in the shoot-to-root control of NO3, uptake is discussed. [source]

ORIGINAL ARTICLE: The Transcriptome of the Fetal Inflammatory Response Syndrome

Sally A. Madsen-Bouterse
Problem, The fetal inflammatory response syndrome (FIRS) is considered the counterpart of the systemic inflammatory response syndrome (SIRS), but similarities in their regulatory mechanisms are unclear. This study characterizes the fetal mRNA transcriptome of peripheral leukocytes to identify key biological processes and pathways involved in FIRS. Method of study, Umbilical cord blood from preterm neonates with FIRS (funisitis, plasma IL-6 >11 pg/mL; n = 10) and neonates with no evidence of inflammation (n = 10) was collected at birth. Results, Microarray analysis of leukocyte RNA revealed differential expression of 541 unique genes, changes confirmed by qRT-PCR for 41 or 44 genes tested. Similar to SIRS and sepsis, ontological and pathway analyses yielded significant enrichment of biological processes including antigen processing and presentation, immune response, and processes critical to cellular metabolism. Results are comparable with microarray studies of endotoxin challenge models and pediatric sepsis, identifying 25 genes across all studies. Conclusion, This study is the first to profile genome-wide expression in FIRS, which demonstrates a substantial degree of similarity with SIRS despite differences in fetal and adult immune systems. [source]

Downstream Processing of Enzymatically Produced Geranyl Glucoside

B. Mattheus de Roode
Geraniol plays an important role in the fragrance and flavor industry. The corresponding glucoside has interesting properties as a "slow release" aroma compound. Therefore, the enzymatic production and downstream processing of geranyl glucoside were investigated. Geranyl glucoside was produced in a spray column reactor with an initial production rate of 0.58 mg U,1 h,1. A pretreated hydrophobic microfiltration membrane was used to prevent migration of the aqueous, enzyme-containing phase to the downstream process. No retention of the glucoside, which accumulated in the geraniol phase, was found. On the basis of examples from the literature, four downstream processes were tested on their viability for this system. Extraction with water and foaming were not suitable to recover geranyl glucoside from geraniol. In the first case, the glucoside selectivity for the geraniol phase was found to be high, which made extraction with water unsuccessful. In the second case it was possible to obtain a stable foam, but significant enrichment of the foam with glucoside did not occur. Adsorption on alumina and distillation under reduced pressure were applied successfully and tested in-line with the bioreactor. A maximum glucoside adsorption of 7.86 mg g,1 was achieved on alumina. After desorption and evaporation of the extractant the pure glucoside was obtained quantitatively. A pure product could not be obtained after distillation because a small amount of glucose was present in the permeate as well, which accumulated in the bottom fraction. It was shown that with this reactor system a production of 1 kg of geranyl glucoside in 2 days is possible using an initial amount of 50,000 units of enzyme. [source]

SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites

CHEMMEDCHEM, Issue 5 2008
Lars Ridder Dr.
Abstract Predictions of potential metabolites based on chemical structure are becoming increasingly important in drug discovery to guide medicinal chemistry efforts that address metabolic issues and to support experimental metabolite screening and identification. Herein we present a novel rule-based method, SyGMa (Systematic Generation of potential Metabolites), to predict the potential metabolites of a given parent structure. A set of reaction rules covering a broad range of phase,1 and phase,2 metabolism has been derived from metabolic reactions reported in the Metabolite Database to occur in humans. An empirical probability score is assigned to each rule representing the fraction of correctly predicted metabolites in the training database. This score is used to refine the rules and to rank predicted metabolites. The current rule set of SyGMa covers approximately 70,% of biotransformation reactions observed in humans. Evaluation of the rule-based predictions demonstrated a significant enrichment of true metabolites in the top of the ranking list: while in total, 68,% of all observed metabolites in an independent test set were reproduced by SyGMa, a large part, 30,% of the observed metabolites, were identified among the top three predictions. From a subset of cytochrome P450 specific metabolites, 84,% were reproduced overall, with 66,% in the top three predicted phase,1 metabolites. A similarity analysis of the reactions present in the database was performed to obtain an overview of the metabolic reactions predicted by SyGMa and to support ongoing efforts to extend the rules. Specific examples demonstrate the use of SyGMa in experimental metabolite identification and the application of SyGMa to suggest chemical modifications that improve the metabolic stability of compounds. [source]

Effects of stream restoration and wastewater treatment plant effluent on fish communities in urban streams

Summary 1. Fish community characteristics, resource availability and resource use were assessed in three headwater urban streams in Piedmont North Carolina, U.S.A. Three site types were examined on each stream; two urban (restored and unrestored) and a forested site downstream of urbanisation, which was impacted by effluent from a wastewater treatment plant (WWTP). Stream basal resources, aquatic macroinvertebrates, terrestrial macroinvertebrates and fish were collected at each site. 2. The WWTPs affected isotope signatures in the biota. Basal resource, aquatic macroinvertebrate and fish ,15N showed significant enrichments in the downstream sites, although ,13C signatures were not greatly influenced by the WWTP. Fish were clearly deriving a significant part of their nutrition from sewage effluent-derived sources. There was a trend towards lower richness and abundance of fish at sewage-influenced sites compared with urban restored sites, although the difference was not significant. 3. Restored stream sites had significantly higher fish richness and a trend towards greater abundance compared with unrestored sites. Although significant differences did not exist between urban restored and unrestored areas for aquatic and terrestrial macroinvertebrate abundances and biotic indices of stream health, there appeared to be a trend towards improvements in restored sites for these parameters. Additional surveys of these sites on a regular basis, along with maintenance of restored features are vital to understanding and maximising restoration effectiveness. 4. A pattern of enriched ,13C in fish in restored and unrestored streams in conjunction with enriched ,13C of terrestrial invertebrates at these sites suggests that these terrestrial subsidies are important to the fish, a conclusion also supported by isotope cross plots. Furthermore, enriched ,13C observed for terrestrial invertebrates is consistent with some utilisation of the invasive C4 plants that occur in the urban riparian areas. [source]