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Xuejun Liu

Publications and source records attributed to Xuejun Liu.

At least 19 recordsLinked to original sources
PubMed2006

Differential feedback regulation of ethylene biosynthesis in pulp and peel tissues of banana fruit.

The feedback regulation of ethylene biosynthesis in banana [Musa sp. (AAA group, Cavendish subgroup) cv. Grand Nain] fruit was investigated in an attempt to clarify the opposite effect of 1-methylcyclopropene (1-MCP), an ethylene action inhibitor, before and after the onset of ripening. 1-MCP pre-treatment completely prevented the ripening-induced effect of propylene in pre-climacteric banana fruit, whereas treatment after the onset of ripening stimulated ethylene production. In pre-climacteric fruit, higher concentrations of propylene suppressed ethylene production more strongly, despite their earlier ethylene-inducing effect. Exposure of the fruit ripened by propylene to 1-MCP increased ethylene production concomitantly with an increase in 1-aminocyclopropane-1-carboxylate (ACC) synthase activity and ACC content, and prevented a transient decrease in MA-ACS1 transcripts in the pulp tissues. In contrast, in the peel of ripening fruit, 1-MCP prevented the increase in ethylene production and subsequently the ripening process by reduction of the increase in MA-ACS1 and MA-ACO1 transcripts and of ACC synthase and ACC oxidase activities. These results suggest that ethylene biosynthesis in ripening banana fruit may be controlled negatively in the pulp tissue and positively in the peel tissue. This differential regulation by ethylene in pulp and peel tissues was also observed for MA-PL, MA-Exp, and MA-MADS genes.

Amino Acids, Cyclic↗
PubMed2006

Solvent effects in thermodynamically controlled multicomponent nanocage syntheses.

The solvent effects on the condensation reaction between tetraformylcavitand 2 and ethylene-1,2-diamine 3 are reported. Earlier, it was found that the trifluoroacetic acid-catalyzed condensation of 2 and 2 equiv of 3 in CHCl(3) provides in 82% yield an octahedral nanocage 1 composed of 6 cavitands that are linked together by 12 -CH=N-CH(2)CH(2)-N=CH- linker groups (Liu, X.; Liu, Y.; Li, G.; Warmuth, R. Angew. Chem., Int. Ed. 2006, 45, 901). In tetrahydrofuran, the same reactants yield a tetrameric nanocage 4 (35% yield), which resembles a distorted tetrahedron built up from four cavitands that occupy the apexes. Each cavitand is doubly linked to one other cavitand and singly linked to the other two cavitands via -CH=N-CH(2)CH(2)N=CH- connectors. In CH(2)Cl(2), the reaction between 8 2 and 16 3 yields a square antiprismatic nanocage 5 (65% yield), in which each cavitand occupies one of the eight corners and is connected to four neighboring cavitands via -CH=N-CH(2)CH(2)-N=CH- linkers. Nanocage 5 is also the main product in CH(2)ClCH(2)Cl (26% yield) and CHCl(2)CHCl(2) (33% yield). Reduction of all imine bonds in 4 and 5 yields polyaminonanocontainers 7 and 8, respectively, which were isolated as trifluoroacetate salts. Contrary to the formation of larger capsules composed of four, six, or eight cavitands in the reaction between 2 and 3, the acid-catalyzed reaction of 2 with 2 equiv of H(2)N-X-NH(2) (X = (CH(2))(n)(=3,4,5), 1,3-C(6)H(4), 1,4-(CH(2))(2)C(6)H(4), or 1,3-(CH(2))(2)C(6)H(4)) quantitatively yields octaiminohemicarcerands 9-14, in which two cavitands are connected with four -CH=N-X-N=CH- linkers. The outcomes of these condensation reactions are rationalized with the different diamine structures and the relative orientation of cavitands in 1, 4, 5, and 9-14.

Journal Article↗
PubMed2006

Probe-level measurement error improves accuracy in detecting differential gene expression.

MOTIVATION: Finding differentially expressed genes is a fundamental objective of a microarray experiment. Numerous methods have been proposed to perform this task. Existing methods are based on point estimates of gene expression level obtained from each microarray experiment. This approach discards potentially useful information about measurement error that can be obtained from an appropriate probe-level analysis. Probabilistic probe-level models can be used to measure gene expression and also provide a level of uncertainty in this measurement. This probe-level measurement error provides useful information which can help in the identification of differentially expressed genes. RESULTS: We propose a Bayesian method to include probe-level measurement error into the detection of differentially expressed genes from replicated experiments. A variational approximation is used for efficient parameter estimation. We compare this approximation with MAP and MCMC parameter estimation in terms of computational efficiency and accuracy. The method is used to calculate the probability of positive log-ratio (PPLR) of expression levels between conditions. Using the measurements from a recently developed Affymetrix probe-level model, multi-mgMOS, we test PPLR on a spike-in dataset and a mouse time-course dataset. Results show that the inclusion of probe-level measurement error improves accuracy in detecting differential gene expression. AVAILABILITY: The MAP approximation and variational inference described in this paper have been implemented in an R package pplr. The MCMC method is implemented in Matlab. Both software are available from http://umber.sbs.man.ac.uk/resources/puma.

Algorithms↗
PubMed2006

Asymmetric synthesis of 1,2-dioxolane-3-acetic acids: synthesis and configurational assignment of plakinic acid A.

The first asymmetric synthesis of 1,2-dioxolane-3-acetic acids is reported. Key features include the stereoselective opening of enantiomerically enriched oxetanes by hydrogen peroxide, conversion of the resulting 4-hydroperoxy-2-alkanols to 3-alkoxy-1,2-dioxolanes, and Lewis acid mediated homologation of the latter with a thioester silyl ketene acetal. The approach is modeled on 3,5-dimethyl-5-hexadecyl-1,2-dioxolane-3-acetic acid (1a), an unnamed natural product, and an optimized strategy is applied to the synthesis of four stereoisomers of plakinic acid A (2), allowing a configurational assignment of this incompletely characterized natural product.

Alcohols↗
PubMed2006

Propagating uncertainty in microarray data analysis.

Microarray technology is associated with many sources of experimental uncertainty. In this review we discuss a number of approaches for dealing with this uncertainty in the processing of data from microarray experiments. We focus here on the analysis of high-density oligonucleotide arrays, such as the popular Affymetrix GeneChip array, which contain multiple probes for each target. This set of probes can be used to determine an estimate for the target concentration and can also be used to determine the experimental uncertainty associated with this measurement. This measurement uncertainty can then be propagated through the downstream analysis using probabilistic methods. We give examples showing how these credibility intervals can be used to help identify differential expression, to combine information from replicated experiments and to improve the performance of principal component analysis.

Computational Biology↗
PubMed2005

Drug-induced oxidative stress in rat liver from a toxicogenomics perspective.

Macrophage activators (MA), peroxisome proliferators (PP), and oxidative stressors/reactive metabolites (OS/RM) all produce oxidative stress and hepatotoxicity in rats. However, these three classes of hepatotoxicants give three distinct gene transcriptional profiles on cDNA microarrays, an indication that rat hepatocytes respond/adapt quite differently to these three classes of oxidative stressors. The differential gene responses largely reflect differential activation of transcription factors: MA activate Stat-3 and NFkB, PP activate PPARa, and OS/RM activate Nrf2. We have used gene signature profiles for each of these three classes of hepatotoxicants to categorize over 100 paradigm (and 50+ in-house proprietary) compounds as to their oxidative stress potential in rat liver. In addition to a role for microarrays in predictive toxicology, analyses of small subsets of these signature profiles, genes within a specific pathway, or even single genes often provide important insights into possible mechanisms involved in the toxicities of these compounds.

Animals↗
PubMed2005

A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips.

MOTIVATION: Affymetrix GeneChip arrays are currently the most widely used microarray technology. Many summarization methods have been developed to provide gene expression levels from Affymetrix probe-level data. Most of the currently popular methods do not provide a measure of uncertainty for the expression level of each gene. The use of probabilistic models can overcome this limitation. A full hierarchical Bayesian approach requires the use of computationally intensive MCMC methods that are impractical for large datasets. An alternative computationally efficient probabilistic model, mgMOS, uses Gamma distributions to model specific and non-specific binding with a latent variable to capture variations in probe affinity. Although promising, the main limitations of this model are that it does not use information from multiple chips and does not account for specific binding to the mismatch (MM) probes. RESULTS: We extend mgMOS to model the binding affinity of probe-pairs across multiple chips and to capture the effect of specific binding to MM probes. The new model, multi-mgMOS, provides improved accuracy, as demonstrated on some bench-mark datasets and a real time-course dataset, and is much more computationally efficient than a competing hierarchical Bayesian approach that requires MCMC sampling. We demonstrate how the probabilistic model can be used to estimate credibility intervals for expression levels and their log-ratios between conditions. AVAILABILITY: Both mgMOS and the new model multi-mgMOS have been implemented in an R package, which is available at http://www.bioinf.man.ac.uk/resources/puma.

Algorithms↗
PubMed2005

[The clinical anatomy of ophthalmic artery and relative arteries].

OBJECTIVE: To discovery the reason of single eye blind that happened when treating the uncontrolled epistaxis by transarterial embolization method and to provide evidence in vessels morphological to avoid the complication. METHOD: The normal origins and distributions of the ophthalmic artery and the central retinal artery, the abnormal origins and distributions of ophthalmic artery, and the communication of ophthalmic artery and maxillary artery were observed and studied in 100 sides of adult brain specimens. RESULT: 95% of the ophthalmic arteries originated from the supraclinoidal segment of internal carotid artery, and 5% are from middle meningeal artery which was a branch of maxillary artery; 80% of the specimens had communication branches between ophthalmic arteries and middle meningeal arteries. All the central retinal arteries were from ophthalmic arteries. CONCLUSION: One of the two reasons of single eye blinding caused by maxillary artery embolization is the abnormal origins of the ophthalmic artery, and the other reason is that the embolus which passed the communication branch of the middle meningeal artery has embolized the ophthalmic artery or central retinal artery.

Adult↗
PubMed2004

A gene expression signature for oxidant stress/reactive metabolites in rat liver.

Formation of free radicals and other reactive molecules is responsible for the adverse effects produced by a number of hepatotoxic compounds. cDNA microarray technology was used to compare transcriptional profiles elicited by training and testing sets of 15 oxidant stressors/reactive metabolite treatments to those produced by approximately 85 other paradigm compounds (mostly hepatotoxicants) to determine a shared signature profile for oxidant stress-associated hepatotoxicity. Initially, 100 genes were chosen that responded significantly different to oxidant stressors/reactive metabolites (OS/RM) compared to other samples in the database, then a 25-gene subset was selected by multivariate analysis. Many of the selected genes (e.g., aflatoxin aldehyde reductase, diaphorase, epoxide hydrolase, heme oxgenase and several glutathione transferases) are well-characterized oxidant stress/Nrf-2-responsive genes. Less than 10 other compounds co-cluster with our training and testing set compounds and these are known to generate OS/RMs as part of their mechanisms of toxicity. Using OS/RM signature gene sets, compounds previously associated with macrophage activation formed a distinct cluster separate from OS/RM and other compounds. A 69-gene set was chosen to maximally separate compounds in control, macrophage activator, peroxisome proliferator and OS/RM classes. The ease with which these 'oxidative stressor' classes can be separated indicates a role for microarray technology in early prediction and classification of hepatotoxicants. The ability to rapidly screen the oxidant stress potential of compounds may aid in avoidance of some idiosyncratic drug reactions as well as overtly toxic compounds.

Animals↗
PubMed2004

Inverse gene expression patterns for macrophage activating hepatotoxicants and peroxisome proliferators in rat liver.

Macrophage activation contributes to adverse effects produced by a number of hepatotoxic compounds. Transcriptional profiles elicited by two macrophage activators, LPS and zymosan A, were compared to those produced by 100 paradigm compounds (mostly hepatotoxicants) using cDNA microarrays. Several hepatotoxicants previously reported to activate liver macrophages produced transcriptional responses similar to LPS and zymosan, and these were used to construct a gene signature profile for macrophage activators in the liver. Measurement of cytokine mRNAs in the same liver samples by RT-PCR independently confirmed that these compounds are associated with macrophage activation. In addition to expected effects on acute phase proteins and metabolic pathways that are regulated by LPS and inflammation, a strong induction was observed for many endoplasmic reticulum-associated stress/chaperone proteins. Additionally, many genes in our macrophage activator signature profile were well-characterized PPARalpha-induced genes which were repressed by macrophage activators. A shared gene signature profile for peroxisome proliferators was determined using a training set of clofibrate, WY 14643, diethylhexylphthalate, diisononylphthalate, perfluorodecanoic acid, perfluoroheptanoic acid, and perfluorooctanoic acid. The signature profile included macrophage activator-induced genes that were repressed by peroxisome proliferators. NSAIDs comprised an interesting pharmacological class in that some compounds, notably diflunisal, co-clustered with peroxisome proliferators whereas several others co-clustered with macrophage activators, possibly due to endotoxin exposure secondary to their adverse effects on the gastrointestinal system. While much of these data confirmed findings from the literature, the transcriptional patterns detected using this toxicogenomics approach showed relationships between genes and biological pathways requiring complex analysis to be discerned.

Animals↗
PubMed2004

Simultaneous analysis of host and pathogen interactions during an in vivo infection reveals local induction of host acute phase response proteins, a novel bacterial stress response, and evidence of a host-imposed metal ion limited environment.

A fundamental goal in the study of infections is to understand the dynamic interplay between host and pathogen; however, direct in vivo interrogation of this disease process via transcriptional profiling has been lacking. Here we describe the development and application of novel bacterial RNA amplification technology to simultaneously identify key elements of both host and pathogen responses in a murine infection model. On the bacterial side, we found induction of an unusual pattern of stress response genes, a response to host-induced metal ion limitation, and a failure to achieve stationary phase in vivo. On the mammalian side, we observed the surprising induction of several genes encoding acute phase response proteins including hepcidin, haptoglobin, complement C3 and metallothionein 1 at the site of infection, as well as other mediators of innate immunity. Thus, our results reveal host-pathogen cross-talk not predicted by previous in vitro analyses and provide the framework to eavesdrop on a broad array of host-pathogen interactions in vivo. As described here, the comprehensive examination of host-pathogen interactions during an infection is critical to the discovery of novel approaches for intervention not predicted by current models.

Acute-Phase Proteins↗
PubMed2004

Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis from transcriptional profiles of laser-captured glomeruli.

The molecular pathogenesis of focal/diffuse proliferative lupus glomerulonephritis was studied by cDNA microarray analysis of gene expression in glomeruli from clinical biopsies. Transcriptional phenotyping of glomeruli isolated by laser-capture microscopy revealed considerable kidney-to-kidney heterogeneity in increased transcript expression, resulting in four main gene clusters that identified the presence of B cells, several myelomonocytic lineages, fibroblast and epithelial cell proliferation, matrix alterations, and expression of type I IFN-inducible genes. Glomerulus-to-glomerulus variation within a kidney was less marked. The myeloid lineage transcripts, characteristic of those found in isolated activated macrophages and myeloid dendritic cells, were widely distributed in all biopsy samples. One major subgroup of the samples expressed fibrosis-related genes that correlated with pathological evidence of glomerulosclerosis; however, decreased expression of TGF-beta1 argued against its role in lupus renal fibrosis. Expression of type I IFN-inducible transcripts by a second subset of samples was associated with reduced expression of fibrosis-related genes and milder pathological features. This pattern of gene expression resembled that exhibited by activated NK cells. A large gene cluster with decreased expression found in all samples included ion channels and transcription factors, indicating a loss-of-function response to the glomerular injury.

Adolescent↗
PubMed2004

Nitrogen fertilization, soil nitrate accumulation, and policy recommendations in several agricultural regions of China.

Excessive nitrogen (N) fertilization and decreasing N recovery rates by crops have caused dramatic increases in non-point source pollution from agriculture in China. The rate of N fertilization across the country varies widely among regions and crops, depending on the stage of economic development. For example, N application rates in the eastern regions and on cash crops are far higher than in western regions of the country and on cereal crops. Moreover, N application rates in wealthier regions are higher than recommended by the Chinese Academy of Sciences. To successfully achieve environmental protection as well as high crop yields, China must formulate relevant agricultural policies to encourage farmers in economically developed areas to reduce their N fertilization rate while also issuing conventional fertilization recommendations for small-scale farming systems and the expanding cultivation of cash crops.

Agriculture↗
PubMed2004

[Effect of reduced N application on N utilization and balance in winter wheat-summer maize cropping system].

A field trial on a calcareous soil was carried out at an experimental station of China Agricultural University with the objective of assessing the effect of reduced nitrogen application on N utilization and N balance in a winter wheat-summer maize cropping system. Before this study, the trial has been conducted for one rotation cycle of wheat and maize with four-fixed N rates of 0, 120, 240 and 360 N kg.hm-2 per crop. In this study, each plot was divided into two sub-plots for two N application rates: normal N application(original rate) and reduced N application(reduced rate). The results showed that the grain yields of wheat and maize reached the platform at N rate of 120 kg.hm-2(N120), and then almost kept the same level regardless of the further increase of N rate(N240 and N360). The N uptake by wheat and maize followed the similar tendency like their yield. The grain yield and N uptake of wheat were not significantly declined with the half reduction of original N rate except the treatment N120. However, the same items in maize significantly declined with the further reduction of N fertilizer to zero. The residual NO3-N(main source of mineral N) in reduced N sub-plots was significantly lower in 0-1 m soil layer, but not different in 1-2 m soil layer compared with those receiving original N rate, indicating that 1-2 m soil NO3-N could hardly be utilized by crops. N balance calculation further showed that the N recovery by crops could be largely raised by the reduction of N fertilizer, while the apparent N loss rate decreased in wheat-maize rotation, respectively. Thus, the reduction of fertilizer N under high N rate can significantly increase N use efficiency and reduce NO3-N accumulation and apparent N loss.

Crops, Agricultural↗
PubMed2004

[Formation of iron plaque on root surface and its effect on plant nutrition and ecological environment].

This paper illustrated the conditions of iron plaque formation on root surface, the morphology, mineralogical composition and deposition site of the plaque, and its function as a Fe reservoir in supplying Fe nutrient and affecting the uptake of other nutrients such as phosphorus and zinc. The environmental and ecological role of the plaque in inhibiting the uptake and translocation of heavy metals such as Cu, Ni, Cd and As through absorption or co-precipitation was called external tolerance mechanism, while its competition with heavy metals for metabolically sensitive sites in plants was called internal tolerance mechanisms. These two mechanisms help plant survive in high acidic and low carbon environment.

Ecosystem↗