Biomedical subjects

Fei Zou

Publications and source records attributed to Fei Zou.

At least 19 recordsLinked to original sources

PubMed2026

PETScan: score-based genome-wide association analysis of RNA-Seq and ATAC-Seq data.

MOTIVATION: High-dimensional sequencing data, such as RNA-Seq for gene expression and ATAC-Seq for chromatin accessibility, are widely used in studying systems biology. Accessible chromatin allows transcription factors and regulatory elements to bind to DNA, thereby regulating transcription through the activation or repression of target genes. The association analysis of RNA-Seq and ATAC-Seq data provides insights into gene regulatory mechanisms. Most existing analytic tools exclusively focus on cis-associations, despite regulatory elements being able to physically interact with distant target genes. Furthermore, conventional approaches often utilize Pearson or Spearman correlations, which ignore the count-based nature of RNA-Seq data. RESULTS: To address these limitations, we introduce PETScan, a computationally efficient genome-wide PEak-Transcript Score-based association analysis, utilizing negative binomial models to better accommodate RNA-Seq data. We leverage score tests and matrix calculations for improved computational efficiency, and combine an empirical permutation method with genomic control to ensure valid p-value calculations in studies with limited sample sizes. In real-world datasets, PETScan achieved three orders of magnitude faster than Wald tests, while identifying similar significant gene-peak pairs. AVAILABILITY: The PETScan R package is available on GitHub at https://github.com/yajing-hao/PETScan.

Chromatin Immunoprecipitation Sequencing↗

PubMed2026

Genetic diversity of Collaborative Cross mice implicates FFAR3 as a target for ILC2 anti-inflammatory reprogramming.

Pulmonary group 2 innate lymphoid cells (ILC2s) are key drivers of Type 2 inflammation in diseases like asthma, yet the molecular mechanisms regulating their function are incompletely understood. Using the genetically diverse Collaborative Cross (CC) mouse panel, we mapped a quantitative trait locus (QTL) that governs ILC2 prevalence in the lung after aeroallergen exposure. This QTL induces a large population of ILC2s in the lung that are resistant to activation and have diminished Type 2 effector function. We identified free-fatty acid receptor 3 (Ffar3) as a gene responsible for this effect and demonstrated that FFAR3 signaling reprograms ILC2s to an anti-inflammatory state by promoting their survival, reducing Type 2 cytokine production, and enhancing IL-10 expression. This anti-inflammatory state is dependent on IL-2 signaling, is characterized by decreased ST2 expression, and is distinct from previously described IL-10-producing ILC2 phenotypes. FFAR3-dependent reprogramming is mediated by epidermal growth factor receptor (EGFR) upregulation, and FFAR3's anti-inflammatory effect is partially conserved in human ILC2s.

Animals↗

PubMed2006

Activation of ATP-sensitive K channels protects hippocampal CA1 neurons from hypoxia by suppressing p53 expression.

Oxygen-sensing and responses to changes in oxygen concentration is a fundamental property of cellular physiology. In the central nervous system (CNS), hippocampal CA1 neurons are known to be extremely vulnerable to low oxygen concentrations or anoxia. Understanding the mechanisms governing tolerance to oxygen depletion is vital for developing strategies to protect the brain from hypoxic-ischemic insult. Our current study demonstrates the protective mechanism of KATP channels on hippocampal CA1 neurons subjected to hypoxic or anoxic conditions. Specifically, we show that CA1 neurons undergo apoptosis when depleted of oxygen for 12 or 24 h. A KATP channels agonist diazoxide inhibits the observed apoptosis. The inhibition of apoptosis is mediated through diazoxide's ability to reduce p53 expression. On the other hand, tolbutamide, a KATP channels antagonist which blocks the cellular sulphonylureas receptor, significantly increases p53 expression and apoptosis under hypoxic/anoxic conditions. Trichostatin (TSA), a p53 inhibitor, can block the effects of tolbutamide, lending further support for a role of p53 in mediating this process. These studies demonstrate that KATP channels act as an upstream antagonist of p53 in hippocampal CA1 neurons, and suggests their protective role in cerebral hypoxia.

Adenosine Triphosphate↗

PubMed2006

[Construction of subtracted cDNA library by suppression subtractive hybridization for differentially expressed genes in eosinophils from asthma patients].

OBJECTIVE: To construct a subtracted cDNA library of differentially expressed genes in eosinophils from asthma patients. METHODS: Suppression subtractive hybridization (SSH) was used to isolate the cDNA fragments of differentially expressed genes in the eosinophils of asthma patients before and after treatment. The cDNA fragments were directly inserted into T/A cloning vector to establish the subtractive library, followed by amplification of the library through E. coli transformation with calcium chloride and screening of blue and white clones of the transformants. One hundred positive bacterial clones were randomly picked and identified by colony PCR. RESULTS: The amplified library contained more than 3,000 positive bacterial clones. Analysis of the randomly selected 100 white clones by PCR showed that 90% of the clones contained 100-500 bp inserts, which might be the cDNA fragments of differentially expressed genes in eosinophils of asthma patients before treatment. CONCLUSION: A subtracted cDNA library of differentially expressed genes in the eosinophils of asthma patients before and after treatment is constructed successfully by SSH and T/A cloning techniques, which lays a solid foundation for screening and cloning new specific differentially.expressed genes in the eosinophils of asthma patients.

Asthma↗

PubMed2006

[Establishment of a rat model of severe heatstroke complicated with endotoxemia].

OBJECTIVE: To establish a rat model of heatstroke complicated by endotoxemia for studying the pathogenesis of severe heatstroke. METHODS: Male specific pathogen-free Wistar rats were randomly assigned into 4 groups, namely normothermic saline group (group C), heat exposure saline group (group H), normothermic LPS group (group L), and heat exposure LPS group (group HL). The rectal temperature (Tr), heart rate (HR), mean arterial pressure (MAP), and respiratory rate (RR) of the rats receiving different treatments were continually monitored and their white blood cell count (WBC) and histology of the lungs were observed at 0, 40, 80 and 120 min after the treatments. RESULTS: The rats in HL-Group displayed significantly higher Tr (43.04+/-0.11 degrees C), HR (660+/-42 beats/min), and RR (150+/-11/min) but lower MAP (49.0+/-3.5 mmHg) as compared with the C Group. There were significant differences in the values of Tr, HR, RR and MAP between HL and group L and in HR and MAP between H groups HL and. The rats in group H displayed significantly higher WBC than group C. In contrast, the rats in L groups HL and had significantly lower WBC. LPS injection and heat stress induced pulmonary edema and features characteristic of acute microvascular lung injury in the rats. CONCLUSION: The rat model established by LPS injection and heat stress can successfully mimic the development of severe heatstroke after LPS challenge and heat stress, and provides a suitable model for studying the primordial role of the lungs in the pathogenesis of severe heatstroke.

Animals↗

PubMed2006

Expression of thioredoxin-binding protein-2/vitamin D3 upregulated protein-1 in peripheral blood eosinophils of asthma patients.

OBJECTIVE: To investigate the expression of vitamin D3 upregulated protein-1 (VDUP1) in peripheral eosinophils at different stages of asthma and its correlation with clinical manifestations of asthma. METHODS: Fourteen normal volunteers and 51 mild to moderate asthma patients, including 16 untreated patients with asthma attack and 35 with asthma remission by continuously corticosterone inhalation. The symptom severity and pulmonary function indices were evaluated and induced sputum eosinophil counts and blood eosinophil count measured. VDUP1 and beta-actin gene fragments were amplified simultaneously by RT-PCR from the total RNA of peripheral eosinophils, and 10 microl of the RT-PCR product underwent agarose gel electrophoresis and the VDUP1/beta-actin ratio was obtained by Gel-Pro software. RESULTS: VDUP1/beta-actin ratio significantly decreased in untreated patients with asthma attacks in comparison with normal volunteers (0.314+/-0.242 vs 0.532 +/-0.279) but not in patients with asthma remission (0.612+/-0.381). In the former patients, a positive correlation of VDUP1/beta-actin ratio was found with FEV1.0% (r=0.587, P=0.046) and %PEF (r=0.563, P=0.033), whereas an inverse one observed with sputum eosinophil count (r=-0.436, P=0.049). CONCLUSION: VDUP1 expression in the eosinophils correlates to eosinophil activation and may influence the disease severity of asthma patients.

Actins↗

PubMed2005

Genetic modifiers of lung disease in cystic fibrosis.

BACKGROUND: Polymorphisms in genes other than the cystic fibrosis transmembrane conductance regulator (CFTR) gene may modify the severity of pulmonary disease in patients with cystic fibrosis. METHODS: We performed two studies with different patient samples. We first tested 808 patients who were homozygous for the DeltaF508 mutation and were classified as having either severe or mild lung disease, as defined by the lowest or highest quartile of forced expiratory volume in one second (FEV1), respectively, for age. We genotyped 16 polymorphisms in 10 genes reported by others as modifiers of disease severity in cystic fibrosis and tested for an association in patients with severe disease (263 patients) or mild disease (545). In the replication (second) study, we tested 498 patients, with various CFTR genotypes and a range of FEV1 values, for an association of the TGFbeta1 codon 10 CC genotype with low FEV1. RESULTS: In the initial study, significant allelic and genotypic associations with phenotype were seen only for TGFbeta1 (the gene encoding transforming growth factor beta1), particularly the -509 and codon 10 polymorphisms (with P values obtained with the use of Fisher's exact test and logistic regression ranging from 0.006 to 0.0002). The odds ratio was about 2.2 for the highest-risk TGFbeta1 genotype (codon 10 CC) in association with the phenotype for severe lung disease. The replication study confirmed the association of the TGFbeta1 codon 10 CC genotype with more severe lung disease in comparisons with the use of dichotomized FEV1 for severity status (P=0.0002) and FEV1 values directly (P=0.02). CONCLUSIONS: Genetic variation in the 5' end of TGFbeta1 or a nearby upstream region modifies disease severity in cystic fibrosis.

Adolescent↗

PubMed2005

Protective and anti-fatigue effects of aspirin against heatstroke in rats.

The purpose of this study is to determine whether aspirin can reduce interleukin-1beta(IL-1beta) concentration and exert protective effects against heatstroke. The heatstroke rat model was established through exposing rat to a high ambient temperature (HAT, Ta 41 degrees C, relative humidity 65%) in a simulative HAT chamber to induce heatstroke. Three parts were performed in the present experiment: (1) To determine the effects of pretreatment with aspirin against heatstroke;(2) To prove the effects of specifically reducing inducible nitric oxide synthase (iNOS) against rat heatstroke by iNOS selective prohibitor aminoguanidine (AG);(3) To determine the effects of aspirin against heatstroke and fatigue. In part 1 and 2, Sprague-Dawley rats were randomly assigned to control and aspirin groups or AG groups respectively. Mean arterial blood pressure (MAP), colonic temperature (T(co)), electrocardiograph (ECG) were monitored during heat exposure (HE) and blood samples were taken 0 and 60 min after HE for IL-1betaassay or nitric oxide (NO) assay. In part 3, additional control and aspirin groups of conscious rats were put in a barrel with 41 degrees C water and kept swimming until drowning over 10 s, and then intervals were recorded as survival time. The results from part 1 showed that from 0 to 50 min after HE, MAPs of control group and aspirin group were not significantly different. About 50-60 min after HE, MAPs of both groups were decreased abruptly and MAPs of control group were decreased significantly in comparison with those of aspirin group. T(co) of both groups was increased until to 42 degrees C, without significant difference. Time of heatstroke onset was not significantly different, while survival time was significantly longer in aspirin group than that in control group. Plasma IL-1betaconcentrations in both groups were significantly increased after HE, and the concentration was significantly higher in the control group than that in aspirin group 60 min after HE. In part 3, the survival time was significantly longer in aspirin group than that in control group. In part 2, MAPs of both groups from 0 to 50 min after HE were not significantly different, whereas 55-60 min after HE, MAPs of control group were decreased significantly in comparison with those of AG group;T(co) of both groups was increased after HE until to 42 degrees C, but without significant difference. The time of the heatstroke onset and survival time of AG group were significantly longer than that of control group;the plasma NO concentrations of two groups were significantly higher 60 min after HE than those 0 min after HE, and the plasma NO concentration of control group was significantly higher than that of AG group 60 min after HE. In conclusion, IL-1betamay contribute to heatstroke through inducing iNOS, which attenuates the tone of peripheral blood vessel, and pretreatment with aspirin can provide preventive effects against heatstroke and reinforce the heat and fatigue endurance, which may be associated with inhibition of systemic IL-1betalevels and local iNOS levels.

Journal Article↗

PubMed2005

Practical FDR-based sample size calculations in microarray experiments.

MOTIVATION: Owing to the experimental cost and difficulty in obtaining biological materials, it is essential to consider appropriate sample sizes in microarray studies. With the growing use of the False Discovery Rate (FDR) in microarray analysis, an FDR-based sample size calculation is essential. METHOD: We describe an approach to explicitly connect the sample size to the FDR and the number of differentially expressed genes to be detected. The method fits parametric models for degree of differential expression using the Expectation-Maximization algorithm. RESULTS: The applicability of the method is illustrated with simulations and studies of a lung microarray dataset. We propose to use a small training set or published data from relevant biological settings to calculate the sample size of an experiment. AVAILABILITY: Code to implement the method in the statistical package R is available from the authors.

Algorithms↗

PubMed2005

Quantitative trait locus analysis using recombinant inbred intercrosses: theoretical and empirical considerations.

We describe a new approach, called recombinant inbred intercross (RIX) mapping, that extends the power of recombinant inbred (RI) lines to provide sensitive detection of quantitative trait loci (QTL) responsible for complex genetic and nongenetic interactions. RIXs are generated by producing F1 hybrids between all or a subset of parental RI lines. By dramatically extending the number of unique, reproducible genomes, RIXs share some of the best properties of both the parental RI and F2 mapping panels. These attributes make the RIX method ideally suited for experiments requiring analysis of multiple parameters, under different environmental conditions and/or temporal sampling. However, since any pair of RIX genomes shares either one or no parental RIs, this cross introduces an unusual population structure requiring special computational approaches for analysis. Herein, we propose an efficient statistical procedure for QTL mapping with RIXs and describe a novel empirical permutation procedure to assess genome-wide significance. This procedure will also be applicable to diallel crosses. Extensive simulations using strain distribution patterns from CXB, AXB/BXA, and BXD mouse RI lines show the theoretical power of the RIX approach and the analysis of CXB RIXs demonstrates the limitations of this procedure when using small RI panels.

Animals↗

PubMed2005

Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples.

One of the key factors contributing to the success of a quantitative trait locus (QTL) mapping experiment is the precision with which QTL positions can be estimated. We show, using simulations, that QTL mapping precision for an experimental cross can be increased by the use of a genotypically selected sample of individuals rather than an unselected sample of the same size. Selection is performed using a previously described method that optimizes the complementarity of the crossover sites within the sample. Although the increase in precision is accompanied by a decrease in QTL detection power at markers distant from QTL, only a modest increase in marker density is needed to obtain equivalent power over the whole map. Selected samples also show a slight reduction in the number of false-positive QTL. We find that two features of selected samples independently contribute to these effects: an increase in the number of crossover sites and increased evenness in crossover spacing. We provide an empirical formula for crossover enrichment in selected samples that is useful in experimental design and data analysis. For QTL studies in which the phenotyping is more of a limiting factor than the generation of individuals and the scoring of genotypes, selective sampling is an attractive strategy for increasing genome-wide QTL map resolution.

Chromosome Mapping↗

PubMed2005

[Effect of hypoxia on the viability of rat brain astrocytes in vitro].

OBJECTIVE: To investigate the effect of hypoxia on the viability of rat brain astrocytes in vitro and determine the optimal duration of hypoxic treatment for studying the biological behavior of the in vitro cultured cells in response to hypoxia. METHODS: Rat astrocytes were cultured and identified by glial fibrillary acidic protein (GFAP) immunofluorescent staining. After incubation with 5%; CO(2)+95%; N(2) for different time to induce hypoxia, the cells were harvested and observed microscopically for morphological changes and counting of the dead cells. The culture media of the cells were also collected and pO(2), concentrations of glucose and lactate as well as lactate dehydrogenase (LDH) activity were analyzed. RESULTS: As the hypoxia prolonged, the astrocytes appeared swollen and floating in the medium with some becoming necrotic. Compared with the cells in the control group, the changes in the number of necrotic cells, concentrations of glucose and lactate, and LDH activity in the cells of the hypoxic group were significantly different after 10 h of hypoxia (P<0.05). However, the flat and polygonal morphology of the astrocytes almost remained unchanged after 8 h of hypoxia in spite of significant changes in the concentrations of glucose and lactate and LDH activity. CONCLUSION: Hypoxia induced injury and necrosis of rat brain astrocytes in vitro, and 8 h of hypoxia can be the optimal time point for studying the biological behaviors of the cells in response to hypoxia.

Animals↗

PubMed2005

[Study of genes that differentially expressed in eosinophils of patients with asthma by suppression subtractive hybridization technology].

OBJECTIVE: To study genes that differentially expressed in peripheral blood eosinophils of patient with asthmatic. METHODS: Total RNA extracted from eosinophils of patient at the time of exacerbation was taken as the tester and the total RNA from eosinophils of the same patient after improvement as driver. The ds cDNA was synthesized by SMART PCR cDNA Synthesis technology. The differentially expressed genes were obtained by suppression subtractive hybridization (SSH) technology and were further identified by Southern blot. RESULTS: Twelve differentially expressed genes including transformation growth factor beta activated kinase like (TAK1L) protein, cGMP gated channel protein were obtained. CONCLUSION: Increased expression of these genes were involved in the regulation of proinflammatory response, signal transduction, energy metabolism and cell apoptosis, which may help to clarify the molecular mechanism of eosinophils in asthma and may provide the theoretical base for finding out the new medicines towards eosinophils.

Asthma↗

PubMed2005

[Mechanism of Ca2+ on the hyperthermia-induced apoptosis of rat hippocampal neurons in vitro].

OBJECTIVE: To study the mechanism of Ca(2+) on the apoptosis induced by hyperthermia in neonate rat hippocampal neurons to provide the applicative evidence of dantrolene for preventing brain injuries. METHODS: Dantrolene, Ca(2+) specific blocking agent, was used in the hyperthermia-induced apoptosis of primary hippocampal neurons in vitro to observe its effect on the apoptosis, fluorescent intensity, and dynamic change of Ca(2+) by flowcytometry and laser confocal microscopy. RESULTS: The rate of apoptosis was decreased significantly after hyperthermia treatment by dantrolene sodium. The intracellular Ca(2+) fluorescent intensity in 42 degrees C treatment group (107.35 +/- 6.0) was significantly lower than that in control group (159.12 +/- 33.8). The concentration of Ca(2+) began to decrease 20 approximately 25 s after adding dantrolene sodium, and reached the lowest level about 50 s later, and then kept lower than the basal level. CONCLUSION: Dantrolene sodium has an important protective effect on hippocampal neurons apoptosis induced by hyperthermia and may have some applicative value of preventing heat-induced brain injury.

Animals↗

PubMed2005

[Differentiation of neonatal rat striatal neural stem cells induced by all-trans retinoic acid].

OBJECTIVE: To investigate the role of all-trans retinoic acid (atRA) in inducing differentiation of neonatal rat striatal neural stem cells (NSCs). METHODS: Neonatal rat striatal NSCs were obtained by mechanical isolation and serum-free culture. The roles of atRA at different concentrations in inducing the differentiation of NSCs were observed by immunofluorescent cytochemical staining, and the expression of retinoic acid receptor (RAR) gene was determined by semi-quantitative RT-PCR. RESULTS: atRA could dose-dependently accelerate the differentiation of NSCs into neuron-like cells, and the physiological concentration of atRA was optimal for inducing NSC differentiation. atRA could induce the expression of RARbeta mRNA in a dose- and time-dependent manner. CONCLUSION: atRA can accelerate differentiation of NSCs into neuron-likes cells and up-regulate the expression of RAR-beta mRNA in neonatal rat striatal NSCs.

Animals↗

PubMed2005

[Effect of doxofylline on calcium-activated potassium channels in human peripheral blood eosinophils in asthma].

OBJECTIVE: To study the effects of doxofylline on calcium-activated potassium (K(Ca)) channels of human peripheral blood eosinophils in asthma. METHODS: Peripheral blood eosinophils from patients with asthma were isolated and divided equally into two groups, a control group and a doxofylline incubated group. The data were recorded using cell-attached configuration of patch-clamp technique and the kinetic changes of K(Ca) channels activated by 0.2 micromol/L platelet activating factor (PAF) were compared. RESULTS: As compared with the control group, the open probability of the K(Ca) channels decreased from 0.135 +/- 0.021 to 0.044 +/- 0.018, the open time from (5.75 +/- 0.40) ms to (2.39 +/- 0.13) ms, while the close time increased from (2.17 +/- 0.50) ms to (23.73 +/- 2.50) ms in the doxofylline incubated group. The differences were significant between the two groups (all P < 0.05). CONCLUSION: Doxofylline could decrease the open probability of the channels as a result of both the shortening of open period and the prolongation of close time.

Adolescent↗

PubMed2004

Assessing genomewide statistical significance in linkage studies.

Assessment of genomewide statistical significance in multipoint linkage analysis is a thorny problem. The existing analytical solutions rely on strong assumptions (i.e., infinitely dense or equally spaced genetic markers that are fully informative and completely observed, and a single type of relative pair) which are rarely satisfied in real human studies, while simulation-based methods are computationally intensive and may not be applicable to complex data structures and sophisticated genetic models. Here, we propose a conceptually simple and numerically efficient Monte Carlo procedure for determining genomewide significance levels that is applicable to all linkage studies. The pedigree structure is completely general; the marker data are totally arbitrary in respect to number, spacing, informativeness, and missingness; the trait can be qualitative, quantitative, or multivariate; the alternative hypothesis can be two-sided or one-sided; and the statistic can be parametric or nonparametric. The usefulness of the proposed approach is demonstrated through extensive simulation studies and an application to the nuclear family data from the Tenth Genetic Analysis Workshop.

Computer Simulation↗

PubMed2004

Nonparametric estimation of the effects of quantitative trait loci.

Interval mapping of quantitative trait loci from breeding experiments plays an important role in understanding the mechanisms of disease, both in humans and other organisms. Standard approaches to estimation involve parametric assumptions for the component distributions and may be sensitive to model misspecification. Some nonparametric tests have been studied. However, nonparametric estimation of the phenotypic distributions has not been considered in the genetics literature, even though such methods might provide essential nonparametric summaries for comparing different loci. We develop a sufficient condition for identifiability of the phenotypic distributions. Simple nonparametric estimators for the distributions are proposed for uncensored and right censored data. They have a closed form and their small and large sample properties are readily established. Their practical utility as numerical summaries which complement nonparametric tests is demonstrated on two recent genetics examples.

Animals↗