Biomedical subjects

Chunmei Liu

Publications and source records attributed to Chunmei Liu.

11 recordsLinked to original sources

PubMed2006

Peptide sequence tag-based blind identification of post-translational modifications with point process model.

UNLABELLED: An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental spectra with theoretical spectra from peptides in a peptide database is very time consuming and may lead to high false positive rate. In this paper, we introduce a new approach that is both efficient and effective for blind PTM identification. Our work consists of the following phases. First, we develop a novel tree decomposition based algorithm that can efficiently generate peptide sequence tags (PSTs) from an extended spectrum graph. Sequence tags are selected from all maximum weighted antisymmetric paths in the graph and their reliabilities are evaluated with a score function. An efficient deterministic finite automaton (DFA) based model is then developed to search a peptide database for candidate peptides by using the generated sequence tags. Finally, a point process model-an efficient blind search approach for PTM identification, is applied to report the correct peptide and PTMs if there are any. Our tests on 2657 experimental tandem mass spectra and 2620 experimental spectra with one artificially added PTM show that, in addition to high efficiency, our ab-initio sequence tag selection algorithm achieves better or comparable accuracy to other approaches. Database search results show that the sequence tags of lengths 3 and 4 filter out more than 98.3% and 99.8% peptides respectively when applied to a yeast peptide database. With the dramatically reduced search space, the point process model achieves significant improvement in accuracy as well. AVAILABILITY: The software is available upon request.

Algorithms↗

PubMed2006

Mechanism of retinoic acid and mitogen-activated protein kinases regulating hyperoxia lung injury.

To investigate the protective effect of retinoic acid (RA) on hyperoxic lung injury and the role of RA as a modulator on mitogen-activated protein kinases (MAPKs), gastation 21 d Sprague-Dawley (SD) fetuses (term = 22 d) were delivered by hysterotomy. Within 12-24 h of birth, premature rat pups were randomly divided into 4 groups (n=12 each): air-exposed control group (group I); hyperoxia-exposed group (group II), air-exposed plus RA group (group III), hyperoxia-exposed plus RA group (group IV). Group I, III were kept in room air, and group II, IV were placed in 85 % oxygen. The pups in groups III and IV were intraperitoneally injected with RA (500 microg/kg every day). All lung tissues of premature rat pups were collected at the 4th day after birth. Terminal transferase d-UTP nick end labeling (TUNEL) staining was used for the detection of cell apoptosis. The expression of PCNA was immunohistochemically detected. Western blot analysis was employed for the determination of phosphorylated and total nonphosphorylated ERKs, JNKs or p38. Our results showed that lungs from the pups exposed to hyperoxia for 4 d exhibited TUNEL-positive nuclei increased markedly throughout the parenchyma (P<0.01), and decreased significantly after RA treatment (P<0.01). The index of PCNA-positive cells was significantly decreased (P<0.01), and was significantly increased by RA treatment (P<0.01). The air-space size was significantly enlarged, secondary crests were markedly decreased in hyperoxia-exposed animals. RA treatment improved lung air spaces and secondary crests in air-exposed pups, but had no effect on hyperoxia-exposure pups. Western blotting showed that the amounts of JNK, p38 and ERK proteins in hyperoxia-exposure or RA-treated lung tissues were same as those in untreated lung tissues (P>0.05), whereas activation of these MAPKs was markedly altered by hyperoxia and RA. After hyperoxia exposure, p-ERK1/2, p-JNK1/2 and p-p38 were dramatically increased (P<0.01), whereas p-JNK1/2 and p-p38 were markedly declined and p-ERK1/2 was further elevated by RA treatment (P<0.01). It is concluded that RA could decrease cell apoptosis and stimulate cell proliferation under hyperoxic condition. The protection of RA on hyperoxia-induced lung injury was related to the regulation of MAP kinase activation.

Animals↗

PubMed2006

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.

Equipment Design↗

PubMed2006

Fast de novo peptide sequencing and spectral alignment via tree decomposition.

De novo sequencing and spectral alignment are computationally important for the prediction of new protein peptides via tandem mass spectrometry (MS/MS). Both approaches are established upon the problem of finding the longest antisymmetric path on formulated graphs. The problem is of high computational complexity and the prediction accuracy is compromised when given spectra involve noisy data, missing mass peaks, or post translational modifications (PTMs) and mutations. This paper introduces a graphical mechanism to describe relationships among mass peaks that, through graph tree decomposition, yields linear and quadratic time algorithms for optimal de novo sequencing and spectral alignment respectively. Our test results show that, in addition to high efficiency, the new algorithms can achieve desired prediction accuracy on spectra containing noisy peaks and PTMs while allowing the presence of both b-ions and y-ions.

Algorithms↗

PubMed2005

The relationship of the expression of estrogen receptor in cartilage cell and osteoarthritis induced by bilateral ovariectomy in guinea pig.

To investigate the estrogen receptor (ER) expression in cartilage cell in the development of osteoarthritis induced by bilateral ovariectomy in guinea pig and to find their relationship. 30 two-month-old female guinea pigs were randomly divided into two groups (n = 15 each): sham operation (control) group and ovariectomized group (OVX); Scanning electorne microscope (SEM) and transmission electron microscope (TEM) were obtained to analysis the cartilage degeneration of the hind limb knee joint after 6 and 12 weeks of ovariectomy. Dextran-Coated-Charcoal (DCC) was taken to quantitively detect the expression of ER. The serum levels of estrogen and gestone were detected by immune contest assay. The results showed that ER do exist in the cartilages of the guinea pigs, with higher expression in the control group than in OVX group at the same time point (P < 0.05). It was increased also at 12 th week after operation than that of preoperation. The blood serum levels of estrogen and gestone showed a similar tendency to the expression of ER. Joint cartilage degeneration detected by SEM and TEM could be found at 6 th week, but severe degenerative lesions at 12 th week in the OVX group compared with the control group (P < 0.01). The data suggested that bilateral ovariectomy in guinea pig lead to severe osteoarthritis which mighgt be related to the lower serum level of estrogen and the downregulation of the expression of ER in the cartilage also.

Animals↗

PubMed2005

Screening candidate genes for mutations in patients with hypogonadotropic hypogonadism using custom genome resequencing microarrays.

OBJECTIVE: The purpose of this study was to determine the consistency of calling single nucleotide polymorphisms (SNPs) by custom genome resequencing microarrays compared with capillary DNA sequencing. STUDY DESIGN: Amplified genomic DNA from 23 patients with hypogonadotropic hypogonadism was hybridized to microarrays containing 30 kilobases of sequence from 6 different candidate genes. Capillary DNA sequencing was performed in 10 patients. RESULTS: For 10 patients with > or =90% of bases called, 49 SNPs in 5 of 6 genes were identified. Of the 490 bases, 75 were ambiguous (read as "N"), and 415 were able to be called an A, C, G, or T. Of 415 called, 401 (96.6%) sequences were confirmed by DNA sequencing. All homozygotes (285/285) were called identically, while sequence from 89.2% (116/130) of heterozygotes agreed by both methods. The level of agreement between microarray calls and capillary DNA sequencing demonstrated substantial accuracy. CONCLUSION: Custom genome resequencing microarrays are highly consistent with capillary sequencing in calling individual bases in genomic DNA from patients with human disease.

Adolescent↗

PubMed2005

The External RNA Controls Consortium: a progress report.

Standard controls and best practice guidelines advance acceptance of data from research, preclinical and clinical laboratories by providing a means for evaluating data quality. The External RNA Controls Consortium (ERCC) is developing commonly agreed-upon and tested controls for use in expression assays, a true industry-wide standard control.

Animals↗

PubMed2005

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

Algorithms↗

PubMed2004

Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays.

BACKGROUND: Primary human tissues are an invaluable widely used tool for discovery of gene expression patterns which characterize disease states. Tissue processing methods remain unstandardized, leading to unanswered concerns of how to best store collected tissues and maintain reproducibility between laboratories. We subdivided uterine myometrial tissue specimens and stored split aliquots using the most common tissue processing methods (fresh, frozen, RNALater) before comparing quantitative RNA expression profiles on the Affymetrix U133 human expression array. Split samples and inclusion of duplicates within each processing group allowed us to undertake a formal genome-wide analysis comparing the magnitude of result variation contributed by sample source (different patients), processing protocol (fresh vs. frozen vs. 24 or 72 hours RNALater), and random background (duplicates). The dataset was randomly permuted to define a baseline pattern of ANOVA test statistic values against which the observed results could be interpreted. RESULTS: 14,639 of 22,283 genes were expressed in at least one sample. Patient subjects provided the greatest sources of variation in the mixed model ANOVA, with replicates and processing method the least. The magnitude of variation conferred by processing method (24 hours RNALater vs 72 hours RNALater vs. fresh vs frozen) was similar to the variability seen within replicates. Subset analysis of the test statistic according to gene functional class showed that the frequency of "outlier" ANOVA results within each functional class is overall no greater than expected by chance. CONCLUSIONS: Ambient storage of tissues for 24 or 72 hours in RNALater did not contribute any systematic shift in quantitative RNA expression results relative to the alternatives of fresh or frozen tissue. This nontoxic preservative enables decentralized tissue collection for expression array analysis without a requirement for specialized equipment.

Analysis of Variance↗

PubMed2002

New developments in high-throughput resequencing and variation detection using high density microarrays.

We developed a high-throughput method for resequencing for single nucleotide polymorphism (SNP) discovery using high-density microarrays. Over the two-year course of this study a number of improvements in sample preparation methods, hybridization assay, array handling, and analysis method were developed and implemented. DNA from 40 unrelated individuals of three different ethnic origins was amplified, labeled, and hybridized to arrays designed with probes representing genomic, coding, and regulatory regions. Protocol improvements including the use of long PCR and semi-automation reduced labeling and fragmentation costs by 33%. Automation improvements include the development of a scanner autoloader for arrays, a faster array wash station, and a linked laboratory tracking and data management system. Validation of a smaller feature size, 20 x 24 microns, allowed the simultaneous screening of 30-kb sense and 30-kb antisense DNA on each microarray, increasing throughput to 1.4 Mb per day per two laboratory personnel. More than 15,000 SNPs were identified in 8.3 Mb of the human genome using high-density resequencing and variation detection arrays (microarrays).

Automation↗

PubMedDate not supplied

Efficient parameterized algorithms for biopolymer structure-sequence alignment.

Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment has to consider not only sequence similarity, but also spatially conserved conformations caused by residue interactions and, consequently, is computationally intractable. It is difficult to cope with the inefficiency without compromising alignment accuracy, especially for structure search in genomes or large databases. This paper introduces a novel method and a parameterized algorithm for structure-sequence alignment. Both the structure and the sequence are represented as graphs, where, in general, the graph for a biopolymer structure has a naturally small tree width. The algorithm constructs an optimal alignment by finding in the sequence graph the maximum valued subgraph isomorphic to the structure graph. It has the computational time complexity O[k(t)N(2)] for the structure of N residues and its tree decomposition of width t. Parameter k, small in nature, is determined by a statistical cutoff for the correspondence between the structure and the sequence. This paper demonstrates a successful application of the algorithm to RNA structure search used for noncoding RNA identification. An application to protein threading is also discussed.

Algorithms↗