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Christopher Lee

Publications and source records attributed to Christopher Lee.

At least 37 records · Page 2Linked to original sources
PubMed2004

Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data.

Alternative splicing has recently emerged as a major mechanism of regulation in the human genome, occurring in perhaps 40-60% of human genes. Thus, microarray studies of functional regulation could, in principle, be extended to detect not only the changes in the overall expression of a gene, but also changes in its splicing pattern between different tissues. However, since changes in the total expression of a gene and changes in its alternative splicing can be mixed in complex ways among a set of samples, separating these effects can be difficult, and is essential for their accurate assessment. We present a simple and general approach for distinguishing changes in alternative splicing from changes in expression, based on detecting systematic anti-correlation between the log-ratios of two different samples versus a pool containing both samples. We have tested this analysis method on microarray data for five human tissues, generated using a standard microarray platform and experimental protocols shown previously to be sensitive to alternative splicing. Our automatic analysis was able to detect a wide variety of tissue-specific alternative splicing events, such as exon skipping,mutually exclusive exons, alternative 3' and alternative 5' splicing, alternative initiation and alternative termination, all of which were validated by independent reverse-transcriptase PCR experiments, with validation rates of 70-85%. Our analysis method also enables hierarchical clustering of genes and samples by the level of similarity to their alternative splicing patterns, revealing patterns of tissue-specific regulation that are distinct from those obtained by hierarchical clustering of gene expression from the same microarray data. Our data and analysis source code are available from http://www.bioinformatics.ucla.edu/ASAP.

Alternative Splicing↗
PubMed2004

Molecular mechanism of AHSP-mediated stabilization of alpha-hemoglobin.

Hemoglobin A (HbA), the oxygen delivery system in humans, comprises two alpha and two beta subunits. Free alpha-hemoglobin (alphaHb) is unstable, and its precipitation contributes to the pathophysiology of beta thalassemia. In erythrocytes, the alpha-hemoglobin stabilizing protein (AHSP) binds alphaHb and inhibits its precipitation. The crystal structure of AHSP bound to Fe(II)-alphaHb reveals that AHSP specifically recognizes the G and H helices of alphaHb through a hydrophobic interface that largely recapitulates the alpha1-beta1 interface of hemoglobin. The AHSP-alphaHb interactions are extensive but suboptimal, explaining why beta-hemoglobin can competitively displace AHSP to form HbA. Remarkably, the Fe(II)-heme group in AHSP bound alphaHb is coordinated by the distal but not the proximal histidine. Importantly, binding to AHSP facilitates the conversion of oxy-alphaHb to a deoxygenated, oxidized [Fe(III)], nonreactive form in which all six coordinate positions are occupied. These observations reveal the molecular mechanisms by which AHSP stabilizes free alphaHb.

Animals↗
PubMed2004

Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation.

Recently there has been much interest in assessing the role of alternative splicing in evolution. We have sought to measure functional selection pressure on alternatively spliced single-exon skips, by calculating the fraction that are an exact multiple of 3 nt in length and therefore preserve protein reading-frame in both the exon-inclusion and exon-skip splice forms. The frame-preservation ratio (defined as the number of exons that are an exact multiple of three in length, divided by the number of exons that are not) was slightly above random for both constitutive exons and alternatively spliced exons as a whole in human and mouse. However, orthologous exons that were observed to be alternatively spliced in the expressed sequence tag data from two or more organisms showed a substantially increased bias to be frame-preserving. This effect held true only for exons within the protein coding region, and not the untranslated region. In five animal genomes (human, mouse, rat, zebrafish, Drosophila), we observed an association between these conserved alternative splicing events and increased selection pressure for frame-preservation. Surprisingly, this effect became stronger as a function of decreasing exon inclusion level: for alternatively spliced exons that were included in a majority of the gene's transcripts, the frame-preservation bias was no higher than that of constitutive exons, whereas for alternatively spliced exons that were included in only a minority of the gene's transcripts, the frame-preservation bias increased nearly 20-fold. These data indicate that a subpopulation of modern alternative splicing events was present in the common ancestors of these genomes, and was under functional selection pressure to preserve the protein reading frame.

Alternative Splicing↗
PubMed2004

Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems.

MOTIVATION: Partial order alignment (POA) has been proposed as a new approach to multiple sequence alignment (MSA), which can be combined with existing methods such as progressive alignment. This is important for addressing problems both in the original version of POA (such as order sensitivity) and in standard progressive alignment programs (such as information loss in complex alignments, especially surrounding gap regions). RESULTS: We have developed a new Partial Order-Partial Order alignment algorithm that optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. Using this algorithm, we show the combined Progressive POA alignment method yields results comparable with the best available MSA programs (CLUSTALW, DIALIGN2, T-COFFEE) but is far faster. For example, depending on the level of sequence similarity, aligning 1000 sequences, each 500 amino acids long, took 15 min (at 90% average identity) to 44 min (at 30% identity) on a standard PC. For large alignments, Progressive POA was 10-30 times faster than the fastest of the three previous methods (CLUSTALW). These data suggest that POA-based methods can scale to much larger alignment problems than possible for previous methods. AVAILABILITY: The POA source code is available at http://www.bioinformatics.ucla.edu/poa

Algorithms↗
PubMed2004

The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures.

Recent evidence of abundant transcript variation (e.g., alternative splicing, alternative initiation, alternative polyadenylation) in complex genomes indicates that cataloging the complete set of transcripts from an organism is an important project. One challenge is the fact that most high-throughput experimental methods for characterizing transcripts (such as EST sequencing) give highly detailed information about short fragments of transcripts or protein products, instead of a complete characterization of a full-length form. We analyze this "multiassembly problem"-reconstructing the most likely set of full-length isoform sequences from a mixture of EST fragment data-and present a graph-based algorithm for solving it. In a variety of tests, we demonstrate that this algorithm deals appropriately with coupling of distinct alternative splicing events, increasing fragmentation of the input data and different types of transcript variation (such as alternative splicing, initiation, polyadenylation, and intron retention). To test the method's performance on pure fragment (EST) data, we removed all mRNA sequences, and found it produced no errors in 40 cases tested. Using this algorithm, we have constructed an Alternatively Spliced Proteins database (ASP) from analysis of human expressed and genomic sequences, consisting of 13,384 protein isoforms of 4422 genes, yielding an average of 3.0 protein isoforms per gene.

Algorithms↗
PubMed2004

Does preoperative rofecoxib (Vioxx) decrease postoperative pain with laparoscopic cholecystectomy?

BACKGROUND: A prospective, randomized, double-blinded clinical trial was designed to study the effects of preemptive rofecoxib (Vioxx) analgesia in patients undergoing elective laparoscopic cholecystectomy. METHODS: One hundred-twenty patients were enrolled in the study over a 21-month period, and 116 completed the study. One half of the patients received 50 mg rofecoxib preoperatively and the other half, placebo. Both groups were demographically similar. Medical information, patient and nursing assessments, and surgical data were evaluated. RESULTS: A significant reduction in requirements for postoperative narcotic analgesic dosing was noted in the rofecoxib group. In addition, patients receiving rofecoxib reported significantly less nausea and improvement in their activity level when compared with the control group. No complications were encountered with the preoperative use of rofecoxib. CONCLUSIONS: We conclude that in patients undergoing laparoscopic cholecystectomy, preoperative administration of rofecoxib in selected patients may facilitate postoperative recovery and decrease postoperative narcotic requirements.

Adult↗
PubMed2004

Toxoplasmosis in HIV/AIDS patients: a current situation.

The seroprevalence of toxoplasmosis among 505 of human immunodeficiency virus (HIV)/AIDS patients was 226 (44.8%; 95% CI 42.64-51.76): 27 (47.4%) and 199 (44.4%) showed Toxoplasma seropositivity with and without toxoplasmic encephalitis (TE), respectively (P <0.05). The majority of these patients were in the 25-34 age group (44 versus 39%), male (86 versus 76%), and Chinese (49 versus 53%), though no statistical significance was found between the two. Significant differences between these two groups were noted, however, in terms of marital status, occupation, and present address. The heterosexual exhibited the most frequent behavior at risk for HIV infection, and accounted for 51 and 59% of patients with and without TE, respectively. Only 17/260 (6.5%) and 1/137 (0.7%) of them later acquired TE after receiving primary chemoprophylaxis (cotrimoxazole) and antiretroviral therapy including HAART (P <0.05). Fifty-seven (11.3%) out of those 505 patients were diagnosed with AIDS-related TE. The most common clinical manifestation was headache (56%). The computed tomography scan findings showed most lesions to be multiple (96.4%), hypodense (66.7%), and in the parietal region (39.3%). Twenty-seven (47.4%) patients had chronic (latent) Toxoplasma infection as evidenced by seropositivity for anti-Toxoplasma (IgG) antibody. At the time of diagnosis, the range of CD4 cell count was from 0-239 with a median of 25 cells/cumm. We also found that a CD4 count of less than 100 cells/cumm was significantly associated with development of TE (P <0.05). Clinical outcomes showed that among those who survived, 21 (36.8%), 16 (28.1%), and 2 (3.5%) of patients had completed treatment, transferred out, and were lost to follow up, respectively. Unfortunately, 18 (31.6%) of the cases were officially pronounced dead. Overall, 7 (12.3%) patients were detected as recurrent TE in this study.

AIDS-Related Opportunistic Infections↗
PubMed2003

Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains.

We have investigated the effects of alternative splicing on transcripts encoding membrane proteins in 1001 human genes. Out of a total of 464 alternatively spliced genes encoding single-pass transmembrane (TM) proteins, in 188 we observed a splice form that specifically removed the TM domain, producing a soluble protein isoform. For example, in syndecan-4, the new alternative splice form closely parallels the proteolytic ectodomain shedding previously shown in this protein, and recognized as an important regulatory mechanism of receptor function. While many of the soluble isoforms produced by alternative splicing have already been validated, most are novel, and in 57 genes showed a statistically significant association (P-value<0.01) with a specific tissue.

Alternative Splicing↗
PubMed2003

Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences.

We report here a genome-wide analysis of alternative splicing in 2 million human expressed sequence tags (ESTs), to identify splice forms that are up-regulated in tumors relative to normal tissues. We found strong evidence (P < 0.01) of cancer-specific splice variants in 316 human genes. In total, 78% of the cancer-specific splice forms we detected are confirmed by human-curated mRNA sequences, indicating that our results are not due to random mis-splicing in tumors; 73% of the genes showed the same cancer-specific splicing changes in tissue-matched tumor versus normal datasets, indicating that the vast majority of these changes are associated with tumorigenesis, not tissue specificity. We have confirmed our EST results in an independent set of experimental data provided by human-curated mRNAs (P-value 10(-5.7)). Moreover, the majority of the genes we detected have functions associated with cancer (P-value 0.0007), suggesting that their altered splicing may play a functional role in cancer. Analysis of the types of cancer-specific splicing shifts suggests that many of these shifts act by disrupting a tumor suppressor function. Sur prisingly, our data show that for a large number (190 in this study) of cancer-associated genes cloned originally from tumors, there exists a previously uncharacterized splice form of the gene that appears to be predominant in normal tissue.

Alternative Splicing↗
PubMed2003

POAVIZ: a Partial order multiple sequence alignment visualizer.

SUMMARY: POAVIZ creates a visualization of a multiple sequence alignment that makes clear the overall structure of how sequences match and diverge in the alignment. POAVIZ can construct visualizations from any multiple sequence alignment source (e.g. PIR and CLUSTAL formats), and is valuable for revealing complex branching structure (such as domains, large-scale insertions / deletions or recombinations), especially in partnership with the Partial Order Alignment (POA) multiple sequence alignment program. AVAILABILITY: The Partial Order multiple sequence Alignment Visualizer (POAVIZ) program is available at http://www.bioinformatics.ucla.edu/poa

Algorithms↗
PubMed2003

Generating consensus sequences from partial order multiple sequence alignment graphs.

MOTIVATION: Consensus sequence generation is important in many kinds of sequence analysis ranging from sequence assembly to profile-based iterative search methods. However, how can a consensus be constructed when its inherent assumption-that the aligned sequences form a single linear consensus-is not true? RESULTS: Partial Order Alignment (POA) enables construction and analysis of multiple sequence alignments as directed acyclic graphs containing complex branching structure. Here we present a dynamic programming algorithm (heaviest_bundle) for generating multiple consensus sequences from such complex alignments. The number and relationships of these consensus sequences reveals the degree of structural complexity of the source alignment. This is a powerful and general approach for analyzing and visualizing complex alignment structures, and can be applied to any alignment. We illustrate its value for analyzing expressed sequence alignments to detect alternative splicing, reconstruct full length mRNA isoform sequences from EST fragments, and separate paralog mixtures that can cause incorrect SNP predictions. AVAILABILITY: The heaviest_bundle source code is available at http://www.bioinformatics.ucla.edu/poa

Algorithms↗
PubMed2003

Motor cortex organization after stroke is related to side of stroke and level of recovery.

BACKGROUND AND PURPOSE: The present study hypothesized that side of stroke and level of recovery influence motor system organization after stroke. METHODS: Functional MRI was performed on 14 control subjects and 21 patients with chronic stroke during index finger tapping (control subjects, right; patients, recovered side). RESULTS: On functional MRI, stroke patients with right arm involvement showed (1) significantly smaller activation in contralateral motor cortexes compared with control subjects; (2) smaller ipsilateral (nonstroke) premotor and larger contralateral (stroke-side) sensorimotor activation compared with patients with left arm involvement, although electromyogram across groups was similar; and (3) 2.7-fold-larger contralateral sensorimotor cortex activation, ventrally, in those with full recovery compared with those with partial recovery, despite similar tapping force, frequency, range of motion, and electromyogram between groups. Supplementary motor area activation was unrelated to level of recovery. CONCLUSIONS: After stroke that causes mild to moderate initial impairment and mild residual hand weakness, cortical organization varies with side of injury and with final motor status. The findings may have implications for treatment after stroke.

Arm↗
PubMed2003

ASAP: the Alternative Splicing Annotation Project.

Recently, genomics analyses have demonstrated that alternative splicing is widespread in mammalian genomes (30-60% of genes reported to have multiple isoforms), and may be one of their most important mechanisms of functional regulation. However, by comparison with other genomics data such as genome annotation, SNPs, or gene expression, there exists relatively little database infrastructure for the study of alternative splicing. We have constructed an online database ASAP (the Alternative Splicing Annotation Project) for biologists to access and mine the enormous wealth of alternative splicing information coming from genomics and proteomics. ASAP is based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. Moreover, it can help biologists design probe sequences for distinguishing specific mRNA isoforms. ASAP is intended to be a community resource for collaborative annotation of alternative splice forms, their regulation, and biological functions. The URL for ASAP is http://www.bioinformatics.ucla.edu/ASAP.

Alternative Splicing↗
PubMed2002

Genome-wide detection of tissue-specific alternative splicing in the human transcriptome.

We have developed an automated method for discovering tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs). Using this approach, we have identified 667 tissue-specific alternative splice forms of human genes. We validated our muscle-specific and brain-specific splice forms for known genes. A high fraction (8/10) were reported to have a matching tissue specificity by independent studies in the published literature. The number of tissue-specific alternative splice forms is highest in brain, while eye-retina, muscle, skin, testis and lymph have the greatest enrichment of tissue-specific splicing. Overall, 10-30% of human alternatively spliced genes in our data show evidence of tissue-specific splice forms. Seventy-eight percent of our tissue-specific alternative splices appear to be novel discoveries. We present bioinformatics analysis of several tissue-specific splice forms, including automated protein isoform sequence and domain prediction, showing how our data can provide valuable insights into gene function in different tissues. For example, we have discovered a novel kidney-specific alternative splice form of the WNK1 gene, which appears to specifically disrupt its N-terminal kinase domain and may play a role in PHAII hypertension. Our database greatly expands knowledge of tissue-specific alternative splicing and provides a comprehensive dataset for investigating its functional roles and regulation in different human tissues.

Alternative Splicing↗
PubMed2002

Treatment of PTSD: stress inoculation training with prolonged exposure compared to EMDR.

The effectiveness of Stress Inoculation Training with Prolonged Exposure (SITPE) was compared to Eye Movement Desensitization and Reprocessing (EMDR). Twenty-four participants who had a diagnosis of Post Traumatic Stress Disorder (PTSD) were randomly assigned to one of the treatment conditions. Participants were also their own wait-list control. Outcome measures included self-report and observer-rated measures of PTSD, and self-report measures of depression. On global PTSD measures, there were no significant differences between the treatments at the end of therapy. However on the subscale measures of the degree of intrusion symptoms, EMDR did significantly better than SITPE. At follow-up EMDR was found to lead to greater gains on all measures.

Adult↗
PubMed2002

A genomic view of alternative splicing.

Recent genome-wide analyses of alternative splicing indicate that 40-60% of human genes have alternative splice forms, suggesting that alternative splicing is one of the most significant components of the functional complexity of the human genome. Here we review these recent results from bioinformatics studies, assess their reliability and consider the impact of alternative splicing on biological functions. Although the 'big picture' of alternative splicing that is emerging from genomics is exciting, there are many challenges. High-throughput experimental verification of alternative splice forms, functional characterization, and regulation of alternative splicing are key directions for research. We recommend a community-based effort to discover and characterize alternative splice forms comprehensively throughout the human genome.

Alternative Splicing↗