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Lei Liu

Publications and source records attributed to Lei Liu.

At least 109 records · Page 6Linked to original sources
PubMed2004

[An experimental study of cell apoptosis and correlative gene expression after tractive spinal cord injury in rats].

OBJECTIVE: To observe the cell apoptosis after tractive spinal cord injury in rats, determine expression of apoptosis correlative genes, and study the molecular mechanism of cell apoptosis. METHODS: The T(13)-L(2) spinal cord of rats was injured by traction after the amplitude of P1-N1 wave decreased to 70% in postoperation than in preoperation through cortical somatosensory evoked potential (CSEP) monitor. Then rats were killed in 30 min, 6 h, 1, 4, 7, 14 and 21 d respectively after operation (n = 4). Cell apoptosis was examined by the flow cytometer and terminal deoxynucleotidyl transferase-mediated DUTP-biotin nick end labeling (TUNEL) reaction, the expression of p53, bax and bc1-2 genes was tested with immunohistochemistry. RESULTS: The flow cytometer test and TUNEL method showed that the apoptosis cell ratio raised in 6 h and reached at peak in 7 d after injury, and then declined till 21 d, they showed significant difference (P < 0.05, 0.01). TUNEL method showed that injured group had a large number of apoptosis glial cells in white matter. Immunohistochemical staining showed that the positive expression of p53, bax and bc1-2 protein raised at 6 h, expression of p53 protein reached at peak in 4 d, bax and bc1-2 protein reached at peak in 7 d after injury. Compared with control group and laminectomy group, the injured group showed significant difference (P < 0.05, 0.01). CONCLUSION: There is cell apoptosis phenomenon after tractive spinal cord injury in rats. Morphology indicates that apoptosis includes neurons and glialcytes, which is an important form of cell death and pathological changes in secondary lesion period after tractive spinal cord. There exist high expression of apoptosis correlative gene p53 and bax after spinal cord injury, they may play an important role in reduction of cells to apoptosis.

Animals↗
PubMed2004

Rapid nongenomic inhibitory effects of glucocorticoids on phagocytosis and superoxide anion production by macrophages.

Traditionally, steroid hormone effects have been described as a result of the modulation of nuclear transcription, thus triggering genomic events that are responsible for physiological effects. Despite early observations of rapid steroid effects that were incompatible with this theory, nongenomic steroid effects have been widely recognized only recently. However, the nongenomic effect of glucocorticoid (GC) on anti-inflammation and immunosuppression has not been reported. Macrophages play important roles in inflammation and the immune response. The present experiment selected macrophages as experimental cells to explore the nongenomic effects and possible mechanisms of GCs on phagocytosis and superoxide anion production. Phagocytosis by macrophages was detected by the neutral red uptake assay. The superoxide anions were measured by cytochrome C reduction assay. It was found that both 10(-4) and 10(-5) mol/L corticosterone (CORT) rapidly inhibited uptake of neutral red by macrophages in less than 30 min, and the inhibition by the former was stronger than that of the latter. CORT (10(-4) to 10(-10) mol/L) rapidly inhibited superoxide anion production by macrophages in less than 30 min. The above-mentioned effects were insensitive to the GC-receptor antagonist mifepristone (RU486) and the translation inhibitor actidione. CORT coupled to bovine serum albumin (BSA-CORT) was able to mimic the rapid inhibitory effects of CORT. The results indicated that CORT could rapidly inhibit phagocytosis and superoxide anion production by mouse peritoneal macrophages in vitro in less than 30 min by a rapid, nongenomic mechanism, which contributes to the anti-inflammatory and immunosuppressive actions of GCs. These data shed a new light on the clinical application of GCs.

Animals↗
PubMed2004

Highly enantioselective phenylacetylene additions to ketones catalyzed by (S)-BINOL-Ti complex.

The readily available and inexpensive (S)-BINOL ligand in combination with Ti(O(i)Pr)(4) is an effective chiral catalyst for the catalytic asymmetric addition of alkynylzinc to unactivated simple ketones. Good to excellent enantioselectivities were achieved. No previous case has been reported successfully using BINOL to catalyze the addition of phenylacetylene to unactivated ketones, and thus the utility of BINOL in asymmetric catalysis is expanded.

Acetylene↗
PubMed2004

ESTIMA, a tool for EST management in a multi-project environment.

BACKGROUND: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. RESULTS: A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. CONCLUSIONS: The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. We have also provided detailed installation instructions and a tutorial at the same website. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee brain EST projects. Non-academic users need to contact the W.M. Keck Center for Functional and Comparative Genomics, University of Illinois at Urbana-Champaign, Urbana, IL, for licensing information.

Animals↗
PubMed2004

A cDNA microarray from the telencephalon of juvenile male and female zebra finches.

Studies over roughly the last decade have emphasized the importance of gene expression in the development of structure and function of the songbird forebrain. However, few tools have been available to efficiently identify the critical factors. To that end, we have produced a normalized cDNA library from juvenile zebra finch telencephalon, and have spotted inserts from 2400 randomly selected cDNA clones on microarrays (1664 unique sequences). We have also added several previously cloned cDNAs of interest, including three representing genes encoded on sex chromosomes. Hybridizations comparing Cy3- and Cy5-labeled cDNA from the telencephalon of day 25 male and female zebra finches confirmed sexually dimorphic expression of the Z- and W-linked genes, demonstrating the utility of these microarrays for detecting differential expression and providing information about the relative expression of these genes in the brains of juveniles of this age.

Animals↗
PubMed2004

Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant.

BACKGROUND: Microarrays are an important tool with which to examine coordinated gene expression. Soybean (Glycine max) is one of the most economically valuable crop species in the world food supply. In order to accelerate both gene discovery as well as hypothesis-driven research in soybean, global expression resources needed to be developed. The applications of microarray for determining patterns of expression in different tissues or during conditional treatments by dual labeling of the mRNAs are unlimited. In addition, discovery of the molecular basis of traits through examination of naturally occurring variation in hundreds of mutant lines could be enhanced by the construction and use of soybean cDNA microarrays. RESULTS: We report the construction and analysis of a low redundancy 'unigene' set of 27,513 clones that represent a variety of soybean cDNA libraries made from a wide array of source tissue and organ systems, developmental stages, and stress or pathogen-challenged plants. The set was assembled from the 5' sequence data of the cDNA clones using cluster analysis programs. The selected clones were then physically reracked and sequenced at the 3' end. In order to increase gene discovery from immature cotyledon libraries that contain abundant mRNAs representing storage protein gene families, we utilized a high density filter normalization approach to preferentially select more weakly expressed cDNAs. All 27,513 cDNA inserts were amplified by polymerase chain reaction. The amplified products, along with some repetitively spotted control or 'choice' clones, were used to produce three 9,728-element microarrays that have been used to examine tissue specific gene expression and global expression in mutant isolines. CONCLUSIONS: Global expression studies will be greatly aided by the availability of the sequence-validated and low redundancy cDNA sets described in this report. These cDNAs and ESTs represent a wide array of developmental stages and physiological conditions of the soybean plant. We also demonstrate that the quality of the data from the soybean cDNA microarrays is sufficiently reliable to examine isogenic lines that differ with respect to a mutant phenotype and thereby to define a small list of candidate genes potentially encoding or modulated by the mutant phenotype.

Cluster Analysis↗
PubMed2004

Phonon spectromicroscopy of carbon nanostructures with atomic resolution.

The vibrational properties of single-wall carbon nanotubes have been probed locally with atomic-scale resolution by inelastic electron tunneling spectroscopy with a low-temperature scanning tunneling microscope. The high spatial resolution has allowed the unraveling of changes in the local phonon spectrum related to topological defects. We demonstrated that the radial breathing mode is suppressed within tube segments of lengths below approximately 3 nm, and that in the cap region phonon modes characteristic of the fullerene hemisphere are emerging. Phonon spectromicroscopy should lead to a better understanding of the mechanisms that limit the transport of heat or electrical charge inside nanostructured carbon materials.

Journal Article↗
PubMed2004

Transamination reactions with multiple turnovers catalyzed by hydrophobic pyridoxamine cofactors in the presence of polyethylenimine polymers.

Pyridoxamines carrying hydrophobic side chains reversibly bind into the hydrophobic core of polyethylenimines and transaminate ketoacids to amino acids with as much as a 725000-fold rate acceleration. Turnover catalysis was achieved by sacrificial oxidative decarboxylation of C-substituted amino acids, which reconverted the pyridoxals to pyridoxamines.

Hydrophobic and Hydrophilic Interactions↗
PubMed2004

Polymeric and dendrimeric pyridoxal enzyme mimics.

Pyridoxal was covalently attached to polyethylenimine polymers, but the resulting materials were found to degrade rapidly. In comparison, the dendrimeric pyridoxals, which possess only one pyridoxal unit at the core of every dendrimer molecule were found to be relatively stable compounds. A total of 12 poly(amidoamine) type dendrimers were synthesized. They range from G1 to G6 with either NMe(2) or NHAc termini. The NMe(2)-terminated pyridoxal dendrimers racemize alpha-amino acids 50-100 times faster than does simple pyridoxal, while the NHAc-terminated pyridoxal dendrimers racemize alpha-amino acids only 3-5 times faster than does simple pyridoxal. Both the NMe(2)- and NHAc-terminated pyridoxal dendrimers decarboxylate 2-amino-2-phenyl-propionic acid 1-3 times faster than simple pyridoxal. The interior polarity in the pyridoxal dendrimers is similar to that of 85:15 water-DMF solution. Furthermore, we successfully incorporated eight lauryl groups to the G5 pyridoxal dendrimer at known positions. The laurylated dendrimer exhibits lower racemization and decarboxylation rates than do the unlaurylated ones, in contrast to the positive rate effects of laurylation in polyethylenimine-pyridoxamines in our previous transamination studies.

Amino Acids↗
PubMed2004

Homolytic C-H and N-H bond dissociation energies of strained organic compounds.

High-level computations at G3, CBS-Q, and G3B3 levels were conducted, and good-quality C-H and N-H bond dissociation energies (BDEs) were obtained for a variety of saturated and unsaturated strained hydrocarbons and amines for the first time. From detailed NBO analyses, we found that the C-H BDEs of hydrocarbons are determined mainly by the hybridization of the parent compound, the hybridization of the radical, and the extent of spin delocalization of the radical. The ring strain has a significant effect on the C-H BDE because it forces the parent compound and radical to adopt certain undesirable hybridization. A structure-activity relationship equation (i.e., BDE (C-H) = 61.1-227.8 (p(parent)% - 0.75)(2) + 152.9 (p(radical)% - 1.00)(2) + 40.4 spin) was established, and it can predict the C-H BDEs of a variety of saturated and unsaturated strained hydrocarbons fairly well. For the C-H BDEs associated with the bridgehead carbons of the highly rigid strained compounds, we found that the strength of the C-H bond can also be predicted from the H-C-C bond angles of the bridgehead carbon. Finally, we found that N-H BDEs show less dependence on the ring strain than C-H BDEs.

Journal Article↗
PubMed2004

NSSR1 promotes neuronal differentiation of mouse embryonic carcinoma P19 cells.

We generated the small interference RNAs to specifically silence the expression of neural salient serine/arginine rich protein 1 (NSSR1) and showed that the inhibition of NSSR1 expression in mouse embryonic carcinoma cells (P19) reduces neuronal differentiation. By contrast, its over-expression promotes the differentiation. Neither inhibition nor over-expression shows distinct effect on cell proliferation. The over-expression increases the inclusion of NCAM L1 exon2 while the inhibition reduces the inclusion. The splicing of kinase insert free isoform of TrkC (TrkC-K1) is increased by the over-expression. The results demonstrate that NSSR1 promotes neuronal differentiation and the splicing of NCAML1 exon2 and TrkC-K1.

Alternative Splicing↗
PubMed2004

First-principle predictions of absolute pKa's of organic acids in dimethyl sulfoxide solution.

MP2/6-311++G(d,p) and B3LYP/6-311++G(2df,p) methods were found to be able to predict the gas-phase acidities of various organic acids with a precision of 2.2 and 2.3 kcal/mol. A PCM cluster-continuum solvation method was developed that could predict the solvation free energies of various neutral, cationic, and anionic organic species in DMSO with a precision of about 2.0 kcal/mol. Using these carefully tested methods, we successfully predicted the pKa's of 105 organic acids in DMSO with a precision of 1.7-1.8 pKa units. We also predicted the pKa's of a variety of organosilanes in DMSO for the first time using the newly developed methods. This study was one of the first that employed first-principle methods for calculating pKa's of unrelated compounds in organic solutions.

Journal Article↗
PubMed2004

Multi-species comparative mapping in silico using the COMPASS strategy.

MOTIVATION: The completion of human and mouse genome sequences provides a valuable resource for decoding other mammalian genomes. The comparative mapping by annotation and sequence similarity (COMPASS) strategy takes advantage of the resource and has been used in several genome-mapping projects. It uses existing comparative genome maps based on conserved regions to predict map locations of a sequence. An automated multiple-species COMPASS tool can facilitate in the genome sequencing effort and comparative genomics study of other mammalian species. RESULTS: The prerequisite of COMPASS is a comparative map table between the reference genome and the predicting genome. We have built and collected comparative maps among five species including human, cattle, pig, mouse and rat. Cattle-human and pig-human comparative maps were built based on the positions of orthologous markers and the conserved synteny groups between human and cattle and human and pig genomes, respectively. Mouse-human and rat-human comparative maps were based on the conserved sequence segments between the two genomes. With a match to human genome sequences, the approximate location of a query sequence can be predicted in cattle, pig, mouse and rat genomes based on the position of the match relatively to the orthologous markers or the conserved segments. AVAILABILITY: The COMPASS-tool and databases are available at http://titan.biotec.uiuc.edu/COMPASS/

Algorithms↗
PubMed2004

Spectral matching factors between Super S25 and New S25 photo cathodes and reflective radiation of objects.

According to the response of photoelectric device to a light source, the formula of spectral matching factor of photo cathode-object combination is deduced. The spectral matching factors of Super S25 and New S25 photo cathodes for green vegetation and rough concrete are calculated and compared. For Super S251, the spectral-matching factors for green vegetation and rough concrete are 0.707 and 0.743, respectively, under the full-moon radiation and are 0.504 and 0.577, respectively, under the clear-star radiation. For Super S252, the full-moon factors are 0.561 (green vegetation) and 0.732 (rough concrete), and those for clear-star radiation are 0.338 (green vegetation) and 0.471 (rough concrete). For New S25, the full-moon factors are 0.741 (green vegetation) and 0.762 (rough concrete), and those for clear-star radiation are 0.603 (green vegetation) and 0.657 (rough concrete). An analysis of results shows that the spectral-matching factor has influence on the performance of a low-light level night vision system and is essential for evaluating the visual range of a night-vision system.

Journal Article↗
PubMed2004

IFN-gamma activates cAMP/PKA/CREB signaling pathway in murine peritoneal macrophages.

Interferon-gamma (IFN-gamma) is a macrophage-activating cytokine that serves critical functions in innate and adaptive immunity and is thought to be mediated by the Jak-Stat signaling pathway. The present study establishes for the first time that cyclic adenosine monophosphate, protein kinase A, and cAMP response element-binding protein (cAMP/PKA/CREB) are coregulators of the IFN-gamma signaling pathway. Experimental data indicate that exogenous IFN-gamma stimulated cAMP accumulation and PKA activation in time-dependent and dose-dependent manners in murine peritoneal macrophages. Moreover, IFN-gamma stimulated CREB phosphorylation and CREB DNA binding, which could be significantly attenuated by PKA inhibition with H89. It appears that a novel cAMP/PKA/CREB signaling pathway is activated by IFN-gamma in macrophages, suggesting that an alternate signaling pathway exists in macrophages in response to IFN-gamma.

Animals↗
PubMed2004

A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates.

A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH(5000) panel to 1913. Of these, 1463 have significant BLASTN hits (E < e(-5)) against the human genome sequence. A cattle-human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle-human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes.

Animals↗
PubMed2004

Shared frailty models for recurrent events and a terminal event.

There has been an increasing interest in the analysis of recurrent event data (Cook and Lawless, 2002, Statistical Methods in Medical Research 11, 141-166). In many situations, a terminating event such as death can happen during the follow-up period to preclude further occurrence of the recurrent events. Furthermore, the death time may be dependent on the recurrent event history. In this article we consider frailty proportional hazards models for the recurrent and terminal event processes. The dependence is modeled by conditioning on a shared frailty that is included in both hazard functions. Covariate effects can be taken into account in the model as well. Maximum likelihood estimation and inference are carried out through a Monte Carlo EM algorithm with Metropolis-Hastings sampler in the E-step. An analysis of hospitalization and death data for waitlisted dialysis patients is presented to illustrate the proposed methods. Methods to check the validity of the proposed model are also demonstrated. This model avoids the difficulties encountered in alternative approaches which attempt to specify a dependent joint distribution with marginal proportional hazards and yields an estimate of the degree of dependence.

Algorithms↗