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Liang Li

Publications and source records attributed to Liang Li.

At least 55 records · Page 3Linked to original sources
PubMed2006

Mass spectrometry-based proteomics combined with bioinformatic tools for bacterial classification.

Timely classification and identification of bacteria is of vital importance in many areas of public health. We present a mass spectrometry (MS)-based proteomics approach for bacterial classification. In this method, a bacterial proteome database is derived from all potential protein coding open reading frames (ORFs) found in 170 fully sequenced bacterial genomes. Amino acid sequences of tryptic peptides obtained by LC-ESI MS/MS analysis of the digest of bacterial cell extracts are assigned to individual bacterial proteomes in the database. Phylogenetic profiles of these peptides are used to create a matrix of sequence-to-bacterium assignments. These matrixes, viewed as specific assignment bitmaps, are analyzed using statistical tools to reveal the relatedness between a test bacterial sample and the microorganism database. It is shown that, if a sufficient amount of sequence information is obtained from the MS/MS experiments, a bacterial sample can be classified to a strain level by using this proteomics method, leading to its positive identification.

Amino Acid Sequence↗
PubMed2006

Effect of 2MEGA labeling on membrane proteome analysis using LC-ESI QTOF MS.

One of the challenges associated with large-scale proteome analysis using tandem mass spectrometry (MS/MS) and automated database searching is to reduce the number of false positive identifications without sacrificing the number of true positives found. In this work, a systematic investigation of the effect of 2MEGA labeling (N-terminal dimethylation after lysine guanidination) on the proteome analysis of a membrane fraction of an Escherichia coli cell extract by 2-dimensional liquid chromatography MS/MS is presented. By a large-scale comparison of MS/MS spectra of native peptides with those from the 2MEGA-labeled peptides, the labeled peptides were found to undergo facile fragmentation with enhanced a1 or a1-related (a(1)-17 and a(1)-45) ions derived from all N-terminal amino acids in the MS/MS spectra; these ions are usually difficult to detect in the MS/MS spectra of nonderivatized peptides. The 2MEGA labeling alleviated the biased detection of arginine-terminated peptides that is often observed in MALDI and ESI MS experiments. 2MEGA labeling was found not only to increase the number of peptides and proteins identified but also to generate enhanced a1 or a1-related ions as a constraint to reduce the number of false positive identifications. In total, 640 proteins were identified from the E. coli membrane fraction, with each protein identified based on peptide mass and sequence match of one or more peptides using MASCOT database search algorithm from the MS/MS spectra generated by a quadrupole time-of-flight mass spectrometer. Among them, the subcellular locations of 336 proteins are presently known, including 258 membrane and membrane-associated proteins (76.8%). Among the classified proteins, there was a dramatic increase in the total number of integral membrane proteins identified in the 2MEGA-labeled sample (153 proteins) versus the unlabeled sample (77 proteins).

Amino Acid Sequence↗
PubMed2006

Morbidity and mortality risk associated with red blood cell and blood-component transfusion in isolated coronary artery bypass grafting.

OBJECTIVE: Our objective was to quantify incremental risk associated with transfusion of packed red blood cells and other blood components on morbidity after coronary artery bypass grafting. DESIGN: The study design was an observational cohort study. SETTING: This investigation took place at a large tertiary care referral center. PATIENTS: A total of 11,963 patients who underwent isolated coronary artery bypass from January 1, 1995, through July 1, 2002. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Among the 11,963 patients who underwent isolated coronary artery bypass grafting, 5,814 (48.6%) were transfused. Risk-adjusted probability of developing in-hospital mortality and morbidity as a function of red blood cell and blood-component transfusion was modeled using logistic regression. Transfusion of red blood cells was associated with a risk-adjusted increased risk for every postoperative morbid event: mortality (odds ratio [OR], 1.77; 95% confidence interval [CI], 1.67-1.87; p<.0001), renal failure (OR, 2.06; 95% CI, 1.87-2.27; p<.0001), prolonged ventilatory support (OR, 1.79; 95% CI, 1.72-1.86; p<.0001), serious infection (OR, 1.76; 95% CI, 1.68-1.84; p<.0001), cardiac complications (OR, 1.55; 95% CI, 1.47-1.63; p<.0001), and neurologic events (OR, 1.37; 95% CI, 1.30-1.44; p<.0001). CONCLUSIONS: Perioperative red blood cell transfusion is the single factor most reliably associated with increased risk of postoperative morbid events after isolated coronary artery bypass grafting. Each unit of red cells transfused is associated with incrementally increased risk for adverse outcome.

Aged↗
PubMed2006

Fingerprint matching based on global comprehensive similarity.

This paper introduces a novel algorithm based on global comprehensive similarity with three steps. To describe the Euclidean space-based relative features among minutiae, we first build a minutia-simplex that contains a pair of minutiae as well as their associated textures, with its transformation-variant and invariant relative features employed for the comprehensive similarity measurement and parameter estimation, respectively. By the second step, we use the ridge-based nearest neighborhood among minutiae to represent the ridge-based relative features among minutiae. With these ridge-based relative features, minutiae are grouped according to their affinity with a ridge. The Euclidean space-based and ridge-based relative features among minutiae reinforce each other in the representation of a fingerprint. Finally, we model the relationship between transformation and the comprehensive similarity between two fingerprints in terms of histogram for initial parameter estimation. Through these steps, our experiment shows that the method mentioned above is both effective and suitable for limited memory AFIS owing to its less than 1k byte template size.

Algorithms↗
PubMed2006

Preparation of conductive polypyrrole-palladium composite nanospheres by inverse microemulsion polymerization.

Conductive polypyrrole-palladium (PPy-Pd) composite nanospheres of about 50 nm in diameter, containing dispersed Pd metal nanoparticles of about 2-4 nm in size, were prepared in a 1-step oxidative polymerization of pyrrole by Pd(NO3)2. Pyrrole was oxidized by Pd(NO3)2 in an inverse microemulsion polymerization system, yielding PPy nanospheres and elemental Pd nanoparticles simultaneously. Palladium nanoparticles were uniformly dispersed in the nanospheres of PPy chains. The latter also exhibited an enhanced effective conjugation. The chemical composition of the PPy-Pd composite nanospheres was characterized by X-ray photoelectron spectroscopy and FTIR spectroscopy. The crystalline structure of the Pd nanoparticles was deduced from X-ray diffraction patterns. The morphology of the composites was revealed by scanning and transmission electron microscopy.

Macromolecular Substances↗
PubMed2006

Water diffusion behavior in epoxy resins with various fluorine contents.

In this work, novolac resin with perfluorinated side chains was synthesized and cured with o-Cresol novolac epoxy resin to obtain epoxy resins with various fluorine contents. Attenuated total reflection Fourier transform infrared spectroscopy (ATR/FT-IR) was used to monitor the in situ water diffusion process in these systems. The diffusion coefficient of water first increased and then slightly decreased with increasing fluorine content, which could be attributed to two opposite effects induced by perfluorinated side chains: enhanced hydrophobicity and increased free volume. In addition, generalized two-dimensional (2D) correlation analysis was employed to investigate both the sorption and the desorption process of water diffusion, and two kinds of water molecules, named bound and free water, were found. It was interesting to find that in the sorption process, the change in the population of bound water molecules occurs earlier than the change in the population of free water molecules, while in the desorption process, the sequence was reversed.

Journal Article↗
PubMed2006

Local control of brain metastases by stereotactic radiosurgery in relation to dose to the tumor margin.

OBJECT: The maximal tolerated dose (MTD) for stereotactic radiosurgery (SRS) for brain tumors was established by the Radiation Therapy Oncology Group (RTOG) in protocol 90-05, which defined three dose groups based on the maximal tumor diameter. The goal in this retrospective study was to determine whether differences in doses to the margins of brain metastases affect the ability of SRS to achieve local control. METHODS: Between 1997 and 2003, 202 patients harboring 375 tumors that met study entry criteria underwent SRS for treatment of one or multiple brain metastases. The median overall follow-up duration was 10.7 months (range 3-83 months). A dose of 24 Gy to the tumor margin had a significantly lower risk of local failure than 15 or 18 Gy (p = 0.0005; hazard ratio 0.277, confidence interval [CI] 0.134-0.573), whereas the 15- and 18-Gy groups were not significantly different from each other (p = 0.82) in this regard. The 1-year local control rate was 85% (95% CI 78-92%) in tumors treated with 24 Gy, compared with 49% (CI 30-68%) in tumors treated with 18 Gy and 45% (CI 23-67%) in tumors treated with 15 Gy. Overall patient survival was independent of dose to the tumor margin. CONCLUSIONS: Use of the RTOG 90-05 dosing scheme for brain metastases is associated with a variable local control rate. Tumors larger than 2 cm are less effectively controlled than smaller lesions, which can be safely treated with 24 Gy. Prospective evaluations of the relationship between dose to the tumor margin and local control should be performed to confirm these observations.

Adult↗
PubMed2006

[A potential role for the bone marrow mesenchymal stem cell in the pathogenesis of osteoporosis by ovariectomy in rat].

The purpose of this paper is to investigate the osteogenesis and adipogenesis in bone marrow mesenchymal stem cells (MSCs) isolated from normal rats and osteoporotic rats by ovariectomy. Osteoporotic animal model was established in 3 month-old and 6 month-old female Sprague-Dawley (SD) rats by ovariectomy. Animal experiments were divided into 4 groups: 1) control-3 group; 2) ovx-3 group; 3) control-6 group and 4) ovx-6 group. MSCs were isolated by means of the density-gradient centrifugation method from each group, respectively. Colony-forming unit-fibroblast (CFU-Fs ) number, CFU-Fs size distribution and cell density in CFU-Fs of primary passage MSCs were measured at the inverted phase contrast microscope. The cell cycle and proliferation index (PI) as well as apoptosis idex (AI) of MSCs were studied by (FCM). After osteogenic induction (OSI), calcium nodes of MSCs were marked by alizarin red staining (ARS); The expression level of alkaline phosphatase(ALP) was detected by dynamics method with substrate of phosphoric acid para-Nitro benzene and the content of osteocalcin (OCN) was detected with the isotope labelling method. After adipogenic induction (ADI), lipid droplet in MSCs were detected by oil red O staining and the mRNA level of lipoprotein lipase (LPL) was measured by RT-PCR. The results showed that CFU-Fs and PI are obviously decresed and AI are increased of MSCs in OVX-3 and OVX-6 groups (P<0.05). The secretory volume of ALP and BGP of MSCs and the content of calcium nods of MSCs are lower in OVX-3 and OVX-6 groups than that in control-3 and control-6 groups after osteogenic induction (P<0.05). The number of lipid droplet and the expression level of LPL mRNA are higher in OVX-3 and OVX-6 groups than that in control-3 and control-6 (P<0.05). The result in our study suggested that depress of osteogenesis and the up-regulation of adipogenesis of MSCs in osteoporotic rats by ovariectomy may be relate close to the pathogenesis of osteoporosis.

Adipocytes↗
PubMed2006

[Studies on the chemical constituents of Lagotis yunnanensis (II)].

OBJECTIVE: To study the chemical constituents of Lagotis yunnanensis W. W. Smith. METHODS: Compounds were isolated from the ethanolic extract of the title herb by silica gel column chromatography, and their structures were identified by physical and chemical evidences and spectral methods. RESULTS: Seven compounds were isolated and identified as artselaeroside A (1),3-hydroxy-5-methoxy-benzyl alcohol (2), tyrosol (3), glycerin-9'-Z-octadecaenate (4), glycerin-docosanate (5), glycerin-tetracosanate (6), tetracosanoic acid (7), respectively. CONCLUSION: All the compounds were isolated from this plant for the first time.

Fatty Acids↗
PubMed2006

[The chemical constituents of Breynia rostrata].

AIM: To study the chemical constituents of Breynia rostrata Merr. METHODS: Chromatography was used to isolate and purify the chemical constituents, their structures were identified by spectral analysis. RESULTS: Four glycosides were identified as 6-O-methylpropanoyl-alpha-D-glucopyranoside (1), 4"-phenolic-6-O-methylpropanoyl-beta-D-glucopyranoside (2), 1-O-galloyl-beta-D-glucopyranoside (3), arbutin (4). CONCLUSION: Compounds 1 and 2 are new compounds; 3 and 4 were isolated from Breynia rostrata Merr. for the first time.

Arbutin↗
PubMed2006

[The effect of mechanical strain on proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells from rats].

In order to investigate the effects of cyclic biaxial mechanical strain on proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells (MSCs)from rats. The MSCs were isolated from bone marrow in the 9-month-old female Sprague-Dawley rats by a density gradient method. After the third passage,1 x 10(5) cells were seeded on the flexible silicone membrane in the cyclic biaxial mechanical strain unit. The amplitude of mechanical strain applied to the cells were 4000 microstrain, at a frequency of one hertz (1 Hz), for periods of 3 repetitions of 2 hours' mechanical strain and a break of 2 hours. The osteoblastic marker such as osteopontin (OPN),alkaline phosphatease (ALP), osteocalcin (OCN), type I collagen (Col I) were detected by RT-PCR. The proliferation of all cells were studied with Flow Cytometry (FCM). ALP and OPN levels significantly increased in the mechanical strained groups and reached the top at 3th day after mechanical strain. COL I level was increase only at 3th day after mechanical strain, and the change of OCN was not obvious in every group. The proliferation index of the medchanical strained groups was increased, compared with the control. These results showed that mechanical strain can improve MSCs proliferation and make MSCs differentiate to osteoblast.

Alkaline Phosphatase↗
PubMed2005

Selection of nonapoptotic spermatozoa as a new tool for enhancing assisted reproduction outcomes: an in vitro model.

Magnetic cell sorting (MACS) using annexin V-conjugated microbeads eliminates apoptotic spermatozoa based on the externalization of phosphatidylserine residues. The procedure delivers two sperm fractions: annexin V-negative (nonapoptotic) and annexin V-positive (apoptotic). Our aim was to determine whether the sperm fertilizing potential can be improved by selecting a nonapoptotic fraction using MACS. Semen samples (n = 35) were subjected to separation on a density gradient followed by MACS. Extent of apoptosis was assessed by measuring levels of activated caspase 3 using fluorescein-labeled inhibitors of caspase, alterations in mitochondrial membrane potential (MMP) using a lipophilic cationic dye, and DNA fragmentation using terminal deoxynucleotidyl transferase-mediated fluorescein-dUTP nick end labeling assay. The sperm fertilization potential was assessed using hamster oocyte penetration assay and hamster oocyte-intracytoplasmic sperm injection (ICSI). Annexin V-negative sperm displayed superior quality in terms of high motility, low caspase 3 activation, MMP integrity, and small extent of DNA fragmentation. Annexin V-negative sperm demonstrated higher oocyte penetration capacity but comparable sperm chromatin decondensation (SCD) following ICSI. Conversely, the annexin V-positive sperm presented with poor quality and fertilization potential. The oocyte penetration rate was negatively correlated with apoptotic marker expression, whereas SCD following ICSI was only associated with apoptosis on sperm-damaged membranes. We conclude that apoptosis appears to impact sperm-oocyte penetration rate; however, it does not seem to affect early stages of fertilization such as SCD in spermatozoa of healthy donors. The selection of nonapoptotic sperm by MACS may be used to enhance results of in vitro fertilization by increasing sperm-oocyte penetration.

Animals↗
PubMed2005

A method for the isolation of covalent DNA-protein crosslinks suitable for proteomics analysis.

The covalent crosslinking of protein to DNA is a form of DNA damage induced by a number of commonly encountered agents, including metals, aldehydes, and radiation as well as chemotherapeutic drugs. DNA-protein crosslinks (DPCs) are potentially bulky and helix distorting and have the potential to block the progression of translocating protein complexes. To fully understand the induction and repair of these lesions, it will be important to identify the crosslinked proteins involved. To take advantage of dramatic improvements in instrument sensitivity that have facilitated the identification of proteins by proteomic approaches, improved methods are required for isolation of DPCs. This article describes a novel method for the isolation of DPCs from mammalian cells that uses chaotropic agents to isolate genomic DNA and stringently remove noncrosslinked proteins followed by DNase I digestion to release covalently crosslinked proteins. This method generates high-quality protein samples in sufficient quantities for analysis by mass spectrometry. In addition, the article presents a modified form of this method that also makes use of chaotropic agents for promoting the adsorption of DNA (with crosslinked proteins) to silica fines, markedly reducing the DPC isolation time and cost. These approaches were applied to radiation- and camptothecin-induced DPCs.

Animals↗
PubMed2005

Identification of mammalian proteins cross-linked to DNA by ionizing radiation.

Ionizing radiation (IR) is an important environmental risk factor for various cancers and also a major therapeutic agent for cancer treatment. Exposure of mammalian cells to IR induces several types of damage to DNA, including double- and single-strand breaks, base and sugar damage, as well as DNA-DNA and DNA-protein cross-links (DPCs). Little is known regarding the biological consequences of DPCs. Identifying the proteins that become cross-linked to DNA by IR would be an important first step in this regard. We have therefore undertaken a proteomics study to isolate and identify proteins involved in IR-induced DPCs. DPCs were induced in AA8 Chinese hamster ovary or GM00637 human fibroblast cells using 0-4 gray of gamma-rays under either aerated or hypoxic conditions. DPCs were isolated using a recently developed method, and proteins were identified by mass spectrometry. We identified 29 proteins as being cross-linked to DNA by IR under aerated and/or hypoxic conditions. The identified proteins include structural proteins, actin-associated proteins, transcription regulators, RNA-splicing components, stress-response proteins, cell cycle regulatory proteins, and GDP/GTP-binding proteins. The involvement of several proteins (actin, histone H2B, and others) in DPCs was confirmed by using Western blot analysis. The dose responsiveness of DPC induction was examined by staining one-dimensional SDS-polyacrylamide gels with SYPRO Tangerine followed by analysis using fluorescence imaging. Quantitation of the fluorescence signal indicated no significant difference in total yields of IR-induced DPCs generated under aerated or hypoxic conditions, although differences were observed for several individual protein bands.

Animals↗
PubMed2005

Antitumor activity of anti-type IV collagenase monoclonal antibody and its lidamycin conjugate against colon carcinoma.

AIM: Type IV collagenase including MMP-2 and -9 plays an important role in cancer cell invasion and metastasis and is an attractive target for mAb-directed therapy. The immunoreactivity of mAb 3G11, a mAb directed against type IV collagenase in human colorectal carcinomas, was studied by immuno-histochemical (IHC) staining. mAb 3G11 was conjugated to an antitumor antibiotic lidamycin (LDM). The antitumor activity of 3G11-LDM conjugate against colon carcinoma was investigated in mice. METHODS: ELISA, gelatin zymography, and Western blot assay were used for the biological characterization of mAb 3G11. The immunoreactivity of mAb 3G11 with human colorectal carcinomas was detected by IHC staining. The cytotoxicity of LDM and 3G11-LDM conjugate to human colon carcinoma HT-29 cells was examined by clonogenic assay and MTT assay. The therapeutic effect of conjugate 3G11-LDM was evaluated with colon carcinoma 26 in mice. RESULTS: As shown in ELISA, mAb 3G11 reacted specifically with type IV collagenase, while 3G11-LDM conjugate also recognized specifically its respective antigen. In IHC assay, mAb 3G11 showed positive immunoreactivity in most cases of colorectal carcinoma, and negative immunoreactivity in the adjacent non-malignant tissues. By gelatin zymography, the inhibition effect of mAb 3G11 on the secretion activity of type IV collagenase was proved. In terms of IC50 values in MTT assay, the cytotoxicity of LDM to human colon carcinoma HT-29 cells was 10,000-fold more potent than that of mitomycin C (MMC) and adriamycin (ADM). 3G11-LDM conjugate also displayed extremely potent cytotoxicity to human colon carcinoma HT-29 cells with an IC50 value of 5.6 x 10(-19) mol/L. 3G11-LDM conjugate at the doses of 0.05 and 0.1 mg/kg inhibited the growth of colon carcinoma 26 in mice by 70.3 and 81.2%, respectively. CONCLUSION: mAb 3G11 is immunoreactive with human colorectal carcinoma and its conjugate with LDM is highly effective against colon carcinoma in mice.

Aminoglycosides↗
PubMed2005

Fabrication and characterization of single-crystalline ZnTe nanowire arrays.

Semiconductor ZnTe nanowire arrays have been synthesized by the pulsed electrochemical deposition from aqueous solutions into porous anodic alumina membranes. X-ray diffraction analyses show that the as-synthesized nanowires have a highly preferential orientation. Scanning electron microscopy, transmission electron microscopy, and high-resolution transmission electron microscopy indicate that high-filling, ordered, and single-crystalline nanowire arrays have been obtained. The optical absorption spectra of the nanowire arrays show that the optical absorption band edge of the ZnTe nanowire array exhibits a blue shift compared with that of bulk ZnTe. The growth mechanism and the electrochemical deposition process are discussed together with the chemical compositions analysis.

Journal Article↗
PubMed2005

Expression of DLK1 in hematopoietic cells results in inhibition of differentiation and proliferation.

The Delta-like (DLK1) gene is overexpressed in CD34+ cells from myelodysplastic syndrome (MDS) patients. DLK1 encodes an EGF-like homeotic transmembrane protein homologous to the notch/delta/serrate family. Although exogenous DLK1 promotes maintenance of murine hematopoietic stem cells, the functional effects of DLK1 overexpression in hematopoietic cells are unknown. We show that ectopically expressed DLK1 significantly inhibits differentiation and proliferation of human promyelocytic HL-60 cells. Unlike preadipocytes, where proteolytic processing of membrane-bound protein and release of a soluble form mediates differentiation inhibition, proteolytic release of the extracellular domain was not required for inhibition of hematopoietic cell differentiation. However, intracellular domain interactions were critical to this DLK1 function. We conclude that DLK1 overexpression in hematopoietic cells has important functional consequences. Our studies identify novel molecular mechanisms and indicate that DLK1 has activity both as a soluble and a transmembrane expressed protein. Our results support further investigation of the role of DLK1 in abnormal hematopoiesis in MDS.

Cell Differentiation↗