Showing papers by "Shanghai Jiao Tong University published in 2010"

International network of cancer genome projects

Abstract: The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Robust Subspace Segmentation by Low-Rank Representation

Abstract: We propose low-rank representation (LRR) to segment data drawn from a union of multiple linear (or affine) subspaces. Given a set of data vectors, LRR seeks the lowest-rank representation among all the candidates that represent all vectors as the linear combination of the bases in a dictionary. Unlike the well-known sparse representation (SR), which computes the sparsest representation of each data vector individually, LRR aims at finding the lowest-rank representation of a collection of vectors jointly. LRR better captures the global structure of data, giving a more effective tool for robust subspace segmentation from corrupted data. Both theoretical and experimental results show that LRR is a promising tool for subspace segmentation.

Dasatinib versus imatinib in newly diagnosed chronic-phase chronic myeloid leukemia.

Abstract: Background Treatment with dasatinib, a highly potent BCR-ABL kinase inhibitor, has resulted in high rates of complete cytogenetic response and progression-free survival among patients with chronic myeloid leukemia (CML) in the chronic phase, after failure of imatinib treatment. We assessed the efficacy and safety of dasatinib, as compared with imatinib, for the first-line treatment of chronic-phase CML. Methods In a multinational study, 519 patients with newly diagnosed chronic-phase CML were randomly assigned to receive dasatinib at a dose of 100 mg once daily (259 patients) or imatinib at a dose of 400 mg once daily (260 patients). The primary end point was complete cytogenetic response by 12 months, confirmed on two consecutive assessments at least 28 days apart. Secondary end points, including major molecular response, were tested at a significance level of 0.0001 to adjust for multiple comparisons. Results After a minimum follow-up of 12 months, the rate of confirmed complete cytogenetic response was higher with dasatinib than with imatinib (77% vs. 66%, P = 0.007), as was the rate of complete cytogenetic response observed on at least one assessment (83% vs. 72%, P = 0.001). The rate of major molecular response was higher with dasatinib than with imatinib (46% vs. 28%, P<0.0001), and responses were achieved in a shorter time with dasatinib (P<0.0001). Progression to the accelerated or blastic phase of CML occurred in 5 patients who were receiving dasatinib (1.9%) and in 9 patients who were receiving imatinib (3.5%). The safety profiles of the two treatments were similar. Conclusions Dasatinib, administered once daily, as compared with imatinib, administered once daily, induced significantly higher and faster rates of complete cytogenetic response and major molecular response. Since achieving complete cytogenetic response within 12 months has been associated with better long-term, progression-free survival, dasatinib may improve the long-term outcomes among patients with newly diagnosed chronic-phase CML. (ClinicalTrials.gov number, NCT00481247.)

The sequence and de novo assembly of the giant panda genome

Abstract: Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Circulating microRNA: a novel potential biomarker for early diagnosis of acute myocardial infarction in humans

Abstract: Aims MicroRNA (miRNA) is reported to be present in the blood of humans and has been increasingly suggested as a biomarker for diseases. We aim to determine the potential of cardiac-specific miRNAs in circulation to serve as biomarkers for acute myocardial infarction (AMI). Methods and results By verifying their tissue expression patterns with real-time polymerase chain reaction (PCR) analysis, muscle-enriched miRNAs (miR-1, miR-133a, and miR-499) and cardiac-specific miR-208a were selected as candidates for this study. With miRNA microarray and real-time PCR analyses, miR-1, miR-133a, and miR-499 were present with very low abundance, and miR-208a was absent in the plasma from healthy people. In the AMI rats, the plasma levels of these miRNAs were significantly increased. Especially, miR-208a in plasma was undetected at 0 h, but was significantly increased to a detectable level as early as 1 h after coronary artery occlusion. Further evaluation of the miRNA levels in plasma from AMI patients ( n = 33) demonstrated that all four miRNA levels were substantially higher than those from healthy people ( n = 30, P < 0.01), patients with non-AMI coronary heart disease ( n = 16, P < 0.01), or patients with other cardiovascular diseases ( n = 17, P < 0.01). Notably, miR-208a remained undetectable in non-AMI patients, but was easily detected in 90.9% AMI patients and in 100% AMI patients within 4 h of the onset of symptoms. By receiver operating characteristic curve analysis, among the four miRNAs investigated, miR-208a revealed the higher sensitivity and specificity for diagnosing AMI. Conclusion Elevated cardiac-specific miR-208a in plasma may be a novel biomarker for early detection of myocardial injury in humans.

Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux.

Abstract: Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely unknown. We demonstrated that central metabolism enzymes in Salmonella were acetylated extensively and differentially in response to different carbon sources, concomitantly with changes in cell growth and metabolic flux. The relative activities of key enzymes controlling the direction of glycolysis versus gluconeogenesis and the branching between citrate cycle and glyoxylate bypass were all regulated by acetylation. This modulation is mainly controlled by a pair of lysine acetyltransferase and deacetylase, whose expressions are coordinated with growth status. Reversible acetylation of metabolic enzymes ensure that cells respond environmental changes via promptly sensing cellular energy status and flexibly altering reaction rates or directions. It represents a metabolic regulatory mechanism conserved from bacteria to mammals.

CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer

Abstract: Long non-coding RNA (lncRNA), highly up-regulated in liver cancer (HULC) plays an important role in tumorigenesis. Depletion of HULC resulted in a significant deregulation of several genes involved in liver cancer. Although up-regulation of HULC expression in hepatocellular carcinoma has been reported, the molecular mechanisms remain unknown. In this study, we used in vivo and in vitro approaches to characterize cancer-dependent alterations in the chromatin organization and find a CREB binding site (encompassing from −67 to −53 nt) in the core promoter. Besides, we also provided evidence that PKA pathway may involved in up-regulation of HULC. Furthermore, we demonstrated HULC may act as an endogenous ‘sponge’, which down-regulates a series of microRNAs (miRNAs) activities, including miR-372. Inhibition of miR-372 leads to reducing translational repression of its target gene, PRKACB, which in turn induces phosphorylation of CREB. Over-expression of miR-372 decreases the association of CREB with the proximal promoter, followed by the dissociation of P300, resulting in a change of the histone ‘code’, such as in deacetylation and methylation. The study elucidates that fine tuning of HULC expression is part of an auto-regulatory loop in which it’s inhibitory to expression and activity of miR-372 allows lncRNA up-regulated expression in liver cancer.

Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice

Abstract: Both genetic variations and diet-disrupted gut microbiota can predispose animals to metabolic syndromes (MS). This study assessed the relative contributions of host genetics and diet in shaping the gut microbiota and modulating MS-relevant phenotypes in mice. Together with its wild-type (Wt) counterpart, the Apoa-I knockout mouse, which has impaired glucose tolerance (IGT) and increased body fat, was fed a high-fat diet (HFD) or normal chow (NC) diet for 25 weeks. DNA fingerprinting and bar-coded pyrosequencing of 16S rRNA genes were used to profile gut microbiota structures and to identify the key population changes relevant to MS development by Partial Least Square Discriminate Analysis. Diet changes explained 57% of the total structural variation in gut microbiota, whereas genetic mutation accounted for no more than 12%. All three groups with IGT had significantly different gut microbiota relative to healthy Wt/NC-fed animals. In all, 65 species-level phylotypes were identified as key members with differential responses to changes in diet, genotype and MS phenotype. Most notably, gut barrier-protecting Bifidobacterium spp. were nearly absent in all animals on HFD, regardless of genotype. Sulphate-reducing, endotoxin-producing bacteria of the family, Desulfovibrionaceae, were enhanced in all animals with IGT, most significantly in the Wt/HFD group, which had the highest calorie intake and the most serious MS phenotypes. Thus, diet has a dominating role in shaping gut microbiota and changes of some key populations may transform the gut microbiota of Wt animals into a pathogen-like entity relevant to development of MS, despite a complete host genome.

Synthesis of visible-light responsive graphene oxide/TiO(2) composites with p/n heterojunction.

Abstract: Graphene oxide/TiO2 composites were prepared by using TiCl3 and graphene oxide as reactants. The concentration of graphene oxide in starting solution played an important role in photoelectronic and photocatalytic performance of graphene oxide/TiO2 composites. Either a p-type or n-type semiconductor was formed by graphene oxide in graphene oxide/TiO2 composites. These semiconductors could be excited by visible light with wavelengths longer than 510 nm and acted as sensitizer in graphene oxide/TiO2 composites. Visible-light driven photocatalytic performance of graphene oxide/TiO2 composites in degradation of methyl orange was also studied. Crystalline quality and chemical states of carbon elements from graphene oxide in graphene oxide/TiO2 composites depended on the concentration of graphene oxide in the starting solution. This study shows a possible way to fabricate graphene oxide/semiconductor composites with different properties by using a tunable semiconductor conductivity type of graphene oxide.

Engineering Homochiral Metal-Organic Frameworks for Heterogeneous Asymmetric Catalysis and Enantioselective Separation

Abstract: Owing to the potential applications in technological areas such as gas storage, catalysis, separation, sensing and nonlinear optics, tremendous efforts have been devoted to the development of porous metal-organic frameworks (MOFs) over the past ten years. Homochiral porous MOFs are particularly attractive candidates as heterogeneous asymmetric catalysts and enantioselective adsorbents and separators for production of optically active organic compounds due to the lack of homochiral inorganic porous materials such as zeolites. In this review, we summarize the recent research progress in homochiral MOF materials, including their synthetic strategy, distinctive structural features and latest advances in asymmetric heterogeneous catalysis and enantioselective separation.

A General Framework for a Class of First Order Primal-Dual Algorithms for Convex Optimization in Imaging Science

Abstract: We generalize the primal-dual hybrid gradient (PDHG) algorithm proposed by Zhu and Chan in [An Efficient Primal-Dual Hybrid Gradient Algorithm for Total Variation Image Restoration, CAM Report 08-34, UCLA, Los Angeles, CA, 2008] to a broader class of convex optimization problems. In addition, we survey several closely related methods and explain the connections to PDHG. We point out convergence results for a modified version of PDHG that has a similarly good empirical convergence rate for total variation (TV) minimization problems. We also prove a convergence result for PDHG applied to TV denoising with some restrictions on the PDHG step size parameters. We show how to interpret this special case as a projected averaged gradient method applied to the dual functional. We discuss the range of parameters for which these methods can be shown to converge. We also present some numerical comparisons of these algorithms applied to TV denoising, TV deblurring, and constrained $l_1$ minimization problems.

Arsenic Trioxide Controls the Fate of the PML-RARα Oncoprotein by Directly Binding PML

Abstract: Arsenic, an ancient drug used in traditional Chinese medicine, has attracted worldwide interest because it shows substantial anticancer activity in patients with acute promyelocytic leukemia (APL). Arsenic trioxide (As2O3) exerts its therapeutic effect by promoting degradation of an oncogenic protein that drives the growth of APL cells, PML-RARalpha (a fusion protein containing sequences from the PML zinc finger protein and retinoic acid receptor alpha). PML and PML-RARalpha degradation is triggered by their SUMOylation, but the mechanism by which As2O3 induces this posttranslational modification is unclear. Here we show that arsenic binds directly to cysteine residues in zinc fingers located within the RBCC domain of PML-RARalpha and PML. Arsenic binding induces PML oligomerization, which increases its interaction with the small ubiquitin-like protein modifier (SUMO)-conjugating enzyme UBC9, resulting in enhanced SUMOylation and degradation. The identification of PML as a direct target of As2O3 provides new insights into the drug's mechanism of action and its specificity for APL.

Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization

Abstract: One of the fundamental goals in proteomics and cell biology is to identify the functions of proteins in various cellular organelles and pathways. Information of subcellular locations of proteins can provide useful insights for revealing their functions and understanding how they interact with each other in cellular network systems. Most of the existing methods in predicting plant protein subcellular localization can only cover three or four location sites, and none of them can be used to deal with multiplex plant proteins that can simultaneously exist at two, or move between, two or more different location sites. Actually, such multiplex proteins might have special biological functions worthy of particular notice. The present study was devoted to improve the existing plant protein subcellular location predictors from the aforementioned two aspects. A new predictor called “Plant-mPLoc” is developed by integrating the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition. It can be used to identify plant proteins among the following 12 location sites: (1) cell membrane, (2) cell wall, (3) chloroplast, (4) cytoplasm, (5) endoplasmic reticulum, (6) extracellular, (7) Golgi apparatus, (8) mitochondrion, (9) nucleus, (10) peroxisome, (11) plastid, and (12) vacuole. Compared with the existing methods for predicting plant protein subcellular localization, the new predictor is much more powerful and flexible. Particularly, it also has the capacity to deal with multiple-location proteins, which is beyond the reach of any existing predictors specialized for identifying plant protein subcellular localization. As a user-friendly web-server, Plant-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results. It is anticipated that the Plant-mPLoc predictor as presented in this paper will become a very useful tool in plant science as well as all the relevant areas.

CXCL12 / CXCR4 / CXCR7 chemokine axis and cancer progression.

Abstract: Chemokines, small pro-inflammatory chemoattractant cytokines that bind to specific G-protein-coupled seven-span transmembrane receptors, are major regulators of cell trafficking and adhesion. The chemokine CXCL12 (also called stromal-derived factor-1) is an important α-chemokine that binds primarily to its cognate receptor CXCR4 and thus regulates the trafficking of normal and malignant cells. For many years, it was believed that CXCR4 was the only receptor for CXCL12. Yet, recent work has demonstrated that CXCL12 also binds to another seven-transmembrane span receptor called CXCR7. Our group and others have established critical roles for CXCR4 and CXCR7 on mediating tumor metastasis in several types of cancers, in addition to their contributions as biomarkers of tumor behavior as well as potential therapeutic targets. Here, we review the current concepts regarding the role of CXCL12 / CXCR4 / CXCR7 axis activation, which regulates the pattern of tumor growth and metastatic spread to organs expressing high levels of CXCL12 to develop secondary tumors. We also summarize recent therapeutic approaches to target these receptors and/or their ligands.

A chelator-free multifunctional [64Cu]CuS nanoparticle platform for simultaneous micro-PET/CT imaging and photothermal ablation therapy.

Abstract: We synthesized and evaluated a novel class of chelator-free [(64)Cu]CuS nanoparticles (NPs) suitable both for PET imaging and as photothermal coupling agents for photothermal ablation. These [(64)Cu]CuS NPs are simple to make, possess excellent stability, and allow robust noninvasive micro-PET imaging. Furthermore, the CuS NPs display strong absorption in the near-infrared (NIR) region (peak at 930 nm); passive targeting prefers the tumor site, and mediated ablation of U87 tumor cells occurs upon exposure to NIR light both in vitro and in vivo after either intratumoral or intravenous injection. The combination of small diameter (∼11 nm), strong NIR absorption, and integration of (64)Cu as a structural component makes these [(64)Cu]CuS NPs ideally suited for multifunctional molecular imaging and therapy.

Current status of machine prognostics in condition-based maintenance: a review

Abstract: Condition-based maintenance (CBM) is a decision-making strategy based on real-time diagnosis of impending failures and prognosis of future equipment health. It is a proactive process that requires the development of a predictive model that can trigger the alarm for corresponding maintenance. Prognostic methodologies for CBM have only recently been introduced into the technical literature and become such a focus in the field of maintenance research and development. There are many research and development on a variety of technologies and algorithms that can be regarded as the steps toward prognostic maintenance. They are needed in order to support decision making and manage operational reliability. In this paper, recent literature that focuses on the machine prognostics has been reviewed. Generally, prognostic models can be classified into four categories: physical model, knowledge-based model, data-driven model, and combination model. Various techniques and algorithms have been developed depending on what models they usually adopt. Based on the review of some typical approaches and new introduced methods, advantages and disadvantages of these methodologies are discussed. From the literature review, some increasing trends appeared in the research field of machine prognostics are summarized. Furthermore, the future research directions have been explored.

European Society of Hypertension International Protocol revision 2010 for the validation of blood pressure measuring devices in adults

Abstract: The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland, dabl Ltd., Blackrock Co., Dublin, Ireland, Hypertension Center, Third University Department of Medicine, Sotiria Hospital, Athens, Greece, Istituto Scientifico Ospedale San Luca, IRCCS, Instituto Auxologico Italiano, Milan, Italy, Societe Francaise d’Hypertension Arterielle, Filiale de la Societe Francaise de Cardiolgie, Paris, France, The Department of Clinical Pharmacology and Therapeutics, Tohoku University Graduate School of Pharmaceutical Science and Medicine, Sendai, Japan, Centre for Epidemiological Studies and Clinical Trials, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China, University Clinic Bonn, Department of Internal Medicine, Bonn, Germany and Guy’s and St Thomas’ Hospitals, London, UK

Inflammatory Cytokine-Induced Intercellular Adhesion Molecule-1 and Vascular Cell Adhesion Molecule-1 in Mesenchymal Stem Cells Are Critical for Immunosuppression

Abstract: Cell–cell adhesion mediated by ICAM-1 and VCAM-1 is critical for T cell activation and leukocyte recruitment to the inflammation site and, therefore, plays an important role in evoking effective immune responses. However, we found that ICAM-1 and VCAM-1 were critical for mesenchymal stem cell (MSC)-mediated immunosuppression. When MSCs were cocultured with T cells in the presence of T cell Ag receptor activation, they significantly upregulated the adhesive capability of T cells due to the increased expression of ICAM-1 and VCAM-1. By comparing the immunosuppressive effect of MSCs toward various subtypes of T cells and the expression of these adhesion molecules, we found that the greater expression of ICAM-1 and VCAM-1 by MSCs, the greater the immunosuppressive capacity that they exhibited. Furthermore, ICAM-1 and VCAM-1 were found to be inducible by the concomitant presence of IFN-γ and inflammatory cytokines (TNF-α or IL-1). Finally, MSC-mediated immunosuppression was significantly reversed in vitro and in vivo when the adhesion molecules were genetically deleted or functionally blocked, which corroborated the importance of cell–cell contact in immunosuppression by MSCs. Taken together, these findings reveal a novel function of adhesion molecules in immunoregulation by MSCs and provide new insights for the clinical studies of antiadhesion therapies in various immune disorders.

Towards multifunctional, targeted drug delivery systems using mesoporous silica nanoparticles – opportunities & challenges

Abstract: One of the big challenges of medicine today is to deliver drugs specifically to defected cells. Nanoparticulate drug carriers have the potential to answer to this call, as nanoparticles can cross physiological barriers and access different tissues, and also be provided in a targetable form aimed at enhancing cell specificity of the carrier. Recent developments within material science and strong collaborative efforts crossing disciplinary borders have highlighted the potential of mesoporous silica nanoparticles (MSNs) for such targeted drug delivery. Here we outline recent advances which in this sense push MSNs to the forefront of drug delivery development. Relatively straightforward inside-out tuning of the vehicles, high flexibility, and potential for sophisticated release mechanisms make these nanostructures promising candidates for targeted drug delivery such as ‘smart’ cancer therapies. Moreover, due to the large surface area and the controllable surface functionality of MSNs, they can be controllably loaded with large amounts of drugs and coupled to homing molecules to facilitate active targeting, simultaneously carrying traceable (fluorescent or magnetically active) modalities, also making them highly interesting as theragnostic agents. However, the increased relative surface area and small size, and flexible surface functionalization which is beneficially exploited in nanomedicine, consequently also includes potential risks in their interactions with biological systems. Therefore, we also discuss some safety issues regarding MSNs and highlight how different features of the drug delivery platform influence their behaviour in a biological setting. Addressing these burning questions will facilitate the application of MSNs in nanomedicine.

Self‐Assembly of Hyperbranched Polymers and Its Biomedical Applications

Abstract: Hyperbranched polymers (HBPs) are highly branched macromolecules with a three-dimensional dendritic architecture. Due to their unique topological structure and interesting physical/chemical properties, HBPs have attracted wide attention from both academia and industry. In this paper, the recent developments in HBP self-assembly and their biomedical applications have been comprehensively reviewed. Many delicate supramolecular structures from zero-dimension (0D) to three-dimension (3D), such as micelles, fibers, tubes, vesicles, membranes, large compound vesicles and physical gels, have been prepared through the solution or interfacial self-assembly of amphiphilic HBPs. In addition, these supramolecular structures have shown promising applications in the biomedical areas including drug delivery, protein purification/detection/delivery, gene transfection, antibacterial/antifouling materials and cytomimetic chemistry. Such developments promote the interdiscipline researches among surpramolecular chemistry, biomedical chemistry, nano-technology and functional materials.

Graphene Oxide as a Matrix for Enzyme Immobilization

Abstract: Graphene oxide (GO), having a large specific surface area and abundant functional groups, provides an ideal substrate for study enzyme immobilization. We demonstrated that the enzyme immobilization on the GO sheets could take place readily without using any cross-linking reagents and additional surface modification. The atomically flat surface enabled us to observe the immobilized enzyme in the native state directly using atomic force microscopy (AFM). Combining the AFM imaging results of the immobilized enzyme molecules and their catalytic activity, we illustrated that the conformation of the immobilized enzyme is mainly determined by interactions of enzyme molecules with the functional groups of GO.

First Dark Matter Results from the XENON100 Experiment

Abstract: The XENON100 experiment, in operation at the Laboratori Nazionali del Gran Sasso in Italy, is designed to search for dark matter weakly interacting massive particles (WIMPs) scattering off 62 kg of liquid xenon in an ultralow background dual-phase time projection chamber. In this Letter, we present first dark matter results from the analysis of 11.17 live days of nonblind data, acquired in October and November 2009. In the selected fiducial target of 40 kg, and within the predefined signal region, we observe no events and hence exclude spin-independent WIMP-nucleon elastic scattering cross sections above 3.4 × 10⁻⁴⁴ cm² for 55 GeV/c² WIMPs at 90% confidence level. Below 20 GeV/c², this result constrains the interpretation of the CoGeNT and DAMA signals as being due to spin-independent, elastic, light mass WIMP interactions.