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Biomedical subjects

Yong Zhang

Publications and source records attributed to Yong Zhang.

At least 73 records · Page 4Linked to original sources
PubMed2006

Protoplast fusion between Geotrichum candidium and Phanerochaete chrysosporium to produce fusants for corn stover fermentation.

Lignin impedes the digestion of corn stover when used as an animal feed. Phanerochaete chrysosporium is an efficient lignindegrader. Geotrichum candidum can be used to produce single-cell protein. In this study, protoplasts of the two fungi were prepared and fused. After screening, one of the fusants, Fusant R1, was selected for corn stover fermentation. It decreased lignin from 109 to 54 g/kg and increased protein from 48 to 67 g/kg in corn stover. Comparison with their parental strains indicated that the fusant obtained the lignin-degrading ability from P. chrysosporium and the protein-accumulating ability from G. candidium.

Biomass↗
PubMed2006

WEGO: a web tool for plotting GO annotations.

Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at http://wego.genomics.org.cn. There are two available mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn. Any suggestions are welcome at wego@genomics.org.cn.

Genes↗
PubMed2006

Phospholipase C-beta3 and -beta1 form homodimers, but not heterodimers, through catalytic and carboxyl-terminal domains.

Phospholipase C-beta (PLC-beta) isoenzymes are key effectors in G protein-coupled signaling pathways. Prior research suggests that some isoforms of PLC-beta may exist and function as dimers. Using coimmunoprecipitation assays of differentially tagged PLC-beta constructs and size-exclusion chromatography of native PLC-beta, we observed homodimerization of PLC-beta3 and PLC-beta1 isoenzymes but failed to detect heterodimerization of these isoenzymes. Size-exclusion chromatography data suggest that PLC-beta3 and PLC-beta1 form higher affinity homodimers than PLC-beta2. Evidence supportive of limited PLC-beta monomer-homodimer equilibrium appears at < or =100 nM. Further assessment of homodimerization status by coimmunoprecipitation assays with differentially tagged PLC-beta3 fragments demonstrated that at least two subdomains of PLC-beta3 are involved in dimer formation, one in the catalytic X and Y domains and the other in the G protein-regulated carboxyl-terminal domain. In addition, we provide evidence consistent with the existence of PLC-beta homodimers in a whole-cell context, using fluorescent protein-tagged constructs and microscopic fluorescence resonance energy transfer assays.

Animals↗
PubMed2006

Surface freezing in normal alkanes: a statistical physics approach.

The present paper aims to understand the surface freezing occurring on the interface between liquid normal alkane and air. After proposing a simple microscopic model, it reveals that the model can describe the surface freezing of normal alkanes. Subsequently, surface freezing is immediately proved to be a first order phase transition, which has been illustrated by numerous experiments. Moreover, our calculation predicts a new first order phase transition on the interface. These two transitions correspond to the liquid to monolayer and monolayer to perfect solid transitions, respectively. A phase diagram is obtained directly from the calculations as well. The model indicates that both van der Waals interaction and the entropy influenced by the surface are essential for explaining the surface phase transition.

Journal Article↗
PubMed2006

Construction of [(eta5-C5Me5)WS3Cu3]-based supramolecular compounds from preformed incomplete cubane-like clusters [PPh4][(eta5-C5Me5)WS3(CuX)3] (X = CN, Br).

Approaches to the assembly of (eta5-C5Me5)WS3Cu3-based supramolecular compounds from two preformed incomplete cubane-like clusters [PPh4][(eta5-C5Me5)WS3(CuX)3] (X = CN, 1a; X = Br, 1b) have been investigated. Treatment of 1a with LiBr/1,4-pyrazine (1,4-pyz), pyridine (py), LiCl/py, or 4,4'-bipyridine (4,4'-bipy) and treatment of 1b with 4,4'-bipy gave rise to a new set of W/Cu/S cluster-based compounds, [Li[((eta5-C5Me5)WS3Cu3(mu3-Br))2(mu-CN)3].C6H6]infinity (2), [(eta5-C5Me5)WS3Cu3(mu-CN)2(py)]infinity (3), [[PPh4][(eta5-C5Me5)WS3Cu3(mu3-Cl)(mu-CN)(CN)].py]infinity (4), [PPh4]2[(eta5-C5Me5)WS3Cu3(CN)2]2(mu-CN)2.(4,4'-bipy) (5), and [[(eta5-C5Me5)WS3Cu3Br(mu-Br)(4,4'-bipy)].Et2O]infinity (6). The structures of 2-6 have been characterized by elemental analysis, IR spectra, and single-crystal X-ray crystallography. Compound 2 displays a 1D ladder-shaped chain structure built of square-like [[(eta5-C5Me5)WS3Cu3(mu3-Br)(mu-CN)]4](mu-CN)2(2-) anions via two pairs of Cu-mu-CN-Cu bridges. Compound 3 consists of a single 3D diamond-like network in which each (eta5-C5Me5)WS3Cu3 unit, serving as a tetrahedral node, interconnects with four other nearby units through Cu-mu-CN-Cu bridges. Compound 4 contains a 1D zigzag chain array made of cubane-like [(eta5-C5Me5)WS3Cu3(mu3-Cl)(mu-CN)(CN)]- anions linked by a couple of Cu-mu-CN-Cu bridges. Compound 5 contains a dimeric structure in which the two incomplete cubane-like [(eta5-C5Me5)WS3(CuCN)2(mu-CN)]- anions are strongly held together via a pair of Cu-mu-CN-Cu bridges. Compound 6 contains a 2D brick-wall layer structure in which dimers of [(eta5-C5Me5)WS3Cu3Br(4,4'-bipy)]2 are interconnected via four Cu-mu-Br-Cu bridges. The successful construction of (eta5-C5Me5)WS3Cu3-based supramolecular compounds 2-6 from the geometry-fixed clusters 1a and 1b may expand the scope of the rational design and construction of cluster-based supramolecular assemblies.

Copper↗
PubMed2006

Dynamic changes in subgraph preference profiles of crucial transcription factors.

Transcription factors with a large number of target genes--transcription hub(s), or THub(s)--are usually crucial components of the regulatory system of a cell, and the different patterns through which they transfer the transcriptional signal to downstream cascades are of great interest. By profiling normalized abundances (A(N)) of basic regulatory patterns of individual THubs in the yeast Saccharomyces cerevisiae transcriptional regulation network under five different cellular states and environmental conditions, we have investigated their preferences for different basic regulatory patterns. Subgraph-normalized abundances downstream of individual THubs often differ significantly from that of the network as a whole, and conversely, certain over-represented subgraphs are not preferred by any THub. The THub preferences changed substantially when the cellular or environmental conditions changed. This switching of regulatory pattern preferences suggests that a change in conditions does not only elicit a change in response by the regulatory network, but also a change in the mechanisms by which the response is mediated. The THub subgraph preference profile thus provides a novel tool for description of the structure and organization between the large-scale exponents and local regulatory patterns.

Cell Cycle↗
PubMed2006

Efforts toward developing direct probes of protein dynamics.

We report the first IR characterization of a single C-D bond within a protein, methyl-d1 Met80 of horse heart cytochrome c. A comparison was made to methyl-d1/d3 methionine as well as methyl-d3 Met80. We found that for methyl-d1 and the asymmetric stretches of methyl-d3, line widths/line shapes are dominated by inhomogeneous broadening, whereas the symmetric stretch of methyl-d3 has a significant homogeneous component. Vibrational energy relaxation calculations found that a significantly stronger Fermi resonance exists for the symmetric stretch than for the asymmetric stretches, thereby suggesting that a difference in intramolecular vibrational relaxation (IVR) causes the observed line width/line shape difference between the symmetric and asymmetric stretches.

Animals↗
PubMed2006

Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.

BACKGROUND: As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective. RESULTS: We reconstructed phylophenetic trees for all available metabolic pathways based on topological similarities, and compared them to the corresponding 16S rRNA-based trees. Similarity values for each pair of trees ranged from 0.044 to 0.297. Using the quartet method, single pathways trees were merged into a comprehensive tree containing information from a large part of the entire metabolic networks. This tree showed considerably higher similarity (0.386) to the corresponding 16S rRNA-based tree than any tree based on a single pathway, but was, on the other hand, sufficiently distinct to preserve unique phylogenetic information not reflected by the 16S rRNA tree. CONCLUSION: We observed that the topology of different metabolic pathways provided different phylogenetic and phenetic information, depicting the compromise between phylogenetic information and varying evolutionary pressures forming metabolic pathway topologies in different organisms. The phylogenetic information content of the comprehensive tree is substantially higher than that of any tree based on a single pathway, which also gave clues to constraints working on the topology of the global metabolic networks, information that is only partly reflected by the topologies of individual metabolic pathways.

Chromosome Mapping↗
PubMed2006

Integrated analysis of multiple data sources reveals modular structure of biological networks.

It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks.

Algorithms↗
PubMed2006

Syndecan-1 and syndecan-4 are overexpressed in an estrogen receptor-negative, highly proliferative breast carcinoma subtype.

Members of the syndecan and glypican families of cell surface heparan sulfate proteoglycans (HSPGs) are modulators of growth factor signaling and cell adhesion. Both loss and gain in expression of syndecans and glypicans has been associated with malignant progression. The goal of this project was to investigate a possible relationship between expression of cell surface HSPGs (syndecan-1, syndecan-4 and glypican-1) and established prognostic factors or clinical outcome in breast carcinomas. Tissue arrays containing 207 human breast carcinoma samples in duplicate were immuno-labeled with antibodies to syndecan-1, syndecan-4, glypican-1, Ki67, E-cadherin, estrogen receptor (ER) and progesterone receptor (PR). Clinical follow-up information was available for up to 18.6 years (median follow-up 6.2 years). Syndecan-1 and syndecan-4 expression in carcinoma cells ranged from complete loss to high expression, but glypican-1 was detected only in a small subset of breast carcinomas. Expression of all three HSPGs was significantly associated with the Ki67 proliferation index (syndecan-1: p=0.0025; syndecan-4: p<0.0001; glypican-1 p=0.01). Syndecan-1 and syndecan-4 expression correlated with ER negativity, grade, and size of the primary tumors. Syndecan-1 expression (but not syndecan-4 nor glypican-1) predicted patient outcome (DFS: p=0.0054; OS: p=0.0086). However, multivariate analysis failed to identify syndecan-1 as an independent prognostic marker, which was due to its significant association with established prognostic factors. The strong association between cell surface HSPGs and the Ki67 proliferation marker would support a biologic role in carcinoma growth regulation. Furthermore, the close correlation between syndecan expression and negative ER status raises the possibility of hormonal regulation or more likely an association with an aggressive, ER-negative carcinoma phenotype.

Adult↗
PubMed2006

Cellular autophagy machinery is not required for vaccinia virus replication and maturation.

The origin of the primary membrane of the vaccinia virus, a double-membrane structure that surrounds the immature virions (IV), is not fully understood. Here we investigated whether the primary membrane originates from the autophagic membrane. Morphologic studies by electron microscopy (EM) showed no apparent difference in viral maturation in the autophagy-deficient cell lines, the atg5(-/-) mouse embryonic fibroblasts (MEFs) and the beclin1(-/-) embryonic stem (ES) cells, compared to their isogenic wild-type counterparts. Moreover, viral growth curves demonstrated that vaccinia viruses replicate and mature in the autophagy-deficient cell lines as efficiently as they do in their isogenic wild type counterpart cells. This study indicates that the cellular autophagy machinery is not required for the life-cycle of vaccinia virus, suggesting that the primary vaccinia viral membrane does not originate from the autophagic membrane.

Animals↗
PubMed2006

Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins.

Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a time-dependent perturbation theory. The system-bath Hamiltonian contains more than the third order coupling terms since we take a normal mode picture as a zeroth order approximation. When we invoke the Markov approximation, our theory reduces to the Maradudin-Fein formula which is used to describe the VER properties of glass and proteins. When the system anharmonicity and the renormalization effect due to the environment vanishes, our formulas reduce to those derived by and Mikami and Okazaki [J. Chem. Phys. 121, 10052 (2004)] invoking the path-integral influence functional method with the second order cumulant expansion. We apply our formulas to VER of the amide I mode of a small amino-acid like molecule, N-methylacetamide, in heavy water.

Amides↗
PubMed2006

Synthesis of homopolymer containing diphenyl end-capped oligothiophene co-oligomer unit in the side chain.

[reaction: see text] A new polymer with the diphenyl end-capped oligothiophene co-oligomer unit in the side chain was obtained by the ROMP method. The polymer showed good photophysical characteristics, thermal stability, and film-forming properties. A photovoltaic cell fabricated from this polymer showed relatively large open-circuit voltage (V(OC) = 0.7 V), moderate short-circuit current (I(SC) = 0.7 microA/cm(2)), and excellent device stability under ambient conditions.

Journal Article↗
PubMed2006

A mammalian organelle map by protein correlation profiling.

Protein localization to membrane-enclosed organelles is a central feature of cellular organization. Using protein correlation profiling, we have mapped 1,404 proteins to ten subcellular locations in mouse liver, and these correspond with enzymatic assays, marker protein profiles, and confocal microscopy. These localizations allowed assessment of the specificity in published organellar proteomic inventories and demonstrate multiple locations for 39% of all organellar proteins. Integration of proteomic and genomic data enabled us to identify networks of coexpressed genes, cis-regulatory motifs, and putative transcriptional regulators involved in organelle biogenesis. Our analysis ties biochemistry, cell biology, and genomics into a common framework for organelle analysis.

Animals↗
PubMed2006

Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication.

BACKGROUND: Staphylococcus aureus or MRSA (Methicillin Resistant S. aureus), is an acquired pathogen and the primary cause of nosocomial infections worldwide. In S. aureus, teichoic acid is an essential component of the cell wall, and its biosynthesis is not yet well characterized. Studies in Bacillus subtilis have discovered two different pathways of teichoic acid biosynthesis, in two strains W23 and 168 respectively, namely teichoic acid ribitol (tar) and teichoic acid glycerol (tag). The genes involved in these two pathways are also characterized, tarA, tarB, tarD, tarI, tarJ, tarK, tarL for the tar pathway, and tagA, tagB, tagD, tagE, tagF for the tag pathway. With the genome sequences of several MRSA strains: Mu50, MW2, N315, MRSA252, COL as well as methicillin susceptible strain MSSA476 available, a comparative genomic analysis was performed to characterize teichoic acid biosynthesis in these S. aureus strains. RESULTS: We identified all S. aureus tar and tag gene orthologs in the selected S. aureus strains which would contribute to teichoic acids sythesis. Based on our identification of genes orthologous to tarI, tarJ, tarL, which are specific to tar pathway in B. subtilis W23, we also concluded that tar is the major teichoic acid biogenesis pathway in S. aureus. Further analyses indicated that the S. aureus tar genes, different from the divergon organization in B. subtilis, are organized into several clusters in cis. Most interesting, compared with genes in B. subtilis tar pathway, the S. aureus tar specific genes (tarI,J,L) are duplicated in all six S. aureus genomes. CONCLUSION: In the S. aureus strains we analyzed, tar (teichoic acid ribitol) is the main teichoic acid biogenesis pathway. The tar genes are organized into several genomic groups in cis and the genes specific to tar (relative to tag): tarI, tarJ, tarL are duplicated. The genomic organization of the S. aureus tar pathway suggests their regulations are different when compared to B. subtilis tar or tag pathway, which are grouped in two operons in a divergon structure.

Amino Acid Sequence↗
PubMed2006

Interaction of SH2-Bbeta with RET is involved in signaling of GDNF-induced neurite outgrowth.

RET receptor signalling is essential for glial-cell-line-derived neurotrophic factor (GDNF)-induced survival and differentiation of various neurons such as mesencephalic neurons. To identify proteins that mediate RET-dependent signaling, yeast two-hybrid screening was performed with the intracellular domain of RET as bait. We identified a new interaction between RET and the adapter protein SH2-Bbeta. Upon GDNF stimulation of PC12-GFRalpha1-RET cells (that stably overexpress GDNF receptor alpha1 and RET), wild-type SH2-Bbeta co-immunoprecipitated with RET, whereas the dominant-negative SH2-Bbeta mutant R555E did not. RET interacted with endogenous SH2-Bbeta both in PC12-GFRalpha1-RET cells and in rat tissues. Mutagenesis analysis revealed that Tyr981 within the intracellular domain of RET was crucial for the interaction with SH2-Bbeta. Morphological evidence showed that SH2-Bbeta and RET colocalized in mesencephalic neurons. Furthermore, functional analysis indicated that overexpression of SH2-Bbeta facilitated GDNF-induced neurite outgrowth in both PC12-GFRalpha1-RET cells and cultured mesencephalic neurons, whereas the mutant R555E inhibited the effect. Moreover, inhibition of SH2-Bbeta expression by RNA interference caused a significant decrease of GDNF-induced neuronal differentiation in PC12-GFRalpha1-RET cells. Taken together, our results suggest that SH2-Bbeta is a new signaling molecule involved in GDNF-induced neurite outgrowth.

Adaptor Proteins, Signal Transducing↗