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Correlation-induced anomalies and extreme sensitivity in fcc-PU1

Description: We have used GGA + U density functional theory to study the effects of correlation on the properties offcc-Pu. We found that the structural and elastic properties offcc-Pu are highly sensitive to the Hubbard U parameter. Within an interval of 0.1 eV ofthe U parameter, the equilibrium lattice constants offcc-Pu can change from 0.44 to 0.47 nm. While the bulk modulus can drop by a factor of5 to 10. The pressure derivative, dB/dp, ofthe bulk modulus can rise dramatically from 5 to 16 and then drop to a negative value before recovering to a more normal value. These observations are partially supported by existing experiments and the prediction of a negative dB/dp needs to be tested in future experiments.
Date: January 1, 2009
Creator: Chen, Shao-ping
Partner: UNT Libraries Government Documents Department

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

Description: RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.
Date: May 26, 2010
Creator: Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S. et al.
Partner: UNT Libraries Government Documents Department

Replica Registration Service - Functional Interface Specification1.0

Description: The goal of the Replica Registration Service (RRS) is toprovide a uniform interface to various file catalogs, replica catalogs,and metadata catalogs. It can be thought of as an abstraction of theconcepts used in such systems to register files and their replicas. Someexperiments may prefer to support their own file catalogs (which may havetheir own specialized structures, semantics, and implementations) ratherthan use a standard replica catalog. Providing an RRS that can interactwith such a catalog (for example by invoking a script) can permit thatcatalog to be invoked as a service in the same way that other replicacatalogs do. If at a later time the experiment wishes to change toanother file catalog or an RLS, it is only a matter of developing an RRSfor that new catalog and replacing the existing catalog. In addition,some systems use metadata catalogs or other catalogs to manage the filename spaces. Our goal is to provide a single interface that supports theregistration of files into such name spaces as well as retrieving thisinformation.
Date: February 28, 2005
Creator: Shoshani, Arie; Sim, Alex & Stockinger, Kurt
Partner: UNT Libraries Government Documents Department

Butt Joint Tool Status: ITER-US-LLNL-NMARTOVETSKY-01312007

Description: Butt joint tool vacuum vessel has been built at C&H Enterprise, Inc. Leak checking and loading tests were taken place at the factory. The conductor could not be pumped down better than to 500 mtorr and therefore we could not check the sealing mechanism of the seal around conductor. But the rest of the vessel, including the flat gasket, one of the difficult seals worked well, no indication of leak at sensitivity 1e-7 l*torr/sec. The load test showed fully functional system of the load mechanism. The conductors were loaded up to 2200 kgf (21560 N) and the pressure between the butts was uniform with 100% of the contact proved by pressure sensitive film. The status of the butt joint tool development is reported.
Date: February 1, 2007
Creator: Martovetsky, N N
Partner: UNT Libraries Government Documents Department

Integration of Phenotypic Metadata and Protein Similarity in Archaea Using a Spectral Bipartitioning Approach

Description: In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. However, it quickly becomes clear that the sequence flexibility allowed a given protein varies significantly among different protein families. The degree to which sequences are conserved not only differs for each protein family, but also is affected by the phylogenetic divergence of the source organisms. Clustering techniques that use similarity thresholds for protein families do not always allow for these variations and thus cannot be confidently used for applications such as automated annotation and phylogenetic profiling. In this work, we applied a spectral bipartitioning technique to all proteins from 53 archaeal genomes. Comparisons between different taxonomic levels allowed us to study the effects of phylogenetic distances on cluster structure. Likewise, by associating functional annotations and phenotypic metadata with each protein, we could compare our protein similarity clusters with both protein function and associated phenotype. Our clusters can be analyzed graphically and interactively online.
Date: January 1, 2009
Creator: Hooper, Sean D.; Anderson, Iain J; Pati, Amrita; Dalevi, Daniel; Mavromatis, Konstantinos & Kyrpides, Nikos C
Partner: UNT Libraries Government Documents Department

Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections

Description: We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, {omega}B97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, {omega}B97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as {omega}B97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.
Date: June 14, 2008
Creator: Chai, Jeng-Da & Head-Gordon, Martin
Partner: UNT Libraries Government Documents Department

Primate-Specific Evolution of an LDLR Enhancer

Description: Sequence changes in regulatory regions have often beeninvoked to explain phenotypic divergence among species, but molecularexamples of this have been difficult to obtain. In this study, weidentified an anthropoid primate specific sequence element thatcontributed to the regulatory evolution of the LDL receptor. Using acombination of close and distant species genomic sequence comparisonscoupled with in vivo and in vitro studies, we show that a functionalcholesterol-sensing sequence motif arose and was fixed within apre-existing enhancer in the common ancestor of anthropoid primates. Ourstudy demonstrates one molecular mechanism by which ancestral mammalianregulatory elements can evolve to perform new functions in the primatelineage leading to human.
Date: June 28, 2006
Creator: Wang, Qian-fei; Prabhakar, Shyam; Wang, Qianben; Moses, Alan M.; Chanan, Sumita; Brown, Myles et al.
Partner: UNT Libraries Government Documents Department

Gaining analytic control of parton showers

Description: Parton showers are widely used to generate fully exclusive final states needed to compare theoretical models to experimental observations. While, in general, parton showers give a good description of the experimental data, the precise functional form of the probability distribution underlying the event generation is generally not known. The reason is that realistic parton showers are required to conserve four-momentum at each vertex. In this paper we investigate in detail how four-momentum conservation is enforced in a standard parton shower and why this destroysthe analytic control of the probability distribution. We show how to modify a parton shower algorithm such that it conserves four-momentum at each vertex, but for which the full analytic form of the probability distribution is known. We then comment how this analytic control can be used to match matrix element calculations with parton showers, and to estimate effects of power corrections and other uncertainties in parton showers.
Date: May 14, 2007
Creator: Tackmann, Frank; Bauer, Christian W. & Tackmann, Frank J.
Partner: UNT Libraries Government Documents Department

Time-periodic solutions of the Benjamin-Ono equation

Description: We present a spectrally accurate numerical method for finding non-trivial time-periodic solutions of non-linear partial differential equations. The method is based on minimizing a functional (of the initial condition and the period) that is positive unless the solution is periodic, in which case it is zero. We solve an adjoint PDE to compute the gradient of this functional with respect to the initial condition. We include additional terms in the functional to specify the free parameters, which, in the case of the Benjamin-Ono equation, are the mean, a spatial phase, a temporal phase and the real part of one of the Fourier modes at t = 0. We use our method to study global paths of non-trivial time-periodic solutions connecting stationary and traveling waves of the Benjamin-Ono equation. As a starting guess for each path, we compute periodic solutions of the linearized problem by solving an infinite dimensional eigenvalue problem in closed form. We then use our numerical method to continue these solutions beyond the realm of linear theory until another traveling wave is reached (or until the solution blows up). By experimentation with data fitting, we identify the analytical form of the solutions on the path connecting the one-hump stationary solution to the two-hump traveling wave. We then derive exact formulas for these solutions by explicitly solving the system of ODE's governing the evolution of solitons using the ansatz suggested by the numerical simulations.
Date: April 1, 2008
Creator: Ambrose , D.M. & Wilkening, Jon
Partner: UNT Libraries Government Documents Department

Primate-specific evolution of an LDLR enhancer

Description: Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. In this study we identified an anthropoid primate-specific sequence element that contributed to the regulatory evolution of the low-density lipoprotein receptor. Using a combination of close and distant species genomic sequence comparisons coupled with in vivo and in vitro studies, we found that a functional cholesterol-sensing sequence motif arose and was fixed within a pre-existing enhancer in the common ancestor of anthropoid primates. Our study demonstrates one molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions in the primate lineage leading to human.
Date: December 1, 2005
Creator: Wang, Qian-Fei; Prabhakar, Shyam; Wang, Qianben; Moses, Alan M.; Chanan, Sumita; Brown, Myles et al.
Partner: UNT Libraries Government Documents Department

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

Description: Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.
Date: September 1, 2006
Creator: Kunin, Victor; Sorek, Rotem & Hugenholtz, Philip
Partner: UNT Libraries Government Documents Department

Transitive closure and metric inequality of weighted graphs:detecting protein interaction modules using cliques

Description: We study transitivity properties of edge weights in complex networks. We show that enforcing transitivity leads to a transitivity inequality which is equivalent to ultra-metric inequality. This can be used to define transitive closure on weighted undirected graphs, which can be computed using a modified Floyd-Warshall algorithm. We outline several applications and present results of detecting protein functional modules in a protein interaction network.
Date: June 2, 2006
Creator: Ding, Chris; He, Xiaofeng; Xiong, Hui; Peng, Hanchuan & Holbrook,Stephen R.
Partner: UNT Libraries Government Documents Department

Advanced Lost Foam Casting Technology - Phase V

Description: Previous research, conducted under DOE Contracts DE-FC07-89ID12869, DE-FC07-93ID12230 and DE-FC07-95ID113358 made significant advances in understanding the Lost Foam Casting (LFC) Process and clearly identified areas where additional developments were needed to improve the process and make it more functional in industrial environments. The current project focused on eight tasks listed as follows: Task 1--Computational Model for the Process and Data Base to Support the Model; Task 2--Casting Dimensional Accuracy; Task 3--Pattern Production; Task 4--Improved Pattern Materials; Task 5--Coating Control; Task 6--In-Plant Case Studies; Task 7--Energy and the Environmental Data; and Task 8--Technology Transfer. This report summarizes the work done on all tasks in the period of October 1, 1999 through September 30, 2004. The results obtained in each task and subtask are summarized in this Executive Summary and details are provided in subsequent sections of the report.
Date: April 29, 2004
Creator: Sun, Wanliang; Littleton, Harry E. & Bates, Charles E.
Partner: UNT Libraries Government Documents Department

Density functional theory study of the structural, electronic, lattice dynamical, and thermodynamic properties of Li4SiO4 and its capability for CO2 capture

Description: The structural, electronic, lattice dynamical, optical, thermodynamic, and CO{sub 2} capture properties of monoclinic and triclinic phases of Li{sub 4}SiO{sub 4} are investigated by combining density functional theory with phonon lattice dynamics calculations. We found that these two phases have some similarities in their bulk and thermodynamic properties. The calculated bulk modulus and the cohesive energies of these two phases are close to each other. Although both of them are insulators, the monoclinic phase of Li{sub 4}SiO{sub 4} has a direct band gap of 5.24 eV while the triclinic Li{sub 4}SiO{sub 4} phase has an indirect band gap of 4.98 eV. In both phases of Li{sub 4}SiO{sub 4}, the s orbital of O mainly contributes to the lower-energy second valence band (VB{sub 2}) and the p orbitals contribute to the fist valence band (VB{sub 1}) and the conduction bands (CBs). The s orbital of Si mainly contributes to the lower portions of the VB1 and VB{sub 2}, and Si p orbitals mainly contribute to the higher portions of the VB{sub 1} and VB{sub 2}. The s and p orbitals of Li contribute to both VBs and to CBs, and Li p orbitals have a higher contribution than the Li s orbital. There is possibly a phonon soft mode existing in triclinic {gamma}-Li{sub 4}SiO{sub 4}; in the monoclinic Li{sub 4}SiO{sub 4}, there are three phonon soft modes, which correspond to the one type of Li disordered over a few sites. Their LO-TO splitting indicates that both phases of Li{sub 4}SiO{sub 4} are polar anisotropic materials. The calculated infrared absorption spectra for LO and TO modes are different for these two phases of Li{sub 4}SiO{sub 4}. The calculated relationships of the chemical potential versus temperature and CO{sub 2} pressure for reaction of Li{sub 4}SiO{sub 4} with CO{sub 2} shows that Li{sub 4}SiO{sub ...
Date: January 1, 2011
Creator: Duan, Yuhua & Parlinski, K.
Partner: UNT Libraries Government Documents Department

Large-scale turnover of functional transcription factor bindingsites in Drosophila

Description: The gain and loss of functional transcription-factor bindingsites has been proposed as a major source of evolutionary change incis-regulatory DNA and gene expression. We have developed an evolutionarymodel to study binding site turnover that uses multiple sequencealignments to assess the evolutionary constraint on individual bindingsites, and to map gain and loss events along a phylogenetic tree. Weapply this model to study the evolutionary dynamics of binding sites ofthe Drosophila melanogaster transcription factor Zeste, using genome-widein vivo (ChIP-chip) binding data to identify functional Zeste bindingsites, and the genome sequences of D. melanogaster, D. simulans, D.erecta and D. yakuba to study their evolution. We estimate that more than5 percent of functional Zeste binding sites in D. melanogaster weregained along the D. melanogaster lineage or lost along one of the otherlineages. We find that Zeste bound regions have a reduced rate of bindingsite loss and an increased rate of binding site gain relative to flankingsequences. Finally, we show that binding site gains and losses areasymmetrically distributed with respect to D. melanogaster, consistentwith lineage-specific acquisition and loss of Zeste-responsive regulatoryelements.
Date: July 14, 2006
Creator: Moses, Alan M.; Pollard, Daniel A.; Nix, David A.; Iyer, VenkyN.; Li, Xiao-Yong; Biggin, Mark D. et al.
Partner: UNT Libraries Government Documents Department

Telomere dysfunction and cell survival: Roles for distinct TIN2-containing complexes

Description: Telomeres are maintained by three DNA binding proteins (TRF1, TRF2 and POT1), and several associated factors. One factor, TIN2, binds TRF1 and TRF2 directly and POT1 indirectly. Along with two other proteins, TPP1 and hRap1, these form a soluble complex that may be the core telomere maintenance complex. It is not clear whether sub-complexes also exist in vivo. We provide evidence for two TIN2 sub-complexes with distinct functions in human cells. We isolated these two TIN2 sub-complexes from nuclear lysates of unperturbed cells and cells expressing TIN2 mutants TIN2-13, TIN2-15C, which cannot bind TRF2 or TRF1, respectively. In cells with wild-type p53 function, TIN2-15C was more potent than TIN2-13 in causing telomere uncapping and eventual growth arrest. In cells lacking p53 function, TIN2-15C was more potent than TIN2-13 in causing telomere dysfunction and cell death. Our findings suggest that distinct TIN2 complexes exist, and that TIN2-15C-sensitive subcomplexes are particularly important for cell survival in the absence of functional p53.
Date: October 2, 2007
Creator: Kim, Sahn-ho; Davalos, Albert R.; Heo, Seok-Jin; Rodier, Francis; Zou, Ying; Beausejour, Christian et al.
Partner: UNT Libraries Government Documents Department

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Description: Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.
Date: September 2, 2007
Creator: Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol et al.
Partner: UNT Libraries Government Documents Department

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Description: Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolatesfrom diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3percent, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport ...
Date: July 30, 2007
Creator: Lapidus, Alla; Kettler, Gregory C.; Martiny, Adam C.; Huang, Katherine; Zucker, Jeremy; Coleman, Maureen L. et al.
Partner: UNT Libraries Government Documents Department

Linear scaling 3D fragment method for large-scale electronic structure calculations

Description: We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39% of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFT calculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N{sup 3}) methods, and the potential for petascale computation using the LS3DF method.
Date: July 11, 2008
Creator: Wang, Lin-Wang; Wang, Lin-Wang; Lee, Byounghak; Shan, HongZhang; Zhao, Zhengji; Meza, Juan et al.
Partner: UNT Libraries Government Documents Department

Progress with PXIE MEBT Chopper

Description: A capability to provide a large variety of bunch patterns is crucial for the concept of the Project X serving MW-range beam to several experiments simultaneously. This capability will be realized by the Medium Energy Beam Transport's (MEBT) chopping system that will divert 80% of all bunches of the initially 5 mA, 2.1 MeV CW 162.5 MHz beam to an absorber according to a pre-programmed bunch-by-bunch selection. Being considered one of the most challenging components, the chopping system will be tested at the Project X Injector Experiment (PXIE) facility that will be built at Fermilab as a prototype of the Pojrect X front end. The bunch deflection will be made by two identical sets of travelling-wave kickers working in sync. Presently, two versions of the kickers are being investigated: a helical 200 Ohm structure with a switching-type 500 V driver and a planar 50 Ohm structure with a linear {+-} 250 V amplifier. This paper describes the chopping system scheme and functional specifications for the kickers, present results of electromagnetic measurements of the models, discuss possible driver schemes, and show a conceptual mechanical design.
Date: May 1, 2012
Creator: Lebedev, V.; Chen, A.; Pasquinelli, R; Peterson, D.; Saewert, G.; Shemyakin, A. et al.
Partner: UNT Libraries Government Documents Department

Surface structure of CdSe Nanorods revealed by combined X-rayabsorption fine structure measurements and ab-initio calculations

Description: We report orientation-specific, surface-sensitive structural characterization of colloidal CdSe nanorods with extended X-ray absorption fine structure spectroscopy and ab-initio density functional theory calculations. Our measurements of crystallographically-aligned CdSe nanorods show that they have reconstructed Cd-rich surfaces. They exhibit orientation-dependent changes in interatomic distances which are qualitatively reproduced by our calculations. These calculations reveal that the measured interatomic distance anisotropy originates from the nanorod surface.
Date: January 27, 2006
Creator: Aruguete, Deborah A.; Marcus, Matthew A.; Li, Liang-shi; Williamson, Andrew; Fakra, Sirine; Gygi, Francois et al.
Partner: UNT Libraries Government Documents Department

DOMINANT EUCLIDEAN CONFIGURATIONS FOR ALL N

Description: The authors identify a class of Euclidean configurations which appear to be dominant in the functional integral of the CP{sup N-1} models. These configurations are point-like topological excitations, and they may be viewed as constituents of instantons, although they are defined independently of instantons through a continuum duality transformation. They show not only that these configurations survive as N {yields} {infinity}, but that in the plasma phase they are responsible for the effects encountered within the 1/N expansion - confinement, {theta}-dependence, and dynamical mass generation. They also discuss the possible types of plasma phase for a statistical mechanical model of the interacting excitations. Possible generalization to QCD is briefly discussed.
Date: April 1, 1980
Creator: Bardakci, K.; Caldi, D.G. & Neuberger, H.
Partner: UNT Libraries Government Documents Department

Involvement of extracellular matrix constituents in breast cancer

Description: It has recently been established that the extracellular matrix is required for normal functional differentiation of mammary epithelia not only in culture, but also in vivo. The mechanisms by which extracellular matrix affects differentiation, as well as the nature of extracellular matrix constituents which have major impacts on mammary gland function, have only now begun to be dissected. The intricate variety of extracellular matrix-mediated events and the remarkable degree of plasticity of extracellular matrix structure and composition at virtually all times during ontogeny, make such studies difficult. Similarly, during carcinogenesis, the extracellular matrix undergoes gross alterations, the consequences of which are not yet precisely understood. Nevertheless, an increasing amount of data suggests that the extracellular matrix and extracellular matrix-receptors might participate in the control of most, if not all, of the successive stages of breast tumors, from appearance to progression and metastasis.
Date: June 1, 1995
Creator: Lochter, Andre & Bissell, Mina J
Partner: UNT Libraries Government Documents Department

MCF-10A-NeoST: A New Cell System for Studying Cell-ECM and Cell-Cell Interactions in Breast Cancer

Description: There is a continuing need for genetically matched cell systems to model cellular behaviors that are frequently observed in aggressive breast cancers. We report here the isolation and initial characterization of a spontaneously arising variant of MCF-10A cells, NeoST, which provides a new model to study cell adhesion and signal transduction in breast cancer. NeoST cells recapitulate important biological and biochemical features of metastatic breast cancer, including anchorage-independent growth, invasiveness in threedimensional reconstituted membranes, loss of E-cadherin expression, and increased tyrosine kinase activity. A comprehensive analysis of tyrosine kinase expression revealed overexpression or functional activation of the Axl, FAK, and EphA2 tyrosine kinases in transformed MCF-10A cells. MCF-10A and these new derivatives provide a genetically matched model to study defects in cell adhesion and signaling that are relevant to cellular behaviors that often typify aggressive breast cancer cells.
Date: August 22, 2001
Creator: Zantek, Nicole Dodge; Walker-Daniels, Jennifer; Stewart, Jane; Hansen, Rhonda K.; Robinson, Daniel; Miao, Hui et al.
Partner: UNT Libraries Government Documents Department