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‣ A 9-nt segment of a cellular mRNA can function as an internal ribosome entry site (IRES) and when present in linked multiple copies greatly enhances IRES activity

Chappell, Stephen A.; Edelman, Gerald M.; Mauro, Vincent P.
Fonte: The National Academy of Sciences Publicador: The National Academy of Sciences
Tipo: Artigo de Revista Científica
Publicado em 15/02/2000 Português
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This study addresses the properties of a newly identified internal ribosome entry site (IRES) contained within the mRNA of the homeodomain protein Gtx. Sequential deletions of the 5′ untranslated region (UTR) from either end did not define distinct IRES boundaries; when five nonoverlapping UTR fragments were tested, four had IRES activity. These observations are consistent with other cellular IRES analyses suggesting that some cellular IRESes are composed of segments (IRES modules) that independently and combinatorially contribute to overall IRES activity. We characterize a 9-nt IRES module from the Gtx 5′ UTR that is 100% complementary to the 18S rRNA at nucleotides 1132–1124. In previous work, we demonstrated that this mRNA segment could be crosslinked to its complement within intact 40S subunits. Here we show that increasing the number of copies of this IRES module in the intercistronic region of a dicistronic mRNA strongly enhances IRES activity in various cell lines. Ten linked copies increased IRES activity up to 570-fold in Neuro 2a cells. This level of IRES activity is up to 63-fold greater than that obtained by using the well characterized encephalomyocarditis virus IRES when tested in the same assay system. When the number of nucleotides between two of the 9-nt Gtx IRES modules was increased...

‣ Isolation and characterization of c-myc, a cellular homolog of the oncogene (v-myc) of avian myelocytomatosis virus strain 29.

Vennstrom, B; Sheiness, D; Zabielski, J; Bishop, J M
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /06/1982 Português
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The chicken genome contains nucleotide sequences homologous to transforming genes (oncogenes) of a number of avian retroviruses. We have isolated chicken DNA (c-myc) that is homologous to the oncogene (v-myc) of the avian myelocytomatosis virus MC29 and have compared the structures of the cellular and viral genes. Results from restriction endonuclease mapping of c-myc and from analysis of heteroduplexes between the DNAs of the cellular and viral genes show that c-myc is homologous to 1,500 nucleotides in v-myc DNA. This homologous region is interrupted in c-myc by an intron-like sequence of 1,100 nucleotides which is absent from v-myc. Nuclear RNA from normal chicken cells contains at least five species of transcripts from c-myc ranging from 2.5 to 6.5 kilobases in length. By contrast, cytoplasm contains only the 2.5-kilobase c-myc RNA. These features of the c-myc gene and its nuclear transcripts are characteristic of normal cellular genes and suggest that the myc gene is of cellular rather than viral origin. The exons in c-myc may define two functional domains in the gene and may therefore facilitate the dissection of the different oncogenic potentials of the MC29 virus.

‣ Hyperphosphorylation of the Rotavirus NSP5 Protein Is Independent of Serine 67 or NSP2, and the Intrinsic Insolubility of NSP5 Is Regulated by Cellular Phosphatases

Sen, Adrish; Agresti, Darin; Mackow, Erich R.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /02/2006 Português
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The NSP5 protein is required for viroplasm formation during rotavirus infection and is hyperphosphorylated into 32- to 35-kDa isoforms. Earlier studies reported that NSP5 is not hyperphosphorylated without NSP2 coexpression or deleting the NSP5 N terminus and that serine 67 is essential for NSP5 hyperphosphorylation. In this report, we show that full-length NSP5 is hyperphosphorylated in the absence of NSP2 or serine 67 and demonstrate that hyperphosphorylated NSP5 is predominantly present in previously unrecognized cellular fractions that are insoluble in 0.2% sodium dodecyl sulfate. The last 68 residues of NSP5 are sufficient to direct green fluorescent protein into insoluble fractions and cause green fluorescent protein localization into viroplasm-like structures; however, NSP5 insolubility was intrinsic and did not require NSP5 hyperphosphorylation. When we mutated serine 67 to alanine we found that the NSP5 mutant was both hyperphosphorylated and insoluble, identical to unmodified NSP5, and as a result serine 67 is not required for NSP5 phosphorylation. Interestingly, treating cells with the phosphatase inhibitor calyculin A permitted the accumulation of soluble hyperphosphorylated NSP5 isoforms. This suggests that soluble NSP5 is constitutively dephosphorylated by cellular phosphatases and demonstrates that hyperphosphorylation does not direct NSP5 insolubility. Collectively these findings indicate that NSP5 hyperphosphorylation and insolubility are completely independent parameters and that analyzing insoluble NSP5 is essential for studies assessing NSP5 phosphorylation. Our results also demonstrate the involvement of cellular phosphatases in regulating NSP5 phosphorylation and indicate that in the absence of other rotavirus proteins...

‣ Lipopolysaccharide (LPS) partial structures inhibit responses to LPS in a human macrophage cell line without inhibiting LPS uptake by a CD14- mediated pathway

Fonte: The Rockefeller University Press Publicador: The Rockefeller University Press
Tipo: Artigo de Revista Científica
Publicado em 01/08/1992 Português
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Lipopolysaccharides (LPS) that lack acyloxyacyl groups can antagonize responses to LPS in human cells. Although the site and mechanism of inhibition are not known, it has been proposed that these inhibitory molecules compete with LPS for a common cellular target such as a cell- surface binding receptor. In the present study, we used an in vitro model system to test this hypothesis and to evaluate the role of CD14 in cellular responses to LPS. Cells of the THP-1 human monocyte- macrophage cell line were exposed to 1,25 dihydroxyvitamin D3 to induce adherence to plastic and expression of CD14, a binding receptor for LPS complexed with LPS-binding protein (LBP). The uptake of picograms of [3H]LPS (agonist) and enzymatically deacylated LPS [3H]dLPS (antagonist) was measured by exposing the cells to the radiolabeled ligands for short incubation periods. The amounts of cell-associated LPS and dLPS were then correlated with cellular responses by measuring the induction of nuclear NF-kappa B binding activity and the production of cell-associated interleukin (IL)-1 beta. We found that similar amounts of [3H]LPS or [3H]dLPS were taken up by the cells. The rate of cellular accumulation of the ligands was greatly enhanced by LBP and blocked by a monoclonal antibody to CD14 (mAb 60b)...

‣ DNA Polymerase Family X: Function, Structure, and Cellular Roles

Yamtich, Jennifer; Sweasy, Joann B.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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The X Family of DNA polymerases in eukaryotic cells consists of Terminal Transferase, and DNA polymerases β, λ, and μ. These enzymes have similar structural portraits, yet different biochemical properties, especially in their interactions with DNA. None of these enzymes possesses a proofreading subdomain, and their intrinsic fidelity of DNA synthesis is much lower than that of a polymerase that functions in cellular DNA replication. In this review, we discuss the similarities and differences of three members of Family X: polymerases β, λ, and μ. We focus on biochemical mechanisms, structural variation, fidelity and lesion bypass mechanisms, and cellular roles. Remarkably, although these enzymes have similar three-dimensional structures, their biochemical properties and cellular functions differ in important ways that impact cellular function.

‣ Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions

Volkmann, Niels
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field.

‣ E3Net: A System for Exploring E3-mediated Regulatory Networks of Cellular Functions*

Han, Youngwoong; Lee, Hodong; Park, Jong C.; Yi, Gwan-Su
Fonte: The American Society for Biochemistry and Molecular Biology Publicador: The American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
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Ubiquitin-protein ligase (E3) is a key enzyme targeting specific substrates in diverse cellular processes for ubiquitination and degradation. The existing findings of substrate specificity of E3 are, however, scattered over a number of resources, making it difficult to study them together with an integrative view. Here we present E3Net, a web-based system that provides a comprehensive collection of available E3-substrate specificities and a systematic framework for the analysis of E3-mediated regulatory networks of diverse cellular functions. Currently, E3Net contains 2201 E3s and 4896 substrates in 427 organisms and 1671 E3-substrate specific relations between 493 E3s and 1277 substrates in 42 organisms, extracted mainly from MEDLINE abstracts and UniProt comments with an automatic text mining method and additional manual inspection and partly from high throughput experiment data and public ubiquitination databases. The significant functions and pathways of the extracted E3-specific substrate groups were identified from a functional enrichment analysis with 12 functional category resources for molecular functions, protein families, protein complexes, pathways, cellular processes, cellular localization, and diseases. E3Net includes interactive analysis and navigation tools that make it possible to build an integrative view of E3-substrate networks and their correlated functions with graphical illustrations and summarized descriptions. As a result...

‣ Cellular Uptakes, Biostabilities and Anti-miR-210 Activities of Chiral Arginine-PNAs in Leukaemic K562 Cells

Manicardi, Alex; Fabbri, Enrica; Tedeschi, Tullia; Sforza, Stefano; Bianchi, Nicoletta; Brognara, Eleonora; Gambari, Roberto; Marchelli, Rosangela; Corradini, Roberto
Fonte: WILEY-VCH Verlag Publicador: WILEY-VCH Verlag
Tipo: Artigo de Revista Científica
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A series of 18-mer peptide nucleic acids (PNAs) targeted against micro-RNA miR-210 was synthesised and tested in a cellular system. Unmodified PNAs, R8-conjugated PNAs and modified PNAs containing eight arginine residues on the backbone, either as C2-modified (R) or C5-modified (S) monomers, all with the same sequence, were compared. Two different models were used for the modified PNAs: one with alternated chiral and achiral monomers and one with a stretch of chiral monomers at the N terminus. The melting temperatures of these derivatives were found to be extremely high and 5 m urea was used to assess differences between the different structures. FACS analysis and qRT-PCR on K562 chronic myelogenous leukaemic cells indicated that arginine-conjugated and backbone-modified PNAs display good cellular uptake, with best performances for the C2-modified series. Resistance to enzymatic degradation was found to be higher for the backbone-modified PNAs, thus enhancing the advantage of using these derivatives rather than conjugated PNAs in the cells in serum, and this effect is magnified in the presence of peptidases such as trypsin. Inhibition of miR-210 activity led to changes in the erythroid differentiation pathway, which were more evident in mithramycin-treated cells. Interestingly...

‣ The structures of non-protein coding RNAs that drive IRES function

Plank, Terra-Dawn M.; Kieft, Jeffrey S.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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Internal Ribosome Entry sites (IRESs) are RNA sequences that can recruit the translation machinery independently of the 5′ end of the messenger RNA. IRESs are found in both viral and cellular RNAs and are important for regulating gene expression. There is great diversity in the mechanisms used by IRESs to recruit the ribosome and this is reflected in a variety of RNA sequences that function as IRESs. The ability of an RNA sequence to function as an IRES is conferred by structures operating at multiple levels from primary sequence through higher-order three-dimensional structures within dynamic RNPs. When these diverse structures are compared, some trends are apparent, but overall it is not possible to find universal rules to describe IRES structure and mechanism. Clearly, many different sequences and structures have evolved to perform the function of recruiting, positioning, and activating a ribosome without using the canonical cap-dependent mechanism. However, as our understanding of the specific sequences, structures, and mechanisms behind IRES function improves, more common features may emerge to link these diverse RNAs.

‣ Mitochondrial dysfunction induced by frataxin deficiency is associated with cellular senescence and abnormal calcium metabolism

Bolinches-Amorós, Arantxa; Mollá, Belén; Pla-Martín, David; Palau, Francesc; González-Cabo, Pilar
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 13/05/2014 Português
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Friedreich ataxia is considered a neurodegenerative disorder involving both the peripheral and central nervous systems. Dorsal root ganglia (DRG) are the major target tissue structures. This neuropathy is caused by mutations in the FXN gene that encodes frataxin. Here, we investigated the mitochondrial and cell consequences of frataxin depletion in a cellular model based on frataxin silencing in SH-SY5Y human neuroblastoma cells, a cell line that has been used widely as in vitro models for studies on neurological diseases. We showed that the reduction of frataxin induced mitochondrial dysfunction due to a bioenergetic deficit and abnormal Ca2+ homeostasis in the mitochondria that were associated with oxidative and endoplasmic reticulum stresses. The depletion of frataxin did not cause cell death but increased autophagy, which may have a cytoprotective effect against cellular insults such as oxidative stress. Frataxin silencing provoked slow cell growth associated with cellular senescence, as demonstrated by increased SA-βgal activity and cell cycle arrest at the G1 phase. We postulate that cellular senescence might be related to a hypoplastic defect in the DRG during neurodevelopment, as suggested by necropsy studies.

‣ TGF-β1 induces the formation of vascular-like structures in embryoid bodies derived from human embryonic stem cells

WANG, YAN; QIAN, DE-JIAN; ZHONG, WEN-YU; LU, JUN-HONG; GUO, XIANG-KAI; CAO, YI-LIN; LIU, JU
Fonte: D.A. Spandidos Publicador: D.A. Spandidos
Tipo: Artigo de Revista Científica
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Human embryonic stem cells (ESCs) can differentiate into endothelial cells in response to stimuli from extracellular cytokines. Transforming growth factor (TGF)-β1 signaling is involved in stem cell renewal and vascular development. Previously, human ESCs were isolated from inner cell mass and a stable ESC line was developed. In the present study, the effects of extracellular TGF-β1 were investigated on human ESC-derived embryoid bodies (EB) in suspension. The structures of the EBs were analyzed with light and electron microscopy, while the cellular composition of the EBs was examined via the expression levels of specific markers. Vascular-like tubular structures and cardiomyocyte-like beating cells were observed in the EBs at day 3 and 8, respectively. The frequencies of vascular-like structures and beating cells in the TGF-β1 treated group were significantly higher compared with the control group (84.31 vs. 12.77%; P<0.001; 37.25 vs. 8.51%; P<0.001, respectively). Electron microscopy revealed the presence of lumens and gap junctions in the sections of the tubular structures. Semiquantitative polymerase chain reaction revealed elevated expression levels of CD31 and fetal liver kinase-1 in EBs cultured with TGF-β1. In addition...

‣ Microstructural Inhomogeneity of Electrical Conductivity in Subcutaneous Fat Tissue

Kruglikov, Ilja L.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 03/03/2015 Português
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Microscopic peculiarities stemming from a temperature increase in subcutaneous adipose tissue (sWAT) after applying a radio-frequency (RF) current, must be strongly dependent on the type of sWAT. This effect is connected with different electrical conductivities of pathways inside (triglycerides in adipocytes) and outside (extra-cellular matrix) the cells and to the different weighting of these pathways in hypertrophic and hyperplastic types of sWAT. The application of the RF current to hypertrophic sWAT, which normally has a strongly developed extracellular matrix with high concentrations of hyaluronan and collagen in a peri-cellular space of adipocytes, can produce, micro-structurally, a highly inhomogeneous temperature distribution, characterized by strong temperature gradients between the peri-cellular sheath of the extra-cellular matrix around the hypertrophic adipocytes and their volumes. In addition to normal temperature effects, which are generally considered in body contouring, these temperature gradients can produce thermo-mechanical stresses on the cells’ surfaces. Whereas these stresses are relatively small under normal conditions and cannot cause any direct fracturing or damage of the cell structure, these stresses can...

‣ Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Publicado em 08/09/2015 Português
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Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

‣ Untersuchungen zur zellulären Aufnahme von zellpenetrierenden Peptiden und der Bioaktivität von HPMA-Peptid-Konjugaten, sowie Charakterisierung eines neuen zellpenetrierenden Peptids aus humanem Lactoferrin; Analysing the cellular uptake of cell penetrating peptides and the bioactivity of HPMA-peptide conjugates, as well as characterisation of a new cell penetrating peptide derived from human lactoferrin

Duchardt, Falk
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
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In dieser Arbeit wird ein neuer und sehr effektiver zellulärer Aufnahmemechanismus für zellpenetrierende Peptide (CPPs) beschrieben. Dieser Aufnahmemechanismus wird ab einer bestimmten Konzentration von extrazellulärem Peptid induziert und führt zu einer zytoplasmatischen Lokalisation der Peptide. Die Konzentration, um diese Aufnahme auszulösen, ist von den Eigenschaften des eingesetzten Peptids abhängig. Sowohl die Ladung als auch die Sekundärstruktur bilden dabei wichtige Parameter. Für R9 konnte gezeigt werden, dass ab einer Konzentration von 10 µM neben einer vesikulären auch eine starke zytoplasmatische Verteilung des Peptids vorliegt. Für das weniger kationische Peptid Penetratin dagegen sind wesentlich höhere Konzentrationen und Änderungen der Membranzusammensetzung notwendig, um den gleichen Effekt zu erreichen. Eine genaue Beobachtung der Aufnahmekinetik von R9 ergab, dass die Aufnahme innerhalb von Minuten stattfindet und mit einer starken Membranaktivität einhergeht. Membranbereiche, in denen die Aufnahme stattfand, wurden als Nucleation Zones bezeichnet. Die elektronenmikroskopische Analyse dieser Zonen ergab keine morphologischen Besonderheiten im Vergleich zwischen Nucleation Zones und anderen Bereichen. Bei der Peptidaufnahme über Nucleation Zones spielen Heparansulfat-Proteoglykane (HSPG) als zelluläre Oberflächenmoleküle eine wichtige Rolle. Der Verlust von HSPG kann die Ausbildung von Nucleation Zones verhindern. Auch der Einsatz von Rottlerin...

‣ Histochemical demonstration and analysis of poly-N-acetyllactosamine structures in normal and malignant human tissues

Ito, N.; yokota, M.; Nagaike, C.; Morimura, Y.; Hatake, K.; Matsunaga, T.
Fonte: Murcia : F. Hernández Publicador: Murcia : F. Hernández
Tipo: Artigo de Revista Científica Formato: application/pdf
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Poly-N-acetyllactosaminyl structures carry a variety of physiologically and pathologically important carbohydrate antigens and are presumed to have essential roles in the process of cellular recognition, differentiation, malignant transformation and cancer metastasis. Monoclonal antibodies, lectins and endo-Bgalactosidase are useful histochemical tools for detecting and analyzing poly-N-acetyllactosamines in tissue sections. 1 (branched structure) and i (linear structure) antigens recognized by monoclonal antibodies have been shown to be differentiation antigens in mouse embryo and mouse and human teratocarcinoma cells as well as in human erythrocytes. They are also oncofoetal antigens and are expressed in carcinoma cells in severa1 tissues and organs. Immobilized lectins specific to po1y-Nacetyllactosamine structures have been successfully applied for fractioning glycoproteins with po1y-Nacetyllactosamine, but histochemical use of these lectins has been restricted to some animal tissues. Arnong them, pokeweed mitogen agglutinin was used to detect branched poly-N-acetyllactosamine in normal and malignant human colon, demonstrating that it has a highly selective affinity for colorectal carcinomas. Griffonia simplicifolia agglutinin-11 staining following endo-B-galactosidase digestion procedure revealed the presence of poly-N-acetyllactosamine structures with or without blood group-specificities in severa1 normal human tissues. By using this procedure...

‣ Rewiring of Cellular Membrane Homeostasis by Picornaviruses

Belov, George A.; Sztul, Elizabeth
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /09/2014 Português
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Viruses are obligatory intracellular parasites and utilize host elements to support key viral processes, including penetration of the plasma membrane, initiation of infection, replication, and suppression of the host's antiviral defenses. In this review, we focus on picornaviruses, a family of positive-strand RNA viruses, and discuss the mechanisms by which these viruses hijack the cellular machinery to form and operate membranous replication complexes. Studies aimed at revealing factors required for the establishment of viral replication structures identified several cellular-membrane-remodeling proteins and led to the development of models in which the virus used a preexisting cellular-membrane-shaping pathway “as is” for generating its replication organelles. However, as more data accumulate, this view is being increasingly questioned, and it is becoming clearer that viruses may utilize cellular factors in ways that are distinct from the normal functions of these proteins in uninfected cells. In addition, the proteincentric view is being supplemented by important new studies showing a previously unappreciated deep remodeling of lipid homeostasis, including extreme changes to phospholipid biosynthesis and cholesterol trafficking. The data on viral modifications of lipid biosynthetic pathways are still rudimentary...

‣ Emergent mechanics of biological structures

Dumont, Sophie; Prakash, Manu
Fonte: The American Society for Cell Biology Publicador: The American Society for Cell Biology
Tipo: Artigo de Revista Científica
Publicado em 05/11/2014 Português
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Mechanical force organizes life at all scales, from molecules to cells and tissues. Although we have made remarkable progress unraveling the mechanics of life's individual building blocks, our understanding of how they give rise to the mechanics of larger-scale biological structures is still poor. Unlike the engineered macroscopic structures that we commonly build, biological structures are dynamic and self-organize: they sculpt themselves and change their own architecture, and they have structural building blocks that generate force and constantly come on and off. A description of such structures defies current traditional mechanical frameworks. It requires approaches that account for active force-generating parts and for the formation of spatial and temporal patterns utilizing a diverse array of building blocks. In this Perspective, we term this framework “emergent mechanics.” Through examples at molecular, cellular, and tissue scales, we highlight challenges and opportunities in quantitatively understanding the emergent mechanics of biological structures and the need for new conceptual frameworks and experimental tools on the way ahead.

‣ Magnetic manipulation and spatial patterning of multi-cellular stem cell aggregates†

Bratt-Leal, Andrés M.; Kepple, Kirsten L.; Carpenedo, Richard L.; Cooke, Marissa T.; McDevitt, Todd C.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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The controlled assembly and organization of multi-cellular systems to mimic complex tissue structures is critical to the engineering of tissues for therapeutic and diagnostic applications. Recent advances in micro-scale technologies to control multi-cellular aggregate formation typically require chemical modification of the interface between cells and materials and lack multi-scale flexibility. Here we demonstrate that simple physical entrapment of magnetic microparticles within the extracellular space of stem cells spheroids during initial formation enables scaffold-free immobilization, translocation and directed assembly of multi-cellular aggregates across multiple length and time scales, even under dynamic suspension culture conditions. The response of aggregates to externally applied magnetic fields was a direct function of microparticle incorporation, allowing for rapid and transient control of the extracellular environment as well as separation of heterogeneous populations. In addition, spatial patterning of heterogeneous spheroid populations as well as individual multi-cellular aggregates was readily achieved by imposing temporary magnetic fields. Overall, this approach provides novel routes to examine stem cell differentiation and tissue morphogenesis with applications that encompass the creation of new model systems for developmental biology...

‣ Gliders, Ether and Triangles

Redeker, Markus
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 01/12/2010 Português
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This is a study of the about structures in one-dimensional cellular automata, with the elementary cellular automaton Rule 54 as example. It uses the formalism of "flexible time" to derive expressions that characterise triangles, gliders, and and periodic background patterns like the ether. A theorem is derived about the existence of simple triangles in one-dimensional cellular automata and their dependence on properties of the transition rule of the automaton. For Rule 54, expressions for its triangles, three of its gliders and its ether are found and used to look into their behaviour in detail.; Comment: There is some overlap with arXiv:1007.2920, but the emphasis is on general theorems: I view it as a "half-new" paper. Submitted to Journal of Cellular Automata. 23 pages, 6 figures, 3 tables

‣ Bulking II: Classifications of Cellular Automata

Delorme, Marianne; Mazoyer, Jacques; Ollinger, Nicolas; Theyssier, Guillaume
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
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This paper is the second part of a series of two papers dealing with bulking: a way to define quasi-order on cellular automata by comparing space-time diagrams up to rescaling. In the present paper, we introduce three notions of simulation between cellular automata and study the quasi-order structures induced by these simulation relations on the whole set of cellular automata. Various aspects of these quasi-orders are considered (induced equivalence relations, maximum elements, induced orders, etc) providing several formal tools allowing to classify cellular automata.