Two-phase stretching of molecular chains

While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the extension energy profile of its individual monomer subunits. Namely, if the effective monomer deformation energy as a function of its extension has a non-convex (concave up) region, the stretched polymer chain separates into two phases: the weakly and strongly stretched monomers. Simplified planar and 3D polymer models are used to illustrate the basic principles of the proposed model. Specifically, we show rigorously that when the secondary structure of a polymer is mostly due to weak non-covalent interactions, the stretching is two-phase, and the force-stretching diagram has the characteristic plateau. We then use realistic coarse-grained models to confirm the main findings and make direct connection to the microscopic structure of the monomers. We demostrate in detail how the two-phase scenario is realized in the \alpha-helix, and in DNA double helix. The predicted plateau parameters are consistent with single molecules experiments. Detailed analysis of DNA stretching demonstrates that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double-helix extends at room temperature. The main strengths of the proposed theory are its generality and direct microscopic connection.Comment: 16 pges, 22 figure

Theory of High-Force DNA Stretching and Overstretching

Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA. We demonstrate that this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the Discrete Persistent Chain, or ``DPC'') that borrows features from both the FJC and the Wormlike Chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple, and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first values for the elastic constants of the stretched state. In particular we find the effective bend stiffness for DNA in this state to be about 10 nm*kbt, a value quite different from either B-form or single-stranded DNAComment: 33 pages, 11 figures. High-quality figures available upon reques

The first Hochschild cohomology group of a schurian cluster-tilted algebra

Given a cluster-tilted algebra B we study its first Hochschild cohomology group HH1(B) with coefficients in the B-B-bimodule B. We find several consequences when B is representation-finite, and also in the case where B is cluster-tilted of type Ã.Fil: Assem, Ibrahim. University of Sherbrooke; CanadáFil: Redondo, Maria Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Matemática Bahía Blanca. Universidad Nacional del Sur. Departamento de Matemática. Instituto de Matemática Bahía Blanca; Argentin

The Intrinsic Fundamental Group of a Linear Category

We provide an intrinsic definition of the fundamental group of a linear category over a ring as the automorphism group of the fibre functor on Galois coverings. If the universal covering exists, we prove that this group is isomorphic to the Galois group of the universal covering. The grading deduced from a Galois covering enables us to describe the canonical monomorphism from its automorphism group to the first Hochschild-Mitchell cohomology vector space.Comment: Final version, to appear in Algebras and Representation Theor

Variation of bone mineral density induced by exercise in postmenopausal women

OBJETIVO: Evaluar la variación de la densidad mineral ósea (DMO) en columna lumbar (CL) y cuello femoral (CF).MÉTODO: 77 mujeres con osteopenia y menopausia, formaron cuatro grupos. Dos con ejercicio físico: uno tratamiento de estrógeno/Calcitonina (n=16), y otro ingesta de Calcio/Vitamina D (n=7). Dos sin ejercicio físico, uno tratamiento estrógeno/Calcitonina (n=27) y otro ingesta Calcio/Vitamina D (n=27). El ejercicio consistió en Fuerza Muscular (65% a 75% de 1RM) y multisaltos de baja a moderada intensidad. La DMO se midió mediante absorciometría. RESULTADOS: En ANOVA 2x2 se encontró homogeneidad (p<0,05) en la DMO tanto en CL y CF entre los tratamientos farmacológicos y nutricionales, heterogeneidad entre los grupos activos y sedentarios (CL p<0,05, CF p<0,01) y heterogeneidad en la interacción (p<0,01) de ambos tratamientos con el ejercicio físico. CONCLUSIONES: El ejercicio físico programado junto con los tratamientos habituales conduce a un mayor incremento de la DMO de en mujeres postmenopáusicasOBJECTIVE: Assess the variation of Bone Mineral Density (BMD) in Lumbar Spine (LS) and Femoral Neck (FN). METHOD: 77 postmenopausal women with osteopenia. Four groups, two groups with exercise: one Estrogen/Calcitonin treatment (n=16), another supplement Calcium/Vitamin D (n=7); two groups without exercise, one Estrogen/Calcitonin treatment (n=27), and another supplement Calcium/Vitamin D (n=27). The exercise program consisted of resistance training (65% to 75% 1RM) and multi-jumps of low-to-moderate intensity. The BMD was evaluated by absorptiometry. RESULTS. ANOVA 2x2, homogeneity (p<0,05) in the BMD in both LS and FN between the pharmacological and nutritional treatments, and heterogeneity between the active and sedentary groups (LS p <0,05, FN p<0,01) as also in the interaction (p<0,01) of the pharmacological/nutritional treatments with the physical exercise were found. CONCLUSION. Physical exercise program with the usual treatments, lead to a greater increase in the BMD of LS and FN in postmenopausal wome

Stretched Polymers in a Poor Solvent

Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest neighbour attraction. The bias corresponds to opposite forces applied to the first and last monomers. We show that both in $d=2$ and $d=3$ a phase transition occurs as this force is increased beyond a critical value, where the polymer changes from a collapsed globule to a stretched configuration. This transition is second order in $d=2$ and first order in $d=3$. For $d=2$ we predict the transition point quantitatively from properties of the unstretched polymer. This is not possible in $d=3$, but even there we can estimate the transition point precisely, and we can study the scaling at temperatures slightly below the collapse temperature of the unstretched polymer. We find very large finite size corrections which would make very difficult the estimate of the transition point from straightforward simulations.Comment: 10 pages, 16 figure

Gene editing of PKLR gene in human hematopoietic progenitors through 5' and 3' UTR modified TALEN mRNA

Pyruvate Kinase Deficiency (PKD) is a rare erythroid metabolic disease caused by mutations in the PKLR gene, which encodes the erythroid specific Pyruvate Kinase enzyme. Erythrocytes from PKD patients show an energetic imbalance and are susceptible to hemolysis. Gene editing of hematopoietic stem cells (HSCs) would provide a therapeutic benefit and improve safety of gene therapy approaches to treat PKD patients. In previous studies, we established a gene editing protocol that corrected the PKD phenotype of PKD-iPSC lines through a TALEN mediated homologous recombination strategy. With the goal of moving toward more clinically relevant stem cells, we aim at editing the PKLR gene in primary human hematopoietic progenitors and hematopoietic stem cells (HPSCs). After nucleofection of the gene editing tools and selection with puromycin, up to 96% colony forming units showed precise integration. However, a low yield of gene edited HPSCs was associated to the procedure. To reduce toxicity while increasing efficacy, we worked on i) optimizing gene editing tools and ii) defining optimal expansion and selection times. Different versions of specific nucleases (TALEN and CRISPR-Cas9) were compared. TALEN mRNAs with 5' and 3' added motifs to increase RNA stability were the most efficient nucleases to obtain high gene editing frequency and low toxicity. Shortening ex vivo manipulation did not reduce the efficiency of homologous recombination and preserved the hematopoietic progenitor potential of the nucleofected HPSCs. Lastly, a very low level of gene edited HPSCs were detected after engraftment in immunodeficient (NSG) mice. Overall, we showed that gene editing of the PKLR gene in HPSCs is feasible, although further improvements must to be done before the clinical use of the gene editing to correct PKD. Institutode Investigacio ' n Sanitaria de la Fundacio '

Gene editing of PKLR gene in human hematopoietic progenitors through 5' and 3' UTR modified TALEN mRNA

TheauthorswouldliketothankMiguelA.MartinforthecarefulmaintenanceofNSGmice,andRebecaSa ́nchezandOmairaAlberquillafortheirtechnicalassistanceinflowcytometry.TheauthorsalsothankFundacio ́n Botı ́n forpromotingtranslationalresearchattheHemato-poieticInnovativeTherapiesDivisionoftheCIEMATPyruvate Kinase Deficiency (PKD) is a rare erythroid metabolic disease caused by mutations in the PKLR gene, which encodes the erythroid specific Pyruvate Kinase enzyme. Erythrocytes from PKD patients show an energetic imbalance and are susceptible to hemolysis. Gene editing of hematopoietic stem cells (HSCs) would provide a therapeutic benefit and improve safety of gene therapy approaches to treat PKD patients. In previous studies, we established a gene editing protocol that corrected the PKD phenotype of PKD-iPSC lines through a TALEN mediated homologous recombination strategy. With the goal of moving toward more clinically relevant stem cells, we aim at editing the PKLR gene in primary human hematopoietic progenitors and hematopoietic stem cells (HPSCs). After nucleofection of the gene editing tools and selection with puromycin, up to 96% colony forming units showed precise integration. However, a low yield of gene edited HPSCs was associated to the procedure. To reduce toxicity while increasing efficacy, we worked on i) optimizing gene editing tools and ii) defining optimal expansion and selection times. Different versions of specific nucleases (TALEN and CRISPR-Cas9) were compared. TALEN mRNAs with 5' and 3' added motifs to increase RNA stability were the most efficient nucleases to obtain high gene editing frequency and low toxicity. Shortening ex vivo manipulation did not reduce the efficiency of homologous recombination and preserved the hematopoietic progenitor potential of the nucleofected HPSCs. Lastly, a very low level of gene edited HPSCs were detected after engraftment in immunodeficient (NSG) mice. Overall, we showed that gene editing of the PKLR gene in HPSCs is feasible, although further improvements must to be done before the clinical use of the gene editing to correct PKD.S

Classes of fast and specific search mechanisms for proteins on DNA

Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.Comment: 65 pages, 23 figure