Lentiviral vectors with amplified beta cell-specific gene expression.

An important goal of gene therapy is to be able to deliver genes, so that they express in a pattern that recapitulates the expression of an endogenous cellular gene. Although tissue-specific promoters confer selectivity, in a vector-based system, their activity may be too weak to mediate detectable levels in gene-expression studies. We have used a two-step transcriptional amplification system to amplify gene expression from lentiviral vectors using the human insulin promoter. In this system, the human insulin promoter drives expression of a potent synthetic transcription activator (the yeast GAL4 DNA-binding domain fused to the activation domain of the Herpes simplex virus-1 VP16 activator), which in turn activates a GAL4-responsive promoter, driving the enhanced green fluorescent protein reporter gene. Vectors carrying the human insulin promoter did not express in non-beta-cell lines, but expressed in murine insulinoma cell lines, indicating that the human insulin promoter was capable of conferring cell specificity of expression. The insulin-amplifiable vector was able to amplify gene expression five to nine times over a standard insulin-promoter vector. In primary human islets, gene expression from the insulin-promoted vectors was coincident with insulin staining. These vectors will be useful in gene-expression studies that require a detectable signal and tissue specificity

Lymphoid priming in human bone marrow begins before expression of CD10 with upregulation of L-selectin.

Expression of the cell-surface antigen CD10 has long been used to define the lymphoid commitment of human cells. Here we report a unique lymphoid-primed population in human bone marrow that was generated from hematopoietic stem cells (HSCs) before onset of the expression of CD10 and commitment to the B cell lineage. We identified this subset by high expression of the homing molecule L-selectin (CD62L). CD10(-)CD62L(hi) progenitors had full lymphoid and monocytic potential but lacked erythroid potential. Gene-expression profiling placed the CD10(-)CD62L(hi) population at an intermediate stage of differentiation between HSCs and lineage-negative (Lin(-)) CD34(+)CD10(+) progenitors. CD62L was expressed on immature thymocytes, and its ligands were expressed at the cortico-medullary junction of the thymus, which suggested a possible role for this molecule in homing to the thymus. Our studies identify the earliest stage of lymphoid priming in human bone marrow

Work and heat probability distributions in out-of-equilibrium systems

We review and discuss the equations governing the distribution of work done on a system which is driven out of equilibrium by external manipulation, as well as those governing the entropy flow to a reservoir in a nonequilibrium system. We take advantage of these equations to investigate the path phase transition in a manipulated mean-field Ising model and the large-deviation function for the heat flow in the asymmetric exclusion process with periodically varying transition probabilities.Comment: Contribution to Proceedings of "Work, Dissipation, and Fluctuations in Nonequilibrium Physics", Brussels, 200

The Zeroth Law of Thermodynamics and Volume-Preserving Conservative Dynamics with Equilibrium Stochastic Damping

We propose a mathematical formulation of the zeroth law of thermodynamics and develop a stochastic dynamical theory, with a consistent irreversible thermodynamics, for systems possessing sustained conservative stationary current in phase space while in equilibrium with a heat bath. The theory generalizes underdamped mechanical equilibrium: $dx=gdt+\{-D\nabla\phi dt+\sqrt{2D}dB(t)\}$, with $\nabla\cdot g=0$ and $\{\cdots\}$ respectively representing phase-volume preserving dynamics and stochastic damping. The zeroth law implies stationary distribution $u^{ss}(x)=e^{-\phi(x)}$. We find an orthogonality $\nabla\phi\cdot g=0$ as a hallmark of the system. Stochastic thermodynamics based on time reversal $\big(t,\phi,g\big)\rightarrow\big(-t,\phi,-g\big)$ is formulated: entropy production $e_p^{\#}(t)=-dF(t)/dt$; generalized "heat" $h_d^{\#}(t)=-dU(t)/dt$, $U(t)=\int_{\mathbb{R}^n} \phi(x)u(x,t)dx$ being "internal energy", and "free energy" $F(t)=U(t)+\int_{\mathbb{R}^n} u(x,t)\ln u(x,t)dx$ never increases. Entropy follows $\frac{dS}{dt}=e_p^{\#}-h_d^{\#}$. Our formulation is shown to be consistent with an earlier theory of P. Ao. Its contradistinctions to other theories, potential-flux decomposition, stochastic Hamiltonian system with even and odd variables, Klein-Kramers equation, Freidlin-Wentzell's theory, and GENERIC, are discussed.Comment: 25 page

Quantum Jarzynski Equality with multiple measurement and feedback for isolated system

In this paper, we derive the Jarzynski equality (JE) for an isolated quantum system in three different cases: (i) the full evolution is unitary with no intermediate measurements, (ii) with intermediate measurements of arbitrary observables being performed, and (iii) with intermediate measurements whose outcomes are used to modify the external protocol (feedback). We assume that the measurements will involve errors that are purely classical in nature. Our treatment is based on path probability in state space for each realization. This is in contrast to the formal approach based on projection operator and density matrices. We find that the JE remains unaffected in the second case, but gets modified in the third case where the mutual information between the measured values with the actual eigenvalues must be incorporated into the relation.Comment: 7 page

Human Developmental Chondrogenesis as a Basis for Engineering Chondrocytes from Pluripotent Stem Cells

Joint injury and osteoarthritis affect millions of people worldwide, but attempts to generate articular cartilage using adult stem/progenitor cells have been unsuccessful. We hypothesized that recapitulation of the human developmental chondrogenic program using pluripotent stem cells (PSCs) may represent a superior approach for cartilage restoration. Using laser-capture microdissection followed by microarray analysis, we first defined a surface phenotype (CD166(low/neg)CD146(low/neg)CD73(+)CD44(low)BMPR1B(+)) distinguishing the earliest cartilage committed cells (prechondrocytes) at 5-6 weeks of development. Functional studies confirmed these cells are chondrocyte progenitors. From 12 weeks, only the superficial layers of articular cartilage were enriched in cells with this progenitor phenotype. Isolation of cells with a similar immunophenotype from differentiating human PSCs revealed a population of CD166(low/neg)BMPR1B(+) putative cartilage-committed progenitors. Taken as a whole, these data define a developmental approach for the generation of highly purified functional human chondrocytes from PSCs that could enable substantial progress in cartilage tissue engineering.Fil: Wu, Ling. University of California at Los Angeles; Estados UnidosFil: Bluguermann, Carolina. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia. Laboratorio de Biología del Desarrollo Celular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of California at Los Angeles; Estados UnidosFil: Kyupelyan, Levon. University of California at Los Angeles; Estados UnidosFil: Latour, Brooke. University of California at Los Angeles; Estados UnidosFil: Gonzalez, Stephanie. University of California at Los Angeles; Estados UnidosFil: Shah, Saumya. University of California at Los Angeles; Estados UnidosFil: Galic, Zoran. University of California at Los Angeles; Estados UnidosFil: Ge, Sundi. University of California at Los Angeles; Estados UnidosFil: Zhu, Yuhua. University of California at Los Angeles; Estados UnidosFil: Petrigliano, Frank A.. University of California at Los Angeles; Estados UnidosFil: Nsair, Ali. University of California at Los Angeles; Estados UnidosFil: Miriuka, Santiago Gabriel. Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia. Laboratorio de Biología del Desarrollo Celular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Li, Xinmin. University of California at Los Angeles; Estados UnidosFil: Lyons, Karen M.. University of California at Los Angeles; Estados UnidosFil: Crooks, Gay M.. University of California at Los Angeles; Estados UnidosFil: McAllister, David R.. University of California at Los Angeles; Estados UnidosFil: Van Handel, Ben. Novogenix Laboratories; Estados UnidosFil: Adams, John S.. University of California at Los Angeles; Estados UnidosFil: Evseenko, Denis. University of California at Los Angeles; Estados Unido

Future Developments in Geographical Agent‐Based Models: Challenges and Opportunities

Despite reaching a point of acceptance as a research tool across the geographical and social sciences, there remain significant methodological challenges for agent‐based models. These include recognizing and simulating emergent phenomena, agent representation, construction of behavioral rules, and calibration and validation. While advances in individual‐level data and computing power have opened up new research avenues, they have also brought with them a new set of challenges. This article reviews some of the challenges that the field has faced, the opportunities available to advance the state‐of‐the‐art, and the outlook for the field over the next decade. We argue that although agent‐based models continue to have enormous promise as a means of developing dynamic spatial simulations, the field needs to fully embrace the potential offered by approaches from machine learning to allow us to fully broaden and deepen our understanding of geographical systems

Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Chemical Reactions

Chemical reaction systems operating in nonequilibrium open-system states arise in a great number of contexts, including the study of living organisms, in which chemical reactions, in general, are far from equilibrium. Here we introduce a theorem that relates forward and re-verse fluxes and free energy for any chemical process operating in a steady state. This rela-tionship, which is a generalization of equilibrium conditions to the case of a chemical process occurring in a nonequilibrium steady state, provides a novel equivalent definition for chemical reaction free energy. In addition, it is shown that previously unrelated theories introduced by Ussing and Hodgkin and Huxley for transport of ions across membranes, Hill for catalytic cycle fluxes, and Crooks for entropy production in microscopically reversible systems, are united in a common framework based on this relationship.Comment: 11 page

Fluctuation Theorems for Entropy Production and Heat Dissipation in Periodically Driven Markov Chains

Asymptotic fluctuation theorems are statements of a Gallavotti-Cohen symmetry in the rate function of either the time-averaged entropy production or heat dissipation of a process. Such theorems have been proved for various general classes of continuous-time deterministic and stochastic processes, but always under the assumption that the forces driving the system are time independent, and often relying on the existence of a limiting ergodic distribution. In this paper we extend the asymptotic fluctuation theorem for the first time to inhomogeneous continuous-time processes without a stationary distribution, considering specifically a finite state Markov chain driven by periodic transition rates. We find that for both entropy production and heat dissipation, the usual Gallavotti-Cohen symmetry of the rate function is generalized to an analogous relation between the rate functions of the original process and its corresponding backward process, in which the trajectory and the driving protocol have been time-reversed. The effect is that spontaneous positive fluctuations in the long time average of each quantity in the forward process are exponentially more likely than spontaneous negative fluctuations in the backward process, and vice-versa, revealing that the distributions of fluctuations in universes in which time moves forward and backward are related. As an additional result, the asymptotic time-averaged entropy production is obtained as the integral of a periodic entropy production rate that generalizes the constant rate pertaining to homogeneous dynamics

Toward physical realizations of thermodynamic resource theories

Conventional statistical mechanics describes large systems and averages over many particles or over many trials. But work, heat, and entropy impact the small scales that experimentalists can increasingly control, e.g., in single-molecule experiments. The statistical mechanics of small scales has been quantified with two toolkits developed in quantum information theory: resource theories and one-shot information theory. The field has boomed recently, but the theorems amassed have hardly impacted experiments. Can thermodynamic resource theories be realized experimentally? Via what steps can we shift the theory toward physical realizations? Should we care? I present eleven opportunities in physically realizing thermodynamic resource theories.Comment: Publication information added. Cosmetic change