Modeling genetic circuit behavior in transiently transfected mammalian cells

Binning cells by plasmid copy number is a common practice for analyzing transient transfection data. In many kinetic models of transfected cells, protein production rates are assumed to be proportional to plasmid copy number. The validity of this assumption in transiently transfected mammalian cells is not clear; models based on this assumption appear unable to reproduce experimental flow cytometry data robustly. We hypothesize that protein saturation at high plasmid copy number is a reason previous models break down and validate our hypothesis by comparing experimental data and a stochastic chemical kinetics model. The model demonstrates that there are multiple distinct physical mechanisms that can cause saturation. On the basis of these observations, we develop a novel minimal bin-dependent ODE model that assumes different parameters for protein production in cells with low versus high numbers of plasmids. Compared to a traditional Hill-function-based model, the bin-dependent model requires only one additional parameter, but fits flow cytometry input-output data for individual modules up to twice as accurately. By composing together models of individually fit modules, we use the bin-dependent model to predict the behavior of six cascades and three feed-forward circuits. The bin-dependent models are shown to provide more accurate predictions on average than corresponding (composed) Hill-function-based models and predictions of comparable accuracy to EQuIP, while still providing a minimal ODE-based model that should be easy to integrate as a subcomponent within larger differential equation circuit models. Our analysis also demonstrates that accounting for batch effects is important in developing accurate composed models.Accepted manuscrip

MicroRNA history : discovery, recent applications and next frontiers

We thank the Department of Scientific Publications at The University of Texas MD Anderson Cancer Center for English language editing of the manuscript.Since 1993, when the first small non-coding RNA was identified, our knowledge about microRNAs has grown exponentially. In this review, we focus on the main progress in this field and discuss the most important findings under a historical perspective. In addition, we examine microRNAs as markers ofdisease diagnosis and prognosis, and as new therapeutic targets.M.I.A is supported by a PhD fellowship (SFRH/BD/47031/2008) from FCT (Fundação para a Ciência e Tecnologia) from Portugal. G.A.C. is supported as a Fellow at The University of Texas MD Anderson Research Trust, as a Fellow of The University of Texas System Regents Research Scholar, and by the CLL Global Research Foundation. Work in Dr. Calin’s laboratory was supported in part by NIH, by DoD, by 2009 Seena Magowitz – Pancreatic Cancer Action Network – AACR Pilot Grant and by the U.S./European Alliance for the Therapy of CLL

Lagrangian Variational Framework for Boundary Value Problems

A boundary value problem is commonly associated with constraints imposed on a system at its boundary. We advance here an alternative point of view treating the system as interacting "boundary" and "interior" subsystems. This view is implemented through a Lagrangian framework that allows to account for (i) a variety of forces including dissipative acting at the boundary; (ii) a multitude of features of interactions between the boundary and the interior fields when the boundary fields may differ from the boundary limit of the interior fields; (iii) detailed pictures of the energy distribution and its flow; (iv) linear and nonlinear effects. We provide a number of elucidating examples of the structured boundary and its interactions with the system interior. We also show that the proposed approach covers the well known boundary value problems.Comment: 41 pages, 3 figure

Alkali Metal Backup Cooling for Stirling Systems - Experimental Results

In a Stirling Radioisotope Power System (RPS), heat must be continuously removed from the General Purpose Heat Source (GPHS) modules to maintain the modules and surrounding insulation at acceptable temperatures. The Stirling convertor normally provides this cooling. If the Stirling convertor stops in the current system, the insulation is designed to spoil, preventing damage to the GPHS at the cost of an early termination of the mission. An alkali-metal Variable Conductance Heat Pipe (VCHP) can be used to passively allow multiple stops and restarts of the Stirling convertor. In a previous NASA SBIR Program, Advanced Cooling Technologies, Inc. (ACT) developed a series of sodium VCHPs as backup cooling systems for Stirling RPS. The operation of these VCHPs was demonstrated using Stirling heater head simulators and GPHS simulators. In the most recent effort, a sodium VCHP with a stainless steel envelope was designed, fabricated and tested at NASA Glenn Research Center (GRC) with a Stirling convertor for two concepts; one for the Advanced Stirling Radioisotope Generator (ASRG) back up cooling system and one for the Long-lived Venus Lander thermal management system. The VCHP is designed to activate and remove heat from the stopped convertor at a 19 C temperature increase from the nominal vapor temperature. The 19 C temperature increase from nominal is low enough to avoid risking standard ASRG operation and spoiling of the Multi-Layer Insulation (MLI). In addition, the same backup cooling system can be applied to the Stirling convertor used for the refrigeration system of the Long-lived Venus Lander. The VCHP will allow the refrigeration system to: 1) rest during transit at a lower temperature than nominal; 2) pre-cool the modules to an even lower temperature before the entry in Venus atmosphere; 3) work at nominal temperature on Venus surface; 4) briefly stop multiple times on the Venus surface to allow scientific measurements. This paper presents the experimental results from integrating the VCHP with an operating Stirling convertor and describes the methodology used to achieve their successful combined operation

Variable Conductance Heat Pipe Cooling of Stirling Convertor and General Purpose Heat Source

In a Stirling Radioisotope Power System (RPS), heat must be continuously removed from the General Purpose Heat Source (GPHS) modules to maintain the modules and surrounding insulation at acceptable temperatures. The Stirling convertor normally provides this cooling. If the Stirling convertor stops in the current system, the insulation is designed to spoil, preventing damage to the GPHS at the cost of an early termination of the mission. An alkali-metal Variable Conductance Heat Pipe (VCHP) can be used to passively allow multiple stops and restarts of the Stirling convertor. In a previous NASA SBIR Program, Advanced Cooling Technologies, Inc. (ACT) developed a series of sodium VCHPs as backup cooling systems for Stirling RPS. The operation of these VCHPs was demonstrated using Stirling heater head simulators and GPHS simulators. In the most recent effort, a sodium VCHP with a stainless steel envelope was designed, fabricated and tested at NASA Glenn Research Center (GRC) with a Stirling convertor for two concepts; one for the Advanced Stirling Radioisotope Generator (ASRG) back up cooling system and one for the Long-lived Venus Lander thermal management system. The VCHP is designed to activate and remove heat from the stopped convertor at a 19 degC temperature increase from the nominal vapor temperature. The 19 degC temperature increase from nominal is low enough to avoid risking standard ASRG operation and spoiling of the Multi-Layer Insulation (MLI). In addition, the same backup cooling system can be applied to the Stirling convertor used for the refrigeration system of the Long-lived Venus Lander. The VCHP will allow the refrigeration system to: 1) rest during transit at a lower temperature than nominal; 2) pre-cool the modules to an even lower temperature before the entry in Venus atmosphere; 3) work at nominal temperature on Venus surface; 4) briefly stop multiple times on the Venus surface to allow scientific measurements. This paper presents the experimental results from integrating the VCHP with an operating Stirling convertor and describes the methodology used to achieve their successful combined operation

The role of a new class of long noncoding RNAs transcribed from ultraconserved regions in cancer

Ultraconserved regions (UCRs) represent a relatively new class of non-coding genomic sequences highly conserved between human, rat and mouse genomes. These regions can reside within exons of protein-coding genes, despite the vast majority of them localizes within introns or intergenic regions. Several studies have undoubtedly demonstrated that most of these regions are actively transcribed in normal cells/tissues, where they contribute to regulate many cellular processes. Interestingly, these non-coding RNAs exhibit aberrant expression levels in human cancer cells and their expression profiles have been used as prognostic factors in human malignancies, as well as to unambiguously distinguish among distinct cancer types. In this review, we first describe their identification, then we provide some updated information about their genomic localization and classification. More importantly, we discuss about the available literature describing an overview of the mechanisms through which some transcribed UCRs (T-UCR) contribute to cancer progression or to the metastatic spread. To date, the interplay between T-UCRs and microRNAs is the most convincing evidence linking T-UCRs and tumorigenesis. The limitations of these studies and the future challenges to be addressed in order to understand the biological role of T-UCRs are also discussed herein. We envision that future efforts are needed to convincingly include this class of ncRNAs in the growing area of cancer therapeutics

Facultative methanotrophs are abundant at terrestrial natural gas seeps

Background: Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the subsurface before it reaches the atmosphere. Methanotrophs are usually obligate, i.e. grow only on methane and not on longer chain alkanes. Bacteria that grow on the other gaseous alkanes in natural gas such as propane have also been characterised, but they do not grow on methane. Recently, it was shown that the facultative methanotroph Methylocella silvestris grew on ethane and propane, other components of natural gas, in addition to methane. Therefore, we hypothesised that Methylocella may be prevalent at natural gas seeps and might play a major role in consuming all components of this potent greenhouse gas mixture before it is released to the atmosphere. Results: Environments known to be exposed to biogenic methane emissions or thermogenic natural gas seeps were surveyed for methanotrophs. 16S rRNA gene amplicon sequencing revealed that Methylocella were the most abundant methanotrophs in natural gas seep environments. New Methylocella-specific molecular tools targeting mmoX (encoding the soluble methane monooxygenase) by PCR and Illumina amplicon sequencing were designed and used to investigate various sites. Functional gene-based assays confirmed that Methylocella were present in all of the natural gas seep sites tested here. This might be due to its ability to use methane and other short chain alkane components of natural gas. We also observed the abundance of Methylocella in other environments exposed to biogenic methane, suggesting that Methylocella has been overlooked in the past as previous ecological studies of methanotrophs often used pmoA (encoding the alpha subunit of particulate methane monooxygenase) as a marker gene. Conclusion: New biomolecular tools designed in this study have expanded our ability to detect, and our knowledge of the environmental distribution of Methylocella, a unique facultative methanotroph. This study has revealed that Methylocella are particularly abundant at natural gas seeps and may play a significant role in biogeochemical cycling of gaseous hydrocarbons

Measurement of 21 cm brightness fluctuations at z ~ 0.8 in cross-correlation

In this letter, 21 cm intensity maps acquired at the Green Bank Telescope are cross-correlated with large-scale structure traced by galaxies in the WiggleZ Dark Energy Survey. The data span the redshift range 0.6 < z < 1 over two fields totaling ~41 deg. sq. and 190 hours of radio integration time. The cross-correlation constrains Omega_HI b_HI r = [0.43 \pm 0.07 (stat.) \pm 0.04(sys.)] x 10^-3, where Omega_HI is the neutral hydrogen HI fraction, r is the galaxy-hydrogen correlation coefficient, and b_HI is the HI bias parameter. This is the most precise constraint on neutral hydrogen density fluctuations in a challenging redshift range. Our measurement improves the previous 21 cm cross-correlation at z ~ 0.8 both in its precision and in the range of scales probed.Comment: 5 pages, 2 figures. As published in Ap