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A cell-free system for polynucleotide amplification and translation is disclosed. Also disclosed are methods for using the system and a composition which allows the various components of the system to function under a common set of reaction conditions.
Multiple scattering radiative transfer results are used to calculate action spectrum weighted irradiances and fractional irradiance changes in terms of a power law in ozone OMEGA, U(OMEGA/200)(sup -RAF), where the new radiation amplification factor (RAF) is just a function of solar zenith angle. Including Rayleigh scattering caused small differences in the estimated 30 year changes in action spectrum-weighted irradiances compared to estimates that neglect multiple scattering. The radiative transfer results are applied to several action spectra and to an instrument response function corresponding to the Solar Light 501 meter. The effect of changing ozone on two plant damage action spectra are shown for plants with high sensitivity to UVB (280-315 run) and those with lower sensitivity, showing that the probability for plant damage for the latter has increased since 1979, especially at middle to high latitudes in the Southern Hemisphere. Similarly, there has been an increase in rates of erythemal skin damage and pre-vitamin D3 production corresponding to measured ozone decreases. An example conversion function is derived to obtain erythemal irradiances and the UV index from measurements with the Solar Light 501 instrument response function. An analytic expressions is given to convert changes in erythemal irradiances to changes in CIE vitamin-D action spectrum weighted irradiances.
Computations are performed to study laminar-turbulent transition due to isolated roughness elements in boundary layers at Mach 3.5 and 5.95, with an emphasis on flow configurations for which experimental measurements from low disturbance wind tunnels are available. The Mach 3.5 case corresponds to a roughness element with right-triangle planform with hypotenuse that is inclined at 45 degrees with respect to the oncoming stream, presenting an obstacle with spanwise asymmetry. The Mach 5.95 case corresponds to a circular roughness element along the nozzle wall of the Purdue BAMQT wind tunnel facility. In both cases, the mean flow distortion due to the roughness element is characterized by long-lived streamwise streaks in the roughness wake, which can support instability modes that did not exist in the absence of the roughness element. The linear amplification characteristics of the wake flow are examined towards the eventual goal of developing linear growth correlations for the onset of transition.
Any cluster of parachute systems is subject to effects on performance due to interactions between the parachutes. One such interaction is the twisting of a riser from one parachute around that of another. Due to friction and relative motion between the risers, it is possible for the tension in the riser near the attach point to be different from the tension in the riser towards the suspension lines or canopy. This could result in system failure due to larger than expected loading. The Orion Capsule Parachute Assembly System (CPAS) designed and executed a test to quantify the amplification of the load in a parachute riser due to twist, rocking rate and angle, cluster size, and canopy load. The design of the testing approach, test matrix, and hardware are discussed along with results and findings.
The Amplification Factor Transport (AFT) transition model proposed by Coder and Maughmer is implemented in the unstructured and curvilinear Reynolds-Averaged Navier-Stokes (RANS) solvers of the Launch Ascent and Vehicle Aerodynamics (LAVA) platform. It is coupled to the Spalart-Allmaras (SA) turbulence model through a modified intermittency variable. As part of the model verification and validation phase, laminar-turbulent transition is studied over 2D flat plates, wind turbine and general aviation airfoils, as well as a 3D inclined prolate spheroid and the JAXA Standard Model (JSM). This work will analyze the sensitivity of the results to grid refinement, grid paradigm, flow conditions and numerical schemes. The numerical efficiency of the unstructured and curvilinear solvers will be compared and convergence acceleration techniques will be explored to address a broad range of aerodynamics applications.
The Arctic is a dynamic region, demonstrated by its remarkable internal variability and rapid response to anthropogenic climate change over the last 40 years. Actionable predictions and projections hold significant value for managing both natural and human systems. The value of these model outputs only grows in a warmer, less icy Arctic. However, substantial gaps exist in our understanding of cross-scale and cross-interface (air-sea ice-ocean) interactions that limit our predictive capabilities. Studies dating back at least 40 years provide evidence that the evolution of the Arctic climate system is sensitive to these cross-scale and cross-interface interactions. This presentation summarizes our understanding of cross-scale and cross-interface interactions relevant to the Arctic’s response to anthropogenic climate change—Arctic Amplification. The presentation emphasizes the influence of surface-type dependent turbulent flux exchanges of heat and moisture, the rectification of episodic atmospheric heat transport events on time-averaged changes, local and remote feedback interactions, and cross-seasonal energy transfers. The presentation concludes with a summary of knowledge gaps and discusses potential pathways for accelerating our understanding of the Arctic climate system.
Arctic amplification (AA) is a coupled atmosphere-sea ice-ocean process. This understanding has evolved from the early concept of AA, as a consequence of snow ice line progressions, through more than a century of research that has clarified the relevant processes and driving mechanisms of AA. The predictions made by early modeling studies, namely the fall/winter maximum, bottom-heavy structure, the prominence of surface albedo feedback, and the importance of stable stratification have withstood the scrutiny of multi-decadal observations and more complex models. Yet, the uncertainty in Arctic climate projections is larger than in any other region of the planet, making the assessment of high-impact, near-term regional changes difficult or impossible. Reducing this large spread in Arctic climate projections requires a quantitative process understanding. This presentation synthesizes current knowledge of AA and describes a set of recommendations to guide future research. It briefly reviews the history of AA science, summarizes observed Arctic changes, discusses modeling approaches and feedback diagnostics, and assesses the current understanding of the most relevant feedbacks to AA. These sections culminate in a conceptual model of the fundamental physical mechanisms causing AA and a collection of recommendations to accelerate progress towards reduced uncertainty in Arctic climate projections. Our conceptual model highlights the need to account for local feedback and remote process interactions within the context of the annual cycle to constrain projected AA.
The Arctic is a dynamic region, demonstrated by its remarkable internal variability and rapid response to anthropogenic climate change over the last >40 years. Actionable predictions and projections hold significant value for managing both natural and human systems. The value of these model outputs only grows in a warmer, less icy Arctic. However, substantial gaps exist in our understanding of cross-scale and cross-interface (air-sea ice-ocean) interactions that limit our predictive capabilities. Studies dating back at least 40 years provide evidence that the evolution of the Arctic climate system is sensitive to these cross-scale and cross-interface interactions. This presentation summarizes our understanding of cross-scale and cross-interface interactions relevant to the Arctic’s response to anthropogenic climate change—Arctic Amplification. The presentation emphasizes the influence of surface-type dependent turbulent flux exchanges of heat and moisture, the rectification of episodic atmospheric heat transport events on time-averaged changes, local and remote feedback interactions, and cross-seasonal energy transfers. The presentation concludes with a summary of knowledge gaps and discusses potential pathways for accelerating our understanding of the Arctic climate system.
The Arctic is a dynamic region, demonstrated by its remarkable internal variability and rapid response to anthropogenic climate change over the last >40 years. Actionable predictions and projections hold significant value for managing both natural and human systems. The value of these model outputs only grows in a warmer, less icy Arctic. However, substantial gaps exist in our understanding of cross-scale and cross-interface (air-sea ice-ocean) interactions that limit our predictive capabilities. Studies dating back at least 40 years provide evidence that the evolution of the Arctic climate system is sensitive to these cross-scale and cross-interface interactions. This presentation summarizes our understanding of cross-scale and cross-interface interactions relevant to the Arctic’s response to anthropogenic climate change—Arctic Amplification. The presentation emphasizes the influence of surface-type dependent turbulent flux exchanges of heat and moisture, the rectification of episodic atmospheric heat transport events on time-averaged changes, local and remote feedback interactions, and cross-seasonal energy transfers. The presentation concludes with a summary of knowledge gaps and discusses potential pathways for accelerating our understanding of the Arctic climate system.
A chirped pulse amplification system includes a laser source providing an input laser pulse along an optical path. The input laser pulse is characterized by a first temporal duration. The system also includes a multi-pass pulse stretcher disposed along the optical path. The multi-pass pulse stretcher includes a first set of mirrors operable to receive input light in a first plane and output light in a second plane parallel to the first plane and a first diffraction grating. The pulse stretcher also includes a second set of mirrors operable to receive light diffracted from the first diffraction grating and a second diffraction grating. The pulse stretcher further includes a reflective element operable to reflect light diffracted from the second diffraction grating. The system further includes an amplifier, a pulse compressor, and a passive dispersion compensator disposed along the optical path.
An analysis of Coherent electron Cooling (CeC) amplifier based on 1D Free Electron Laser (FEL) theory was previously performed with exact solution of the dispersion relation, assuming electrons having Lorentzian energy distribution. At high gain limit, the asymptotic behavior of the FEL amplifier can be better understood by Taylor expanding the exact solution of the dispersion relation with respect to the detuning parameter. In this work, we make quadratic expansion of the dispersion relation for Lorentzian energy distribution and investigate how longitudinal space charge and electrons’ energy spread affect the FEL amplification process.
Our approach to prokaryotic single-cell Whole Genome Amplification at the JGI continues to evolve. To increase both the quality and number of single-cell genomes produced, we explore all aspects of the process from cell sorting to sequencing. For example, we now utilize specialized reagents, acoustic liquid handling, and reduced reaction volumes eliminate non-target DNA contamination in WGA reactions. More specifically, we use a cleaner commercial WGA kit from Qiagen that employs a UV decontamination procedure initially developed at the JGI, and we use the Labcyte Echo for tip-less liquid transfer to set up 2uL reactions. Acoustic liquid handling also dramatically reduces reagent costs. In addition, we are exploring new cell lysis methods including treatment with Proteinase K, lysozyme, and other detergents, in order to complement standard alkaline lysis and allow for more efficient disruption of a wider range of cells. Incomplete lysis represents a major hurdle for WGA on some environmental samples, especially rhizosphere, peatland, and other soils. Finding effective lysis strategies that are also compatible with WGA is challenging, and we are currently assessing the impact of various strategies on genome recovery.
An apparatus for chip-based sorting, amplification, detection, and identification of a sample having a planar substrate. The planar substrate is divided into cells. The cells are arranged on the planar substrate in rows and columns. Electrodes are located in the cells. A micro-reactor maker produces micro-reactors containing the sample. The micro-reactor maker is positioned to deliver the micro-reactors to the planar substrate. A microprocessor is connected to the electrodes for manipulating the micro-reactors on the planar substrate. A detector is positioned to interrogate the sample contained in the micro-reactors.
The present invention, in part, relates to methods and apparatuses for on-chip amplification and/or detection of various targets, including biological targets and any amplifiable targets. In some examples, the microculture apparatus includes a single-use, normally-closed fluidic valve that is initially maintained in the closed position by a valve element bonded to an adhesive coating. The valve is opened using a magnetic force. The valve element includes a magnetic material or metal. Such apparatuses and methods are useful for in-field or real-time detection of targets, especially in limited resource settings.
The present invention, in part, relates to methods and apparatuses for on-chip amplification and/or detection of various targets, including biological targets and any amplifiable targets. In some examples, the microculture apparatus includes a single-use, normally-closed fluidic valve that is initially maintained in the closed position by a valve element bonded to an adhesive coating. The valve is opened using a magnetic force. The valve element includes a magnetic material or metal. Such apparatuses and methods are useful for in-field or real-time detection of targets, especially in limited resource settings.
Disclosed are methods for isothermal nucleic acid amplification and detection.
We report on an organic-based photodetector that integrates a dual-gate organic thin-film transistor (DG-OTFT) with an organic photodiode (OPD) to produce a device with a high effective responsivity at low optical power and video-rate compatible response. In this device, the OPD operates in photovoltaic mode, instead of the commonly used photoconductive mode, to modulate one of the gate voltages of the DG-OTFT. Effective responsivity values of 10 A W –1 are measured at optical power values lower than 10 nW at 635 nm. Here, modeling of the operation of this new photodetector suggests that effective responsivity values up to 10 5 A W –1 can be achieved at optical powers of 1 nW using current printing technology and state-of-the-art organic semiconductors.
Rational engineering strategies that seek to harness the remarkable diversity of microbial metabolism can be limited by incomplete biological knowledge. As described here, a novel approach to address this challenge involved replacing a native pathway for degrading lignin-derived aromatic compounds via ortho cleavage of protocatechuate in Acinetobacter baylyi ADP1 with a foreign meta-cleavage pathway that uses different enzymes, metabolites, and redox carriers. This alteration may improve lignin valorization and coordinate catabolism with bioproduction strategies. When a 14-kbp region of foreign DNA was inserted in the chromosome, the heterologous genes failed to confer growth on target substrates. Regional gene dosage was increased using a synthetic DNA fragment to promote recombination, and higher copy number enabled growth. During adaptive laboratory evolution, compensatory mutations arose that permit growth with one copy of the foreign genes. This complex metabolic remodeling was accomplished without assumptions about the impediments that initially prevented growth. To understand the changes that emerged, a novel transformation assay identified a combination of mutations sufficient for the new phenotype. Three unexpected changes were revealed: loss of one foreign enzyme, loss of one native enzyme, and loss of a two-component transcriptional regulatory system. This study establishes that large multicopy tandem arrays of poorly adapted pathway genes can confer new functions and improve understanding of metabolism.