Promoter architecture dictates cell-to-cell variability in gene expression

Variability in gene expression among genetically identical cells has emerged as a central preoccupation in the study of gene regulation; however, a divide exists between the predictions of molecular models of prokaryotic transcriptional regulation and genome-wide experimental studies suggesting that this variability is indifferent to the underlying regulatory architecture. We constructed a set of promoters in Escherichia coli in which promoter strength, transcription factor binding strength, and transcription factor copy numbers are systematically varied, and used messenger RNA (mRNA) fluorescence in situ hybridization to observe how these changes affected variability in gene expression. Our parameter-free models predicted the observed variability; hence, the molecular details of transcription dictate variability in mRNA expression, and transcriptional noise is specifically tunable and thus represents an evolutionarily accessible phenotypic parameter

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

One of the paramount goals of synthetic biology is to have the ability to tune transcriptional networks to targeted levels of expression at will. As a step in that direction, we have constructed a set of 18 unique binding sites for E. coli RNA Polymerase (RNAP) σ^(70) holoenzyme, designed using a model of sequence-dependent binding energy combined with a thermodynamic model of transcription to produce a targeted level of gene expression. This promoter set allows us to determine the correspondence between the absolute numbers of mRNA molecules or protein products and the predicted promoter binding energies measured in K_(B)T energy units. These binding sites adhere on average to the predicted level of gene expression over orders of magnitude in constitutive gene expression, to within a factor of in both protein and mRNA copy number. With these promoters in hand, we then place them under the regulatory control of a bacterial repressor and show that again there is a strict correspondence between the measured and predicted levels of expression, demonstrating the transferability of the promoters to an alternate regulatory context. In particular, our thermodynamic model predicts the expression from our promoters under a range of repressor concentrations between several per cell up to over 100 per cell. After correcting the predicted polymerase binding strength using the data from the unregulated promoter, the thermodynamic model accurately predicts the expression for the simple repression strains to within 30%. Demonstration of modular promoter design, where parts of the circuit (such as RNAP/TF binding strength and transcription factor copy number) can be independently chosen from a stock list and combined to give a predictable result, has important implications as an engineering tool for use in synthetic biology

Making a Grand Contribution: Professional Development Resources for Leveraging Assessment Data to Advance Equity

Describes professional development opportunities collected by the Grand Challenges Equity Implementation Team to advance equity in institutional assessment. Julene L. Jones, Ciji A. Heiser and Glenn A. Phillips. Making a Grand Contribution: Professional Development Resources for Leveraging Assessment Data to Advance Equity Assessment Update Vol. 36 Iss. 1 (2024) p. 11 - 14 ISSN: 1536-072

Effect of dusts on tomato production

The phytotoxicity of bauxite, cement flue, mud lake, alumina and kaolin dusts were examined on tomatoes. Mud lake white dust caused severe leaf scorch, affected plant growth and resulted in no harvestable yield. Flue dust applied daily depressed market yield of fruit from 64 t ha to 42 t ha. Flue dust applied at 3.1 t ha had no effect. There was no phytotoxic effect from bauxite, alumina or kaolin

Received...

One of the paramount goals of synthetic biology is to have the ability to tune transcriptional networks to targeted levels of expression at will. As a step in that direction, we have constructed a set of 18 unique binding sites for E. coli RNA Polymerase (RNAP) s70 holoenzyme, designed using a model of sequence-dependent binding energy combined with a thermodynamic model of transcription to produce a targeted level of gene expression. This promoter set allows us to determine the correspondence between the absolute numbers of mRNA molecules or protein products and the predicted promoter binding energies measured in kBT energy units. These binding sites adhere on average to the predicted level of gene expression over 3 orders of magnitude in constitutive gene expression, to within a factor of 3 in both protein and mRNA copy number. With these promoters in hand, we then place them under the regulatory control of a bacterial repressor and show that again there is a strict correspondence between the measured and predicted levels of expression, demonstrating the transferability of the promoters to an alternate regulatory context. In particular, our thermodynamic model predicts the expression from our promoters under a range of repressor concentrations between several per cell up to over 100 per cell. After correcting the predicted polymerase binding strength using the data from the unregulated promoter, the thermodynamic model accurately predicts the expression for the simple repression strains to within 30%. Demonstration of modular promoter design, where parts of the circuit (such as RNAP/TF binding strength and transcription factor cop

Minimizing Induced Drag with Weight Distribution, Lift Distribution, Wingspan, and Wing-Structure Weight

Because the wing-structure weight required to support the critical wing section bending moments is a function of wingspan, net weight, weight distribution, and lift distribution, there exists an optimum wingspan and wing-structure weight are presented for rectangular wings with four different sets of design constraints. These design constraints are fixed lift distribution and net weight combined with 1) fixed maximum stress and wing loading, 2) fixed maximum deflection and wing loading, 3) fixed maximum stress and stall speed and 4) fixed maximum deflection and stall speed. For each of these analytic solutions, the optimum wing-structure weight is found to depend only on the net weight, independent of the arbitrary fixed lift distribution. Analytic solutions for optimum weight and lift distributions are also presented for the same four sets of design constraints. Depending on the design constraints, the optimum lift distribution can differ significantly from the elliptic lift distribution. Solutions for two example wing designs are presented, which demonstrate how the induced drag varies with lift distribution, wingspan, and wing-structure weight in the design space near the optimum solution. Although the analytic solutions presented here are restricted to rectangular wings, these solutions provide excellent test cases for verifying numerical algorithms used for more general multidisciplinary analysis and optimization

Minimum Induced Drag for Tapered Wings Including Structural Constraints

For a wing in steady level flight, the lift distribution that minimizes induced drag depends on a tradeoff between wingspan and wing-structure weight. In 1933, Prandtl suggested that tapered wings have an advantage over rectangular wings due to this tradeoff. However, Prandtl’s solutions were obtained using assumptions that correspond to rectangular wings. Therefore, his claim was not analytically proven by his 1933 publication. Here, an approach similar to Prandtl’s is taken with more general approximations that apply to wings of arbitrary planform. This more general development is used to study Prandtl’s claim about tapered wings. Closed-form solutions for the optimum wingspan and corresponding induced drag are presented for wings having elliptic and linearly-tapered planforms with constraints of fixed wing loading and maximum stress. It is shown that induced drag is minimized with a triangular planform, which gives a reduction in induced drag of up to 24.44% over the rectangular planform and up to 11.71% over the elliptic planform. Numerical solutions for the lift distributions that minimize induced drag for each planform are also presented. It is shown that the optimum lift distribution produces up to 5.94% less induced drag than the elliptic lift distribution when the triangular planform is used

Plasma heat shock protein 27 is associated with coronary artery disease, abdominal aortic aneurysm and peripheral artery disease

Low protein levels of Hsp27 have been reported in atherosclerotic plaques. In addition, human studies have indicated that circulating Hsp27 levels are lower in coronary artery disease patients compared with controls. It remains, however, unclear whether this applies to other forms of atherosclerotic disease. Plasma Hsp27 from 280 subjects was examined by ELISA. The cohort included 80 coronary artery disease (CAD), 40 peripheral artery disease (PAD) and 80 abdominal aortic aneurysm (AAA) patients. Eighty elderly subjects, without any clinical history of vascular diseases, were used as a control group. Receiver operating curve (ROC) and logistic regression model analysis were performed to evaluate the potential value of Hsp27 as a circulating biomarker. Patients with atherosclerotic vascular diseases had significantly lower levels of Hsp27 than control subjects (p < 0.001). Moreover, Hsp27 was significantly lower in CAD patients than other atherosclerotic vascular disease groups (p < 0.001). There was no difference in Hsp27 levels between the AAA and PAD groups. Using the ROC-generated optimal cut-off values for Hsp27, logistic regression modeling indicated that low plasma Hsp27 was independently associated with the presence of multiple forms of atherosclerotic disease. In conclusion, circulating Hsp27 is significantly lower in patients with multiple forms of atherosclerotic arterial disease

On the selective deposition of tin and tin oxide on various glasses using a high power diode laser

The deposition of SnO2 using a 120 W high power diode laser (HPDL) on both fused silica and soda-lime-silica glass has been successfully demonstrated. Deposition on both glass substrates was carried out with laser power densities of 650-1600 W cm-2 and at rates of 420-1550 mm min-1. The thickness of the deposited layers was typically around 250 m. The maximum theoretical coverage rate that it may be possible to achieve using the HPDL was calculated as being 3.72 m2 h-1. Owing to the wettability characteristics of Sn, it proved impossible to deposit the metal on either glass substrate. Evidence of solidified microstructures was observed, with the microstructures differing considerably across the same deposited track. These differences were attributed to variations in the solidification rate, R, and the thermal gradient, G. Adhesion of the SnO2 with the soda-lime-silica glass was found to be due to mechanical bonding. The adhesion of the SnO2 with the fused silica was seen to the result of a chemical bond arising from an interface region between the SnO2 and the fused silica glass substrate. This interface region was found to be comprised of mainly Si and rich with Sn3O4

Comparison of Theoretical and High-Fidelity Aerostructural Solutions

As contemporary aerostructural research in aircraft design trends toward high-fidelity computational methods, aerostructural solutions based on theory are often neglected or forgotten. In fact, in many modern aerostructural wing optimization studies, the elliptic lift distribution is used as a benchmark in place of theoretical aerostructural solutions with more appropriate constraints. In this paper, we review several theoretical aerostructural solutions that could be used as benchmark cases for wing design studies, and we compare them to high-fidelity solutions with similar constraints. Solutions are presented for studies with 1) constraints related to the wing integrated bending moment, 2) constraints related to the wing root bending moment, and 3) structural constraints combined with constraints on either wing stall or wing loading. It is shown that for each set of design constraints, the theoretical optimum lift distribution consistently shows excellent agreement with high-fidelity results. It follows that theoretical optimum lift distributions can often serve as a good benchmark for higher fidelity aerostructural wing optimization methods. Moreover, a review of solutions for the optimum wingspan and corresponding drag reveals important insights into the effects of viscosity, aeroelasticity, and compressibility on the aerodynamic and structural coupling involved in wing design and optimization