Structural fingerprints of transcription factor binding site regions

Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data

Americans Support for Renewable Energy is Disconnected from their Understanding of Powerline Infrastructure as a Mechanism to Mitigate Climate Change

As nations are transitioning to renewable energy sources, they will need to expand and upgrade their energy infrastructure, including high-voltage power lines (HVPL). We have conducted the first nation-wide survey in the last thirty years to assess public attitudes toward HVPL in the USA. The study evaluates perceptions, knowledge, and attitudes toward building new transmission lines, as these relate to renewable energy, place attachment, and environmental impacts. Our results show that Americans do not recognize how new HVPL could help reduce greenhouse gas emissions; instead, respondents favor moving from centralized energy (large power stations and HVPL) to decentralized energy (local power supply and small scale solar panels and wind turbines. Our findings are consistent with studies from Europe in that citizens recognize negative human impacts on the natural world and support renewable energy, however, they have a limited understanding of the role of HVPL infrastructure in mitigating climate change

Bod1, a novel kinetochore protein required for chromosome biorientation

We have combined the proteomic analysis of Xenopus laevis in vitro–assembled chromosomes with RNA interference and live cell imaging in HeLa cells to identify novel factors required for proper chromosome segregation. The first of these is Bod1, a protein conserved throughout metazoans that associates with a large macromolecular complex and localizes with kinetochores and spindle poles during mitosis. Small interfering RNA depletion of Bod1 in HeLa cells produces elongated mitotic spindles with severe biorientation defects. Bod1-depleted cells form syntelic attachments that can oscillate and generate enough force to separate sister kinetochores, suggesting that microtubule–kinetochore interactions were intact. Releasing Bod1-depleted cells from a monastrol block increases the frequency of syntelic attachments and the number of cells displaying biorientation defects. Bod1 depletion does not affect the activity or localization of Aurora B but does cause mislocalization of the microtubule depolymerase mitotic centromere- associated kinesin and prevents its efficient phosphorylation by Aurora B. Therefore, Bod1 is a novel kinetochore protein that is required for the detection or resolution of syntelic attachments in mitotic spindles

High Spatial Resolution Observations of Two Young Protostars in the R Corona Australis Region

We present multi-wavelength, high spatial resolution imaging of the IRS 7 region in the R Corona Australis molecular cloud. Our observations include 1.1 mm continuum and HCO^+ J = $3 \to 2$ images from the SMA, ^{12}CO J = $3 \to 2$ outflow maps from the DesertStar heterodyne array receiver on the HHT, 450 $\mu$m and 850 $\mu$m continuum images from SCUBA, and archival Spitzer IRAC and MIPS 24 \micron images. The accurate astrometry of the IRAC images allow us to identify IRS 7 with the cm source VLA 10W (IRS 7A) and the X-ray source X_W. The SMA 1.1 mm image reveals two compact continuum sources which are also distinguishable at 450 $\mu$m. SMA 1 coincides with X-ray source CXOU J190156.4-365728 and VLA cm source 10E (IRS 7B) and is seen in the IRAC and MIPS images. SMA 2 has no infrared counterpart but coincides with cm source VLA 9. Spectral energy distributions constructed from SMA, SCUBA and Spitzer data yield bolometric temperatures of 83 K for SMA 1 and $\leq$70 K for SMA 2. These temperatures along with the submillimeter to total luminosity ratios indicate that SMA 2 is a Class 0 protostar, while SMA 1 is a Class 0/Class I transitional object (L=$17\pm6$ \Lsun). The ^{12}CO J = $3 \to 2$ outflow map shows one major and possibly several smaller outflows centered on the IRS 7 region, with masses and energetics consistent with previous work. We identify the Class 0 source SMA 2/VLA 9 as the main driver of this outflow. The complex and clumpy spatial and velocity distribution of the HCO^+ J = $3 \to 2$ emission is not consistent with either bulk rotation, or any known molecular outflow activity.Comment: 31 pages, 8 figures, Accepted to Ap

NASA Centers and Universities Collaborate in Annual Smallsat Technology Partnerships

The Small Spacecraft Technology program within the NASA Space Technology Mission Directorate sponsors the Smallsat Technology Partnerships (STP) initiative. The STP initiative awards cooperative agreements between NASA centers and university teams for technology development efforts that advance the capabilities of small spacecraft to achieve NASA mission objectives in unique and more affordable ways. NASA’s announcement to return humans to the Moon by 2024 raises new opportunities for Smallsats to contribute to missions in cislunar space, though technical challenges are to be overcome to establish their value in this environment. Precursor missions utilizing small spacecraft will blaze the trail for lunar exploration, establishing infrastructure such as communication and navigation networks, and performing assembly and repair services for larger structures and human habitats. To achieve these goals, certain novel Smallsat technologies will need to be developed and demonstrated. The 2020 STP solicitation sought proposals for specific technologies to enable these lunar missions. For the 2020 STP cycle, NASA selected nine university teams to mature new systems and capabilities in the laboratory, and in some cases, demonstrate in suborbital or orbital spaceflights. This paper describes the STP portfolio, past and present efforts, and the nine partnerships selected

SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications.

We present the SSIPTools suite of programs. SSIPTools is a collection of software modules enabling the use of the Surface Site Interaction Point (SSIP) molecular descriptors, used for the modeling of noncovalent interactions in neutral organic molecules. It contains an implementation of the workflow for the generation of the SSIP descriptors, as well as the Functional Group Interaction Profiles (FGIPs) and Solvent Similarity Indexes (SSIs) applications, based on the SSIMPLE (Surface Site Interaction model for the Properties of Liquids at Equilibria) approach.Engineering and Physical Sciences Research Council (EP/M506485/1

Generalized Lévy walks and the role of chemokines in migration of effector CD8+ T cells.

Chemokines have a central role in regulating processes essential to the immune function of T cells, such as their migration within lymphoid tissues and targeting of pathogens in sites of inflammation. Here we track T cells using multi-photon microscopy to demonstrate that the chemokine CXCL10 enhances the ability of CD8+ T cells to control the pathogen Toxoplasma gondii in the brains of chronically infected mice. This chemokine boosts T-cell function in two different ways: it maintains the effector T-cell population in the brain and speeds up the average migration speed without changing the nature of the walk statistics. Notably, these statistics are not Brownian; rather, CD8+ T-cell motility in the brain is well described by a generalized Lévy walk. According to our model, this unexpected feature enables T cells to find rare targets with more than an order of magnitude more efficiency than Brownian random walkers. Thus, CD8+ T-cell behaviour is similar to Lévy strategies reported in organisms ranging from mussels to marine predators and monkeys, and CXCL10 aids T cells in shortening the average time taken to find rare targets

A Surface Site Interaction Point Method for Dissipative Particle Dynamics Parametrization: Application to Alkyl Ethoxylate Surfactant Self-Assembly.

Dissipative particle dynamics (DPD) is a coarse-grained approach to the simulation of large supramolecular systems, but one limitation has been that the parameters required to describe the noncovalent interactions between beads are not readily accessible. A first-principles computational method has been developed so that bead interaction parameters can be calculated directly from ab initio gas-phase molecular electrostatic potential surfaces of the molecular fragments that represent the beads. A footprinting algorithm converts the molecular electrostatic potential surfaces into a discrete set of surface site interaction points (SSIPs), and these SSIPs are used in the SSIMPLE (surface site interaction model for the properties of liquids at equilibrium) algorithm to calculate the free energies of transfer of one bead into a solution of any other bead. The bead transfer free energies are then converted into the required DPD interaction parameters for all pairwise combinations of different beads. The reliability of the parameters was demonstrated using DPD simulations of a range of alkyl ethoxylate surfactants. The simulations reproduce the experimentally determined values of the critical micelle concentration and mean aggregation number well for all 22 surfactants studied.Engineering and Physical Sciences Research Counci