The Integration of Proteome-Wide PTM Data with Protein Structural and Sequence Features Identifies Phosphorylations that Mediate 14-3-3 Interactions.

14-3-3s are abundant proteins that regulate essentially all aspects of cell biology, including cell cycle, motility, metabolism, and cell death. 14-3-3s work by docking to phosphorylated Ser/Thr residues on a large network of client proteins and modulating client protein function in a variety of ways. In recent years, aided by improvements in proteomics, the discovery of 14-3-3 client proteins has far outpaced our ability to understand the biological impact of individual 14-3-3 interactions. The rate-limiting step in this process is often the identification of the individual phospho-serines/threonines that mediate 14-3-3 binding, which are difficult to distinguish from other phospho-sites by sequence alone. Furthermore, trial-and-error molecular approaches to identify these phosphorylations are costly and can take months or years to identify even a single 14-3-3 docking site phosphorylation. To help overcome this challenge, we used machine learning to analyze predictive features of 14-3-3 binding sites. We found that accounting for intrinsic protein disorder and the unbiased mass spectrometry identification rate of a given phosphorylation significantly improves the identification of 14-3-3 docking site phosphorylations across the proteome. We incorporated these features, coupled with consensus sequence prediction, into a publicly available web app, called "14-3-3 site-finder". We demonstrate the strength of this approach through its ability to identify 14-3-3 binding sites that do not conform to the loose consensus sequence of 14-3-3 docking phosphorylations, which we validate with 14-3-3 client proteins, including TNK1, CHEK1, MAPK7, and others. In addition, by using this approach, we identify a phosphorylation on A-kinase anchor protein-13 (AKAP13) at Ser2467 that dominantly controls its interaction with 14-3-3.

Atmospheric Carbon and Transport - America (ACT-America) Data Sets: Description, Management, and Delivery.

The ACT-America project is a NASA Earth Venture Suborbital-2 mission designed to study the transport and fluxes of greenhouse gases. The open and freely available ACT-America data sets provide airborne in situ measurements of atmospheric carbon dioxide, methane, trace gases, aerosols, clouds, and meteorological properties, airborne remote sensing measurements of aerosol backscatter, atmospheric boundary layer height and columnar content of atmospheric carbon dioxide, tower-based measurements, and modeled atmospheric mole fractions and regional carbon fluxes of greenhouse gases over the Central and Eastern United States. We conducted 121 research flights during five campaigns in four seasons during 2016-2019 over three regions of the US (Mid-Atlantic, Midwest and South) using two NASA research aircraft (B-200 and C-130). We performed three flight patterns (fair weather, frontal crossings, and OCO-2 underflights) and collected more than 1,140 h of airborne measurements via level-leg flights in the atmospheric boundary layer, lower, and upper free troposphere and vertical profiles spanning these altitudes. We also merged various airborne in situ measurements onto a common standard sampling interval, which brings coherence to the data, creates geolocated data products, and makes it much easier for the users to perform holistic analysis of the ACT-America data products. Here, we report on detailed information of data sets collected, the workflow for data sets including storage and processing of the quality controlled and quality assured harmonized observations, and their archival and formatting for users. Finally, we provide some important information on the dissemination of data products including metadata and highlights of applications of ACT-America data sets.

Fundamental image quality limits for microcomputed tomography in small animals.

Small-animal imaging has become increasingly more important as transgenic and knockout mice are produced to model human diseases. One imaging technique that has emerged is microcomputed tomography (micro-CT). For live-animal imaging, the precision in the images will be determined by the x-ray dose given to the animal. As a result, we propose a simple method to predict the noise performance of an x-ray micro-CT system as a function of dose and image resolution. An ideal, quantum-noise limited micro-CT scanner, assumed to have perfect resolution and ideal efficiency, was modeled. Using a simplified model, the coefficient of variation (COV) of the linear attenuation coefficient was calculated for a range of entrance doses and isotropic voxel sizes. COV calculations were performed for the ideal case and with simulated imperfections in efficiency and resolution. Our model was validated in phantom studies and mouse images were acquired with a specimen scanner to illustrate the results. A simplified model of noise propagation in the case of isotropic resolution indicates that the COV in the linear attenuation coefficient is proportional to (dose)(-1/2) and to the (isotropic voxel size)(-2) in the reconstructed volume. Therefore an improvement in the precision can be achieved only by increasing the isotropic voxel size (thereby decreasing the resolution of the image) or by increasing the x-ray dose. For the ideal scanner, a COV of 1% in the linear attenuation coefficient for an image of a mouse exposed to 0.25 Gy is obtained with a minimum isotropic voxel size of 135 microm. However, the same COV is achieved at a dose of 5.0 Gy with a 65 microm isotropic voxel size. Conversely, for a 68 mm diameter rat, a COV of 1% obtained from an image at 5.0 Gy would require an isotropic voxel size of 100 microm. These results indicate that short-term, potentially lethal, effects of ionizing radiation will limit high-resolution live animal imaging. As improvements in detector technology allow the resolution to improve, by decreasing the detector element size to tens of microns or less, high quality images will be limited by the x-ray dose administered. For the highest quality images, these doses will approach the lethal dose or LD50 for the animals. Approaching the lethal dose will affect the way experiments are planned, and may reduce opportunities for experiments involving imaging the same animal over time. Dose considerations will become much more important for live small-animal imaging as the limits of resolution are tested.

A precise radiographic technique for the measurement of dimensional changes in heart valve biomaterials following fixation.

Accurate tissue thickness measurements are difficult to acquire by present techniques. Error is introduced by tissue compression during measurements or by tissue processing prior to measurement. In the field of valve replacement, tissue dimensional changes from fixation prior to implantation may predispose implants to premature tissue failure and it becomes important to have an accurate method for comparing cusp dimensions pre- and post-fixation. A new approach is to use high-resolution digital radiography to make thickness maps of entire specimens. For 25 matched porcine aortic valve cusps, we have evaluated this technique's ability to measure and compare thickness, surface area and volume before and after 7 days of aldehyde fixation. Digital radiographs were acquired pre- and post-0.5% glutaraldehyde (n=13) or 10% formaldehyde (n=12) fixation. Mean thickness, surface area, volume and four measurements to evaluate shape differences with fixation were obtained and compared pre- and post-fixation using paired t tests. The results demonstrate that this X-ray imaging technique can provide dimensions of matched fresh and fixed specimens and is sensitive enough to show statistically significant changes due to fixation. These findings also illustrate that aldehyde fixation can cause tissue contraction resulting in a significant overall increase in tissue thickness and a decrease in surface area. This technique could be used to gain further insights into tissue anatomy and mechanics.

Rapid small-animal dual-energy X-ray absorptiometry using digital radiography.

Although dual-energy X-ray absorptiometry (DEXA) is an established technique for clinical assessment of areal bone mineral density (BMD), the spatial resolution, signal-to-noise ratio, scan time, and availability of clinical DEXA systems may be limiting factors for small-animal investigations using a large number of specimens. To avoid these limitations, we have implemented a clinical digital radiography system to perform rapid area DEXA analysis on in vitro rat bone specimens. A crossed step-wedge (comprised of epoxy-based materials that mimic the radiographic properties of tissue and bone) was used to calibrate the system. Digital radiographs of bone specimens (pelvis, spine, femur, and tibia from sham-ovariectomized [SHAM] and ovariectomized [OVX] rats) were obtained at 40 kilovolt peak (kVp) and 125 kVp, and the resulting areal BMD values were compared with those obtained with a clinical fan-beam DEXA system (Hologics QDR 4500). Our investigation indicates that the cross-wedge calibrated (CWC) DEXA technique provides high-precision measurements of bone mineral content (BMC; CV = 0.6%) and BMD (CV = 0.8%) within a short acquisition time (<30 s). Areal BMD measurements reported by the CWC-DEXA system are within 8.5% of those reported by a clinical fan-beam scanner, and BMC values are within 5% of the known value of test specimens. In an in vivo application, the CWC-DEXA system is capable of reporting significant differences between study groups (SHAM and OVX) that are not reported by a clinical fan-beam DEXA system, because of the reduced variance and improved object segmentation provided by the CWC-DEXA system.

Bone mineral measurement of phalanges: comparison of radiographic absorptiometry and area dual X-ray absorptiometry.

With a standard, image-intensifier-based, digital radiographic system, high-spatial-resolution images of the hand were acquired for analysis of phalangeal bone mineral density with dual x-ray absorptiometry (DXA). Results with phalangeal DXA had precision of plus or minus 0.67% and accuracy of 4.1% and correlated well with those with radiographic absorptiometry. This phalangeal DXA technique is potentially useful for clinical diagnosis of osteoporosis.