Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 3′-untranslated region (UTR) and CpG di-nucleotides in the 5′-UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells.

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

Recent advances in DNA sequencers are accelerating genome sequencing, especially in microbes, and complete and draft genomes from various species have been sequenced in rapid succession. Here, we present a comprehensive gene prediction tool, the MetaGeneAnnotator (MGA), which precisely predicts all kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having a variety of lengths. The MGA integrates statistical models of prophage genes, in addition to those of bacterial and archaeal genes, and also uses a self-training model from input sequences for predictions. As a result, the MGA sensitively detects not only typical genes but also atypical genes, such as horizontally transferred and prophage genes in a prokaryotic genome. In this paper, we also propose a novel approach for analyzing the ribosomal binding site (RBS), which enables us to detect species-specific patterns of the RBSs. The MGA has the ingenious RBS model based on this approach, and precisely predicts translation starts of genes. The MGA also succeeds in improving prediction accuracies for short sequences by using the adapted RBS models (96% sensitivity and 93% specificity for 700 bp fragments). These features of the MGA expedite wide ranges of microbial genome studies, such as genome annotations and metagenome analyses.

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

Soil moisture induced droughts are expected to become more frequent under future global climate change. Precipitation has been previously assumed to be mainly responsible for variability in summer soil moisture. However, little is known about the impacts of precipitation frequency on summer soil moisture, either interannually or spatially. To better understand the temporal and spatial drivers of summer drought, 415 site yr measurements observed at 75 flux sites world wide were used to analyze the temporal and spatial relationships between summer soil water content (SWC) and the precipitation frequencies at various temporal scales, i.e., from half-hourly, 3, 6, 12 and 24 h measurements. Summer precipitation was found to be an indicator of interannual SWC variability with r of 0.49 (p < 0.001) for the overall dataset. However, interannual variability in summer SWC was also significantly correlated with the five precipitation frequencies and the sub-daily precipitation frequencies seemed to explain the interannual SWC variability better than the total of precipitation. Spatially, all these precipitation frequencies were better indicators of summer SWC than precipitation totals, but these better performances were only observed in non-forest ecosystems. Our results demonstrate that precipitation frequency may play an important role in regulating both interannual and spatial variations of summer SWC, which has probably been overlooked or underestimated. However, the spatial interpretation should carefully consider other factors, such as the plant functional types and soil characteristics of diverse ecoregions.

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An underestimated role of precipitation frequency in regulating summer soil moisture

The surface reactions of electrolytes with a silicon anode in lithium ion cells have been investigated. The investigation utilizes two novel techniques that are enabled by the use of binder-free silicon (BF-Si) nanoparticle anodes. The first method, transmission electron microscopy with energy dispersive X-ray spectroscopy, allows straightforward analysis of the BF-Si solid electrolyte interphase (SEI). The second method utilizes multi-nuclear magnetic resonance spectroscopy of D2O extracts from the cycled anodes. The TEM and NMR data are complemented by XPS and FTIR data, which are routinely used for SEI studies. Coin cells (BF-Si/Li) were cycled in electrolytes containing LiPF6 salt and ethylene carbonate or fluoroethylene carbonate solvent. Capacity retention was significantly better for cells cycled with LiPF6/FEC electrolyte than for cells cycled with LiPF6/EC electrolyte. Our unique combination of techniques establishes that for LiPF6/EC electrolyte the BF-Si SEI continuously grows during the first ...

https://digitalcommons.uri.edu/cgi/viewcontent.cgi?article=1220&context=oa_diss

Anode solid electrolyte interphase (sei) of lithium ion battery characterized by microscopy and spectroscopy

The butterfly family Nymphalidae contains some of the most important non-drosophilid insect model systems for evolutionary and ecological studies, yet the evolutionary history of the group has remained shrouded in mystery. We have inferred a robust phylogenetic hypothesis based on sequences of 10 genes and 235 morphological characters for exemplars of 400 of the 540 valid nymphalid genera representing all major lineages of the family. By dating the branching events, we infer that Nymphalidae originated in the Cretaceous at 90 Ma, but that the ancestors of 10–12 lineages survived the end-Cretaceous catastrophe in the Neotropical and Oriental regions. Patterns of diversification suggest extinction of lineages at the Cretaceous/Tertiary boundary (65 Ma) and subsequent elevated speciation rates in the Tertiary.

/pdf/nymphalid-butterflies-diversify-following-near-demise-at-the-30248ty592.pdf

Nymphalid butterflies diversify following near demise at the Cretaceous/Tertiary boundary

Introduction: Astronauts soaring through space modules with the grace of birds seems counterintuitive. How do they adapt to the weightless environment? Previous spaceflights have shown that astronauts in orbit adapt their motor strategies to each change in their gravitational environment. During adaptation, performance is degraded and can lead to mission-threatening injuries. If adaptation can occur before a mission, productivity during the mission might improve, minimizing risk. The goal is to combine kinetic and kinematic data to examine translational motions during microgravity adaptations. Methods: Experiments were performed during parabolic flights aboard NASA's C-9. Five subjects used their legs to push off from a sensor, landing on a target 3.96 m (13 ft) away. The sensor quantified the kinetics during contact, while four cameras recorded kinematics during push-off. Joint torques were calculated for a subset of traverses (N = 50) using the forces, moments, and joint angles. Results: During the 149 traverses, the average peak force exerted onto the sensor was 224.6 ± 74.6 N, with peak values ranging between 65.8―461.9 N. Two types of force profiles were observed, some having single, strong peaks (N = 64) and others having multiple, weaker peaks (N = 86). Conclusions: The force data were consistent with values recorded previously in sustained microgravity aboard Mir and the Space Shuttle. A training program for astronauts might be designed to encourage fine-control motions (i.e., multiple, weaker peaks) as these reduce the risk of injury and increase controllability. Additionally, a kinematic and kinetic sensor suite was successfully demonstrated in the weightless environment onboard the C-9 aircraft.

Kinetics and kinematics for translational motions in microgravity during parabolic flight.

An accurate knowledge of the satellites, space debris, and other objects orbiting Earth is critical to mission planning and avoiding on-orbit collisions. Numerous ground and space-based space situational awareness platforms have been developed to aid in the identification and tracking of these objects, collectively known as resident space objects. While space situational awareness satellites are ideal for identifying and tracking space debris, many other satellites have sensors that may be able to contribute to space situational awareness. This paper examines the feasibility of leveraging several existing sensor technologies to aid in identifying and tracking resident space objects. Specifically, we investigate how Synthetic Aperture Radars (SARs), laser rangefinders, Light Detection and Ranging (LIDAR) devices, and laser communication devices can provide range measurements between the observing platform and the resident space object. Based on this survey, we believe that investigating the feasibility of utilizing LIDAR devices for RSO ranging is worth further study.

Feasibility of Gathering Resident Space Object Range Measurements Using In-Orbit Observers

In space, it is usually not possible to repair equipment when things go wrong. While astronauts ventured into space aboard the Space Shuttle to repair the infamously flawed Hubble Space Telescope, these types of repair missions are extremely expensive and rare. Limited repair options make spacecraft engineers turn their attention to reliability in an attempt to avoid failures altogether. Building a reliable system starts with a robust design, incorporates proven parts, and—most importantly—involves a lot of testing.

Testing satellite control systems with drones

GNSS-denied navigation has been the topic of much research for decades. Interference and occlusion by the surrounding environment limit GNSS access in urban environments. Poor GNSS coverage in the Arctic is another reason to pursue local navigation systems independent on satellite coverage. Our solution is to develop specially designed beacon systems that transmit the beacons' position data to a vehicle over radio signals. The receiving vehicle then uses the signal strength to estimate its position relative to the beacons. This paper provides the design and implementation of a low-cost beacon system that provides position information required for navigation in GNSS-denied environments. 

Design and Implementation of a Low-Cost Local Beacon System for GPS-Denied Environments

The ability of drones to navigate through remote terrain and avoid ground-based vehicular traffic has led to an increase in remote sensing studies and drone-based transportation services. Such applications require a payload to be suspended from the drone via a cable which can introduce instability in the drone's flight resulting from the sway of the suspended payload. Therefore, to maintain a stable flight it is key to measure the position of the payload relative to the drone. This study uses a Vicon motion capture system to measure the position of the drone and simulated Light Detection and Ranging (LiDAR) measurements for the position of the payload. LiDAR measurements are simulated using a LiDAR noise model developed from experimental results using the Velodyne VLP-16 sensor. A nonlinear dynamic model of a drone-based single cable-suspended payload is developed and a discrete Extended Kalman Filter is used to obtain an accurate estimate of the position of the drone and the position of the payload relative to the drone. 

Philip Ferguson

Papers

Kinetics and kinematics for translational motions in microgravity during parabolic flight.

Feasibility of Gathering Resident Space Object Range Measurements Using In-Orbit Observers

Testing satellite control systems with drones

Design and Implementation of a Low-Cost Local Beacon System for GPS-Denied Environments

Drone-Based Cable-Suspended Payload Tracking and Estimation Using Simulated LiDAR Measurements and an Extended Kalman Filter