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Predicting spatiotemporal patterns of road mortality for medium-large mammals
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Influence of intrinsic and extrinsic attributes on neonate survival in an invasive large mammal
Abstract Understanding factors influencing survival of neonates for wild species is important for successful management, particularly for determining drivers of population dynamics. Wild pigs ( Sus scrofa ) are invasive and populations are rapidly increasing in part due to high reproductive capacity. Survival of adults is generally high, however, survival of piglets, and particularly neonates, is largely unknown. We located neonates at the natal nest and quantified survival in relation to individual and maternal biological attributes, and environmental variables. During 2017–2020, we captured 50 neonates from 13 litters and documented 28 mortalities (56%) over six weeks. Survival was positively influenced by pelage coloration, likely as a form of camouflage from predators. Male neonates had higher survival. They were born larger than females, which could be beneficial for thermoregulation and competition for milk. Neonates born to larger sows had lower survival. Sow size was positively correlated with litter size, and this finding may reflect the increased nutritional demands of sustaining large litters, or difficulties in defending more neonates against predators. Neonates born in warmer months had higher survival than those born in cooler months. Neonates are inefficient thermoregulators, thus being born in warmer months could be beneficial for maintaining homeostasis as well as access to more food resources. These are the largest and most complete data for neonate wild pig survival and will inform population models for the development of management strategies to reduce negative impacts of this destructive invasive species on native ecosystems.
Selenium-mediated arsenic excretion in mammals: a synchrotron-based study of whole-body distribution and tissue-specific chemistry
Abstract not provided
Crystal Structures of GCN2 Protein Kinase C-terminal Domains Suggest Regulatory Differences in Yeast and Mammals
Abstract not provided
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.
Mass-independent maximal metabolic rate predicts geographic range size of placental mammals
Not Available
Identification of ancestral gnathostome Gli3 enhancers with activity in mammals
Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15–21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. In conclusion, these results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.
X-ray CT Scans - New Mexico Mammals - Set 1
A collection of x-ray computed tomography scans of specimens from the Museum of Southwestern Biology.
System wide analyses have underestimated protein abundances and the importance of transcription in mammals
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8000–16 000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170 000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 12% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R2 = 0.13). Based on this, our second strategy suggests that mRNA levels explain ~81% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller role. Finally, the above estimates only apply to those genes whose mRNA and protein expression was detected. Based on a detailed analysis by Hebenstreit et al. (2012), we estimate that approximately 40% of genes in a given cell within a population express no mRNA. Since there can be no translation in the absence of mRNA, we argue that differences in translation rates can play no role in determining the expression levels for the ~40% of genes that are non-expressed.
Disposition of legacy mammal specimens; Presentation for the Natural Resources Damage Assessment Trustee Council Meeting
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Assessing endothelial function using a blood pressure cuff
Methods and apparatus are provided for assessing endothelial function in a mammal. In certain embodiments the methods involve applying to the artery a substantially constant external pressure that causes the tension in the arterial wall to be reduced, where the pressure is provided via a cuff adjacent to and/or around a region of the mammal's body; determining, over the course of one or more cardiac cycles, changes in pressure in the cuff resulting from cardiac activity of the mammal to establish a baseline value for a parameter related to endothelial function in the mammal; applying a stimulus to the mammal; determining, over the course of one or more cardiac cycles, changes in pressure in the cuff resulting from cardiac activity of the mammal to establish a stimulus-effected value for a parameter related to endothelial function in the mammal; wherein the baseline value is determined from measurements made when the mammal is not substantially effected by the stimulus; and wherein differences in the baseline value and the stimulus-effected value provide a measure of endothelial function in the mammal.
Acoustic characterization of sensors used for marine environmental monitoring
We report active acoustic sensors are widely used in oceanographic and environmental studies. Although many have nominal operating frequencies above the range of marine mammal hearing, they can produce out-of-band sound that may be audible to marine mammals. Acoustic emissions from four active acoustic transducers were characterized and compared to marine mammal hearing thresholds. All four transducers had nominal operating frequencies above the reported upper limit of marine mammal hearing, but produced measurable sound below 160 kHz. A spatial map of the acoustic emissions of each sonar is used to evaluate potential effects on marine mammal hearing when the transducer is continuously operated from a stationary platform. Based on the cumulative sound exposure level metric, the acoustic emissions from the transducers are unlikely to cause temporary threshold shifts in marine mammals, but could affect animal behavior. The extent of audibility is estimated to be, at most, on the order of 100 m.
FINAL TECHNICAL REPORT: Underwater Active Acoustic Monitoring Network For Marine And Hydrokinetic Energy Projects
This project saw the completion of the design and development of a second generation, high frequency (90-120 kHz) Subsurface-Threat Detection Sonar Network (SDSN). The system was deployed, operated, and tested in Cobscook Bay, Maine near the site the Ocean Renewable Power Company TidGen™ power unit. This effort resulted in a very successful demonstration of the SDSN detection, tracking, localization, and classification capabilities in a high current, MHK environment as measured by results from the detection and tracking trials in Cobscook Bay. The new high frequency node, designed to operate outside the hearing range of a subset of marine mammals, was shown to detect and track objects of marine mammal-like target strength to ranges of approximately 500 meters. This performance range results in the SDSN system tracking objects for a significant duration - on the order of minutes - even in a tidal flow of 5-7 knots, potentially allowing time for MHK system or operator decision-making if marine mammals are present. Having demonstrated detection and tracking of synthetic targets with target strengths similar to some marine mammals, the primary hurdle to eventual automated monitoring is a dataset of actual marine mammal kinematic behavior and modifying the tracking algorithms and parameters which are currently tuned to human diver kinematics and classification.
Review of Recent Literature Relevant to the Environmental Effects of Marine and Hydrokinetic Energy Devices, Task 2.1.3: Effects on Aquatic Organisms – Fiscal Year 2011 Progress Report Environmental Effects of Marine and Hydrokinetic Energy
A literature search was conducted by using the Web of Science® Databases component of the ISI Web of KnowledgeSM to identify recent articles that would be useful to help assess the potential environmental effects of renewable energy development in the ocean, with emphasis on marine mammals, seabirds, and fish. Several relatively recent general review articles that included possible effects of marine renewable energy devices on marine mammals and seabirds were examined to begin the search process (e.g., Boehlert et al. 2008; Thompson et al. 2008; Simas et al. 2009). From these articles, several general topics of potential environmental effects on marine mammals, seabirds, and fish were derived. These topics were used as the primary search factors. Searches were conducted with reference to the potential effects of offshore wind farms and MHK devices on marine mammals, seabirds, and fish. Additional sources were identified by cross-checking the Web of Science databases for articles that cited the review articles. It also became clear that often the potential effects were offered as hypotheses that often were not supported by the presentation of appropriate documentation. Therefore, the search was refined and focused on trying to obtain the necessary information to support or challenge a proposed potential effect to a specific concern. One of the expressed concerns regarding MHK devices is that placing wave parks in coastal waters could compromise the migration patterns of whales. Disruption of the annual migration of the gray whale (Eschrichtius robustus), which swims at least 30,000 km on its round trip from breeding grounds in Baja California to feeding areas in the Bering Sea, is of particular concern. Among the hypothesized effects on the migrating gray whales are increased predation risk by constricting migration corridor to between array and shore or by forcing the whales to swim into deeper waters, increased metabolic energy costs and delays in reaching the destinations, and interrupting feeding by blocking access to benthic areas under arrays. The literature search focused on identifying published studies that could provide information to evaluate these concerns. The results were developed into a case study that evaluated the potential effects of the placement of wave parks in coastal waters along the migration route of the gray whale. Wave parks and other MHK arrays may have additional effects on gray whales and other marine mammals, including entanglement in mooring lines and interference with communications among other effects, that were not included in this case study. The case study results were rewritten into a simpler form that would be suitable for placement on a web blog