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Defining the HIV Capsid Binding Site of Nucleoporin 153
The human immunodeficiency virus (HIV) can infect nondividing cells by interacting with the host nuclear pore complex. The host nuclear pore protein NUP153 directly interacts with the HIV capsid to promote viral nuclear entry.
Bat Acoustic Survey Data Collected June 2024 in and near Self Sufficiency Parcel-2 (SSP2) on the Oak Ridge Reservation (ORR)
The US Department of Energy (DOE) Oak Ridge Reservation (ORR) is located in Anderson and Roane Counties, Tennessee. A portion of the ORR, known as Self-Sufficiency Parcel 2 (SSP2) is planned for transfer for private use. The SSP2 Site is approximately 670 acres (Figure 1-1), although the current plan is to only clear and develop a portion of this acreage. Any inquiries about the land transfer and future development should be directed to DOE Oak Ridge Environmental Management, as this is beyond the scope of the Natural Resources Management Team (NRMT). NRMT records bat data for the entire ORR, including acoustic monitoring, mist netting and cave surveys. A few surveys have previously been conducted for small land transfers adjacent to SSP2 (See Appendix A), but not for the entire SSP2 area. Since bats have a large range, it was decided that collecting data while SSP2 was still accessible would be beneficial for the NRMT dataset. Acoustic data was therefore collected within and near SSP2 during the summer of 2024. This write-up is not a Biological Assessment (BA). However, the data and information provided can be used during the creation of a BA and consultations with US Fish and Wildlife Service (USFWS) in order to comply with federal directives of the Endangered Species Act of 1973 (16 U. S. C. 153 et seq.). The SSP2 site was surveyed during summer roosting/maternity season of 2024 using ultrasonic acoustic monitors to record calls from all bat species whose home ranges include the ORR. Special note was taken for presence of Federally listed Endangered and Threatened (T&E) bat species, as well as bat species which are Proposed for Federal listing, Candidate for federal listing, and state listed. Summer roosting season, from May 15 to August 15, is crucial to forest-dwelling T&E bat species for rearing young and foraging. Results of these surveys indicate the presence of three Federally listed bat species: Gray bat (Myotis grisescens--Endangered), Indiana bat (Myotis sodalis--Endangered), and Northern long-eared bat (Myotis septentrionalis--Endangered). Two additional bat species were present on the SSP2 Site: Tricolored bat (Perimyotis subflavus--Proposed for Federal listing) and Little brown bat (Myotis lucifugus—Candidate for Federal listing).
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation
Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. Here, we demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.
Spallation Neutron Source Second Target Station Construction Project: Biological Assessment
The Endangered Species Act of 1973 (16 U.S.C. 153 et seq.), as amended (ESA or Act) in section 7(a)(1) directs Federal agencies to conserve and recover listed species and use their authorities in the furtherance of the purposes of the Act by carrying out programs for the conservation of endangered and threatened species so that listing is no longer necessary (50 CFR §402). Furthermore, the Act in section 7(a)(2) directs Federal agencies to consult (referred to as section 7 consultation) with the U.S. Fish and Wildlife Service (USFWS) when their activities “may affect” a listed species or designated critical habitat. This biological assessment (BA) analyzes the potential effects of the proposed Spallation Neutron Source Second Target Station STS construction project on the U. S. Department of Energy Oak Ridge Reservation (ORR) on Federal listed threatened, endangered, proposed, and under consideration for Federal listing bat species, pursuant to section 7(a)(2) of the ESA.
Assessing springtime vertebrate prey of sympatric mesopredators in the southeastern United States using metabarcoding analysis
Coyotes (Canis latrans) colonized the eastern United States over the last century and formed a 3-species predator guild with bobcats (Lynx rufus) and gray foxes (Urocyon cinereoargenteus) across much of the southeastern United States. Diets among the three species vary along with respective impacts on game species such as white-tailed deer (Odocoileus virginianus) and wild turkeys (Meleagris gallopavo). To determine predation impacts on vertebrate prey and dietary overlap in consumption of prey items, we assessed diets of coyote, bobcat, and gray fox during spring, coinciding with white-tailed deer fawning and wild turkey nesting and brood rearing. We sampled across three sites along the Savannah River in South Carolina from mid-May through mid-June of 2020–2021. We collected 180 scat samples along 295.9 kilometers (71.1–122.4 km/site) of unpaved secondary roads and used DNA metabarcoding to determine vertebrate diet items. We identified predator species of scat using DNA metabarcoding and species-specific mtDNA fragment analysis (153 were coyote, 20 bobcat, and seven gray fox). Overall, we found evidence that two species, coyote and bobcat, consumed deer while all three consumed turkeys. Frequency of deer in the diet varied across sites for coyotes from 62–86% and wild turkey was present with a frequency of occurrence of 9% for coyotes, 5% for bobcats, and 14% for gray fox. Vertebrate diet specialization was evident across predator species with high frequency of deer in coyote diets, rabbits and small mammals in bobcat diets, and herpetofauna in gray fox diets. During deer fawning and wild turkey nesting and brood rearing, dietary overlap appears to be mediated by disparate selection of prey items, which reduced competition among coyotes, bobcats, and gray foxes. Use of DNA metabarcoding may augment our understanding of dietary preferences within this predator guild by providing increased resolution of diet composition among important game species.