A Spatiotemporal Assessment of Fish Assemblage Response to Land-Use Change and the Evaluation of eDNA Metabarcoding for Describing Diverse Fish Communities

Fish assemblages are often assessed as a biological proxy for environmental health. While humans value healthy environments for the ecosystem services and recreational opportunities they provide, it is increasingly evident that such resources can be paradoxically degraded by anthropogenic activities. In this investigation, we studied the relationship between different intensities of anthropogenic land-use change and habitat-driven fish assemblage response across multiple spatiotemporal scales. Secondarily, we explored the efficacy of eDNA metabarcoding against conventional electrofishing techniques for the purpose of describing complete fish communities. This study was conducted in the Tuckahoe Creek basin near Richmond, Virginia. This James River tributary serves as an optimal case-study due to a myriad of land-use changes that have continued to occur throughout the basin, in conjunction with a diverse fish assemblage that has been studied across a unique fisheries dataset that originated in 1869. Our findings indicate that fish assemblage dynamics are driven by localized, low-intensity development, and are therefore longitudinally discontinuous throughout the Tuckahoe Creek basin. Further, we observed that eDNA metabarcoding outperformed electrofishing in determining fish biodiversity throughout the system

Age- and sex-based variation in helminth infection of helmeted guineafowl (Numida meleagris) with comments on Swainson's spurfowl (Pternistis swainsonii) and Orange River francolin (Scleroptila levaillantoides)

Gastrointestinal tracts from 48 helmeted guineafowl (Numida meleagris), five Swainson's spurfowl (Pternistis swainsonii) and a single Orange River francolin (Scleroptila levaillantoides) were examined for helminth parasites. Twelve species of helminths were found in helmeted guineafowl, comprising six nematodes, five cestodes and a single acanthocephalan. Six species of nematodes were recovered from Swainson's spurfowl and a single nematode was recovered from the Orange River francolin. First-year guineafowl had more than twice the intensity of infection than did adult guineafowl, particularly regarding the acanthocephalan Mediorhynchus gallinarum, the caecal nematodes Subulura dentigera and S. suctoria, and the cestodes Octopetalum numida, Hymenolepis cantaniana and Numidella numida. Female guineafowl had significantly higher intensities of infection than males, especially concerning M. gallinarum, S. dentigera and N. numida and the nematode Gongylonema congolense. The recovery of the cestode Retinometra sp. from helmeted guineafowl constitutes a new host-parasite record

The Endowment Effect in Orangutans

The endowment effect is the tendency to, seemingly irrationally, immediately value a possessed item more than the opportunity to acquire the identical item when one does not already possess it. Although endowment effects are reported in chimpanzees (Brosnan, Jones, Lambeth, Mareno, Richardson, & Shapiro, 2007) and capuchin monkeys (Lakshminarayanan, Chen, & Santos, 2008), both species share social traits with humans that make convergence as likely an evolutionary mechanism as homology. Orangutans (Pongo spp.) provide a unique insight into the evolution of the endowment effect, along with other apparently irrational behaviors, because their less frequent social interactions and relatively more solitary social organization distinguishes them from the more gregarious apes, allowing a test of evolutionary homology. In the present study, we used pairs of both food and non-food objects, as in an earlier test on chimpanzees (Brosnan et al., 2007). We established the apes’ preferences in forced-choice tasks, then tested whether they showed an endowment effect in an exchange task, in which subjects were given one of the objects, followed by the option to exchange it for the other. Here, we report the first evidence of the endowment effect in a relatively less social primate, the orangutan. This indicates that this behavior may have evolved as a homology within the primates, rather than being due to convergent social pressures. These findings provide stronger evidence for the hypothesis that at least one bias, the endowment effect, may be common in primates and, potentially, other species

SPIDR: Small-Molecule Peptide-Influenced Drug Repurposing

Background: Conventional de novo drug design is costly and time consuming, making it accessible to only the best resourced research organizations. An emergent approach to new drug development is drug repurposing, in which compounds that have already gone through some level of clinical testing are examined for efficacy against diseases divergent than their original application. Repurposing of existing drugs circumvents the time and considerable cost of early stages of drug development, and can be accelerated by using software to screen existing chemical databases to identify suitable drug candidates. Results: Small-molecule Peptide-Influenced Drug Repurposing (SPIDR) was developed to identify small molecule drugs that target a specific receptor by exploring the conformational binding space of peptide ligands. SPIDR was tested using the potent and selective 16-amino acid peptide α-conotoxin MII ligand and the α3β2-nicotinic acetylcholine receptor (nAChR) isoform. SPIDR incorporates a genetic algorithm-based, heuristic search procedure, which was used to explore the ligand binding domain of the α3β2-nAChR isoform using a library consisting of 640,000 α-conotoxin MII peptide analogs. The peptides that exhibited the highest affinity for α3β2-nAChR were used as models for a small-molecule structure similarity search of the PubChem Compound database. SPIDR incorporates the SimSearcher utility, which generates shape distribution signatures of molecules and employs multi-level K-means clustering to insure fast database queries. SPIDR identified non-peptide drugs with estimated binding affinities nearly double that of the native α-conotoxin MII peptide. Conclusions: SPIDR has been generalized and integrated into DockoMatic v 2.1. This software contains an intuitive graphical interface for peptide mutant screening workflow and facilitates mapping, clustering, and searching of local molecular databases, making DockoMatic a valuable tool for researchers in drug design and repurposing

Evidence for a late glacial advance near the beginning of the Younger Dryas in western New York State: An event postdating the record for local Laurentide ice sheet recession

Widespread evidence of an unrecognized late glacial advance across preexisting moraines in western New York is confirmed by 40 14C ages and six new optically stimulated luminescence analyses between the Genesee Valley and the Cattaraugus Creek basin of eastern Lake Erie. The Late Wisconsin chronology is relatively unconstrained by local dating of moraines between Pennsylvania and Lake Ontario. Few published 14C ages record discrete events, unlike evidence in the upper Great Lakes and New England. The new 14C ages from wood in glacial tills along Buttermilk Creek south of Springville, New York, and reevaluation of numerous 14C ages from miscellaneous investigations in the Genesee Valley document a significant glacial advance into Cattaraugus and Livingston Counties between 13,000 and 13,300 cal yr B.P., near the Greenland Interstadial 1b (GI-1b) cooling leading into the transition from the Bölling-Alleröd to the Younger Dryas. The chronology from four widely distributed sites indicates that a Late Wisconsin advance spread till discontinuously over the surface, without significantly modifying the preexisting glacial topography. A short-lived advance by a partially grounded ice shelf best explains the evidence. The advance, ending 43 km south of Rochester and a similar distance south of Buffalo, overlaps the revised chronology for glacial Lake Iroquois, now considered to extend from ca. 14,800–13,000 cal yr B.P. The spread of the radiocarbon ages is similar to the well-known Two Creeks Forest Bed, which equates the event with the Two Rivers advance in Wisconsin

ETDs in Lock-Down: Trends, Analyses and Faculty Perspectives on ETD Embargoes

Owen, Terry, Timothy Hackman and Thomas Harrod. 2009. “ETDs in Lock-Down: Trends, Analyses and Faculty Perspectives on ETD Embargoes.” ETD 2009: 12th International Symposium on Electronic Theses and Dissertations, Pittsburgh, PA, June 10-13, 2009. Also available at http://conferences.library.pitt.edu/ocs/viewabstract.php?id=679&cf=7.Since September 2006, graduate students at the University of Maryland have had the option of restricting access to their ETD in the university’s digital repository (DRUM) for either a one- or six-year period. Embargo requests must be approved by the student’s faculty advisor and submitted to the Graduate School prior to uploading the ETD. Since the beginning of the program, an average of 32% of the ETDs that have been submitted each semester have been embargoed. While Engineering has the largest number of embargoes (150), Chemical and Life Sciences has the greatest percentage (54%), followed closely by Agriculture and Natural Resources (51%) and Business (47%). The College of Arts and Humanities, specifically the English Department, has the largest number of six-year embargoes (75). Faculty advisors who had approved at least one embargo request since 2006 were surveyed to gain insight into their perspectives on publicly available ETDs and ascertain their reasons for approving embargo requests. In general, faculty advisors indicated that they approve ETDs without attempting to change the students’ choice of embargo period, indicating that the student plays a major role in deciding whether or not to embargo their ETD. In addition, faculty stated that the primary reason for approving embargoes was to protect opportunities for future publication. While the percentage of embargoes has remained relatively constant each semester, our goal is to decrease the number of embargoes by educating faculty and students on the benefits of making their research widely available. We are working with the Graduate School and library faculty to develop a scholarly communications program that not only educates faculty and graduate students about the consequences of embargoes, but also makes them more aware of open access issues in general

Simultaneous vehicle routing and charging station siting for commercial Electric Vehicles

As organizations electrify their vehicle fleets in order to lower costs, reduce emissions, and improve their pub-lic image, they face the problem of providing charging access to their vehicles on the road. Electric vehicle

Testing Hydrodynamic Models of LMC X-4 with UV and X-ray Spectra

We compare the predictions of hydrodynamic models of the LMC X-4 X-ray binary system with observations of UV P Cygni lines with the GHRS and STIS spectrographs on the Hubble Space Telescope. The hydrodynamic model determines density and velocity fields of the stellar wind, wind-compressed disk, accretion stream, Keplerian accretion disk, and accretion disk wind. We use a Monte Carlo code to determine the UV P Cygni line profiles by simulating the radiative transfer of UV photons that originate on the star and are scattered in the wind. The qualitative orbital variation predicted is similar to that observed, although the model fails to reproduce the strong orbital asymmetry (the observed absorption is strongest for phi>0.5). The model predicts a mid-eclipse X-ray spectrum, due almost entirely to Compton scattering, with a factor 4 less flux than observed with ASCA. We discuss how the model may need to be altered to explain the spectral variability of the system.Comment: 11 figures, accepted by Ap

Sequencing PDX1 (insulin promoter factor 1) in 1788 UK individuals found 5% had a low frequency coding variant, but these variants are not associated with Type 2 diabetes

OnlineOpen Article. This is a copy of an article published in Diabetic Medicine. This journal is available online at: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1464-5491Genome-wide association studies have identified >30 common variants associated with Type 2 diabetes (>5% minor allele frequency). These variants have small effects on individual risk and do not account for a large proportion of the heritable component of the disease. Monogenic forms of diabetes are caused by mutations that occur in <1:2000 individuals and follow strict patterns of inheritance. In contrast, the role of low frequency genetic variants (minor allele frequency 0.1-5%) in Type 2 diabetes is not known. The aim of this study was to assess the role of low frequency PDX1 (also called IPF1) variants in Type 2 diabetes