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Erie, PA, United States

Foulk M.S.,Brown University | Foulk M.S.,Mercyhurst University | Urban J.M.,Brown University | Casella C.,Brown University | And 2 more authors.
Genome Research

Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand-independent λ-exo biases in NSseq and validated this approach at the rDNA locus. The λ-exo-controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na+ instead of K+ in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq. © 2015 Foulk et al. Source

McIntyre P.J.,University of California at Berkeley | Thorne J.H.,University of California at Davis | Dolanc C.R.,University of California at Davis | Dolanc C.R.,University of Montana | And 5 more authors.
Proceedings of the National Academy of Sciences of the United States of America

We document changes in forest structure between historical (1930s) and contemporary (2000s) surveys of California vegetation through comparisons of tree abundance and size across the state and within several ecoregions. Across California, tree density in forested regions increased by 30% between the two time periods, whereas forest biomass in the same regions declined, as indicated by a 19% reduction in basal area. These changes reflect a demographic shift in forest structure: larger trees (>61 cm diameter at breast height) have declined, whereas smaller trees (<30 cm) have increased. Large tree declines were found in all surveyed regions of California, whereas small tree increases were found in every region except the south and central coast. Large tree declines were more severe in areas experiencing greater increases in climaticwater deficit since the 1930s, based on a hydrologicmodel of water balance for historical climates through the 20th century. Forest composition in California in the last century has also shifted toward increased dominance by oaks relative to pines, a pattern consistent with warming and increased water stress, and also with paleohistoric shifts in vegetation in California over the last 150,000 y. Source

Hefner J.T.,Central Identification Laboratory | Ousley S.D.,Mercyhurst University
Journal of Forensic Sciences

Ancestry assessments using cranial morphoscopic traits currently rely on subjective trait lists and observer experience rather than empirical support. The trait list approach, which is untested, unverified, and in many respects unrefined, is relied upon because of tradition and subjective experience. Our objective was to examine the utility of frequently cited morphoscopic traits and to explore eleven appropriate and novel methods for classifying an unknown cranium into one of several reference groups. Based on these results, artificial neural networks (aNNs), OSSA, support vector machines, and random forest models showed mean classification accuracies of at least 85%. The aNNs had the highest overall classification rate (87.8%), and random forests show the smallest difference between the highest (90.4%) and lowest (76.5%) classification accuracies. The results of this research demonstrate that morphoscopic traits can be successfully used to assess ancestry without relying only on the experience of the observer. © 2014 American Academy of Forensic Sciences. Source

Lesciotto K.M.,Mercyhurst University
Journal of Forensic Sciences

Forensic anthropologists anticipated a significant impact from the 1993 Supreme Court Daubert decision, which addressed the standard of admissibility for expert testimony. In response, many forensic articles cited Daubert in the search for objective techniques or a critique of established subjective methods. This study examines challenges to forensic anthropological expert testimony to evaluate whether Daubert has actually affected the admissibility of such testimony. Thirty cases were identified that addressed the admissibility of the testimony, including 14 cases prior to Daubert and 16 after Daubert. Examination of these cases indicates that post-Daubert cases do not result in more exclusions. Yet, this lack of exclusions may instead be viewed as a manifestation of the field's overall surge toward more objective and quantifiable techniques in a self-regulating response to Daubert. © 2015 American Academy of Forensic Sciences. Source

Persico L.,Mercyhurst University | Meyer G.,University of New Mexico
Earth Surface Processes and Landforms

Two centuries of human activities in the Greater Yellowstone Ecosystem (GYE) have strongly influenced beaver activity on small streams, raising questions about the suitability of the historical (Euro-American) period for establishing stream reference conditions. We used beaver-pond deposits as proxy records of beaver occupation to compare historical beaver activity to that throughout the Holocene. Forty-nine carbon-14 (14C) ages on beaver-pond deposits from Grand Teton National Park indicate that beaver activity was episodic, where multi-century periods lacking dated beaver-pond deposits have similar timing to those previously documented in Yellowstone National Park. These gaps in the sequence of dated deposits coincide with episodes of severe, prolonged drought, e.g. within the Medieval Climatic Anomaly 1000-600calyr bp, when small streams likely became ephemeral. In contrast, many beaver-pond deposits date to 500-100calyr bp, corresponding to the colder, effectively wetter Little Ice Age. Abundant historical beaver activity in the early 1900s is coincident with a climate cooler and wetter than present and more abundant willow and aspen, but also regulation of beaver trapping and the removal of wolves (the beaver's main predator), all favorable for expanded beaver populations. Reduced beaver populations after the 1920s, particularly in the northern Yellowstone winter range, are in part a response to elk overbrowsing of willow and aspen that later stemmed from wolf extirpation. Beaver populations on small streams were also impacted by low streamflows during severe droughts in the 1930s and late 1980s to present. Thus, both abundant beaver in the 1920s and reduced beaver activity at present reflect the combined influence of management practices and climate, and underscore the limitations of the early historical period for defining reference conditions. The Holocene record of beaver activity prior to Euro-American activities provides a better indication of the natural range of variability in beaver-influenced small stream systems of the GYE. © 2012 John Wiley & Sons, Ltd. Source

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