A novel NGS library preparation method to characterize native termini of fragmented DNA.

Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes?7 of which are novel?from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g fromEarly andMiddle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal 15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement 9,000 years ago.Fil: Roca Rada, Xavier. Centre For Ancient Dna, University Of Adelaide; AustraliaFil: Politis, Gustavo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Messineo, Pablo Geronimo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Scheifler, Nahuel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Scabuzzo, Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia de Entre Ríos. Universidad Nacional de Entre Ríos. Centro de Investigaciones y Transferencia de Entre Ríos; ArgentinaFil: Gonzalez, Mariela Edith. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Harkins, Kelly M.. University of California; Estados UnidosFil: Reich, David. Harvard Medical School; Estados UnidosFil: Souilmi, Yassine. University of Adelaide; AustraliaFil: Teixeira, Joao C. T.. University of Adelaide; AustraliaFil: Llamas, Bastien. University of Adelaide; AustraliaFil: Fehren Schmitz, Lars. University of California; Estados Unido

The Grizzly, February 7, 2002

The Bluelight Hits a Stoplight: Kmart Files for Chapter 11 • Reinstatement of Zeta Chi Charter On Hold • Alan Morrison and Friends to Perform at Heefner Organ Recital • Opinions: Not Everyone Loves Valentine\u27s Day; Tri Sig Strikes Back; Nowhere to Park • Wynton Marsalis is Coming to Campus! • Berman Museum: A Fun and Relaxing Alternative • When the Weather Outside is Frightful • Comparative Pricing Report: Cell Phone Plans • Spring Fashion Preview for Women • Record Breaking Results at Widener Invitational for UC Track & Field • Hussey Twins are Double Trouble • Bears Turn the Bullet in the Opposite Direction • Gymnastics Gods Shine on Johnson; Girls Set Three School Records in Second Straight Win • Men\u27s Basketball Splits Two League Games • UC Women\u27s Basketball Hits Three Game Winning Streak • UC Women\u27s Lacrosse Aiming for Final Four in 2002 • Bears Swimming Claws Their way Through the Water, Falling Short to a Powerful Franklin and Marshall Teamhttps://digitalcommons.ursinus.edu/grizzlynews/1506/thumbnail.jp

Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation

The Grizzly, February 28, 2002

Doug Farah Pays a Visit to Ursinus • Ursinus Students in Who\u27s Who List • Mysterious Rash Hits School Children Across the Country • Welcome to the Real World • Xanax Abuse • Controversy in the World of Figure Skating • Opinions: Spring Break; Sprinklers: Where are They?; Italy for a Semester • Experience the Beauty of Spring at the Philadelphia Flower Show • Marisol: A Different but Successful Performance at Ursinus College • Some Hot Tips for an Exciting and Safe Spring Break in Sunny Mexico • Track Team\u27s Results from Haverford • Men\u27s Basketball Falls Short at F&M • Men\u27s Rugby Team Admitted to Eastern Pennsylvania Rugby Union • Kings of the Court • Aivazian says Bye, Bye, Bye to the Division I Competition at UPenn • UC Swimmers Turn Up the Heat in the Water at the 2002 CC Championship Meethttps://digitalcommons.ursinus.edu/grizzlynews/1509/thumbnail.jp

The Grizzly, February 14, 2002

Salt Lake City Says Hello to the 2002 Winter Olympics • Black History Month at Ursinus: How Diverse is the Campus? • Lorelei: Blast or Bust? • All About Enron: Latest in the Scandal • Parking on Campus: Will There be Enough? • Opinions: Is the Bookstore Slighting Us?; New Dance Studio Missing One Thing: Dancers; Women Drinking While Pregnant: Is That Acceptable? • Exclusive Interview with Jamie Kennedy, Host of The Jamie Kennedy Experiment • The Silver-Brown Dance Company Stomps the Night Away • Is Digital TV Coming to Your House? • Introducing the Wellness Center • Black History Month at Ursinus: The Truth • What the Class of 2002 can Expect in the Real World • UC Women\u27s B-Ball Chops Down Washington on Friday, but Kneels to Swarthmore on Sunday • Ursinus Seeks Women\u27s Golf Coach and Prospective Players • UC Invitational Huge Success for Bears • Men\u27s Basketball Clinches Play-off Berth With Two Dominating Wins! • UC Bears Make a Splash in the Pool, Being Out-Touched by a Strong Bryn Mawr Teamhttps://digitalcommons.ursinus.edu/grizzlynews/1507/thumbnail.jp

The Grizzly, September 12, 2002

America. No Longer the Beautiful • September 11, 2002: A Changed Nation Remembers • Omwake Party Closed for Overcrowding • The Dangers of Limerick: KI Pills Soon • The Freshman Fifteen: A Preventable Phenomenon for Students • Opinions: Too Much Liberty in Calling it a Diner; Zack\u27s Without the Power; Orientation Evaluation; New Laundry Detergent Testing: Bad Idea! • Remembering September 11th: Student Essays • September 11th: A National Holiday? I Think Not • Theater Booming at Ursinus • WVOU: Ursinus\u27 Pride and Joy • Redline Visits Ursinus • Comparative Pricing Report: Healthy Foods • Volleyball Crushes Albright College • Ursinus Looks to Next Game After Loss to W&J • Field Hockey Wins Season Opener • Women\u27s Soccer Loses Back-to-back in OThttps://digitalcommons.ursinus.edu/grizzlynews/1518/thumbnail.jp

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.Facultad de Ciencias Naturales y Muse

The Big Drink Debate: perceptions of the impact of price on alcohol consumption from a large scale cross-sectional convenience survey in north west England

<p>Abstract</p> <p>Background</p> <p>A large-scale survey was conducted in 2008 in north west England, a region with high levels of alcohol-related harm, during a regional 'Big Drink Debate' campaign. The aim of this paper is to explore perceptions of how alcohol consumption would change if alcohol prices were to increase or decrease.</p> <p>Methods</p> <p>A convenience survey of residents (≥ 18 years) of north west England measured demographics, income, alcohol consumption in previous week, and opinions on drinking behaviour under two pricing conditions: low prices and discounts and increased alcohol prices (either 'decrease', 'no change' or 'increase'). Multinomial logistic regression used three outcomes: 'completely elastic' (consider that lower prices increase drinking and higher prices decrease drinking); 'lower price elastic' (lower prices increase drinking, higher prices have no effect); and 'price inelastic' (no change for either).</p> <p>Results</p> <p>Of 22,780 drinkers surveyed, 80.3% considered lower alcohol prices and discounts would increase alcohol consumption, while 22.1% thought raising prices would decrease consumption, making lower price elasticity only (i.e. lower prices increase drinking, higher prices have no effect) the most common outcome (62%). Compared to a high income/high drinking category, the lightest drinkers with a low income (adjusted odds ratio AOR = 1.78, 95% confidence intervals CI 1.38-2.30) or medium income (AOR = 1.88, CI 1.47-2.41) were most likely to be lower price elastic. Females were more likely than males to be lower price elastic (65% vs 57%) while the reverse was true for complete elasticity (20% vs 26%, P < 0.001).</p> <p>Conclusions</p> <p>Lower pricing increases alcohol consumption, and the alcohol industry's continued focus on discounting sales encourages higher drinking levels. International evidence suggests increasing the price of alcohol reduces consumption, and one in five of the surveyed population agreed; more work is required to increase this agreement to achieve public support for policy change. Such policy should also recognise that alcohol is an addictive drug, and the population may be prepared to pay more to drink the amount they now feel they need.</p