26 Works

Data from: High-throughput sequencing of the T-cell receptor beta chain gene distinguishes two subgroups of cutaneous T-cell lymphoma

Jie Wang, Bryan Rea, Paul Haun, Ryan Emerson, Ilan Kirsch & Adam Bagg
HTS of the TCR beta chain distinguishes two subgroups of CTCLT-cell repertoire characterization data are provided herein as a supplement to: High-Throughput Sequencing of the T-cell receptor beta chain gene distinguishes two subgroups of cutaneous T-cell lymphoma By Jie Wang, MD, Bryan Rea, MD, Paul Haun, MD, Ryan Emerson, PhD, Ilan Kirsch, MD, and Adam Bagg, MD

Data from: Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster

Emily L. Behrman, Virginia M. Howick, Martin Kapun, Fabian Staubach, Alan O. Bergland, Dmitri A. Petrov, Brian P. Lazzaro & Paul S. Schmidt
Understanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes across a range of taxa. Here, we use immune defence in natural populations of Drosophila melanogaster to understand the rate of evolution in natural populations and the genetics underlying rapid change. We probed the immune system using the natural...

Data from: CHIIMP: an automated high-throughput microsatellite genotyping approach reveals greater allelic diversity in wild chimpanzees

Hannah J. Barbian, Andrew Jesse Connell, Alexa N. Avitto, Ronnie M. Russell, Andrew G. Smith, Madhurima S. Gundlapally, Alexander L. Shazad, Yingying Li, Frederic Bibollet-Ruche, Emily E. Wroblewski, Deus Mjungu, Elizabeth V. Lonsdorf, Fiona A. Stewart, Alexander K. Piel, Anne E. Pusey, Paul M. Sharp & Beatrice H. Hahn
Short tandem repeats (STRs), also known as microsatellites, are commonly used to non-invasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park,...

Data from: Distributed rhythm generators underlie Caenorhabditis elegans forward locomotion

Anthony D Fouad, Shelly Teng, Julian R Mark, Alice Liu, Pilar Alvarez-Illera, Hongfei Ji, Angelica Du, Priya D Bhirgoo, Eli Cornblath, Sihui Asuka Guan & Christopher Fang-Yen
Coordinated rhythmic movements are ubiquitous in animal behavior. In many organisms, chains of neural oscillators underlie the generation of these rhythms. In C. elegans, locomotor wave generation has been poorly understood; in particular, it is unclear where in the circuit rhythms are generated, and whether there exists more than one such generator. We used optogenetic and ablation experiments to probe the nature of rhythm generation in the locomotor circuit. We found that multiple sections of...

Directed Evolution of AAV for Efficient Gene Delivery to Canine and Primate Retina - Raw counts of variants from deep sequencing

Leah Byrne, Timothy Day, Meike Visel, Deniz Dalkara, Valerie Dufour, Felipe Pompeo Marinho, William Merigan, Gustavo Aguirre, William Beltran, David Schaffer & John Flannery
Efficient AAV-mediated gene delivery remains a significant obstacle to effective retinal gene therapies. Here, we apply the process of directed evolution – guided by deep sequencing and followed by direct in vivo secondary selection of high-performing vectors with a GFP-barcoded library – to create AAV viral capsids with new capabilities to deliver genes to the outer retina in large animals. The resulting vectors resulted in efficient targeting of photoreceptors, bipolar cells, and RPE cells in...

Data from: Phenotypic correlation between queen and worker brood care supports the role of maternal care in the evolution of eusociality

Justin T. Walsh, Lisa Signorotti, Timothy A. Linksvayer & Patrizia D'Ettorre
Cooperative brood care by siblings, a defining feature of eusociality, is hypothesized to be evolutionarily derived from maternal care via shifts in the timing of the expression of genes underlying maternal care. If sibling and maternal care share a genetic basis, the two behaviors are expected to be genetically and phenotypically correlated. We tested this prediction in the black garden ant Lasius niger by quantifying the brood retrieval rate of queens and their first and...

Data from: An inversion supergene in Drosophila underpins latitudinal clines in survival traits

Esra Durmaz, Clare Benson, Martin Kapun, Paul Schmidt & Thomas Flatt
Chromosomal inversions often contribute to local adaptation across latitudinal clines, but the underlying selective mechanisms remain poorly understood. We and others have previously shown that a clinal inversion polymorphism in Drosophila melanogaster, In(3R)Payne, underpins body size clines along the North American and Australian east coasts. Here we ask whether this polymorphism also contributes to clinal variation in other fitness-related traits, namely survival traits (lifespan, survival upon starvation, and survival upon cold shock). We generated homokaryon...

Data from: An inverse latitudinal gradient in speciation rate for marine fishes

Daniel L. Rabosky, Jonathan Chang, Pascal O. Title, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll & Michael E. Alfaro
Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity gradient propose that warm reef environments serve as evolutionary ‘hotspots’ for species formation5,6,7,8. Here we test the relationship between latitude, species richness and speciation rate...

Data from: Placental H3K27me3 establishes female resilience to prenatal insults

Bridget M. Nugent, Carly M. O'Donnell, C. Neill Epperson & Tracy L. Bale
Although sex biases in disease presentation are well documented, the mechanisms mediating vulnerability or resilience to diseases are unknown. In utero insults are more likely to produce detrimental health outcomes for males versus females. In our mouse model of prenatal stress, male offspring experience long-term dysregulation of body weight and hypothalamic pituitary adrenal stress axis dysfunction, endophenotypes of male-biased neurodevelopmental disorders. Placental function is critical for healthy fetal development, and we previously showed that sex...

Data from: Racial differences in recurrent ischemic stroke risk and recurrent stroke case fatality

Karen C. Albright, Lei Huang, Justin Blackburn, George Howard, Michael Mullen, Vera Bittner, Paul Muntner & Virginia Howard
Objective: To determine black-white differences in 1-year recurrent stroke and 30-day case fatality following a recurrent stroke in older US adults. Methods: We conducted a retrospective cohort study using a 5% random sample of Medicare beneficiaries with fee-for-service health insurance coverage who were hospitalized for ischemic stroke between 1999 and 2013. Hazard ratios (HR) for recurrent ischemic stroke and risk ratios (RR) for 30-day case fatality comparing blacks to whites were calculated with adjustment for...

Data from: Influenza hemagglutination-inhibition antibody titer as a mediator of vaccine-induced protection for influenza B

Benjamin J. Cowling, Wey Wen Lim, Ranawaka A.P.M. Perera, Vicky J. Fang, Gabriel M. Leung, J.S. Malik Peiris, Eric J. Tchetgen Tchetgen, Ranawaka A P M Perera & J S Malik Peiris
Background: The hemagglutination inhibition (HAI) assay is an established correlate of protection for the inactivated influenza vaccine, but the proportion of vaccine-induced protection that is mediated by the post-vaccination HAI titer has not been assessed. Methods: We used data from a randomized placebo-controlled trial of a split-virion inactivated influenza vaccine in children 6-17 years of age. Sera were collected before and 30 days after receipt of vaccination or placebo, and tested by the HAI assay...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

Data from: The effects of skeletal asymmetry on interpreting biological variation and taphonomy in the fossil record

Brandon P. Hedrick, Emma R. Schachner, Gabriel Rivera, Peter Dodson & Stephanie E. Pierce
Biological asymmetry is present in all bilaterally symmetric organisms as a result of normal developmental instability. However, fossilized organisms, which have undergone distortion due to burial, may have additional asymmetry as a result of taphonomic processes. To investigate this issue, we evaluated the magnitude of shape variation resulting from taphonomy on vertebrate bone using a novel application of fluctuating asymmetry. We quantified the amount of total variance attributed to asymmetry in a taphonomically distorted fossil...

Data from: White matter lesions: spatial heterogeneity, links to risk factors, cognition, genetics, atrophy

Mohamad Habes, Sotiras Aristeidis, Erus Guray, Jon B. Toledo, Janowitz Deborah, Wolk David A., Shou Haochang, Bryan Nick R, Doshi Jimit, Völzke Henry, Schminke Ulf, Hoffmann Wolfgang, Resnick Susan M., Grabe Hans J. & Davatzikos Christos
Objectives: To investigate spatial heterogeneity of white matter lesions or hyperintensities (WMH). Methods: MRI scans of 1836 participants (median age 52.2±13.16) encompassing a wide age range (22–84 years) from the cross-sectional Study of Health in Pomerania (SHIP, Germany) were included as discovery set identifying spatially distinct components of WMH using a structural covariance approach. Scans of 307 participants (median age 73.8±10.2, with 747 observations) from the Baltimore Longitudinal Study of Aging (BLSA, USA) were included...

Data from: Developmental shifts in social cognition: socio-emotional biases across the lifespan in rhesus monkeys

Alexandra G. Rosati, Alyssa M. Arre, Michael L. Platt & Laurie R. Santos
Humans exhibit a suite of developmental changes in social cognition across the lifespan. To what extent are these developmental patterns unique? We first review several social domains in which humans undergo critical ontogenetic changes in socio-cognitive processing, including social attention and theory of mind. We then examine whether one human developmental transition—a shift in socioemotional preferences—also occurs in nonhuman primates. Specifically, we experimentally measured socioemotional processing in a large population of rhesus macaques (Macaca mulatta)...

Data from: Spatiotemporal dynamics and genome-wide association analysis of desiccation tolerance in Drosophila melanogaster

Subhash Rajpurohit, Eran Gefen, Alan O. Bergland, Dmitri A. Petrov, Allen G. Gibbs & Paul S. Schmidt
Water availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over spatial and temporal scales and is an important physiological determinant of fitness in natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations of Drosophila melanogaster using: 1) natural populations sampled across latitudes and seasons; 2) experimental evolution in field mesocosms over seasonal time; 3) genome-wide associations to identify SNPs/genes associated...

Data from: Evolution of transmission mode in conditional mutualisms with spatial variation in symbiont quality

Alexandra Lynne Brown, Erol Akcay & Alexandra Brown
Many symbioses have costs and benefits to their hosts that vary with the environmental context, which itself may vary in space. The same symbiont may be a mutualist in one location and a parasite in another. Such spatially conditional mutualisms pose a dilemma for hosts, who might evolve (higher or lower) horizontal or vertical transmission to increase their chances of being infected only where the symbiont is beneficial. To determine how transmission in hosts might...

Data from: Dietary challenges differentially affect activity and sleep/wake behavior in mus musculus: isolating independent associations with diet/energy balance and body weight

Isaac J. Perron, Brendan T. Keenan, Karthikeyani Chellappa, Nicholas F. Lahens, Nicole Y. Yohn, Keith R. Shockley, Allan I. Pack & Sigrid C. Veasey
Background and Aims: Associated with numerous metabolic and behavioral abnormalities, obesity is classified by metrics reliant on body weight (such as body mass index). However, overnutrition is the common cause of obesity, and may independently contribute to these obesity-related abnormalities. Here, we use dietary challenges to parse apart the relative influence of diet and/or energy balance from body weight on various metabolic and behavioral outcomes. Materials and Methods: Seventy male mice (mus musculus) were subjected...

Data from: Identifying the morphologic basis for radiomic features in distinguishing different Gleason grades of prostate cancer on MRI: preliminary findings

Gregory Penzias, Asha Singanamalli, Robin Elliott, Jay Gollamudi, Natalie Shih, Michael Feldman, Phillip D. Stricker, Warick Delprado, Sarita Tiwari, Maret Böhm, Anne-Maree Haynes, Lee Ponsky, Pingfu Fu, Pallavi Tiwari, Satish Viswanath & Anant Madabhushi
Translation of radiomics into the clinic may require a more comprehensive understanding of the underlying morphologic tissue characteristics they reflect. In the context of prostate cancer (PCa), some studies have correlated gross histological measurements of gland lumen, epithelium, and nuclei with disease appearance on MRI. Quantitative histomorphometry (QH), like radiomics for radiologic images, is the computer based extraction of features for describing tumor morphology on digitized tissue images. In this work, we attempt to establish...

Data from: A sequel to Sanger: amplicon sequencing that scales

Paul D.N. Hebert, Thomas W.A. Braukmann, Sean W.J. Prosser, Sujeevan Ratnasingham, Jeremy R. DeWaard, Natalia V. Ivanova, Daniel H. Janzen, Winnie Hallwachs, Suresh Naik, Jayme E. Sones & Evgeny V. Zakharov
Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system. By examining templates from more than 5,000 species and 20,000 specimens,...

Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage

Marketa Kaucka, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, Karl Annusver, Maria Kasper, Orsolya Symmons, Leslie Pan, Francois Spitz, Jozef Kaiser, Maria Hovorakova, Tomas Zikmund, Kazunori Sunadome, Michael P. Matise, Hui Wang, Ulrika Marklund, Hind Abdo, Patrik Ernfors, Pascal Maire, Maud Wurmser, Andrei S. Chagin, Kaj Fried … & Igor Adameyko
Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly,...

Data from: Despite high levels of expression in thymic epithelial cells, miR-181a1 and miR-181b1 are not required for thymic development

Heather E. Stefanski, Yan Xing, Patricia A. Taylor, Stefano Maio, Jorge Henao-Meija, Adam Williams, Richard A. Flavell, Georg A. Hollander & Bruce R. Blazar
MicroRNAs (miRNAs) have been shown to be key modulators of post-transcriptional gene silencing in many cellular processes. In previous studies designed to understand the role of miRNAs in thymic development, we globally deleted miRNA exclusively in thymic epithelial cells (TECs), which are critical in thymic selection. This resulted in the loss of stromal cells that instruct T cell lineage commitment and affect thymocyte positive selection, required for mature T cell development. Since murine miR-181 is...

Data from: The nearshore cradle of early vertebrate diversification

Lauren Sallan, Matt Friedman, Robert S. Sansom, Charlotte M. Bird & Ivan J. Sansom
Ancestral vertebrate habitats are subject to controversy and obscured by limited, often contradictory paleontological data. We assembled fossil vertebrate occurrence and habitat datasets spanning the middle Paleozoic (480 million to 360 million years ago) and found that early vertebrate clades, both jawed and jawless, originated in restricted, shallow intertidal-subtidal environments. Nearshore divergences gave rise to body plans with different dispersal abilities: Robust fishes shifted shoreward, whereas gracile groups moved seaward. Fresh waters were invaded repeatedly,...

Data from: Faster processing of moving compared to flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion

Manivannan Subramaniyan, Alexander S. Ecker, Saumil S. Patel, R. James Cotton, Matthias Bethge, Xaq Pitkow, Philipp Berens & Andreas S. Tolias
When the brain has determined the position of a moving object, due to anatomical and processing delays, the object will have already moved to a new location. Given the statistical regularities present in natural motion, the brain may have acquired compensatory mechanisms to minimize the mismatch between the perceived and the real position of moving objects. A well-known visual illusion — the flash lag effect — points towards such a possibility. Although many psychophysical models...

Data from: High mutation rates limit evolutionary adaptation in Escherichia coli

Kathleen Sprouffske, José Aguilar-Rodríguez, Paul Sniegowski & Andreas Wagner
Mutation is fundamental to evolution, because it generates the genetic variation on which selection can act. In nature, genetic changes often increase the mutation rate in systems that range from viruses and bacteria to human tumors. Such an increase promotes the accumulation of frequent deleterious or neutral alleles, but it can also increase the chances that a population acquires rare beneficial alleles. Here, we study how up to 100-fold increases in Escherichia coli’s genomic mutation...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Pennsylvania
  • Yale University
  • University of Michigan-Ann Arbor
  • Duke University
  • University of Manchester
  • Stanford University
  • University of Virginia
  • University of Minnesota
  • University of Lausanne
  • University of Fribourg