117 Works

Data from: Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Alan O. Bergland, Ray Tobler, Josefa Gonzalez, Paul Schmidt, Dimitri A. Petrov & Dmitri Petrov
Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America...

Data from: Gender disparity in physician authorship among commentary articles in high impact medical journals

Mira Mamtani, Frances Shofer, Anita Mudan, Utsha Khatri, Rachael Walker, Jaya Aysola & Jeanmarie Perrone
Background: There is an attrition of women physicians in academic medicine hierarchy. Scholarship in medical journals plays a direct role in career advancement, promotion, and authoritative recognition, and women physician authors are underrepresented in original research articles. Objectives: We sought to determine if women physician authors are similarly underrepresented in commentary articles within high impact journals. Design/Setting/Participants: In this observational study, we abstracted gender, degree, and authorship position from January 1, 2014 to October 16,...

Data from: Nanoaperture fabrication via colloidal lithography for single molecule fluorescence analysis

Shawn H. Pfeil, Kevin Y. Chen, Yale E. Goldman, Shane A. Fiorenza, Ryan M. Jamiolkowski & Alyssa M. Tate
In single molecule fluorescence studies, background emission from labeled substrates often restricts their concentrations to non-physiological nanomolar values. One approach to address this challenge is the use of zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that physically and optically confine the observation volume allowing much higher concentrations of fluorescent substrates. Standard fabrication of ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are made using a self-assembled mask of polystyrene microspheres, enabling...

Hepatic estrogen sulfotransferase distantly sensitizes mice to hemorrhagic shock-induced acute lung injury

Yang Xie, Anne Barbosa, Meishu Xu, Patrick Oberly, Songrong Ren, Robbert Gibbs, Samuel Poloyac, Wenchao Song, Jie Fan & Wen Xie
Hemorrhagic shock (HS) is a potential life-threatening condition that may lead to injury to multiple organs, including the lung. The estrogen sulfotransferase (EST, or SULT1E1) is a conjugating enzyme that sulfonates and deactivates estrogens. In this report, we showed that the expression of Est was markedly induced in the liver, but not in the lung of female mice subject to hemorrhagic shock and resuscitation (HS/R). Genetic ablation or pharmacological inhibition of Est effectively protected female...

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: Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations

Hsin-Hung Chou, Nigel F. Delaney, Jeremy A. Draghi & Christopher J. Marx
How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncover the fitness landscape defined by gene expression levels. We found strong antagonism and sign epistasis between these beneficial mutations. Mutations with the largest individual benefit interacted the most...

Data from: Chimpanzees breed with genetically dissimilar mates

Kara K. Walker, Rebecca S. Rudicell, Yingying Li, Beatrice H. Hahn, Emily Wroblewski & Anne E. Pusey
Inbreeding adversely affects fitness, whereas heterozygosity often augments it. Therefore, mechanisms to avoid inbreeding and increase genetic distance between mates should be advantageous in species where adult relatives reside together. Here we investigate mate choice for genetic dissimilarity in chimpanzees, a species in which many females avoid inbreeding through dispersal, but where promiscuous mating and sexual coercion can limit choice when related adults reside together. We take advantage of incomplete female dispersal in Gombe National...

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

Hannah J. Barbian, Andrew J. 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 & Andrew Jesse Connell
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...

Data from: Family network size and survival across the lifespan of female macaques

Lauren J. N. Brent, Angelina Ruiz Lambides, Michael L. Platt & M. L. Platt
Two decades of research suggest social relationships have a common evolutionary basis in humans and other gregarious mammals. Critical to the support of this idea is growing evidence that mortality is influenced by social integration, but when these effects emerge and how long they last is mostly unknown. Here, we report in adult female macaques that the impact of number of close adult female relatives, a proxy for social integration, on survival is not experienced...

Data from: Clinical factors associated with long-term complete remission versus poor response to chemotherapy in HIV-infected children and adolescents with Kaposi sarcoma receiving bleomycin and vincristine: a retrospective observational study

Nader Kim El-Mallawany, William Kamiyango, Jeremy S. Slone, Jimmy Villiera, Carrie L. Kovarik, Carrie M. Cox, Dirk P. Dittmer, Saeed Ahmed, Gordon E. Schutze, Michael E. Scheurer, Peter N. Kazembe & Parth S. Mehta
Kaposi sarcoma (KS) is the most common HIV-associated malignancy in children and adolescents in Africa. Pediatric KS is distinct from adult disease. We evaluated the clinical characteristics associated with long-term outcomes. We performed a retrospective observational analysis of 70 HIV-infected children and adolescents with KS less than 18 years of age diagnosed between 8/2010 and 6/2013 in Lilongwe, Malawi. Local first-line treatment included bleomycin and vincristine plus nevirapine-based highly active anti-retroviral therapy (HAART). Median age...

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: 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: Stability of the gorilla microbiome despite simian immunodeficiency virus infection

Andrew H. Moeller, Martine Peeters, Ahidjo Ayouba, Eitel Mpoudi Ngole, Amadine Esteban, Beatrice H. Hahn & Howard Ochman
Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we...

Data from: Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

Shadi Shokralla, Teresita M. Porter, Joel F. Gibson, Rafal Dobosz, Daniel H. Janzen, Winnie Hallwachs, G. Brian Golding & Mehrdad Hajibabaei
Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina...

Data from: Evolution of mutation rates in hypermutable populations of Escherichia coli propagated at very small effective population size

Tanya Singh, Meredith Hyun & Paul Sniegowski
Mutation is the ultimate source of the genetic variation—including variation for mutation rate itself—that fuels evolution. Natural selection can raise or lower the genomic mutation rate of a population by changing the frequencies of mutation rate modifier alleles associated with beneficial and deleterious mutations. Existing theory and observations suggest that where selection is minimized, rapid systematic evolution of mutation rate either up or down is unlikely. Here, we report systematic evolution of higher and lower...

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: A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans

William M. Roberts, Steven B. Augustine, Kristy J. Lawton, Theodore H. Lindsay, Tod R. Thiele, Eduardo J. Izquierdo, Serge Faumont, Rebecca A. Lindsay, Matthew Cale Britton, Navin Pokala, Cornelia I. Bargmann, Shawn R. Lockery, Eduardo J Izquierdo, Tod R Thiele, Theodore H Lindsay, Cornelia I Bargmann, William M Roberts, Shawn R Lockery & Steven B Augustine
Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral...

Data from: A phylogenomic analysis of turtles

Nicholas G. Crawford, James F. Parham, Anna B. Sellas, Brant C. Faircloth, Travis C. Glenn, Theodore J. Papefuss, James B. Henderson, Madison H. Hansen, W. Brian Simison & Theodore J. Papenfuss
Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2,381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust...

Data from: Dietary regulation of the gut microbiota engineered by a minimal defined bacterial consortium

Gary D. Wu, Evelyn Hsu, Ting-Chin Shen, Christel Chehoud, Aubrey Bailey, Josephine Ni, Ying-Yu Chen, Frederic D. Bushman, Alice Laughlin, Kyle Bittinger, Ting-Chin David Shen, Gary D Wu & Frederic D Bushman
We have recently reported that Altered Schaedler Flora (ASF) can be used to durably engineer the gut microbiota to reduce ammonia production as an effective modality to reduce morbidity and mortality in the setting of liver injury. Here we investigated the effects of a low protein diet on ASF colonization and its ability to engineer the microbiota. Initially, ASF inoculation was similar between mice fed a normal protein diet or low protein diet, but the...

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, Eric J Tchetgen Tchetgen, Benjamin J Cowling, Ranawaka A P M Perera, Vicky J Fang, Gabriel M Leung & 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...

Risk factors for cardiovascular disease (CVD) in adults with type 1 diabetes: findings from prospective real-life T1D exchange registry

Nicole Foster, Viral N Shah, Ryan Bailey, Mengdi Wu, Rodica Pop-Busui, Michelle Katz, Jill Crandall, Fida Bacha, Kristen Nadeau, Ingrid Libman, Paul Hiers, Kara Mizokami-Stout, Linda A DiMeglio, Jennifer Sherr, Richard Pratley, Shivani Agarwal, Janet Snell-Bergeon, Eda Cengiz, Sarit Polsky & Sanjeev N Mehta
Context Cardiovascular disease (CVD) is a major cause of mortality in adults with type 1 diabetes. Objective We prospectively evaluated CVD risk factors in a large, contemporary cohort of adults with type 1 diabetes living in the United States. Design Observational study of CVD and CVD risk factors over a median of 5.3 years. Setting The T1D Exchange clinic network. Patients Adults (age ≥18 years) with type 1 diabetes and without known CVD diagnosed before...

Data from: Locomotory abilities and habitat of the Cretaceous bird Gansus yumenensis inferred from limb length proportions

Robert L. Nudds, Jessie Atterholt, Xia Wang, H. L. You, Gareth J. Dyke, J. Atterholt, R. L. Nudds, X. Wang & H.-L. You
The relative length proportions of the three bony elements of the pelvic (femur, tibiotarsus and tarsometatarsus) and pectoral (humerus, ulna and manus) limbs of the early Cretaceous bird Gansus yumenensis, a well-represented basal ornithuromorph from China are investigated and compared to those of extant taxa. Ternary plots show that the pectoral limb length proportions of Gansus are most similar to Apodiformes (swifts and hummingbirds), which plot away from all other extant birds. In contrast, the...

Data from: The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development

Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson & Timothy A. Linksvayer
The caste fate of developing female honey bee larvae is strictly socially regulated by adult nurse workers. As a result of this social regulation, nurse-expressed genes as well as larval-expressed genes may affect caste expression and evolution. We used a novel transcriptomic approach to identify genes with putative direct and indirect effects on honey bee caste development, and we subsequently studied the relative rates of molecular evolution at these caste-associated genes. We experimentally induced the...

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...

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