54 Works

Data from: Genome-wide evolutionary dynamics of influenza B viruses on a global scale

Pinky Langat, Jayna Raghwani, Gytis Dudas, Thomas A. Bowden, Stephanie Edwards, Astrid Gall, Trevor Bedford, Andrew Rambaut, Rodney S. Daniels, Colin A. Russell, Oliver G. Pybus, John McCauley, Paul Kellam & Simon J. Watson
The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study...

Data from: The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific manner

Candida Bhagwandin, Erin L. Ashbeck, Michael Whalen, Joanna Bandola-Simon, Paul A. Roche, Adam Szajman, Sarah Mai Truong, Betsy C. Wertheim, Yann C. Klimentidis, Satoshi Ishido, Benjamin J. Renquist & Lonnie Lybarger
Type 2 diabetes is typified by insulin-resistance in adipose tissue, skeletal muscle, and liver, leading to chronic hyperglycemia. Additionally, obesity and type 2 diabetes are characterized by chronic low-grade inflammation. Membrane-associated RING-CH-1 (MARCH1) is an E3 ubiquitin ligase best known for suppression of antigen presentation by dendritic and B cells. MARCH1 was recently found to negatively regulate the cell surface levels of the insulin receptor via ubiquitination. This, in turn, impaired insulin sensitivity in mouse...

Data from: Marking mosquitoes in their natural larval sites using 2H-enriched water: a promising approach for tracking over extended temporal and spatial scales

Roy Faiman, Adama Dao, Alpha Yaro, Moussa Diallo, Samake Djibril, Zana L. Sonogo, Yossi Ousmane, Margerie Sullivan, Laura Veru, Benjamin Krajacich, Asha Krishna, Joy Matthews, Christine France, Gabriel Hamer, Keith Hobson & Tovi Lehmann
1. Background. Tracking mosquitoes using current methods of mark-release-recapture are limited to small spatial and temporal scales exposing major gaps in understanding long-range movements and extended survival. Novel approaches to track mosquitoes may yield fresh insights into their biology which improves intervention activities to reduce disease transmission. Stable isotope enrichment of natural mosquito breeding sites allows large-scale marking of wild mosquitoes absent human handling. Mosquito larvae that develop in 2H-enriched water are expected to be...

Data from: Distributed acoustic cues for caller identity in macaque vocalization

Makoto Fukushima, Alexandra M. Doyle, Matthew P. Mullarkey, Mortimer Mishkin, Bruno B. Averbeck & Alex M. Doyle
Individual primates can be identified by the sound of their voice. Macaques have demonstrated an ability to discern conspecific identity from a harmonically structured ‘coo’ call. Voice recognition presumably requires the integrated perception of multiple acoustic features. However, it is unclear how this is achieved, given considerable variability across utterances. Specifically, the extent to which information about caller identity is distributed across multiple features remains elusive. We examined these issues by recording and analysing a...

Data from: Genome sequencing highlights the dynamic early history of dogs

Adam H. Freedman, Ilan Gronau, Rena M. Schweizer, Diego Ortega-Del Vecchyo, Eunjung Han, Pedro M. Silva, Marco Galaverni, Zhenxin Fan, Peter Marx, Belen Lorente-Galdos, Holly Beale, Oscar Ramirez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R. Boyko, Heidi G. Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos D. Bustamante, Timothy T. Harkins … & John Novembre
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow....

Data from: Integrating influenza antigenic dynamics with molecular evolution

Trevor Bedford, Marc A. Suchard, Philippe Lemey, Gytis Dudas, Victoria Gregory, Alan J. Hay, John W. McCauley, Colin A. Russell, Derek J. Smith, Andrew Rambaut, Colin A Russell, Alan J Hay, John W McCauley, Derek J Smith & Marc A Suchard
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata,...

Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

Matthieu Leray, Joy Y. Yang, Christopher P. Meyer, Suzanne C. Mills, Natalia Agudelo, Ranwez Vincent, Joel T. Boehm & Ryuji J. Machida
Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the...

Preface

Michele Ellison & Robin C. Vanderpool
Connected cancer care is of increasing importance in light of the COVID-19 pandemic. The Linking & Amplifying User-Centered Networks through Connected Health (L.A.U.N.C.H.) Collaborative in Appalachian Kentucky has pioneered a new roadmap for equipping communities with the transformative power of broadband to innovate around the future of cancer care and to better scale their ideas. The roadmap involves reaching across disciplines, including public health, anthropology, telecommunications, and user-centered design. The goal is to leverage connectivity...

Barn-Raising on the Digital Frontier

Bradford W. Hesse, David Ahern, Michele Ellison, Eliah Aronoff-Spencer, Robin C. Vanderpool, Karen Onyeije, Michael C. Gibbons, Timothy W. Mullett, Ming-Yuan Chih, Victoria Attencio, Grant Patterson, Jessica Boten, Christopher Hartshorn, Ben Bartolome, Katie Gorscak, Melanie McComsey, Alexandra Hubenko, Bin Huang, Corey Baker & Don Norman
A meta-analysis of oncology papers from around the world revealed that cancer patients who lived more than 50 miles away from hospital centers routinely presented with more advanced stages of disease at diagnosis, exhibited lower adherence to prescribed treatments, presented with poorer diagnoses, and reported a lower quality of life than patients who lived nearer to care facilities. Connected health approaches—or the use of broadband and telecommunications technologies to evaluate, diagnose, and monitor patients beyond...

Data from: Maternal effects and population regulation: maternal density-induced reproduction suppression impairs offspring capacity in response to immediate environment in root voles Microtus oeconomus

Jiang-Hui Bian, Shou-Yang Du, Yan Wu, Yi-Fan Cao, Xu-Heng Nie, Hui He & Zhi-Bing You
1. The hypothesis that maternal effects act as an adaptive bridge in translating maternal environments into offspring phenotypes and thereby affecting population dynamics has not been studied in the well-controlled fields. 2. In this study, the effects of maternal population-density on offspring stress axis, reproduction and population dynamics were studied in root voles (Microtus oeconomus). Parental enclosures for breeding offspring were established by introducing 6 adults per sex into each of 4 (low density) and...

Data from: Existing infection facilitates establishment and density of malaria parasites in their mosquito vector

Laura C. Pollitt, Joshua T. Bram, Simon Blanford, Matthew J. Jones & Andrew F. Read
Very little is known about how vector-borne pathogens interact within their vector and how this impacts transmission. Here we show that mosquitoes can accumulate mixed strain malaria infections after feeding on multiple hosts. We found that parasites have a greater chance of establishing and reach higher densities if another strain is already present in a mosquito. Mixed infections contained more parasites but these larger populations did not have a detectable impact on vector survival. Together...

Data from: Imperfect vaccination can enhance the transmission of highly virulent pathogens

Andrew F. Read, Susan J. Baigent, Claire Powers, Lydia B. Kgosana, Luke Blackwell, Lorraine P. Smith, David A. Kennedy, Stephen W. Walkden-Brown & Venugopal K. Nair
Could some vaccines drive the evolution of more virulent pathogens? Conventional wisdom is that natural selection will remove highly lethal pathogens if host death greatly reduces transmission. Vaccines that keep hosts alive but still allow transmission could thus allow very virulent strains to circulate in a population. Here we show experimentally that immunization of chickens against Marek's disease virus enhances the fitness of more virulent strains, making it possible for hyperpathogenic strains to transmit. Immunity...

Data from: Quantifying hummingbird preference for floral trait combinations: the role of selection on trait interactions in the evolution of pollination syndromes

Charles B. Fenster, Richard J. Reynolds, Christopher W. Williams, Robert Makowsky & Michele R. Dudash
Darwin recognized the flower's importance for the study of adaptation and emphasized that the flower's functionality reflects the coordinated action of multiple traits. Here we use a multi-trait manipulative approach to quantify the potential role of selection acting on floral trait combinations underlying the divergence and maintenance of three related North American species of Silene (Caryophyllaceae). We artificially generated 48 plant phenotypes corresponding to all combinations of key attractive traits differing among the three Silene...

Data from: Tracing the origin of the early wet-season Anopheles coluzzii in the Sahel

Tovi Lehmann, David Weetman, Diana L. Huestis, Alpha S. Yaro, Yaya Kassogue, Moussa Diallo, Martin J. Donnelly & Adama Dao
In arid environments the source of the malaria mosquito populations that re-establish soon after first rains remains a puzzle and alternative explanations have been proposed. Using genetic data, we evaluated whether the early Rainy Season (RS) population of Anopheles coluzzii is descended from the preceding late-RS generation at the same locality, consistent with dry season (DS) dormancy (aestivation), or from migrants from distant locations. Distinct predictions derived from these two hypotheses were assessed, based on...

Data from: NK-CD11c+ cell crosstalk in diabetes enhances IL-6-mediated inflammation during mycobacterium tuberculosis infection

Satyanarayana Swamy Cheekatla, Deepak Tripathi, Sambasivan Venkatasubramanian, Pavan K. Nathella, Padmaja Paidipally, Munenori Ishibashi, Elwyn Welch, Amy R. Tvinnereim, Mitsuo Ikebe, Vijaya Lakshmi Valluri, Subash Babu, Hardy Kornfeld, Ramakrishna Vankayalapati & Pavan Kumar Nathella
In this study, we developed a mouse model of type 2 diabetes mellitus (T2DM) using streptozotocin and nicotinamide and identified factors that increase susceptibility of T2DM mice to infection by Mycobacterium tuberculosis (Mtb). All Mtb-infected T2DM mice and 40% of uninfected T2DM mice died within 10 months, whereas all control mice survived. In Mtb-infected mice, T2DM increased the bacterial burden and pro- and anti-inflammatory cytokine and chemokine production in the lungs relative to those in...

Data from: A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

François Blanquart, Mary Kate Grabowski, Joshua Herbeck, Fred Nalugoda, David Serwadda, Michael A. Eller, Merlin L. Robb, Ronald Gray, Godfrey Kigozi, Oliver Laeyendecker, Katrina A. Lythgoe, Gertrude Nakigozi, Thomas C. Quinn, Steven J. Reynolds, Maria J. Wawer, Christophe Fraser, Maria J Wawer, Katrina A Lythgoe, Thomas C Quinn & Steven J Reynolds
Evolutionary theory hypothesizes that intermediate virulence maximizes pathogen fitness as a result of a trade-off between virulence and transmission, but empirical evidence remains scarce. We bridge this gap using data from a large and long-standing HIV-1 prospective cohort, in Uganda. We use an epidemiological-evolutionary model parameterised with this data to derive evolutionary predictions based on analysis and detailed individual-based simulations. We robustly predict stabilising selection towards a low level of virulence, and rapid attenuation of...

Data from: Urban colonization through multiple genetic lenses: the city-fox phenomenon revisited

Alexandra L. DeCandia, Kristin E. Brzeski, Elizabeth Heppenheimer, Catherine V. Caro, Glauco Camenisch, Peter Wandeler, Carlos Driscoll & Bridgett M. VonHoldt
Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty traversing human-modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes...

Data from: The role of platelets in mediating a response to human influenza infection

Milka Koupenova, Heather A. Corkrey, Olga Vitseva, Giorgia Manni, Catherine J. Pang, Lauren Clancy, Chen Yao, Jeffrey Rade, Daniel Levy, Jennifer P. Wang, Robert W. Finberg, Evelyn A. Kurt-Jones & Jane E. Freedman
Influenza infection increases the incidence of myocardial infarction but the reason is unknown. Platelets mediate vascular occlusion through thrombotic functions but are also recognized to have immunomodulatory activity. To determine if platelet processes are activated during influenza infection, we collected blood from 18 patients with acute influenza infection. Microscopy reveals activated platelets, many containing viral particles and extracellular- DNA associated with platelets. To understand the mechanism, we isolated human platelets and treated them with influenza...

Data from: Thyroid hormone receptor beta mutations alter photoreceptor development and function in Danio rerio (zebrafish)

Ciana Deveau, Xiaodong Jiao, Sachihiro Suzuki, Asha Krishnakumar, Takeshi Yoshimatsu, J Fielding Hejtmancik & Ralph Nelson
We investigate mutations in trβ2, a splice variant of thrb, identifying changes in function, structure, and behavior in larval and adult zebrafish retinas. Two N-terminus CRISPR mutants were identified. The first is a 6BP+1 insertion deletion frameshift resulting in a truncated protein. The second is a 3BP in frame deletion with intact binding domains. ERG recordings of isolated cone signals showed that the 6BP+1 mutants did not respond to red wavelengths of light while the...

Data from: Persistent chaos of measles epidemics in the prevaccination United States caused by a small change in seasonal transmission patterns

Benjamin D. Dalziel, Ottar N. Bjornstad, Willem G. Van Panhuis, Donald S. Burke, C Jessica E. Metcalf, Bryan T. Grenfell, Ottar N. Bjørnstad & C. Jessica E. Metcalf
Epidemics of infectious diseases often occur in predictable limit cycles. Theory suggests these cycles can be disrupted by high amplitude seasonal fluctuations in transmission rates, resulting in deterministic chaos. However, persistent deterministic chaos has never been observed, in part because sufficiently large oscillations in transmission rates are uncommon. Where they do occur, the resulting deep epidemic troughs break the chain of transmission, leading to epidemic extinction, even in large cities. Here we demonstrate a new...

Data from: Quantitative detection of rare interphase chromosome breaks and translocations by high-throughput imaging

Bharat Burman, Tom Misteli & Gianluca Pegoraro
We report a method for the sensitive detection of rare chromosome breaks and translocations in interphase cells. HiBA-FISH (High-throughput break-apart FISH) combines high-throughput imaging with the measurement of the spatial separation of FISH probes flanking target genome regions of interest. As proof-of-principle, we apply hiBA-FISH to detect with high sensitivity and specificity rare chromosome breaks and translocations in the anaplastic large cell lymphoma breakpoint regions of NPM1 and ALK. This method complements existing approaches to...

Data from: High throughput functional genomics identifies modulators of TCE metabolite genotoxicity and candidate susceptibility genes

Vanessa Y. De La Rosa, Jonathan Asfaha, Michael Fasullo, Alex Loguinov, Peng Li, Lee E. Moore, Nathaniel Rothman, Jun Nakamura, James A. Swenberg, Ghislaine Scelo, Luoping Zhang, Martyn T. Smith & Chris D. Vulpe
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites....

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 & Nicole L. Yohn
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: Emergence and evolution of novel reassortant influenza A viruses in canines in southern China

Ying Chen, Nídia S. Trovão, Guojun Wang, Weifeng Zhao, Ping He, Huabo Zhou, Yanning Mo, Zuzhang Wei, Kang Ouyang, Weijiang Huang, Adolfo García-Sastre, Martha I. Nelson & Weijian Huang
The capacity of influenza A viruses (IAVs) to host jump from animal reservoir species to humans presents an ongoing pandemic threat. Birds and swine are considered major reservoirs of viral genetic diversity, whereas equines and canines have historically been restricted to one or two stable IAV lineages with no transmission to humans. Here, by sequencing the complete genomes of 16 IAVs obtained from canines in southern China (Guangxi Zhuang Autonomous Region [Guangxi]) in 2013 to...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

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