91 Works

Multimodal Molecular Imaging of Human Kidney Tissue From a 66 Year Old White Female Donor

Jeffrey Spraggins, Elizabeth Neumann, Nathan Patterson, David Anderson, Kavya Sharman, Lukasz Migas, Jamie Allen, Maya Brewer, Jennifer Harvey, Haichun Yang, Raymond Harris, Agnes Fogo, Mark deCaestecker, Danielle Gutierrez, Richard Caprioli & Raf Van de Plas
Multimodal molecular imaging data collected from the Left Kidney of a 66 year old White Female donor by the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University. BIOMIC is a Tissue Mapping Center that is part of the NIH funded Human Biomolecular Atlas Program (HuBMAP). Datasets generated by BIOMIC combine MALDI imaging mass spectrometry with various microscopy modalities including autofluorescence and stained microscopy. Support was provided by the NIH Common Fund and National Institute of...

On What States Do Prices Depend? Answers from Ecuador

Craig Benedict, Mario J. Crucini & Anthony Landry
In this paper, we argue that differences in the cost structures across sectors play an important role in firms’ decisions to adjust their prices. We develop a menu-cost model of pricing in which retail firms intermediate trade between producers and consumers. An important facet of our analysis is that the labor-cost share of retail production differs across goods and services in the consumption basket. For example, the price of gasoline at the retail pump is...

Temporal Inflection Points in Decorated Pottery: a Bayesian Refinement of the Late Formative Chronology in the Southern Lake Titicaca Basin, Bolivia

Christine Hastorf, Erik Marsh, Andrew Roddick, Maria Bruno, Scott Smith & John Janusek
The Late Formative Period immediately precedes the emergence of Tiwanaku, one of the earliest South American states, yet is one of the most poorly understood periods in the southern Lake Titicaca Basin (Bolivia). In this paper, we refine this period’s ceramic chronology with large sets of dates from eight sites, focusing on temporal inflection points in decorated ceramic styles. These points, estimated here by Bayesian models, index specific moments of change: (1) cal AD 140...

Data from: Selection on multiple sexual signals in two Central- and Eastern-European populations of the barn swallow

Peter Laszlo Pap, Attila Fülöp, Marie Adamkova-Kotasova, Jaroslav Cepak, Romana Michalkova, Rebecca J. Safran, Alexandru N. Stermin, Oldrich Tomasek, Csongor I. Vágási, Orsolya Vincze, Matthew R. Wilkins & Tomas Albrecht
Variation in intensity and targets of sexual selection on multiple traits has been suggested to play a major role in promoting phenotypic differentiation between populations, although the divergence in selection may depend on year, local conditions or age. In this study, we quantified sexual selection for two putative sexual signals across two Central and East European barn swallow (Hirundo rustica rustica) populations from Czech Republic and Romania over multiple years. We then related these differences...

Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data

Xing-Xing Shen, Jacob Steenwyk & Antonis Rokas
Topological conflict or incongruence is widespread in phylogenomic data. Concatenation- and coalescent-based approaches often result in incongruent topologies, but the causes of this conflict can be difficult to characterize. We examined incongruence stemming from conflict between likelihood-based signal (quantified by the difference in gene-wise log likelihood score or ΔGLS) and quartet-based topological signal (quantified by the difference in gene-wise quartet score or ΔGQS) for every gene in three phylogenomic studies in animals, fungi, and plants,...

Molecular basis for the evolved instability of a human G-protein coupled receptor

Laura Chamness, Nathan Zelt, Charles Kuntz, Brian Bender, Wesley Penn, Joshua Ziarek, Jens Meiler, Jonathan Schlebach & Haley Harrington
Membrane proteins are prone to misfolding and degradation. This is particularly true for mammalian forms of the gonadotropin-releasing hormone receptor (GnRHR). Although they function at the plasma membrane, mammalian GnRHRs accumulate within the secretory pathway. Their apparent instability is believed to have evolved through selection for attenuated GnRHR activity. Nevertheless, the molecular basis of this adaptation remains unclear. We show that adaptation coincides with a C-terminal truncation that compromises the translocon-mediated membrane integration of its...

Data from: Pop-out search instigates beta-gated feature selectivity enhancement across V4 layers

Jacob Westerberg, Elizabeth Sigworth, Jeffrey Schall & Alexander Maier
Visual search is a work-horse for investigating how attention interacts with processing of sensory information. Attentional selection has been linked to altered cortical sensory responses and feature preferences (i.e., tuning). However, attentional modulation of feature selectivity during search is largely unexplored. Here we map the spatiotemporal profile of feature selectivity during singleton search. Monkeys performed search where a pop-out feature determined the target of attention. We recorded laminar neural responses from visual area V4. We...

Data from: Dietary responses of Sahul (Pleistocene Australia–New Guinea) megafauna to climate and environmental change

Larisa R.G. DeSantis, Judith H. Field, Stephen Wroe & John R. Dodson
Throughout the late Quaternary, the Sahul (Pleistocene Australia–New Guinea) vertebrate fauna was dominated by a diversity of large mammals, birds, and reptiles, commonly referred to as megafauna. Since ca. 450–400Ka, approximately 88 species disappeared in Sahul, including kangaroos exceeding 200kg in size, wombat-like animals the size of hippopotamuses, flightless birds, and giant monitor lizards that were likely venomous. Ongoing debates over the primary cause of these extinctions have typically favored climate change or human activities....

Data from: An alternative pathway to eusociality: exploring the molecular and functional basis of fortress defense

Sarah P. Lawson, Leah Sigle, Abigail L. Lind, Andrew W. Legan, Jessica N. Mezzanotte, Hans-Willi Honegger, Patrick Abbot & Leah T. Sigle
Some animals express a form of eusociality known as 'fortress defense', in which defense rather than brood care is the primary social act. Aphids are small plant-feeding insects, but like termites, some species express division of labor and castes of aggressive juvenile 'soldiers'. What is the functional basis of fortress defense eusociality in aphids? Previous work showed that the acquisition of venoms might be a key innovation in aphid social evolution. We show that the...

Data from: The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia

Robert M. Brucker
Although the gut microbiome influences numerous aspects of organismal fitness, its role in animal evolution and the origin of new species is largely unknown. Here we present evidence that beneficial bacterial communities in the guts of closely related species of the genus Nasonia form species-specific phylosymbiotic assemblages that cause lethality in interspecific hybrids. Bacterial constituents and abundance are irregular in hybrids relative to parental controls, and antibiotic curing of the gut bacteria significantly rescues hybrid...

Data from: Loss of mTORC2 signaling in oligodendrocyte precursor cells delays myelination

Mark D. Grier, Kathryn L. West, Nathaniel D. Kelm, Cary Fu, Mark D. Does, Brittany Parker, Eleanor McBrier, Andre H. LaGrange, Kevin C. Ess & Robert P. Carson
Myelin abnormalities are increasingly being recognized as an important component of a number of neurologic developmental disorders. The integration of many signaling pathways and cell types are critical for correct myelinogenesis. The PI3-K and mechanistic target of rapamycin (mTOR) pathways have been found to play key roles. mTOR is found within two distinct complexes, mTORC1 and mTORC2. mTORC1 activity has been shown to play a major role during myelination, while the role of mTORC2 is...

Data from: Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal

Esteban J. Parra, Andrew Mazurek, Christopher R. Gignoux, Alexandra Sockell, Michael Agostino, Andrew P. Morris, Lauren E. Petty, Craig L. Hanis, Nancy J. Cox, Adan Valladares-Salgado, Jennifer E. Below & Miguel Cruz
We carried out an admixture mapping study of lipid traits in two samples from Mexico City. Native American locus ancestry was significantly associated with triglyceride levels in a broad region of chromosome 11 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping analysis of this region using dense genome-wide data, rs964184 is the only marker included in the 99% credible set of SNPs, providing strong support for rs964184 as the causal variant within this...

Data from: Bile diversion to the distal small intestine has comparable metabolic benefits to bariatric surgery

Charles Robb Flynn, Vance L. Albaugh, Steven Cai, Joyce Cheung-Flynn, Phillip E. Williams, Robert M. Brucker, Seth R. Bordenstein, Yan Guo, David H. Wasserman & Naji N. Abumrad
Roux-en-Y gastric bypass (RYGB) is highly effective in reversing obesity and associated diabetes. Recent observations in humans suggest a contributing role of increased circulating bile acids in mediating such effects. Here we use a diet-induced obesity (DIO) mouse model and compare metabolic remission when bile flow is diverted through a gallbladder anastomosis to jejunum, ileum or duodenum (sham control). We find that only bile diversion to the ileum results in physiologic changes similar to RYGB,...

Data from: Transcriptional profile and differential fitness in a specialist milkweed insect across host plants varying in toxicity

Stephanie S.L. Birnbaum, David C. Rinker, Nicole M. Gerardo, Patrick Abbot & Stephanie S. L. Birnbaum
Interactions between plants and herbivorous insects have been models for theories of specialization and coevolution for over a century. Phytochemicals govern many aspects of these interactions and have fostered the evolution of adaptations by insects to tolerate or even specialize on plant defensive chemistry. While genomic approaches are providing new insights into the genes and mechanisms insect specialists employ to tolerate plant secondary metabolites, open questions remain about the evolution and conservation of insect counter-defenses,...

Data from: Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer

Luigi Formisano, Yao Lu, Alberto Servetto, Ariella B. Hanker, Valerie M. Jansen, Joshua A. Bauer, Dhivya R. Sudhan, Angel L. Guerrero-Zotano, Sarah Croessmann, Yan Guo, Paula Gonzalez, Kyung-Min Lee, Melissa J. Nixon, Luis J. Schwarz, Melinda E. Sanders, Teresa C. Dugger, Marcelo Rocha Cruz, Amir Behdad, Massimo Cristofanilli, Aditya Bardia, Joyce O'Shaughnessy, Rebecca J. Nagy, Richard B. Lanman, Nadia Solovieff, Wei He … & Carlos L. Arteaga
Using an ORF kinome screen in MCF-7 cells treated with the CDK4/6 inhibitor ribociclib plus fulvestrant, we identified FGFR1 as a mechanism of drug resistance. FGFR1-amplified/ER+ breast cancer cells and MCF-7 cells transduced with FGFR1 were resistant to fulvestrant ± ribociclib or palbociclib. This resistance was abrogated by treatment with the FGFR tyrosine kinase inhibitor (TKI) lucitanib. Addition of the FGFR TKI erdafitinib to palbociclib/fulvestrant induced complete responses of FGFR1-amplified/ER+ patient-derived-xenografts. Next generation sequencing of...

Data from: The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia

Robert M. Brucker & Seth R. Bordenstein
Although the gut microbiome influences numerous aspects of organismal fitness, its role in animal evolution and the origin of new species is largely unknown. Here we present evidence that beneficial bacterial communities in the guts of closely related species of the genus Nasonia form species-specific phylosymbiotic assemblages that cause lethality in interspecific hybrids. Bacterial constituents and abundance are irregular in hybrids relative to parental controls, and antibiotic curing of the gut bacteria significantly rescues hybrid...

Data from: Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis

Matthew H. Becker, Jenifer B. Walke, Lindsey Murrill, Douglas C. Woodhams, Laura K. Reinert, Louise A. Rollins-Smith, Elizabeth A. Burzynski, Thomas P. Umile, Kevin P. C. Minbiole & Lisa K. Belden
The introduction of next-generation sequencing has allowed for greater understanding of community composition of symbiotic microbial communities. However, determining the function of individual members of these microbial communities still largely relies on culture-based methods. Here, we present results on the phylogenetic distribution of a defensive functional trait of cultured symbiotic bacteria associated with amphibians. Amphibians are host to a diverse community of cutaneous bacteria and some of these bacteria protect their host from the lethal...

Data from: Prevention, diagnosis, and treatment of high-throughput sequencing data pathologies

Xiaofan Zhou & Antonis Rokas
High Throughput Sequencing (HTS) technologies generate millions of sequence reads from DNA/RNA molecules rapidly and cost-effectively, enabling single investigator laboratories to address a variety of “omics” questions in non-model organisms, fundamentally changing the way genomic approaches are used to advance biological research. One major challenge posed by HTS is the complexity and difficulty of data quality control (QC). While QC issues associated with sample isolation, library preparation, and sequencing are well known and protocols for...

Data from: Emerging Representational Geometries in the Visual System Predict Reaction Times for Object Categorization

J. Brendan Ritchie, David A. Tovar & Thomas A. Carlson
Recognizing an object takes just a fraction of a second, less than the blink of an eye. Applying multivariate pattern analysis, or "brain decoding", methods to magnetoencephalography (MEG) data has allowed researchers to characterize, in high temporal resolution, the emerging representation of objects that underlie our capacity for rapid recognition. Shortly after stimulus onset, exemplar stimuli cluster by category in high-dimensional activation spaces. In these emerging activation spaces, the decodability of exemplar category varies over...

Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)

Jennifer R. Mandel, Edward V. McAssey, Katherine M. Roland & David E. McCauley
Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1,...

Data from: Real-time decision-making during emergency disease outbreaks

William J. M. Probert, Chris P. Jewell, Marleen Werkman, Christopher J. Fonnesbeck, Yoshitaka Goto, Michael C. Runge, Satoshi Sekiguchi, Katriona Shea, Matt J. Keeling, Matthew J. Ferrari & Michael J. Tildesley
In the event of a new infectious disease outbreak, mathematical and simulation models are commonly used to inform policy by evaluating which control strategies will minimize the impact of the epidemic. In the early stages of such outbreaks, substantial parameter uncertainty may limit the ability of models to provide accurate predictions, and policymakers do not have the luxury of waiting for data to alleviate this state of uncertainty. For policymakers, however, it is the selection...

Data from: Reconstructing geographic range size dynamics from fossil data

Simon A.F. Darroch & Erin E. Saupe
Ecologists and paleontologists alike are increasingly using the fossil record as a spatial data set, in particular to study the dynamics and distribution of geographic range sizes among fossil taxa. However, no attempts have been made to establish how accurately range sizes and range-size dynamics can be preserved. Two fundamental questions are: Can common paleo range-size reconstruction methods accurately reproduce known species’ ranges from locality (i.e., point) data? And, are some reconstruction methods more reliable...

Data from: Evidence for convergent evolution of ultrasonic hearing in toothed whales (Cetacea: Odontoceti)

Rachel A. Racicot, Robert W. Boessenecker, Simon A.F. Darroch & Jonathan H. Geisler
Toothed whales (Cetacea: Odontoceti) are the most diverse group of modern cetaceans, originating during the Eocene/Oligocene transition ~38 million years ago. All extant odontocetes echolocate; a single origin for this behavior is supported by a unique facial source for ultrasonic vocalizations and a cochlea adapted for hearing the corresponding echoes. The craniofacial and inner ear morphology of Oligocene odontocetes support a rapid (Simocetus and Olympicetus suggest an ability to generate ultrasonic sound, until now, the...

Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau

Elizabeth Scordato, Chris C. R. Smith, Georgy A. Semenov, Yu Liu, Matthew R. Wilkins, Wei Liang, Alexander Rubtsov, Gomboobaatar Sundev, Kazuo Koyama, Sheela P. Turbek, Michael B. Wunder, Craig A. Stricker & Rebecca Safran
Migratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, it is difficult to test the relative contributions of migratory behavior vs. other divergent traits to reproductive isolation. Comparing hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behavior to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive...

Permeability of Neotropical agricultural lands to a key native ungulate – are well-connected forests important?

Maria Luisa S. P. Jorge, Jennifer L. Bradham, Alexine Keuroghlian, Julia E. F. Oshima & Milton C. Ribeiro
Much of what remains of the Earth’s tropical forests is embedded within agricultural landscapes, where forest is reduced and fragmented. As native forest ungulates are critical to maintaining forest function, it is imperative to understand how this functional group responds to declines in forest cover and connectivity resulting from agricultural expansion. We addressed this issue by evaluating selection of forest cover and forest connectivity by a key native ungulate of Neotropical forests, the white-lipped peccary...

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