38 Works

Stepwise-edited, human melanoma models reveal mutations’ effect on tumor and microenvironment

Eran Hodis & Elena Torlai Triglia
Establishing causal relationships between genetic alterations of human cancers and the specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly disrupted melanoma pathways forming nine genetically distinct cellular models of melanoma. We connected mutant melanocyte genotypes to malignant cell expression programs in vitro and in vivo, replicative immortality, malignancy, rapid tumor growth, pigmentation, metastasis, and histopathology. Mutations in malignant cells also...

TCCON data from Indianapolis (US), Release GGG2020.R0

L. T. Iraci, J. R. Podolske, P. W. Hillyard, C. Roehl, P. O. Wennberg, J.-F. Blavier, J. Landeros, N. Allen, D. Wunch, J. Zavaleta, E. Quigley, G. B. Osterman, E. Barrow & J. Barney
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at Indianapolis, Indiana, USA

Profiling, monitoring and conserving caterpillar fungus in the Himalayan region using anchored hybrid enrichment markers

Zhengyang Wang
The collection of caterpillar fungus accounts for 50-70% of the household income of thousands of Himalayan communities and has an estimated market value of $5-11 billion across Asia. However, Himalayan collectors are at multiple economic disadvantages compared with collectors on the Tibetan plateau because their product is not legally recognized. Using a customized hybrid-enrichment probe set and market-grade caterpillar fungus (with samples up to 30 years old) from 94 production zones across Asia, we uncovered...

Changes in temperature alter competitive interactions and overall structure of fig wasp communities

Khin Me Me Aung, Huan-Huan Chen, Simon Segar, Yan-Qiong Peng & Cong Liu
1. Organisms exist within ecological networks, connected through interactions such as parasitism, predation and mutualism which can modify their abundance and distribution within habitat patches. Differential species responses make it hard to predict the influence of climate change at the community scale. Understanding the interplay between climate and biotic interactions can improve our predictions of how ecosystems will respond to current global warming. 2. We aim to understand how climate affects the multi-trophic biotic interactions...

Population and single dopamine neuron activity during classical conditioning

Ryunosuke Amo, Sara Matias, Naoshige Uchida & Mitsuko Watabe-Uchida
We trained naive or trained mice to associate odor cues with outcome (water, air puff or no outcome), and recorded dopamine cell body activity in the vetral tegmental area (VTA), dopamine axon activity in the ventral striatum (VS) or dopamine release in VS with optic fiber fluorometry (photometry). In different set of mice, single dopamine neuron activiy was recorded with 2-photon microscope. In some of these mice, we reversed odor-outcome contingency so that an odor...

Game Design Considerations for Screening, Interim, and Diagnostic Educational Assessments

David Dockterman, Yaacov Petscher, Alison McAfee, Eric Klopfer, Scot Osterweil & Cody Diefenthaler
To inform instruction, screening and diagnostic assessments must collect accurate data about the current state of the learner. Unfortunately, students may find assessments unengaging, intimidating, or irrelevant, undermining the quality of their effort and the quality of the data. The application of gaming to assessments may provide a way to boost and sustain effortful test-taker engagement, an integration that has thus far yielded mixed results, at best. Our interdisciplinary team reviewed and evaluated existing gamification...

Demographic data collection in STEM organizations

Nicholas Burnett, Alyssa Hernandez, Emily King, Richelle Tanner & Kathryn Wilsterman
Professional organizations in STEM (science, technology, engineering, and mathematics) can use demographic data to quantify recruitment and retention (R&R) of underrepresented groups within their memberships. However, variation in the types of demographic data collected can influence the targeting and perceived impacts of R&R efforts - e.g., giving false signals of R&R for some groups. We obtained demographic surveys from 73 U.S.-affiliated STEM organizations, collectively representing 712,000 members and conference-attendees. We found large differences in the...

Histological and life history data for small-bodied mammals from: Multituberculate mammals show evidence of a life history strategy similar to that of placentals, not marsupials

Lucas Weaver, Henry Fulghum, David Grossnickle, William Brightly, Zoe Kulik, Gregory Wilson Mantilla & Megan Whitney
The remarkable evolutionary success of placental mammals has been partly attributed to their reproductive strategy of prolonged gestation and birthing of relatively precocial, quickly weaned neonates. Although this strategy was conventionally considered derived relative to that of marsupials with highly altricial neonates and long lactation periods, mounting evidence has challenged this view. Until now, the fossil record has been relatively silent on this debate, but here we find that proportions of different bone tissue microstructures...

Barcoded Bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

Alex N. Nguyen Ba, Katherine Lawrence, Artur Rego-Costa, Shreyas Gopalakrishnan, Daniel Temko, Franziska Michor & Michael Desai
Mapping the genetic basis of complex traits is critical to uncovering the biological mechanisms that underlie disease and other phenotypes. Genome-wide association studies (GWAS) in humans and quantitative trait locus (QTL) mapping in model organisms can now explain much of the observed heritability in many traits, allowing us to predict phenotype from genotype. However, constraints on power due to statistical confounders in large GWAS and smaller sample sizes in QTL studies still limit our ability...

TCCON data from Jet Propulsion Laboratory (US), 2011, Release GGG2020.R0

P. O. Wennberg, C. M. Roehl, J.-F. Blavier, D. Wunch & N. T. Allen
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at Jet Propulsion Laboratory, Pasadena, California, USA

Doryteuthis pealeii embyronic transcriptome individual stages 16-27 pooled and annotation

Kristen Koenig
Photoreception is a ubiquitous sensory ability found across the Metazoa, and photoreceptive organs are intricate and diverse in their structure. Although the morphology of the compound eye in Drosophila and the single-chambered eye in vertebrates have elaborated independently, the amount of conservation within the 'eye' gene regulatory network remains controversial, with few taxa studied. To better understand the evolution of photoreceptive organs, we established the cephalopod Doryteuthis pealeii as a lophotrochozoan model for eye development....

Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains

Zhengyang Wang & Naomi Pierce
The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host...

β-cell-specific deletion of Zfp148 improves nutrient-stimulated β-cell Ca2+ responses

Christopher Emfinger, Alan Attie, Matthew Merrins, Eleonora De Klerk, Matthias Hebrok, Richard Kibbey, Rebecca Cardone, Kathryn Schueler, Mary Rabaglia, Shane Simonett, Donnie Stapleton, Kelly Mitok, Sophie Lewandowski, Ziyue Wang, Christina Kendziorski, Mark Keller, Hannah Foster, Stephen Gygi, Xinyue Liu, Joao Paulo, Qinq Yu & José Perales
Insulin secretion from pancreatic β-cells is essential for glucose homeostasis. An insufficient response to the demand for insulin results in diabetes. We previously showed that β-cell-specific deletion of Zfp148 (β-Zfp148KO) improves glucose tolerance and insulin secretion in mice. Here, we performed Ca2+ imaging of islets from β‑Zfp148KO and control mice on both a chow and a Western-style diet. β-Zfp148KO islets demonstrate improved sensitivity and sustained Ca2+ oscillations in response to elevated glucose. β-Zfp148KO islets also...

Data from: Ontogeny and evolution of the elasmosaurid neck highlight a greater diversity of Antarctic plesiosaurians

Arthur S. Brum, Tiago R. Simões, Geovane A. Souza, André E. P. Pinheiro, Rodrigo G. Figueiredo, Michael W. Caldwell, Juliana M. Sayão & Alexander W. A. Kellner
The Antarctic plesiosaurian record is critical for understanding the evolution of elasmosaurids in the southern hemisphere. Elasmosaurids exhibit some of the most remarkable modifications of the vertebrate axial skeleton given their extreme elongation of the cervical region. Despite a considerable amount of information available on vertebral counts within Plesiosauria throughout the decades, we have a considerably more limited understanding of the diversity of cervical vertebral shapes in elasmosaurids and how these have changed throughout ontogeny...

Species-level termite methane production rates

Yong Zhou, Carla Staver & Andrew Davies
Termites consume substantial amounts of plant material across tropical and subtropical ecosystems. During the process of lignocellulose digestion, the symbiotic methanogenesis within termites’ guts produces the potent greenhouse gas methane (CH4). Termites contribute an estimated 1-5% of global CH4 emissions, with these estimates derived from the product of termite biomass and termite CH4 production rate per unit of termite biomass. However, termite CH4 production rates vary significantly across species, genus, family, and feeding group, yet...

TCCON data from East Trout Lake, SK (CA), Release GGG2020.R0

D. Wunch, J. Mendonca, O. Colebatch, N. T. Allen, J.-F. Blavier, K. Kunz, S. Roche, J. Hedelius, G. Neufeld, S. Springett, D. Worthy, R. Kessler & K. Strong
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at East Trout Lake, Canada

TCCON data from Jet Propulsion Laboratory (US), 2007, Release GGG2020.R0

P. O. Wennberg, D. Wunch, Y. Yavin, G. C. Toon, J.-F. Blavier, N. T. Allen, G. Keppel-Aleks & C.M. Roehl
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at Jet Propulsion Laboratory, Pasadena, California, USA

TCCON data from Lamont (US), Release GGG2020.R0

P. O. Wennberg, D. Wunch, C. M. Roehl, J.-F. Blavier, G. C. Toon & N. T. Allen
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at Lamont, Oklahoma, USA

Data from: An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

Stephanie Marciniak, Christina Bergey, Ana Maria Silva, Agata Hałuszko, Mirosław Furmanek, Barbara Veselka, Petr Velemínský, Giuseppe Vercellotti, Joachim Wahl, Gunita Zarina, Cristina Longhi, Jan Kolář, Rafael Garrido-Pena, Raúl Flores-Fernández, Ana M. Herrero-Corral, Angela Simalcsik, Werner Müller, Alison Sheridan, Žydrūnė Miliauskienė, Rimantas Jankauskas, Vyacheslav Moiseyev, Kitti Köhler, Ágnes Király, Beatriz Gamarra, Olivia Cheronet … & George H. Perry
Human culture, biology, and health were shaped dramatically by the onset of agriculture ~12,000 years before present (BP). This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across...

New opabiniid diversifies the weirdest wonders of the euarthropod stem group

Joanna Wolfe, Stephen Pates, Rudy Lerosey-Aubril, Allison C. Daley & Javier Ortega-Hernández
Once considered ‘weird wonders’ of the Cambrian, the emblematic Burgess Shale animals Anomalocaris and Opabinia are now recognized as lower stem group euarthropods and have provided crucial data for constraining the polarity of key morphological characters in the group. Anomalocaris and its relatives (radiodonts) had a worldwide distribution and survived until at least the Devonian. However, despite intense study, Opabinia remains the only formally described opabiniid to date. Here we reinterpret a fossil from the...

Data from: Whole-genome phylogeography of the Blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome

Scott Edwards, John Burley, Sophie Orzechowski & Yun Wa Sin
Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the Blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and...

TCCON data from Park Falls (US), Release GGG2020.R0

P. O. Wennberg, C. M. Roehl, D. Wunch, G. C. Toon, J.-F. Blavier, R. Washenfelder, G. Keppel-Aleks & N. T. Allen
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at Park Falls, Wisconsin, USA

Limited increases in savanna carbon stocks over decades of fire suppression

Yong Zhou, Jenia Singh, John Butnor, Corli Coetsee, Peter Boucher, Madelon Case, Evan Hockridge, Andrew Davies & Carla Staver
Savannas cover a fifth of the land surface and contribute a third of terrestrial net primary production, accounting for three quarters of global area burned and over half of global fire-driven carbon emissions. Fire suppression and afforestation have been proposed as tools to increase carbon sequestration in these ecosystems. A robust quantification of whole-ecosystem carbon storage in savannas is lacking, however, especially under altered fire regimes. Here, we provide the first direct estimates of whole-ecosystem...

Data for: A hypothesis to explain polarization color vision in butterflies, with an example from the Australian Imperial Blue, Jalmenus evagoras

Richard Rabideau Childers
The Australian lycaenid butterfly, Jalmenus evagoras, has iridescent wings that are sexually dimorphic in both spectral reflection and degree of polarization, suggesting that these wing properties are likely to be important in mate recognition. We first describe the results of a field experiment showing that free-flying individuals of J. evagoras can discriminate between visual stimuli that vary in polarization content in a wavelength-dependent manner. We then present detailed reflectance spectrophotometry measurements of the polarization content...

Dopamine activity in the tail of the striatum, DeepLabCut and MoSeq during novel object exploration

Mitsuko Watabe-Uchida, Korleki Akiti, Iku Tsutsui-Kimura, Yudi Xie, Alexander Mathis, Jeffrey Markowitz, Rockwell Anyoha, Sandeep Robert Datta, Mackenzie Weygandt Mathis & Naoshige Uchida
In this study, we characterized dynamics of novelty exploration using multi-point tracking (DeepLabCut) and behavioral segmentation (MoSeq). Mice were habituated in an arena, and then a object was placed at the corner of the arena. We compared 4 groups of mice: one with presentation of a novel object (stimulus novelty), one with a presentation of a familiar object (contextual novelty), one with presentation of a novel object after ablation of dopamine neuorns that project to...

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  • Harvard University
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  • Jet Propulsion Laboratory, Pasadena, CA (US)
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  • California Institute of Technology, Pasadena, CA (US)
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  • Department of Physics, University of Toronto, Toronto, ON (CA)
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