105 Works

Data from: A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life history adaptation

Annalise B. Paaby, Alan O. Bergland, Emily L. Behrman & Paul S. Schmidt
Finding the specific nucleotides that underlie adaptive variation is a major goal in evolutionary biology, but polygenic traits pose a challenge because the complex genotype-phenotype relationship can obscure the effects of individual alleles. However, natural selection working in large wild populations can shift allele frequencies and indicate functional regions of the genome. Previously, we showed that the two most common alleles of a complex amino acid insertion-deletion polymorphism in the Drosophila insulin receptor show independent,...

Data from: Essential gene disruptions reveal complex relationships between phenotypic robustness, pleiotropy, and fitness

Christopher R. Bauer, Shuang Li & Mark L. Siegal
The concept of robustness in biology has gained much attention recently, but a mechanistic understanding of how genetic networks regulate phenotypic variation has remained elusive. One approach to understand the genetic architecture of variability has been to analyze dispensable gene deletions in model organisms; however, the most important genes cannot be deleted. Here, we have utilized two systems in yeast whereby essential genes have been altered to reduce expression. Using high‐throughput microscopy and image analysis,...

Data from: Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

Annalise B. Paaby, Amelia G. White, David D. Riccardi, Kristin C. Gunsalus, Fabio Piano & Matthew V. Rockman
Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of C. elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants...

Data from: Memory and fitness optimization of bacteria under fluctuating environments

Guillaume Lambert & Edo Kussell
Bacteria prudently regulate their metabolic phenotypes by sensing the availability of specific nutrients, expressing the required genes for their metabolism, and repressing them after specific metabolites are depleted. It is unclear, however, how genetic networks maintain and transmit phenotypic states between generations under rapidly fluctuating environments. By subjecting bacteria to fluctuating carbon sources (glucose and lactose) using microfluidics, we discover two types of non-genetic memory in Escherichia coli and analyze their benefits. First, phenotypic memory...

Data from: High-frequency resonance in the gerbil medial superior olive

Jason Mikiel-Hunter, Vibhakar Kotak & John Rinzel
A high-frequency, subthreshold resonance in the guinea pig medial superior olive (MSO) was recently linked to the efficient extraction of spatial cues from the fine structure of acoustic stimuli. We report here that MSO neurons in gerbil also have resonant properties and, based on our whole-cell recordings and computational modeling, that a low-voltage-gated potassium current, IKLT, underlies the resonance. We show that resonance was lost following dynamic clamp replacement of IKLT with a leak conductance...

Data from: Towards the automatic classification of avian flight calls for bioacoustic monitoring

Justin Salamon, Juan Pablo Bello, Andrew Farnsworth, Matt Robbins, Sara Keen, Holger Klinck & Steve Kelling
Automatic classification of animal vocalizations has great potential to enhance the monitoring of species movements and behaviors. This is particularly true for monitoring nocturnal bird migration, where automated classification of migrants’ flight calls could yield new biological insights and conservation applications for birds that vocalize during migration. In this paper we investigate the automatic classification of bird species from flight calls, and in particular the relationship between two different problem formulations commonly found in the...

Data from: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales

Francine Kershaw, Inês Carvalho, Jacqueline Loo, Cristina Pomilla, Peter B. Best, Ken P. Findlay, Salvatore Cerchio, Tim Collins, Marcia H. Engel, Gianna Minton, Peter Ersts, Jaco Barendse, P. G. H. Kotze, Yvette Razafindrakoto, Solange Ngouessono, Michael Meӱer, Meredith Thornton & Howard C. Rosenbaum
Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample,...

Data from: The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization

David R. Nelson, Basel Khraiwesh, Weiqi Fu, Saleh Alseekh, Ashish Jaiswal, Amphun Chaiboonchoe, Khaled Hazzouri, Matthew J. O’Connor, Glenn L. Butterfoss, Nizar Drou, Jillian D. Rowe, Jamil Harb, Alisdair R. Fernie, Kristin C. Gunsalus & Kourosh Salehi-Ashtiani
To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero...

Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

Jae Young Choi & Michael D. Purugganan
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between...

Data from: Symbiont community stability through severe coral bleaching in a thermally extreme lagoon

Edward G. Smith, Grace O. Vaughan, Remi N. Ketchum, Dain McParland & John A. Burt
Coral reefs are threatened by climate change as coral-algal symbioses are currently living close to their upper thermal limits. The resilience of the algal partner plays a key role in determining the thermal tolerance of the coral holobiont and therefore, understanding the acclimatory limits of present day coral-algal symbioses is fundamental to forecasting corals’ responses to climate change. This study characterised the symbiont community in a highly variable and thermally extreme (Max = 37.5 °C,...

Data from: Walking on ashes: insect trace fossils from Laetoli indicate poor grass cover associated with early hominin environments

Jorge F. Genise & Terry Harrison
More than 4000 insect trace fossils collected in recent years from Pliocene deposits at Laetoli in northern Tanzania provide new insights on early hominin palaeoenvironments. These trace fossils include: Fictovichnus gobiensis, Coprinisphaera murguiai, C. kheprii, Coprinisphaera ispp., Quirogaichnus isp., Teisseirei linguatus isp. nov., Celliforma ritchiei isp. nov., C. spirifer, C. germanica, C. cfr. curvata, Celliforma ispp., Rosellichnus isp., Vondrichnus planoglobus, Laetolichnus kwekai igen. et isp. nov. and Krausichnidae indet. They reveal that at least one...

Data from: The rice paradox: multiple origins but single domestication in Asian rice

Jae Young Choi, Adrian E Platts, Dorian Q Fuller, Yue-Ie Hsing, Rod A Wing & Michael D Purugganan
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic...

Data from: The role of familiarity in signaler-receiver interactions

Wei Ji Ma & James P. Higham
Code - Chance calculationgetchance.mCode - Choices over days calculationgetchoices_overdays.mCode - Choices per day calculationgetchoices_perday.mCode - Decision Learnergetdecision_learner.mCode - Decision nonlearnergetdecision_nonlearner.mCode - measurementsgetmeasurements.mCode - parametersgetparameters.mCode - paternitygetpaternity.mMaster CodeMASTER.mCode - Plot figureplotFigure1.mCode - resultsplotresults.mCode - simulatesimulate.mREAD ME

2010 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

2015 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

2016 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

Anand Ranjan, Vu Q. Nguyen, Sheng Liu, Jan Wisniewski, Kim Jee Min, Xiaona Tang, Gaku Mizuguchi, Vivian Jou, Timothy J. Nickels, Brian P. English, Qinsi Zheng, Ed Luk, Timothee Lionnet, Luke D. Lavis, Carl Wu & Ejlal Elalaoui
The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit...

Domestication phenotype linked to vocal behavior in marmoset monkeys

Asif Ghazanfar, Lauren Kelly, Daniel Takahashi, Sandra Winters, Rebecca Terrett & James Higham
The domestication syndrome refers to a set of traits that are the incidental by-products of artificial selection for increased tolerance towards humans. One hypothesis is that some species like humans and bonobos “self domesticated”, that they have been under selection for that same suite of domesticated phenotypes. However, the evidence for this has been largely circumstantial. Here, we provide evidence that in marmoset monkeys, the size of a domestication phenotype—a white facial fur patch—is linked...

Serial thin section movie of every third section from the DTC to the distal extensions of Sh1 in a young adult hermaphrodite posterior gonad arm

Theadora Tolkin, Ariz Mohammed, Todd Starich, Ken C. Q. Nguyen, David H. Hall, Tim Schedl, E. Jane Albert Hubbard & David Greenstein
Gap-junctional signaling mediates myriad cellular interactions in metazoans. Yet, how gap junctions control the positioning of cells in organs is not well understood. Innexins compose gap junctions in invertebrates and affect organ architecture. Here, we investigate the roles of gap-junctions in controlling distal somatic gonad architecture and its relationship to underlying germline stem cells in Caenorhabditis elegans. We show that a reduction of soma-germline gap-junctional activity causes displacement of distal sheath cells (Sh1) towards the...

Demographics for all four breeds of broiler chickens

Iris Chan, Becca Franks & Matthew Hayek
In 2018, over nine billion chickens were slaughtered in the United States. As the demand for chickens increases, so too have concerns regarding the welfare of the chickens in these systems and the damage such practices cause to the surrounding ecosystems. To address welfare concerns, there is large-scale interest in raising chickens on pasture and switching to slower-growing, higher-welfare breeds as soon as 2024. We created a box model of US chicken demographics to characterize...

Data from: Optimal lineage principle for age-structured populations

Yuichi Wakamoto, Alexander Y Grosberg & Edo Kussell
We present a formulation of branching and aging processes that allows distributions along lineages to be studied within populations, and provides a new interpretation of classical results in the theory of aging. We establish a variational principle for the stable age distribution along lineages. Using this optimal lineage principle, we show that the response of a population’s growth rate to age-specific changes in mortality and fecundity – a key quantity which was first calculated by...

Data from: Assessing the potential information content of multicomponent visual signals: a machine learning approach

William L. Allen & James P. Higham
Careful investigation of the form of animal signals can offer novel insights into their function. Here, we deconstruct the face patterns of a tribe of primates, the guenons (Cercopithecini), and examine the information that is potentially available in the perceptual dimensions of their multicomponent displays. Using standardized colour-calibrated images of guenon faces, we measure variation in appearance both within and between species. Overall face pattern was quantified using the computer vision ‘eigenface’ technique, and eyebrow...

Data from: Closing the achievement gap through modification of neurocognitive and neuroendocrine function: results from a cluster randomized controlled trial of an innovative approach to the education of children in kindergarten

Clancy Blair & C. Cybele Raver
Effective early education is essential for academic achievement and positive life outcomes, particularly for children in poverty. Advances in neuroscience suggest that a focus on self-regulation in education can enhance children’s engagement in learning and establish beneficial academic trajectories in the early elementary grades. Here, we experimentally evaluate an innovative approach to the education of children in kindergarten that embeds support for self-regulation, particularly executive functions, into literacy, mathematics, and science learning activities. Results from...

Data from: Lateralization in alpha-band oscillations predicts the locus and spatial distribution of attention

Akiko Ikkai, Sangita Dandekar & Clayton E. Curtis
Attending to a task-relevant location changes how neural activity oscillates in the alpha band (8–13Hz) in posterior visual cortical areas. However, a clear understanding of the relationships between top-down attention, changes in alpha oscillations in visual cortex, and attention performance are still poorly understood. Here, we tested the degree to which the posterior alpha power tracked the locus of attention, the distribution of attention, and how well the topography of alpha could predict the locus...

Data from: The kinetochore prevents centromere-proximal crossover recombination during meiosis

Nadine Vincenten, Lisa-Marie Kuhl, Isabel Lam, Ashwini Oke, Alastair R. W. Kerr, Andreas Hochwagen, Jennifer C. Fung, Scott Keeney, Gerben Vader & Adèle L. Marston
During meiosis, crossover recombination is essential to link homologous chromosomes and drive 22 faithful chromosome segregation. Crossover recombination is non-random across the genome, 23 and centromere-proximal crossovers are associated with an increased risk of aneuploidy, 24 including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub- 25 complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers 26 in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the 27...

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Affiliations

  • New York University
    96
  • Hansen Experimental Physics Laboratory, Stanford University
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  • Electrical Engineering and Computer Science Department, University of Michigan
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  • SUPA School of Physics and Astronomy, University of Glasgow
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