107 Works

Improved route to a diphenoxide-based precursor for CVD of parylene AF-4

Daniel Kast, Gerhard Franz & Jay J. Senkevich
In this work, we present an easy synthesis of a alternative precursor for CVD of parylene AF-4 to the widely used standard, Octafluoro[2.2]paracyclophane. The standard precursor suffers from uncertainties in its supply chain and its synthesis is of low yield. A comparison between different reaction parameters and solvents are being discussed by means of thermal, laboratory scale and microwave assisted reactions and qNMR studies.

Data from: Shear-induced orientational dynamics and spatial heterogeneity in suspensions of motile phytoplankton

Michael T. Barry, Roberto Rusconi, Jeffrey S. Guasto & Roman Stocker
Fluid flow, ubiquitous in natural and man-made environments, has the potential to profoundly impact the transport of microorganisms, including phytoplankton in aquatic habitats and bioreactors. Yet, the effect of ambient flow on the swimming behavior of phytoplankton has remained poorly understood, largely due to the difficulty of observing cell-flow interactions at the microscale. Here, we present microfluidic experiments where we tracked individual cells for four species of motile phytoplankton exposed to a spatially non-uniform fluid...

Data from: Surface energies of elemental crystals

Richard Tran, Zihan Xu, Balachandran Radhakrishnan, Donald Winston, Wenhao Sun, Kristin A. Persson & Shyue Ping Ong
The surface energy is a fundamental property of the different facets of a crystal that is crucial to the understanding of various phenomena like surface segregation, roughening, catalytic activity, and the crystal’s equilibrium shape. Such surface phenomena are especially important at the nanoscale, where the large surface area to volume ratios leads to properties that are significantly different from the bulk. In this work, we present the largest database of the calculated surface energies of...

Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus

Nadav Kashtan, Sara E. Roggensack, Sébastien Rodrigue, Jessie W. Thompson, Steven J. Biller, Allison Coe, Huiming Ding, Pekka Marttinen, Rex R. Malmstrom, Roman Stocker, Michael J. Follows, Ramunas Stepanauskas & Sallie W. Chisholm
Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct “genomic backbones,” each backbone consisting of a different set of...

Data from: Processing political misinformation: comprehending the Trump phenomenon

Briony Swire, Adam J. Berinsky, Stephan Lewandowsky & Ullrich K. H. Ecker
This study investigated the cognitive processing of true and false political information. Specifically, it examined the impact of source credibility on the assessment of veracity when information comes from a polarizing source (Experiment 1), and effectiveness of explanations when they come from one's own political party or an opposition party (Experiment 2). These experiments were conducted prior to the 2016 Presidential election. Participants rated their belief in factual and incorrect statements that President Trump made...

Data from: Effects of diet on cranial morphology and biting ability in musteloid mammals

Chris J. Law, Emma Duran, Nancy Hung, Ekai Richards, Isaac Santillan & Rita S. Mehta
Size and shape are often considered important variables that lead to variation in performance. In studies of feeding, size‐corrected metrics of the skull are often used as proxies of biting performance; however, few studies have examined the relationship between cranial shape in its entirety and estimated bite force across species and how dietary ecologies may affect these variables differently. Here, we used geometric morphometric and phylogenetic comparative approaches to examine relationships between cranial morphology and...

Data from: A new giant titanosaur sheds light on body mass evolution among sauropod dinosaurs

Jose L. Carballido, Diego Pol, Alejandro Otero, Ignacio Cerda, Leonardo Salgado, Alberto C. Garrido, Jahandar Ramezani, Nestor R. Cúneo & Javier M. Krause
Titanosauria was the most diverse and successful lineage of sauropod dinosaurs. This clade had its major radiation during the middle Early Cretaceous and survived up to the end of that period. Among sauropods, this lineage has the most disparate values of body mass, including the smallest and largest sauropods known. Although recent findings have improved our knowledge on giant titanosaur anatomy, there are still many unknown aspects about their evolution, especially for the most gigantic...

Data from: Pioneer cells established by the [SWI+] prion can promote dispersal and out-crossing in yeast

Gregory A. Newby & Susan Lindquist
To thrive in an ever-changing environment, microbes must widely distribute their progeny to colonize new territory. Simultaneously, they must evolve and adapt to the stresses of unpredictable surroundings. In both of these regards, diversity is key—if an entire population moved together or responded to the environment in the same way, it could easily go extinct. Here, we show that the epigenetic prion switch [SWI+] establishes a specialized subpopulation with a “pioneer” phenotypic program in Saccharomyces...

Data from: Relation between stability and resilience determines the performance of early warning signals under different environmental drivers

Lei Dai, Kirill S. Korolev & Jeff Gore
Shifting patterns of temporal fluctuations have been found to signal critical transitions in a variety of systems, from ecological communities to human physiology. However, failure of these early warning signals in some systems calls for a better understanding of their limitations. In particular, little is known about the generality of early warning signals in different deteriorating environments. In this study, we characterized how multiple environmental drivers influence the dynamics of laboratory yeast populations, which was...

Data from: Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle

Jacob R. Waldbauer, Sebastien Rodrigue, Maureen L. Coleman & Sallie W. Chisholm
BACKGROUND: Growth of the ocean’s most abundant primary producer, the cyanobacterium Prochlorococcus, is tightly synchronized to the natural 24-hour light-dark cycle. We sought to quantify the relationship between transcriptome and proteome dynamics that underlie this obligate photoautotroph’s highly choreographed response to the daily oscillation in energy supply. METHODOLOGY/PRINCIPAL FINDINGS: Using Illumina RNA-sequencing transcriptomics and mass spectrometry-based quantitative proteomics, we measured timecourses of paired mRNA-protein abundances for 312 genes every 2 hours over a light-dark cycle....

Data from: International collaboration and spatial dynamics of US patenting in Central and Eastern Europe 1981-2010

Mariann Leskó & Balázs Lengyel
How did post-socialist transition and a parallel shift in international labor division restructure regional innovation systems in Central and Eastern Europe? This question is increasingly important, because current EU innovation policy is combined with regional development in Smart Specialization Strategies; however, spatial trends of innovation in Central and Eastern Europe are not fully understood which might lead to less than perfectly efficient policy. In this paper we describe the spatial dynamics of inventor activity in...

Data from: Metamorphosis is ancestral for crown euarthropods, and evolved in the Cambrian or earlier

Joanna M. Wolfe
Macroevolutionary developmental biology employs fossilized ontogenetic data and phylogenetic comparative methods to probe the evolution of development at ancient nodes. Despite the prevalence of ecologically differentiated larval forms in marine invertebrates, it has been frequently presumed that the ancestors of arthropods were direct developers, and that metamorphosis may not have evolved until the Ordovician or later. Using fossils and new dated phylogenies, I infer that metamorphosis was likely ancestral for crown arthropods, contradicting this assumption....

Data from: Horizontal gene transfer constrains the timing of methanogen evolution

Joanna M. Wolfe & Gregory P. Fournier
Microbial methanogenesis may have been a major component of Earth’s carbon cycle during the Archaean eon, generating a methane greenhouse that increased global temperatures enough for a liquid hydrosphere, despite the Sun’s lower luminosity at the time. Evaluation of potential solutions to the ‘faint young Sun’ hypothesis by determining the age of microbial methanogenesis has been limited by ambiguous geochemical evidence and the absence of a diagnostic fossil record. To overcome these challenges, we use...

Data from: Seasonal variation in life history traits in two Drosophila species

Emily L. Behrman, Samuel S. Watson, Katherine R. O'Brien, Shane M. Heschel & Paul S. Schmidt
Seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. In species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. Here, we investigate how two closely related species of Drosophila in a temperate orchard respond to environmental changes across seasonal time. Natural populations of Drosophila melanogaster and D. simulans were sampled at four timepoints from June...

Data from: Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?

Derya Akkaynak, Liese Siemann, Alexandra Barbosa & Lydia M. Mäthger
Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation of perfect camouflage in which flounder and background were assumed to have identical spectral distribution. Computations were...

Data from: Paleozoic diversification of terrestrial chitin-degrading bacterial lineages

Danielle S. Gruen, Joanna M. Wolfe & Gregory P. Fournier
Background: Establishing the divergence times of groups of organisms is a major goal of evolutionary biology. This is especially challenging for microbial lineages, due to the near-absence of preserved physical evidence (diagnostic body fossils or geochemical biomarkers). Horizontal gene transfer (HGT), can serve as a temporal scaffold between microbial groups and other fossil-calibrated clades, potentially improving these estimates. Specifically, HGT to or from organisms with fossil-calibrated age estimates can propagate these constraints to additional groups...

Data from: Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Daniel I. Chasman, Erik Ingelsson … & Paul W. Franks
Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G·E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G·E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ=0.401 for triglycerides, and ρ=0.236 for BMI) compared...

Data from: Evolutionary history and biogeographical patterns of barnacles endemic to deep-sea hydrothermal vents

Santiago Herrera & Timothy M. Shank
The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep-sea hydrothermal vent barnacles represent an excellent model for testing biogeographic hypotheses regarding the origin, dispersal, and diversity of modern vent fauna. Here we characterize the global genetic diversity of vent barnacles to infer their time of radiation, place of origin, mode of dispersal, and diversification. Our approach was to target a...

Data from: A new lineage of Galapagos giant tortoises identified from museum samples

Evelyn L. Jensen, Maud C. Quinzin, Joshua M. Miller, Michael A. Russello, Ryan Garrick, Danielle L. Edwards, Scott Glaberman, Ylenia Chiari, Nikos Poulakakis, Washington Tapia, James P. Gibbs & Adalgisa Caccone
The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased individuals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave...

Data from: Strength of species interactions determines biodiversity and stability in microbial communities

Christoph Ratzke, Julien Barrere & Jeff Gore
Organisms, especially microbes, tend to live in complex communities. While some of these ecosystems are very bio-diverse, others aren′t, and while some are very stable over time others undergo strong temporal fluctuations. Despite a long history of research and a plethora of data it is not fully understood what sets biodiversity and stability of ecosystems. Theory as well as experiments suggest a connection between species interaction, biodiversity, and stability of ecosystems, where an increase of...

Preservation of erniettomorph fossils in clay-rich siliciclastic deposits from the Ediacaran Wood Canyon Formation, Nevada

James Hall, Emmy Smith, Nobumichi Tamura, Sirine Fakra & Tanja Bosak
Three-dimensionally preserved Ediacaran fossils occur globally within sandstone beds. Sandy siliciclastic deposits of the Ediacaran Wood Canyon Formation (WCF) in the Montgomery Mountains, Nevada, contain two taphomorphs of erniettomorphs, soft-bodied organisms with uncertain taxonomic affinities. One taphomorph exhibits mm-scale ridges and a distinct lower boundary, the other is devoid of these diagnostic features but is similar in size and shape. We explore the cast-and-mould preservation of both taphomorphs by petrography, Raman spectroscopy, X-ray fluorescence microprobe,...

Data from: Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

Steven J. Biller, Paul M. Berube, Jessie W. Berta-Thompson, Libusha Kelly, Sara E. Roggensack, Lana Awad, Kathryn H. Roache-Johnson, Huiming Ding, Stephen J. Giovannoni, Lisa R. Moore & Sallie W. Chisholm
The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To...

Data from: Combining role-play with interactive simulation to motivate informed climate action: evidence from the World Climate simulation

Juliette N. Rooney-Varga, John D. Sterman, Eduardo Fracassi, Travis Franck, Florian Kapmeier, Victoria Kurker, Ellie Johnston, Andrew P. Jones & Kenneth Rath
Climate change communication efforts grounded in the information deficit model have largely failed to close the gap between scientific and public understanding of the risks posed by climate change. In response, simulations have been proposed to enable people to learn for themselves about this complex and politically charged topic. Here we assess the impact of a widely-used simulation, World Climate, which combines a socially and emotionally engaging role-play with interactive exploration of climate change science...

Data from: Cataract surgery visual outcomes and associated risk factors in secondary level eye care centers of L V Prasad Eye Institute, India

Rohit C. Khanna, Sumathi Matta, Gullapalli Rao, Jiwon Park, Ghanshyam Palamaner Subash Shantha & Gullapalli N. Rao
Purpose: To evaluate cataract surgery visual outcomes and associated risk factors in rural secondary level eye care centers of L V Prasad Eye Institute (LVPEI), India. Methods: The Eye Health pyramid of LVPEI has a network of rural secondary care centres (SCs) and attached vision centres (VCs) that provide high quality comprehensive eye care with permanent infrastructure to the most disadvantaged sections of society. The most common procedure performed at SCs is cataract surgery. We...

Label-free three-photon imaging of intact human cerebral organoids: Tracking early events in brain development and deficits in Rett Syndrome

Murat Yildirim, Chloe Delepine, Danielle Feldman, Vincent Pham, Stephanie Chou, Jacque Ip, Alexi Nott, Li-Huei Tsai, Guo-Li Ming, Peter So & Mriganka Sur
Human cerebral organoids are unique in their development of progenitor-rich zones akin to ventricular zones from which neuronal progenitors differentiate and migrate radially. Analyses of cerebral organoids thus far have been performed in sectioned tissue or in superficial layers due to their high scattering properties. Here, we demonstrate label-free three-photon imaging of whole, uncleared intact organoids (~2 mm depth) to assess early events of early human brain development. Optimizing a custom-made three-photon microscope to image...

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  • Massachusetts Institute of Technology
  • Harvard University
  • Woods Hole Oceanographic Institution
  • University of California, Davis
  • University of Washington
  • University of California, Berkeley
  • Lawrence Berkeley National Laboratory
  • Howard Hughes Medical Institute
  • Zhejiang University
  • University of Pennsylvania