19 Works

Large-scale neural recordings with single neuron resolution using Neuropixels probes in human cortex

Angelique C Paulk, Yoav Kfir, Arjun R Khanna, Martina L Mustroph, Eric M Trautmann, Dan J Soper, Sergey D Stavisky, Marleen Welkenhuysen, Barundeb Dutta, Krisha V Shenoy, Leigh R Hochberg, R. Mark Richardson, Ziv M Williams & Sydney S Cash
Recent advances in multi-electrode array technology have made it possible to monitor large neuronal ensembles at cellular resolution in animal models. In humans, however, current approaches restrict recordings to few neurons per penetrating electrode or combine the signals of thousands of neurons in local field potential (LFP) recordings. Here, we describe a new probe variant and set of techniques which enable simultaneous recording from over 200 well-isolated cortical single units in human participants during intraoperative...

Revisiting a classic hybrid zone: movement of the northern flicker hybrid zone in contemporary times

Stepfanie Aguillon & Vanya Rohwer
Natural hybrid zones have provided important insights into the evolutionary process, and their geographic dynamics over time can help to disentangle the underlying biological processes that maintain them. Here, we leverage replicated sampling of an identical transect across the hybrid zone between yellow-shafted and red-shafted flickers in the Great Plains to assess its stability over ~60 years (1955-1957 to 2016-2018). We identify a ~73 km westward shift in the hybrid zone center towards the range...

Mitochondrial and ER membrane protein trafficking CRISPR screens

David Yao & Robert Coukos
The trafficking of specific protein cohorts to the correct subcellular location at the correct time is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or FACS. To broadly empower the study of protein trafficking processes...

Fractal Characterization of Multimodal, Multiscale Images of Shale Rock Fracture Networks

Bolivia Vega & Anthony Kovscek
Images associated to paper of the same name by B. Vega, A.R. Kovscek This research was funded by the Center for Mechanistic Control of Unconventional Formations (CMC-UF), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science under DOE (BES) Award DE-SC0019165.

Single-Cell RNA-sequencing of neural precursor cells from an Alzheimer's mouse model, wild-type mice, and Alzheimer's mice rescued with Usp16 haploinsufficiency

Elizabeth Chen, Robert Jones, Michael Clarke & Stephen Quake
Alzheimer’s disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify an earlier targetable phenotype. Utilizing a mouse model of AD we found that cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it one of the earlier defects in the evolution...

Data and code repository for the manuscript: JC Selinger, JL Hicks, RW Jackson, CM Wall-Scheffler, D Chang, and SL Delp. Running in the Wild: Using large-scale wearable data to understand ecological running speed preferences. Current Biology (2022).

Jessica Selinger, Jennifer Hicks, Rachel Jackson, Cara Wall-Scheffler, Derek Chang & Scott Delp
Human runners have long been thought to have the ability to consume a near constant amount of energy per distance traveled regardless of speed, allowing speed to be adapted to particular task demands with minimal energetic consequence. However, recent and more precise laboratory measures indicate that humans may in fact have an energy-optimal running speed. Here we characterize runners’ speeds in a free-living environment and determine if preferred speed is consistent with task or energy...

Resilient consumers accelerate the plant decomposition in a naturally acidified seagrass ecosystem

Juhyung Lee, Maria Cristina Gambi, Kristy Kroeker, Marco Munari, Kabir Peay & Fiorenza Micheli
Anthropogenic stressors are predicted to alter biodiversity and ecosystem functioning worldwide. However, scaling up from species to ecosystem responses poses a challenge, as species and functional groups can exhibit different capacities to adapt, acclimate, and compensate under changing environments. We used a naturally acidified seagrass ecosystem (the endemic Mediterranean Posidonia oceanica) as a model system to examine how ocean acidification (OA) modifies the community structure and functioning of plant detritivores, which play vital roles in...

Census and phenotype data supporting Drosophila adaptive tracking

Seth Rudman, Paul Schmidt, Subhash Rajpurohit, Sharon Greenblum & Dmitri Petrov
Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked evolution of fitness-associated phenotypes and allele frequencies genome-wide in ten replicate field populations of Drosophila melanogaster over ten generations from summer to late fall. Adaptation was evident over each sampling interval (1-4 generations) with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent...

Data from: Scaling of maneuvering performance in baleen whales: larger whales outperform expectations

Paolo Segre
Despite their enormous size, whales make their living as voracious predators. To catch their much smaller, more maneuverable prey, they have developed several unique locomotor strategies that require high energetic input, high mechanical power output, and a surprising degree of agility. To better understand how body size affects maneuverability at the largest scale, we used bio-logging data, aerial photogrammetry, and a high-throughput approach to quantify the maneuvering performance of seven species of free-swimming baleen whales....

10Be concentrations constraining surface age and valley growth rate in a seepage-derived drainage network in the Apalachicola River basin, Florida

Emma Harrison, Brandon McElroy & Jane Willenbring
Measuring rates of valley head migration and determining the timing of canyon-opening are insightful quantifications for the history and evolution of planetary surfaces. Horizontal spatial gradients of in situ-produced cosmogenic nuclide concentrations provide a framework for assessing the migration of these and similar topographic features. We developed a theoretical model for the concentration of in situ produced cosmogenic radionuclides in valley walls during retreat of a valley head. The retreat rate is inversely proportional to...

Hair phenotype diversity across Indriidae lemurs

Elizabeth Tapanes, Rachel Jacobs, Ian Harryman, , Mitchell Irwin, Jason Kamilar & Brenda Bradley
Objectives: Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution—serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun). Materials...

Flash intensity and duration

Jamie Zeitzer, Daniel Joyce & Manuel Spitschan
These data were obtained by having individuals participate in a series of 16-day studies, each with a 34-hour in-laboratory period. In this between-subjects design, we examined phase shifting in response to variable-intensity (3-9500 photopic lux) flashes at fixed duration (2 ms; n=28 participants) and variable-duration (10 μs-10 s) flashes at fixed intensity (2000 photopic lux; n=31 participants) for 1 hour with 15 s between flashes . Acute melatonin suppression, objective alertness, and subjective sleepiness during...

Data for: Inhibition of Ca2+-triggered secretion by hydrocarbon-stapled peptides

Axel Brunger, Ying Lai, Giorgio Fois, Jose Flores, Michael Tuvim, Qiangjun Zhou, Kailu Yang, Jeremy Leitz, John Peters, Yunxiang Zhang, Richard Pfuetzner, Luis Esquivies, Philip Jones, Manfred Frick & Burton Dickey
Ca2+-triggered membrane fusion is orchestrated by a conserved set of proteins to mediate synaptic neurotransmitter release, mucin secretion, and other regulated exocytic processes. For neurotransmitter release, the Ca2+ sensitivity is introduced by interactions between the Ca2+ sensor synaptotagmin and the SNARE complex, and sequence conservation and functional studies suggest this mechanism is also conserved for mucin secretion. Disruption of Ca2+-triggered membrane fusion by a pharmacologic agent would have therapeutic value for mucus hypersecretion since it...

Maternal and perinatal obesity induce bronchial obstruction and pulmonary hypertension via IL-6-FoxO1-axis in later life

Jaco Selle, Katharina Dinger, Vanessa Jentgen, Daniela Zanetti, Johannes Will Will, Theodoros Georgomanolis, Christina Vohlen, Rebecca Wilke, Baktybek Kojonazarov, Oleksiy Klymenko, Jasmine Mohr, Silke V. Koningsbruggen-Rietschel, Christopher J. Rhodes, Anna Ulrich, Dharmesh Hirani, Tim Nestler, Margarete Odenthal, Esther Mahabir, Sreenath Nayakanti, Swati Dabral, Thomas Wunderlich, James Priest, Werner Seeger, Jörg Dötsch, Soni S. Pullamsetti … & Miguel A. Alejandre Alcazar
Obesity is a pre-disposing condition for chronic obstructive pulmonary disease, asthma, and pulmonary arterial hypertension. Accumulating evidence suggests that metabolic influences during development can determine chronic lung diseases (CLD). We demonstrate that maternal obesity causes early metabolic disorder in the offspring. Here, interleukin-6 induced bronchial and microvascular smooth muscle cell (SMC) hyperproliferation and increased airway and pulmonary vascular resistance. The key anti-proliferative transcription factor FoxO1 was inactivated via nuclear exclusion. These findings were confirmed using...

Data from: a physics-based digital twin for model predictive control of autonomous unmanned aerial vehicle landing

Andrew McClellan, Joseph Lorenzetti, Marco Pavone & Charbel Farhat
This paper proposes a two-level, data-driven, digital twin concept for the autonomous landing of aircraft, under some assumptions. It features a digital twin instance for model predictive control; and an innovative, real-time, digital twin prototype for fluid-structure interaction and flight dynamics to inform it. The latter digital twin is based on the linearization about a pre-designed glideslope trajectory of a high-fidelity, viscous, nonlinear computational model for flight dynamics; and its projection onto a low-dimensional approximation...

The effects of light intensity and flow speed on biogeochemical variability within a fringing coral reef in Onna-son, Okinawa, Japan

Max Rintoul, Travis Courtney, Julia Dohner, Sarah Giddings, Samuel Kekuewa, Stephen Monismith, Ariel Pezner, Andreas Andersson & Satoshi Mitarai
Global warming and ocean acidification are driving gradual declines in seawater dissolved oxygen concentrations and pH. Predicting how these changes will affect shallow, near-shore environments including coral reefs is challenging due to high natural variability on both spatial (10 m to km) and temporal (diel to seasonal) scales. To make predictions, it is first necessary to identify and quantify the drivers of this natural variability. While significant efforts have been devoted to characterising the influence...

Carry-over effects of larval food stress on adult energetics and life history in a nectar-feeding butterfly

Carol Boggs & Kristjan Niitepold
Stressful juvenile developmental conditions can affect performance and fitness later in life. In holometabolous insects such as butterflies, development under stressful conditions may lead to smaller adult size, lower reproductive output and shorter lifespan. However, how larval developmental stress affects energy intake and expenditure in adult individuals is poorly understood. We subjected last-instar larvae of Speyeria mormonia Edwards (Lepidoptera: Nymphalidae) to periodic dietary restriction (DR) to examine the allocation of energy and nutrients among different...

Supplementary material for: nQMaker: estimating time non-reversible amino acid substitution models

Cuong Dang, Minh Bui, Hanon McShea, Joanna Masel, Jennifer James, Vinh Le & Robert Lanfear
Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly-used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation...

The limits of convergence in the collective behavior of competing marine taxa

Benjamin Burford
Collective behaviors in biological systems, such as coordinated movements, have important ecological and evolutionary consequences. While many studies examine within-species variation in collective behavior, explicit comparisons between functionally similar species from different taxonomic groups are rare. Therefore, a fundamental question remains: how do collective behaviors compare between taxa with morphological and physiological convergence, and how might this relate to functional ecology and niche partitioning? We examined the collective motion of two ecologically similar species from...

Registration Year

  • 2022
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  • Stanford University
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  • University of Puerto Rico-Mayaguez
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  • Max Planck Institute for Heart and Lung Research
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  • University of California, San Diego
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