16 Works

Vachellia drepanolobium nutrient translocation in response to smoke

Katherine Angier, Richard Rabideau-Childers, Brendan Dean, Meghan Blumstein, Walker Darling, Annina Kennedy-Yoon, Clayton Ziemke, Christian Perez-Martinez, Donghao Wu, Wenqing Ye, Inam Yekwayo, Duncan Kimuyu, Dino Martins & Naomi Pierce
1. Fire is a major selective force on arid grassland communities, favoring traits such as the smoke-induced seed germination response seen in a wide variety of plant species. However, little is known about the relevance of smoke as a cue for plants beyond the seedling stage. 2. We exposed a fire-adapted savanna tree, Vachellia (=Acacia) drepanolobium, to smoke and compared nutrient concentrations in leaf and root tissues to unexposed controls. Experiments were performed on three...

RNA sequencing of PET127 mutants overexpressed using the galactose inducible promoter

Daniel Corbi & Angelika Amon
In Saccharomyces cerevisiae, PET127 is a mitochondrial RNA exonuclease known to interact with the mitochondrial RNA polymerase RPO41. The nature of the interaction between PET127 and RPO41 is unclear. Here, we overexpressed different PET127 mutants for five hours utilizing the galactose inducible promoter on high-copy plasmids, collected samples, and performed RNA sequencing to understand the mitochondrial RNA landscape in each condition. The mutants tested were PET127 lacking the nuclease activity (pet127-nd) and two truncated forms...

Data from: Functional attractors in microbial community assembly

Sylvie Estrela, Jean Vila, Nanxi Lu, Djordje Bajic, Maria Rebolleda-Gomez, Chang-Yu Chang, Josh Goldford, Alicia Sanchez-Gorostiaga & Alvaro Sanchez
For microbiome biology to become a more predictive science, we must identify which descriptive features of microbial communities are reproducible and predictable, which are not, and why. We address this question by experimentally studying parallelism and convergence in microbial community assembly in replicate glucose-limited habitats. Here, we show that the previously observed family-level convergence in these habitats reflects a reproducible metabolic organization, where the ratio of the dominant metabolic groups can be explained from a...

A helicase-tethered ORC flip enables bidirectional helicase loading

Shalini Gupta
Replication origins are licensed by loading two Mcm2‑7 helicases around DNA in a head-to-head conformation poised to initiate bidirectional replication. This process requires ORC, Cdc6, and Cdt1. Although different Cdc6 and Cdt1 molecules load each helicase, whether two ORC proteins are required is unclear. Using colocalization single-molecule spectroscopy combined with FRET, we investigated interactions between ORC and Mcm2‑7 during helicase loading. In the large majority of events, we observed a single ORC molecule recruiting both...

Neural representations of space in the hippocampus of a food-caching bird

Hannah Payne, Galen Lynch & Dmitriy Aronov
Spatial memory in vertebrates requires brain regions homologous to the mammalian hippocampus. Between vertebrate clades, however, these regions are anatomically distinct and appear to produce different spatial patterns of neural activity. We asked whether hippocampal activity is fundamentally different even between distant vertebrates that share a strong dependence on spatial memory. We studied tufted titmice, food-caching birds capable of remembering many concealed food locations. We found mammalian-like neural activity in the titmouse hippocampus, including sharp-wave...

COMSOL models of fluid flow in the sarcomere

Sage Malingen, Kaitlyn Hood, Eric Lauga, Anette Hosoi & Thomas Daniel
A highly organized and densely packed lattice of molecular machinery within the sarcomeres of muscle cells powers contraction. Although many of the proteins that drive contraction have been studied extensively, the mechanical impact of fluid shearing within the lattice of molecular machinery has received minimal attention. It was recently proposed that fluid flow augments substrate transport in the sarcomere, however, this analysis used analytical models of fluid flow in the molecular machinery that could not...

Inferred ancestry of scytonemin biosynthesis proteins in cyanobacteria indicates a response to Paleoproterozoic oxygenation

Erik Tamre & Gregory P. Fournier
Protection from radiation damage is an important adaptation for phototrophic microbes. In the case of cyanobacteria, surface, shallow water, and peritidal environments are especially exposed to long- wavelength ultraviolet (UVA) radiation. Several groups of cyanobacteria within these environments are protected from UVA damage by the production of the pigment scytonemin. Paleontological evidence of cyanobacteria in UVA-exposed environments from the Proterozoic, and possibly as early as the Archaean, suggests a long evolutionary history of radiation protection...

RNA sequencing of nuclease dead PET127 conditions

Daniel Corbi & Angelika Amon
PET127, is thought to be a mitochondrial RNA exonuclease and loss of PET127 is thought to cause accumulation of untrimmed RNA in the mitochondria. Here we show RNA sequencing of Saccharomyces cerevisiae in four PET127 conditions: PET127 wild-type, pet127∆, pet127-nd (nuclease dead)/pet127∆, and pet127-nd/PET127. The resulting sequences show that regions of mitochondrial RNA accumulate in the pet127∆ background, and the RNA sequencing profile of PET127 containing disruptive mutations in the conserved exonuclease active site mimics...

Drainage Canals in Southeast Asian Peatland

Nathan Dadap, Alison M Hoyt, Alexander R Cobb, Doruk Oner, Mateusz Kozinski, Pascal V Fua, Krishna Rao, Charles F Harvey & Alexandra G Konings
These images depict drainage canals and roads in peatlands in Borneo, Sumatra, and Peninsular Malaysia at 5 meter resolution. These canals were detected from July-September 2017 Planet Basemaps satellite imagery using a convolutional neural network. Please contact Nathan Dadap (ndadap@stanford.edu) with any questions.

Dataset for the study of Ultrafast energy transfer between lipid-linked chromophores and plant Light-Harvesting Complex II

Ashley Hancock, Minjung Son, Muath Nairat, Tiejun Wei, Lars Jeuken, Christopher Duffy, Gabriela Schlau-Cohen & Peter Adams
This dataset shows the raw data, analysed data and documentation related to figures and tables from the study “Ultrafast energy transfer between lipid-linked chromophores and plant Light-Harvesting Complex II". This includes: absorbance and fluorescence spectra; molecular dynamics images and associated files; calculations of excitation energy transfer; other graphical analyses; tabulated numerical data.

Data from: The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages

Gregory Fournier, Kelsey Moore, L. Thiberio Rangel, Jack Payette, Lily Momper & Tanja Bosak
The record of the co-evolution of oxygenic phototrophs and the environment is preserved in three forms: genomes of modern organisms, diverse geochemical signals of surface oxidation, and diagnostic Proterozoic microfossils. When calibrated by fossils, genomic data form the basis of molecular clock analyses. However, different interpretations of the geochemical record, fossil calibrations, and evolutionary models produce a wide range of age estimates that are often conflicting. Here, we show that multiple interpretations of the cyanobacterial...

Data from: Secure and secret cooperation in robot swarms

Eduardo Castelló Ferrer, Thomas Hardjono, Alex Pentland & Marco Dorigo
The importance of swarm robotics systems in both academic research and real-world applications is steadily increasing. However, to reach widespread adoption, new models that ensure the secure cooperation of large groups of robots need to be developed. This work introduces a method to encapsulate cooperative robotic missions in an authenticated data structure known as Merkle tree. With this method, operators can provide the "blueprint" of the swarm's mission without disclosing its raw data. In other...

Guidelines for conducting ethical AI research in neurology: Supplementary materials

Sharon Chiang, Rosalind Picard, Winston Chiong, Robert Moss, Gregory Worrell, Vikram Rao & Daniel Goldenholz
Pre-emptive recognition of the ethical implications of study design and algorithm choices in artificial intelligence (AI) research is an important but challenging process. AI applications have begun to transition from a promising future to clinical reality in neurology. As the clinical management of neurology is often concerned with discrete, often unpredictable, and highly consequential events linked to multimodal data streams over long timescales, forthcoming advances in AI have great potential to transform care for patients....

Data from: Deep learning unlocks X‐ray microtomography segmentation of multiclass microdamage in heterogeneous materials

Reed Kopp, Joshua Joseph, Xinchen Ni, Nicholas Roy & Brian L. Wardle
Four-dimensional quantitative characterization of heterogeneous materials using in situ synchrotron radiation computed tomography can reveal 3D sub-micron features, particularly damage, evolving under load, leading to improved materials. However, dataset size and complexity increasingly require time-intensive and subjective semi-automatic segmentations. Here, we present the first deep learning (DL) convolutional neural network (CNN) segmentation of multiclass microscale damage in heterogeneous bulk materials, teaching on advanced aerospace-grade composite damage using ≈65,000 (trained) human-segmented tomograms. The trained CNN machine...

Supplementary data, code, and information for ‘Atlantic Hurricane Trends linked to Climate Change’ (Mann et al. 2006)

M.E. Mann & K. Emanuel
Increases in key measures of Atlantic hurricane activity over recent decades are believed to reflect, in large part, contemporaneous increases in tropical Atlantic warmth [e.g., Emanuel, 2005]. Some recent studies [e.g., Goldenberg et al., 2001] have attributed these increases to a natural climate cycle termed the Atlantic Multidecadal Oscillation (AMO), while other studies suggest that climate change may instead be playing the dominant role [Emanuel, 2005; Webster et al., 2005]. Using a formal statistical analysis...

SMRT sequencing data on four hypersuppressive Saccharomyces cereviciae mitochondrial DNAs

Daniel Corbi & Angelika Amon
Hypersuppressive mitochondrial DNAs are thought to be linear tandem repeats of the base unit of specific ORI regions on the mitochondrial genome. Here we confirm the linear tandem repeats using SMRT sequencing technology on four hypersuppressive clones. Mitochondrial DNA from four Saccharomyces cervisiae hypersuppressive mutants and a wild-type control was enriched and sequenced using SMRT sequencing technology.

Registration Year

  • 2021

Resource Types

  • Dataset


  • Massachusetts Institute of Technology
  • Zhejiang University
  • University of Washington
  • Stanford University
  • Columbia University
  • Princeton University
  • University of Cambridge
  • Université Libre de Bruxelles
  • University of Wisconsin–Madison
  • University of Leeds