132 Works

Monitoring Data from Pilot-Scale Open-Water Unit Process Wetland Treatment of Reverse Osmosis Concentrate from Water Reuse

Rachel Scholes, Jack King, Michael Vega, Josh Sharp, William Mitch & David Sedlak
This workbook provides monitoring data from a pilot-scale ozone/open-water wetland treatment system for reverse osmosis concentrate from the Silicon Valley Advanced Water Purification Center (San Jose, CA). Water quality analyses included common water quality parameters, nutrients, trace metals, and trace organics. These analyses were performed by UC Berkeley, Stanford University, Valley Water's Water Quality Lab, and a contract lab (Eurofins). Functional gene analyses (qPCR) were conducted at Colorado School of Mines for samples of the...

Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

Carrie Tribble, Jesús Martínez-Gómez, Fernando Alzate-Guarín, Carl Rothfels & Chelsea Specht
Many species from across the vascular plant tree-of-life have modified standard plant tissues into tubers, bulbs, corms, and other underground storage organs (USOs), unique innovations which allow these plants to retreat underground. Our ability to understand the developmental and evolutionary forces that shape these morphologies is limited by a lack of studies on certain USOs and plant clades; Bomarea multiflora (Alstroemeriaceae) fills a key gap in our understanding of USO molecular development as the first...

Disease scores and microbial densities for seedlings in phage pre-treatment trials

Catherine Hernandez
This dataset contains two files of results associated with a project testing phage pre-treatment of tomato seedlings prior to infection with Pseudomonas syringae pv. tomato strain DC3000. One file contains the disease scores of each seedling over time, and the other contains bacteria and phage densities at the endpoint of sampling. Bacterial densities were quantified using two methods (colony forming units and droplet digital PCR), and phage densities were quantified solely with droplet digital PCR.

Intraspecific variation in thermal acclimation and tolerance between populations of the winter ant, Prenolepis imparis

Maria Tonione, So Mi Cho, Gary Richmond, Christian Irian & Neil Tsutsui
Thermal phenotypic plasticity, otherwise known as acclimation, plays an essential role in how organisms respond to short‐term temperature changes. Plasticity buffers the impact of harmful temperature changes; therefore, understanding variation in plasticity in natural populations is crucial for understanding how species will respond to the changing climate. However, very few studies have examined patterns of phenotypic plasticity among populations, especially among ant populations. Considering that this intraspecies variation can provide insight into adaptive variation in...

Recreating giants impacts in the laboratory: Shock compression of MgSiO3 bridgmanite to 14 Mbar

Marius Millot, Shuai Zhang, Dayne Fratanduono, Federica Coppari, Sebastien Hamel, Burkhard Militzer, Dariia Simonova, Svyatoslav Shcheka, Natalia Dubrovinskaia, Leonid Dubrovinsky & Jon Eggert
Understanding giant impacts requires accurate description of how extreme pressures and temperatures affect the physical properties of the constituent materials. Here, we report shock experiments on two polymorphs of MgSiO3: enstatite and bridgmanite (perovskite) crystals. We obtain pressure-density shock equation of state to 14 Mbar and more than 9 g/cm3 a 40 % increase in density from previous data on MgSiO3. Density-functional-theory molecular dynamics (DFT-MD) simulations provide predictions for the shock Hugoniot curves for bridgmanite...

Data from: Complex interactions between temperature, sexual signals, and mate choice in a desert-dwelling jumping spider

Erin Brandt, Malcolm Rosenthal & Damian Elias
Environmental context is a crucial factor that influences sexual communication systems. Particularly in ectotherms, which cannot metabolically regulate their body temperature, temperature has an outsized effect on these intraspecific interactions. Using a desert-dwelling jumping spider Habronattus clypeatus, we assessed how temperature impacts various parts of the male signal and female mate choice for the signal. These spiders have multimodal, temporally-structured courtship displays that begin with visual-only “sidling” displays and proceed to multimodal visual and vibratory...

Data from: Ecological convergence of secondary phytochemicals along elevational gradients

Sergio Rasmann, Moe Bakhtiari, Emmanuel Defossez & Gaetan Glauser
Biologists still strive to identify the ecological and evolutionary drivers of phytochemical variation that mediate biotic interactions. We hypothesized that plant species growing at sites characterized by high herbivore pressure would converge to produce highly toxic blends of secondary metabolites, independent of phylogenetic constraints. To address the role of shared evolutionary history and ecological niches in driving variation in plant phytochemistry, we combined targeted metabolomics with insect herbivore bioassays and with a set of growth-related...

Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 2)

Samantha Grist, Andoni Mourdoukoutas & Amy Herr
Immunoassays and mass spectrometry are powerful single-cell protein analysis tools; however, interfacing and throughput bottlenecks remain. Here, we introduce three-dimensional single-cell immunoblots to detect both cytosolic and nuclear proteins. The 3D microfluidic device is a photoactive polyacrylamide gel with a microwell array-patterned face (x-y) for cell isolation and lysis. Single-cell lysate in each microwell is ‘electrophoretically projected’ into the 3rd dimension (z-axis), separated by size, and photo-captured in the gel for immunoprobing and confocal/light-sheet imaging....

Supporting data: 3D projection electrophoresis for single-cell immunoblotting (Part 4)

Samantha Grist, Amy Herr & Andoni Mourdoukoutas
Immunoassays and mass spectrometry are powerful single-cell protein analysis tools; however, interfacing and throughput bottlenecks remain. Here, we introduce three-dimensional single-cell immunoblots to detect both cytosolic and nuclear proteins. The 3D microfluidic device is a photoactive polyacrylamide gel with a microwell array-patterned face (x-y) for cell isolation and lysis. Single-cell lysate in each microwell is ‘electrophoretically projected’ into the 3rd dimension (z-axis), separated by size, and photo-captured in the gel for immunoprobing and confocal/light-sheet imaging....

Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

Jennifer Walsh, Stepfanie Aguillon, Yvonne Chan, Peter Arcese, Phred Benham, Irby Lovette & Chloe Mikles
Elucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent’s most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range-wide persistence. We focus here on six morphologically distinct subspecies resident in...

Olive ridley blood volume by nesting strategy

Gabriela Arango
Sea turtles dive with a full lung of air and these O2 stores are supplemented by O2 stored in blood and muscle. Olive ridley sea turtles exhibit polymorphic nesting behavior; mass nesting behavior called arribada, where up to 25,000 turtles will nest at once, and solitary nesting behavior. The potential physiological differences between the individuals using these strategies are not well understood. We measured blood volume and associated variables, including blood hemoglobin content and hematocrit,...

Resources for gasAcu1-4, a new stickleback reference genome

Garrett Roberts Kingman, Heidi Chen, David Kingsley, Deven Vyas, Krishna Veeramah, Felicity Jones & Mike Bell
gasAcu1-4 is a new version of the stickleback reference genome. It only minorly differs from the 2017 Hi-C guided assembly by Peichel, Sullivan, Liachko, and White (https://doi.org/10.1093/jhered/esx058) to improve the subtelomeric Pitx1 locus and the mitochondrial genome. We here present basic resources for utilizing this version of the reference genome: the fasta sequence of the assembly and liftOver chains for converting coordinates between this reference version and the original (Broad S1) gasAcu1 assembly (https://www.nature.com/articles/nature10944). This...

Tributary confluences are dynamic thermal refuges for a juvenile salmonid in a warming river network

Terrance Wang, Suzanne Kelson, George Greer, Sally Thompson & Stephanie Carlson
As rivers warm, cold-water fish species may alleviate thermal stress by moving into localized thermal refuges such as cold-water plumes created by cool tributary inflows. We quantified use of two tributary confluence plumes by juvenile steelhead, Oncorhynchus mykiss, throughout the summer, including how trout positioned themselves in relation to temperature within confluence plumes. At two confluences, Cedar and Elder creeks, along the South Fork Eel River, California, USA, we monitored temperatures using in-situ logger grids...

Three eco-physiological strategies of response to drought maintain the form and function of a tropical montane grassland

Ilaíne Matos
1. Ecologists seek a general scheme to classify the diversity of plant responses to environmental factors into a few strategies (e.g. competitor -C, stress-tolerant -S, ruderal-R), while plant physiologists seek a mechanistic scheme to explain such different responses (e.g. tolerance, escape, avoidance). So far, few attempts have been made to combine both perspectives into plant eco-physiological strategies. Moreover, the relative contribution of different strategies to maintain both community structure and ecosystem functioning during drought has...

Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility

Jonathan Liu, Elizabeth Eck & Hernan Garcia
Thermodynamic models of gene regulation can predict transcriptional regulation in bacteria, but in eukaryotes chromatin accessibility and energy expenditure may call for a different framework. Here we systematically tested the predictive power of models of DNA accessibility based on the Monod-Wyman-Changeux (MWC) model of allostery, which posits that chromatin fluctuates between accessible and inaccessible states. We dissected the regulatory dynamics of hunchback by the activator Bicoid and the pioneer-like transcription factor Zelda in living Drosophila...

Data from: Allocation of gene products to daughter cells is determined by the age of the mother in single Escherichia coli cells

Ulla Rang, Chao Shi, Lin Chao, Audrey Proenca, Andrew Qiu & Jasper Chao
Gene expression and growth rate are highly stochastic in E. coli. Some of the growth rate variations result from the deterministic and asymmetric partitioning of damage by the mother to its daughters. One daughter, denoted the old daughter, receives more damage, grows more slowly, and ages. To determine if expressed gene products are also allocated asymmetrically, we compared the levels of expressed green fluorescence protein in growing daughters descending from the same mother. Our results...

Data and code for: Microalgae-blend tilapia feed eliminates fishmeal and fish oil, improves growth, and is cost viable

Pallab Sarker, Anne Kapuscinski, Brandi McKuin, Devin Fitzgerald, Hannah Nash & Connor Greenwood
Aquafeed manufacturers have reduced, but not fully eliminated, fishmeal and fish oil and are seeking cost competitive replacements. We combined two commercially available microalgae, to produce a high-performing fish-free feed for Nile tilapia (Oreochromis niloticus) —the world’s second largest group of farmed fish. We substituted protein-rich defatted biomass of Nannochloropsis oculata (leftover after oil extraction for nutraceuticals) for fishmeal and whole cells of docosahexaenoic acid (DHA)-rich Schizochytrium sp. as substitute for fish oil. Here, we...

Phylogenomics of white-eyes, a ‘great speciator,’ reveals Indonesian archipelago as the center of lineage diversity

Chyi Yin Gwee, Kritika Garg, Balaji Chattopadhyay, Keren Sadanandan, Dewi Prawiradilaga, Martin Irestedt, Fu-Min Lei, Luke Bloch, Jessica Lee, Mohammad Irham, Tri Haryoko, Malcolm Soh, Kelvin Peh, Karen Rowe, Teuku Ferasyi, Shaoyuan Wu, Guinevere Wogan, Rauri Bowie & Frank Rheindt
Archipelagoes serve as important ‘natural laboratories’ which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a ‘great speciator’, comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods...

Data from: When policy and psychology meet: mitigating the consequences of bias in schools

Jason Okonofua
Harsh exclusionary discipline predicts major negative life outcomes, including adult incarceration and unemployment. This breeds racial inequality, because Black students are disproportionately at risk for this type of discipline. Can a combination of policy and psychological interventions reduce this kind of discipline and mitigate this inequality? Two preregistered experiments (Nexperiment1 = 246 teachers; Nexperiment2 = 243 teachers) used an established paradigm to systematically test integration of two and then three policy and psychological interventions to...

First come, first served: possible role for priority effects in marine populations under different degrees of dispersal potential

Christiaan De Leeuw, Katja Peijnenburg, Rosemary Gillespie, Diede Maas, Naoto Hanzawa, Yosephine Tuti, Abdul Toha, Ludi Aji & Leontine Becking
Aim Studying clearly delineated populations in marine lakes, islands of sea, we investigate the interplay of habitat size, immigration, and priority effects in shaping marine population genetic structure. Location Marine lakes and coastal locations in Indonesia, Palau, Papua New-Guinea and Australia. Taxon Mussels (Mytillidae, Brachidontes spp.) Methods Populations were sampled from four coastal locations and 22 marine lakes of similar age (~8,000 years), yet differing in size (0.04 - 4.7 km2) and degree of connection...

Data from: Vascular epiphytes show low physiological resistance and high recovery capacity to episodic, short-term drought in Monteverde, Costa Rica

Cameron Williams, Jessica Murray, Andrew Glunk, Todd Dawson, Nalini Nadkarni & Sybil Gotsch
Tropical montane cloud forests support abundant epiphytic vascular plant communities that serve important ecosystem functions, but their reliance on atmospheric inputs of water may make them susceptible to the drying effects of rising cloud bases and more frequent droughts. We conducted a common garden experiment to explore the combined effects of decreasing cloud influence—lower humidity, warmer temperature, brighter light—and meteorological drought (i.e., absence of rain) on the physiology and morphology of vascular epiphytes native to...

Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance

Nicholas Mason, Nicholas Fletcher, Brian Gill, Chris Funk & Kelly Zamudio
Species are a fundamental unit of biodiversity that are delimited via genetic data and coalescent-based methods with increasing frequency. Despite the widespread use of coalescent-based species delimitation, we do not fully understand the sensitivity of these methods to potential sources of bias and violations of their underlying assumptions. One implicit assumption of coalescent-based species delimitation is that geographic sampling is adequate and representative of genetic variation among populations within the lineage of interest. Yet exhaustive...

Data matrices for: Phylogenomics of peacock spiders and their kin (Salticidae, Maratus), with implications for the evolution of male courtship displays

Damian Elias & Marshal Hedin
Understanding diversity has been a pursuit in evolutionary biology since its inception. A challenge arises when sexual selection has played a role in diversification. Questions of what constitutes a “species”, homoplasy versus synapomorphy, and whether sexually-selected traits show phylogenetic signal have hampered work on many systems. Peacock spiders are famous for sexually selected male courtship dances and peacock-like abdominal ornamentation. This lineage of jumping spiders currently includes over 90 species classified into two genera, Maratus...

Five-years of ocrelizumab in relapsing multiple sclerosis: OPERA studies open-label extension

Stephen L Hauser, Ludwig Kappos, Douglas L Arnold, Amit Bar-Or, Bruno Brochet, Robert T Naismith, Anthony Traboulsee, Jerry S Wolinsky, Shibeshih Belachew, Harold Koendgen, Victoria Levesque, Marianna Manfrini, Fabian Model, Stanislas Hubeaux, Lahar Mehta & Xavier Montalban
Objective To assess over 3 years of follow-up, the effects of maintaining or switching to ocrelizumab (OCR) therapy on clinical and MRI outcomes and safety measures in the open-label extension (OLE) phase of the pooled OPERA studies in relapsing multiple sclerosis. Methods After 2 years of double-blind, controlled treatment, patients continued OCR (600 mg infusions every 24 weeks) or switched from interferon (IFN) β-1a (44 μg 3 times weekly) to OCR when entering the OLE...

Tree functional traits as predictors of microburst-associated treefalls in tropical wet forests

Alana Rader, Amy Cotrell, Anna Kudla, Tiffany Lum, David Henderson & Harshad Karandikar
On 19 May 2018 a microburst caused 600 isolated forest gaps in a Costa Rican tropical forest. We surveyed fallen and standing trees within gaps to determine if certain variables are associated with treefalls. Our results highlight considerations for future research to understand the impacts of microbursts in tropical forests. Our results show that at the scale and locality of our study, treefall vulnerability to microbursts and characteristics of fall events are independent of the...

Registration Year

  • 2020
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Affiliations

  • University of California, Berkeley
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