14 Works

Data from: Differential requirements for the RAD51 paralogs in genome repair and maintenance in human cells

Edwige B. Garcin, Stéphanie Gon, Meghan R. Sullivan, Gregory J. Brunette, Anne De Cian, Jean-Paul Concordet, Carine Giovannangeli, Wilhelm G. Dirks, Sonja Eberth, Kara A. Bernstein, Rohit Prakash, Maria Jasin & Mauro Modesti
Deficiency in several of the classical human RAD51 paralogs [RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition and Fanconi anemia. To investigate their functions, isogenic disruption mutants for each were generated in non-transformed MCF10A mammary epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and HEK293 cells, viable ablated clones were readily isolated for each RAD51 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are cell-essential in MCF10A...

Data from: Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila

Qanber Raza, Jae Young Choi, Yang Li, Roisin M. O'Dowd, Simon C. Watkins, Yang Hong, Maria Chikina, Nathan L. Clark & Adam V. Kwiatkowski
The adherens junction couples the actin cytoskeletons of neighboring cells to provide the foundation for multicellular organization. The core of the adherens junction is the cadherin-catenin complex that arose early in the evolution of multicellularity to link actin to intercellular adhesions. Over time, evolutionary pressures have shaped the signaling and mechanical functions of the adherens junction to meet specific developmental and physiological demands. Evolutionary rate covariation (ERC) identifies proteins with correlated fluctuations in evolutionary rate...

Data from: Proximity to roads disrupts rodents’ contributions to seed dispersal services and subsequent recruitment dynamics

Wenwen Chen, Jie Zhong, Walter Carson, Zhanhui Tang, Zongqiang Xie, Shucun Sun & Youbing Zhou
1. Seed dispersal and subsequent recruitment dynamics play a crucially important role in regulating species coexistence and structuring tree diversity in diverse forests. Wildlife, which can dually shape the tree recruitment process by simultaneously functioning as natural enemies and seed dispersers, are undergoing widespread changes in population and behaviour due to the detrimental effects of expanding global road networks. However, the impact of these changes on recruitment dynamics through the alteration of seed dispersal processes...

Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

Vaughn Cooper, Caroline Turner, Sean Buskirk & Katrina Harris
Natural environments are rarely static; rather selection can fluctuate on time scales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with Burkholderia cenocepacia, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation...

Effects of latitudinal, seasonal, and daily temperature variations on chytrid fungal infections in a North American frog

Corinne Richards-Zawacki, Julia Sonn & Ryan Utz
As human activities alter environmental conditions, the emergence and spread of disease represents an increasing threat to wildlife. Studies that examine how host–pathogen relationships play out across seasons and latitudes can serve as proxies for understanding how natural and anthropogenic changes in climate may influence infection and disease dynamics. Amphibians are ideal host organisms for studying the impacts of climate on disease because they are ectothermic and threatened by chytridiomycosis, a recently emerged and globally...

Hepatic estrogen sulfotransferase distantly sensitizes mice to hemorrhagic shock-induced acute lung injury

Yang Xie, Anne Barbosa, Meishu Xu, Patrick Oberly, Songrong Ren, Robbert Gibbs, Samuel Poloyac, Wenchao Song, Jie Fan & Wen Xie
Hemorrhagic shock (HS) is a potential life-threatening condition that may lead to injury to multiple organs, including the lung. The estrogen sulfotransferase (EST, or SULT1E1) is a conjugating enzyme that sulfonates and deactivates estrogens. In this report, we showed that the expression of Est was markedly induced in the liver, but not in the lung of female mice subject to hemorrhagic shock and resuscitation (HS/R). Genetic ablation or pharmacological inhibition of Est effectively protected female...

Data from: Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: is disturbance an alternative explanation?

Eric A. Griffin, Joshua G. Harrison, Steven W. Kembel, Alyssa A. Carrell, S. Joseph Wright & Walter P. Carson
1. Bacterial endophytes may be fairly host specific; nonetheless, an important subset of taxa may be shared among numerous host species forming a community-wide core microbiome. Moreover, other key factors, particularly the supply of limiting macronutrients and disturbances, may supersede the importance of host identity. 2. We tested the following four non-mutually exclusive hypotheses: 1. The Host Identity Hypothesis: endophytes vary substantially among different host plant species. 2. The Core Microbiome Hypothesis: a subset of...

Data from: The potential for mass ratio and trait divergence effects to explain idiosyncratic impacts of nonnative invasive plants on carbon mineralization of decomposing leaf litter

Sara E. Kuebbing & Mark A. Bradford
1. Invasive plant effects on litter decomposition tend to be idiosyncratic among species and ecosystems, which may arise from variation in the invader’s relative abundance (mass ratio effect), its relative functional difference to other species (trait divergence effect), and/or from species’ litter mixing that causes non-additive decomposition rates relative to single-species decomposition. 2. We use experimental microcosms to quantify the potential for mass ratio and trait divergence to explain effects of invasive litters on carbon...

Data from: Human retinal pigment epithelium: in vivo cell morphometry, multispectral autofluorescence, and relationship to cone mosaic

Charles E. Granger, Qiang Yang, Hongxin Song, Kenichi Saito, Koji Nozato, Lisa R. Latchney, Bianca T. Leonard, Mina M. Chung, David R. Williams & Ethan A. Rossi
Purpose: To characterize in vivo morphometry and multispectral autofluorescence of the retinal pigment epithelial (RPE) cell mosaic and its relationship to cone cell topography across the macula. Methods: RPE cell morphometrics were computed in regularly spaced regions of interest (ROIs) from contiguous short-wavelength autofluorescence (SWAF) and photoreceptor reflectance images collected across the macula in one eye of 10 normal participants (23–65 years) by using adaptive optics scanning light ophthalmoscopy (AOSLO). Infrared autofluorescence (IRAF) images of...

Data from: HIV infection is an independent risk factor for decreased 6-minute walk test distance

Tom E. Robertson, Mehdi Nouraie, Shulin Qin, Kristina A. Crothers, Cathy J. Kessinger, Deborah McMahon, Divay Chandra, Lawrence A. Kingsley, Ruth M. Greenblatt, Laurence Huang, Meghan F. Fitzpatrick & Alison Morris
Background: Ambulatory function predicts morbidity and mortality and may be influenced by cardiopulmonary dysfunction. Persons living with HIV (PLWH) suffer from a high prevalence of cardiac and pulmonary comorbidities that may contribute to higher risk of ambulatory dysfunction as measured by 6-minute walk test distance (6-MWD). We investigated the effect of HIV on 6-MWD. Methods: PLWH and HIV-uninfected individuals were enrolled from 2 clinical centers and completed a 6-MWD, spirometry, diffusing capacity for carbon monoxide...

Data from: A clinical decision support system learned from data to personalize treatment recommendations towards preventing breast cancer metastasis

Xia Jiang, Alan Wells, Adam Brufsky & Richard Neapolitan
Objective: A Clinical Decision Support System (CDSS) that can amass Electronic Health Record (EHR) and other patient data holds promise to provide accurate classification and guide treatment choices. Our objective is to develop the Decision Support System for Making Personalized Assessments and Recommendations Concerning Breast Cancer Patients (DPAC), which is a CDSS learned from data that recommends the optimal treatment decisions based on a patient’s features. Method: We developed a Bayesian network architecture called Causal...

Data from: Associative learning of flowers by generalist bumble bees can be mediated by microbes on the petals

Avery L. Russell & Tia-Lynn Ashman
Communication is often vital to the maintenance of mutualisms. In plant-pollinator mutualisms, plants signal pollinators via floral displays, composed of olfactory, visual, and other plant-derived cues. While plants are understood to be associated with microbes, only recently has the role of microbial (yeast and bacteria) inhabitants of flowers as intermediaries of plant-pollinator communication been recognized. Animals frequently use microbial cues to find resources, yet no study has examined whether microbes directly mediate learned and innate...

Data from: Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: an approximate Bayesian computation approach

Tracy L. Stepien, Holley E. Lynch, Shirley X. Yancey, Laura Dempsey & Lance A. Davidson
Advanced imaging techniques generate large datasets that are capable of describing the structure and kinematics of tissue spreading in embryonic development, wound healing, and the progression of many diseases. Information in these datasets can be integrated with mathematical models to infer important biomechanical properties of the system. Standard computational tools for estimating relevant parameters rely on methods such as gradient descent and typically identify a single set of optimal parameters for a single experiment. These...

Revisiting the origin of octoploid strawberry

Aaron Liston, Na Wei, Jacob Tennessen, Jumin Li, Ming Dong & Ashman Tia-Lynn
The cultivated strawberry (Fragaria ×ananassa) is an octoploid, and the identity of its four subgenomes has long been a mystery. In their recent strawberry genome publication, Edger et al. present a novel hypothesis: each subgenome originated from a different extant diploid progenitor, and the hexaploid species Fragaria moschata was a direct ancestor. We reanalyzed the four octoploid subgenomes in a phylogenomic context and our results support only two extant diploids progenitors; we also found no...

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of Pittsburgh
  • Northwestern University
  • West Chester University
  • University of Pennsylvania
  • University of Washington
  • University of Rochester Medical Center
  • Oregon State University
  • Capital Medical University
  • University of Wyoming
  • Hangzhou Normal University