26 Works

SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation

Patricia Richard, Shuang Feng, Yueh-Lin Tsai, Wencheng Li, Paola Rinchetti, Ubayed Muhith, Juan Irizarry-Cole, Katharine Stolz, Lionel A. Sanz, Stella Hartono, Mainul Hoque, Saba Tadesse, Hervé Seitz, Francesco Lotti, Michio Hirano, Frédéric Chédin, Bin Tian & James L. Manley
SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, whereas recessive mutations are responsible for ataxia called ataxia with oculomotor apraxia type 2 (AOA2). How mutations in the same protein can lead to different phenotypes...

Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins

Premal Shah, Rafael Campos, H.R. Sagara Wijeratne, Mariano Garcia-Blanco & Shelton Bradrick
The ribosomal stalk proteins, RPLP1 and RPLP2 (RPLP1/2), which form the ancient ribosomal stalk, were discovered decades ago but their functions remain mysterious. We had previously shown that RPLP1/2 are exquisitely required for replication of dengue virus (DENV) and other mosquito-borne flaviviruses. Here, we show that RPLP1/2 function to relieve ribosome pausing within the DENV envelope coding sequence, leading to enhanced protein stability. We evaluated viral and cellular translation in RPLP1/2-depleted cells using ribosome profiling...

Ecological divergence and the history of gene flow in the Nearctic milksnakes (Lampropeltis triangulum complex)

Frank Burbrink, Justin Bernstein, Arianna Kuhn, Marcelo Gehara & Sara Ruane
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers to gene flow. These studies may conclude absence of population structure, lineage structure that indicates unique species have been discovered, or suggest more research is needed prior to delimitation. Comparative risks of delimiting species incorrectly or failing to delimit species are usually not weighed and a more detailed return to these problems with more data...

Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta)

Chung Hyun Cho, Seung In Park, Claudia Ciniglia, Eun Chan Yang, Louis Graf, Debashish Bhattacharya & Hwan Su Yoon
The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of extremophilic eukaryotes, little is known about the molecular evolution of their mitochondrial genomes (mitogenomes). To fill this knowledge gap, we sequenced five mitogenomes from representative clades of Cyanidiophyceae and identified two major groups, here referred to as Galdieria-type (G-type) and Cyanidium-type (C-type). G-type mitogenomes...

Data from: Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi

Stephanie Marciniak, Mehreen R. Mughal, Laurie R. Godfrey, Richard J. Bankoff, Heritiana Randrianatoandro, Brooke E. Crowley, Christina M. Bergey, Kathleen M. Muldoon, Jeannot Randrianasy, Brigitte M. Raharivololona, Stephan C. Schuster, Ripan S. Malhi, Anne D. Yoder, , Logan Kistler & George H. Perry
No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal ‘subfossil’ remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well into the past millennium. Yet much about the evolutionary biology of these now extinct species...

New England Seismic Transect

A planned linear array of broadband seismometers across New England (New Hampshire and Vermont) aimed at understanding the crust and upper mantle structure. The experiment targets the so-called Northern Appalachian Anomaly (NAA) in the upper mantle, which may represent a recently formed mantle upwelling.

Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment

Ryan Almeida, Kevin Smith, Alexander Berro, Alston Lippert, Jake Clary, Sam McKlin & Erin Scott
Land-use change is a significant cause of anthropogenic extinctions, which are likely to continue and accelerate as habitat conversion proceeds in most biomes. One way to understand the effects of habitat loss on biodiversity is through improved tools for predicting the number and identity of species losses in response to habitat loss. There are relatively few methods for predicting extinctions and even fewer opportunities for rigorously assessing the quality of these predictions. In this paper...

Data from: Antibiotics in hives and their effects on honey bee physiology and behavioral development

Yarira Ortiz-Alvarado, David Clark, Carlos Vega-Melendez, Zomary Flores-Cruz, Maria Dominguez-Bello & Tugrul Giray
Recurrent honey bee losses make it critical to understand the impact of human interventions, such as antibiotics use in apiculture. Antibiotics are used to prevent or treat bacterial infections in colonies. However, little is known about their effects on honey bee development. We studied the effect of two commercial beekeeping antibiotics on the bee physiology and behavior throughout development. Our results show that antibiotic treatments have an effect on amount of lipids and rate of...

Data from: Chronotropic incompetence limits aerobic exercise capacity in patients taking beta-blockers

Krzysztof Smarz, Maciej Tysarowski, Beata Zaborska, Ewa Pilichowska-Paszkiet, Malgorzata Sikora-Frac, Andrzej Budaj & Tomasz Jaxa-Chamiec
Background: Chronotropic incompetence in patients taking beta-blockers is associated with poor prognosis; however, its impact on exercise capacity (EC) remains unclear. Hypothesis: Chronotropic incompetence in patients taking beta-blockers is associated with lower EC. Methods: We retrospectively analyzed data from consecutive patients taking beta-blockers referred for cardiopulmonary exercise testing. EC was expressed as peak oxygen uptake (VO2peak; mL/kg/min). Chronotropic incompetence was defined as chronotropic index (CI) ≤ 62%. CI was calculated as [(HR at peak–resting HR)...

Data from: Finding clarity in ecological outcomes using empirical integrated social-ecological systems: a case study of agriculture-dependent grassland birds

Michael Allen, Julie Lockwood & Joanna Burger
1. Efforts to monitor and conserve populations and ecosystems in human-dominated landscapes can benefit from an empirical social-ecological systems approach. 2. Here we illustrate how latent variable structural equation modelling of regional time series data can effectively describe interconnected drivers of population fluctuations in dynamic landscapes and can help to reveal previously unknown system drivers. 3. Using a declining farmland-dependent bird species (Ammodramus savannarum) in the eastern United States (1994-2015) as a case study, our...

SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation

Patricia Richard, Shuang Feng, Yueh-Lin Tsai, Wencheng Li, Paola Rinchetti, Ubayed Muhith, Juan Irizarry-Cole, Katharine Stolz, Lionel A. Sanz, Stella Hartono, Mainul Hoque, Saba Tadesse, Hervé Seitz, Francesco Lotti, Michio Hirano, Frédéric Chédin, Bin Tian & James L. Manley
SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, whereas recessive mutations are responsible for ataxia called ataxia with oculomotor apraxia type 2 (AOA2). How mutations in the same protein can lead to different phenotypes...

Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex)

Frank Burbrink, Marcelo Gehara, Alexander McKelvy & Edward Myers
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the “gray zone” of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes...

Data from Beyond MAP: A guide to dimensions of rainfall variability for tropical ecology

Naomi Schwartz, Benjamin R. Lintner, Xue Feng & Jennifer S. Powers
Tropical ecologists have long recognized rainfall as the key climate filter shaping tropical ecosystem structure and function across space and time. Still, tropical ecologists have historically had a limited toolkit for characterizing rainfall, largely relying on simple metrics like mean annual precipitation (MAP) and dry season length to characterize rainfall regimes that vary along many more dimensions. Here, we review methods for quantifying dimensions of rainfall variability on multiple time scales, with a focus on...

The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population

Dina Navon, Paul Hatini, Lily Zogbaum & Craig Albertson
Adaptive radiations are often stereotypical, as populations repeatedly specialize along conserved environmental axes. Phenotypic plasticity may be similarly stereotypical, as individuals respond to environmental cues. These parallel patterns of variation, which are often consistent across traits, have led researchers to propose that plasticity can facilitate predictable patterns of evolution along environmental gradients. This “flexible stem” model of evolution raises questions about the genetic nature of plasticity, including: How complex is the genetic basis for plasticity?...

Long non-coding RNA XIST promotes the progression of esophageal squamous cell carcinoma through sponging miR-129-5p and upregulating CCND1 expression

Haoran Wang, Haomiao Li, Yongkui Yu, Qingfeng Jiang, Ruixiang Zhang, Haibo Sun, Wenqun Xing & Yin Li
Long non-coding RNA (lncRNA) X inactive specific transcript (XIST) has been identified as an oncogenic lncRNA in a series of human cancers, including esophageal squamous cell carcinoma (ESCC). In this study, we aimed to further explore the underlying mechanism of XIST on ESCC progression. qRT-PCR assay was used to determine the levels of XIST and miR-129-5p. Western blot analysis was performed to assess cyclin D1 (CCND1) expression. Bioinformatic analysis was performed using starBase v2.0 software....

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...

Characterizing uncertainty in climate impact projections: a case study with seven marine species on the North American continental shelf

James Morley, Thomas Froelicher & Malin Pinsky
Projections of climate change impacts on living resources are being conducted frequently, and the goal is often to inform policy. Species projections will be more useful if uncertainty is effectively quantified. However, few studies have comprehensively characterized the projection uncertainty arising from greenhouse gas scenarios, Earth system models, and both structural and parameter uncertainty in species distribution modeling. Here we conducted 8964 unique 21st century projections for shifts in suitable habitat for seven economically important...

Data from: Crop production in the USA is frequently limited by a lack of pollinators

James Reilly, Derek Artz, David Biddinger, Kyle Bobiwash, Natalie Boyle, Claire Brittain, Julia Brokaw, Josh Campbell, Jaret Daniels, Elizabeth Elle, Jamie Ellis, Shelby Fleischer, Jason Gibbs, Robert Gillespie, Knute Gundersen, Larry Gut, George Hoffman, Neelendra Joshi, Ola Lundin, Keith Mason, Carley McGrady, Steve Peterson, Theresa Pitts-Singer, Sujaya Rao, Nikki Rothwell … & Rachael Winfree
Most of the world’s crops depend on pollinators, so declines in both managed and wild bees raise concerns about food security. However, the degree to which insect pollination is actually limiting current crop production is poorly understood, as is the role of wild species (as opposed to managed honey bees) in pollinating crops, particularly in intensive production areas. We established a nation-wide study to assess the extent of pollinator limitation in seven crops at 131...

Data from: The shape of avian eggs: assessment of a novel metric for quantifying eggshell conicality

Ian Reid Hays & Iva Ljubičić
Studying avian egg shape and other aspects of its morphology has recently undergone a renaissance. Yet, most studies rely solely on two metrics for the quantification of egg shape: elongation and asymmetry. The difficulty of additionally quantifying the curvature of an eggshell has yielded many attempts including those with complex equations and spatial modeling techniques based on digitized images. These have lacked an independent single-variable metric, hampering comparative studies. We propose a metric for one...

Changes in taxonomic and phylogenetic diversity in the Anthropocene

Daijiang Li, Julian Olden, Julie Lockwood, Sydne Record, Michael McKinney & Benjamin Baiser
To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness and evolutionary history across spatial scales is needed. Here we compiled 162 datasets for fish, bird, and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at different spatial scales (within site α diversity and between sites spatial β diversity). Biodiversity change is measured from these datasets in three ways: across land use gradients,...

Data on assessing the effects of genetic divergence and morphology on Anolis lizard mating

Emmanuel D'Agostino, Colin Donihue, Jonathan Losos & Anthony Geneva
The brown anole (Anolis sagrei) is a widespread neotropical lizard found on many islands in the West Indies as well as the coast of Central America. Across their range, brown anole populations show extensive ecomorphological trait variation and substantial genetic divergence. It is unclear, however, whether this genetic and morphological divergence results in reproductive isolation between populations. We investigated variation in mating behavior across populations by analyzing four hours of video of each of 234...

Data from: Assessing support for Blaberoidea phylogeny suggests optimal locus

Dominic Evangelista, Sabrina Simon, Megan M. Wilson, Akito Y. Kawahara, Manpreet K. Kohli, Jessica L. Ware, Benjamin Wipfler, Olivier Béthoux, Grandcolas Philippe & Frédéric Legendre
Phylogenomics seeks to use next-generation data to robustly infer an organism’s evolutionary history. Yet, the practical caveats of phylogenomics motivates investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in...

Data from: Multiple factors affect the evolution of repertoire size across birds

Gavin Leighton & Tucker Birmingham
Changes in signaling repertoires across species allow for insight into the macroevolutionary forces that control signaling systems. Signaling systems are theorized to be affected by both the social and ecological environments of species. With respect to social variables, increased social complexity is thought to lead to increased vocal complexity. Although ecology can affect signaling systems in numerous ways, one potential effect of ecology is that more cluttered habitats should lead to greater reliance on non-visual...

Preconception alcohol exposure increases the susceptibility to diabetes in the offspring

Ali Al-Yasari, Shaima Jabbar, Miguel Cabrera, Bénédicte Rousseau & Dipak Sarkar
Preconception alcohol exposure in mothers has recently been shown to increase stress responses and anxiety behaviors in their offspring during the adult period. One hypothesis is that alcohol-induced genetic modifications in germ cells of the mother could have been transmitted to the offspring to manifest the endophenotypes. In this study, transcriptome analysis of germ cells of female rats given binge-like alcohol identified altered stress gene regulation networks involving glucose metabolism and diabetes mellitus. Endocrine tests...

Data from: Temporal scale-dependence of plant-pollinator networks

Benjamin Schwarz, Diego Vázquez, Paul CaraDonna, Tiffany Knight, Gita Benadi, Carsten Dormann, Benoit Gauzens, Elena Motivans, Julian Resasco, Nico Blüthgen, Laura Burkle, Qiang Fang, Christopher Kaiser-Bunbury, Ruben Alarcón, Justin Bain, Natacha Chacoff, Shuang-Quan Huang, Gretchen LeBuhn, Molly MacLeod, Theodora Petanidou, Claus Rasmussen, Michael Simanonok, Amibeth Thompson, Daniel Cariveau, Michael Roswell … & Jochen Fründ
The study of mutualistic interaction networks has led to valuable insights into ecological and evolutionary processes. However, our understanding of network structure may depend upon the temporal scale at which we sample and analyze network data. To date, we lack a comprehensive assessment of the temporal scale-dependence of network structure across a wide range of temporal scales and geographic locations. If network structure is temporally scale-dependent, networks constructed over different temporal scales may provide very...

Registration Year

  • 2020

Resource Types

  • Dataset


  • Rutgers University
  • Rutgers, The State University of New Jersey
  • University of Minnesota
  • American Museum of Natural History
  • North West Agriculture and Forestry University
  • University of Massachusetts Amherst
  • Zhejiang University
  • Huazhong University of Science and Technology
  • Duke University
  • Murdoch University