194 Works

Data from: Data-driven discovery of the spatial scales of habitat choice by elephants

Andrew F. Mashintonio, Stuart L. Pimm, Grant M. Harris, Rudi J. Van Aarde & Gareth J. Russell
Setting conservation goals and management objectives relies on understanding animal habitat preferences. Models that predict preferences combine location data from tracked animals with environmental information, usually at a spatial resolution determined by the available data. This resolution may be biologically irrelevant for the species in question. Individuals likely integrate environmental characteristics over varying distances when evaluating their surroundings; we call this the scale of selection. Even a single characteristic might be viewed differently at different...

Data from: Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses

Allison L. Hicks & Siobain Duffy
The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures. This substitution rate variation may be explained by differences in virus ecology or intrinsic genomic properties. We generated nucleotide substitution rate estimates for mammalian RNA viruses and compiled comparable published rates, yielding a dataset of 118...

Data from: Comparing van Oosterhout and Chybicki-Burczyk methods of estimating null allele frequencies for inbred populations

Pascal Campagne, Peter E. Smouse, Georges Varouchas, Jean-Francois Silvain, Bruno Le Rü, J.-F. Silvain & B. Leru
In spite of the usefulness of codominant markers in population genetics, the existence of null alleles raises challenging estimation issues in natural populations that are characterized by positive inbreeding coefficients (F > 0). Disregarding the possibility of F > 0 in a population will generally lead to overestimates of null allele frequencies. Conversely, estimates of inbreeding coefficients (F) may be strongly biased upwards (excess homozygotes), in the presence of nontrivial frequencies of null alleles. An...

How much do rare and crop-pollinating bees overlap in identity and flower preferences?

Molly MacLeod, James Reilly, Daniel Cariveau, Mark Genung, Michael Roswell, Jason Gibbs & Rachael Winfree
1. The biodiversity-centered approach to conservation prioritizes rare species, whereas the ecosystem services approach prioritizes species that provide services to people. The two approaches align when rare species provide ecosystem services, or when both groups of species benefit from the same management action. We use data on bee pollinators and the plant species they forage on to determine if there are rare species among the most important crop pollinators, and the extent to which plant...

Data from: Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

Sara Branco, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Helene Badouin, Chris E. Ellison, Nhu H. Nguyen, Rytas Vilgalys, Kabir G. Peay, John W. Taylor, Thomas D. Bruns & Christopher E. Ellison
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and...

Data from: Turbulence induces metabolically costly behaviors and inhibits food capture in oyster larvae, causing net energy loss

Heidi L. Fuchs, Jaclyn A. Specht, Diane K. Adams & Adam J. Christman
Planktotrophic invertebrate larvae require energy to develop, disperse, and settle successfully, and it is unknown how their energetics is impacted by turbulence. Ciliated larvae gain metabolic energy from their phytoplankton food to offset the energetic costs of growth, development, and ciliary activity for swimming and feeding. Turbulence may affect the energetic balance by inducing behaviors that alter the metabolic costs and efficiency of swimming, by raising the encounter rate with food particles, and by inhibiting...

Data from: Confirmation of independent introductions of an exotic plant pathogen of Cornus species, Discula destructiva, on the east and west coasts of North America

Kristie Mantooth, Denita Hadziabdic, Sarah Boggess, Mark Windham, Stephen Miller, Cai Guohong, Joseph Spatafora, Ning Zhang, Meg Staton, Bonnie Ownley, Robert Trigiano & Guohong Cai
Cornus florida (flowering dogwood) and C. nuttallii (Pacific dogwood) are North American native tree species that belong to the big-bracted group of dogwoods. Cornus species are highly valued for their ornamental characteristics, and have fruits that contain high fat content for animals. Also, they are an important understory tree in natural forests. Dogwood anthracnose, caused by Discula destructiva, was observed in the late 1970s on the east and west coasts of the United States and...

Data from: Mosaic evolution in the middle Miocene planktonic foraminifera Fohsella lineage

Weimin Si, William A. Berggren & Marie-Pierre Aubry
Recent studies have shown that modes of evolution, namely directional trend, random walk, and stasis, vary across morphologic traits and over the geographic range of a taxon. If so, is it possible that our interpretation of evolutionary modes is actually driven by our selection of traits in a study? In an attempt to answer this question, we have restudied the middle Miocene planktonic foraminifera Fohsella lineage, an iconic example of gradual morphologic evolution. In contrast...

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...

Data from: Allometric and trait-based patterns in parasite stoichiometry

Rachel E. Paseka & Rita L. Grunberg
We measured the elemental content (%C, N, and P) and ratios (C:N, C:P, N:P) of a diverse assemblage of parasitic helminths to ask whether taxonomy or traits were related to stoichiometric variation among species. We sampled 27 macroparasite taxa, spanning 4 phyla, infecting vertebrate and invertebrate hosts from freshwater ecosystems in New Jersey. Macroparasites varied widely in elemental content, exhibiting 4.7-fold variation in %N, 4.6-fold variation in %P, and 11.5-fold variation in N:P. Across all...

A new method for integrating ecological niche modeling with phylogenetics to estimate ancestral distributions

Wilson Guillory & Jason Brown
Ancestral range estimation and projection of niche models into the past have both become common in evolutionary studies where the ancient distributions of organisms are in question. However, these methods are hampered by complementary hurdles: discrete characterization of areas in ancestral range estimation can be overly coarse, especially at shallow timescales, and niche model projection neglects evolution. Phylogenetic niche modeling accounts for both of these issues by incorporating knowledge of evolutionary relationships into a characterization...

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Aurora kinase A is essential for meiosis in mouse oocytes

Karen Schindler, Cecilia S. Blengini, Patricia Ibrahimian, Michaela Vaskovicova, David Drutovic, Petr Solc & Karen Schindler
The Aurora protein kinases are well-established regulators of spindle building and chromosome segregation in mitotic and meiotic cells. In mouse oocytes, there is significant Aurora kinase A (AURKA) compensatory abilities when the other Aurora kinase homologs are deleted. Whether the other homologs, AURKB or AURKC can compensate for loss of AURKA is not known. Using a conditional mouse oocyte knockout model, we demonstrate that this compensation is not reciprocal because female oocyte-specific knockout mice are...

Data from: Predator-induced collapse of niche structure and coexistence on islands

Robert M. Pringle, Tyler R. Kartzinel, Todd M. Palmer, Timothy J. Thurman, Kena Fox-Dobbs, Charles C. Y. Xu, Matthew C. Hutchinson, Tyler C. Coverdale, Joshua H. Daskin, Dominic A. Evangelista, Kiyoko M. Gotanda, , Johanna E. Wegener, Jason J. Kolbe, Thomas W. Schoener, David A. Spiller, Jonathan B. Losos & Rowan D. H. Barrett
Biological invasions represent both a pressing environmental challenge and an opportunity to investigate fundamental ecological processes, such as the role of top predators in regulating species diversity and food-web structure. In whole-ecosystem manipulations of small Caribbean islands where brown anole lizards (Anolis sagrei) were the native top predator, we experimentally staged invasions by competitors (green anoles, A. smaragdinus) and/or novel top predators (curly-tailed lizards, Leiocephalus carinatus). We show that curly-tails destabilized coexistence of competing prey...

Data from: An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

Dominic A. Evangelista, Benjamin Wipfler, Olivier Béthoux, Alexander Donath, Mari Fujita, Manpreet K. Kohli, Frédéric Legendre, Shanlin Liu, Ryuichiro Machida, Berhard Misof, Ralph Peters, Lars Podsiadlowski, Jes Rust, Kai Schuette, Ward Tollenaar, Jessica L. Ware, Torsten Wappler, Xin Zhou, Karen Meusemann & Sabrina Simon
READMEREADME of Supplementary Archives and included files of Evangelista et al. 2019Evangelista_et_al_README_DRYAD.pdfSupplementary Archive 1Files included in Supplementary Archive 1, see Evangelista_et_al_README_DRYAD.pdfSupplementary_Archive_1.zipSupplementary Archive 2Files included in Supplementary Archive 2, see Evangelista_et_al_README_DRYAD.pdfSupplementary_Archive_2.zip

Circular RNA circ_0089153 acts as a competing endogenous RNA to regulate colorectal cancer development by the miR-198/SUMO-specific peptidase 1 (SENP1) axis

Guan Fang, Tingting Chen, Ruibo Mao, Xiaming Huang & Ling Ji
Increasing evidence has indicated the implications of circular RNAs (circRNAs) in the development of colorectal cancer (CRC). In this study, we investigated the functional role and mechanism of circ_0089153 in CRC pathogenesis. The expression levels of circ_0089153, microRNA (miR)-198, and SUMO-specific peptidase 1 (SENP1) were gauged by quantitative real-time PCR (qRT-PCR) or western blot. Cell proliferation, sphere formation, tube formation, and apoptosis abilities were detected by 5-Ethynyl-2ʹ-Deoxyuridine (EdU), sphere formation, tube formation, and flow cytometry...

Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic β cells

Yunjin Zhang, Qingrui Zhao, Shenghan Su, Lingfeng Dan, Xuebei Li, Yu Wang, Yuqing Lin, Zhen Tian, Changhao Sun & Huimin Lu
Chronic exposure to high concentrations of circulating palmitic acid and stearic acid leads to impaired β cell function, which accelerates the development of type 2 diabetes. However, differences in the mechanisms underlying this process between these two saturated fatty acids remain largely unknown. In this study, we screened for potential circular RNAs (circRNAs) and their associated regulatory pathways in palmitic acid- and stearic acid-induced mouse β-TC6 cell dysfunction. CircRNA high-throughput sequencing, gene ontology enrichment and...

Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic β cells

Yunjin Zhang, Qingrui Zhao, Shenghan Su, Lingfeng Dan, Xuebei Li, Yu Wang, Yuqing Lin, Zhen Tian, Changhao Sun & Huimin Lu
Chronic exposure to high concentrations of circulating palmitic acid and stearic acid leads to impaired β cell function, which accelerates the development of type 2 diabetes. However, differences in the mechanisms underlying this process between these two saturated fatty acids remain largely unknown. In this study, we screened for potential circular RNAs (circRNAs) and their associated regulatory pathways in palmitic acid- and stearic acid-induced mouse β-TC6 cell dysfunction. CircRNA high-throughput sequencing, gene ontology enrichment and...

Varied oxygen simulations with WACCM6 (Proterozoic to pre-industrial atmosphere)

Gregory Cooke, Daniel Marsh, Catherine Walsh, Benjamin Black & Jean-François Lamarque
The history of molecular oxygen (O2) in Earth’s atmosphere is still debated; however, geological evidence supports at least two major episodes where O2 increased by an order of magnitude or more: the Great Oxidation Event (GOE) and the Neoproterozoic Oxidation Event. O2 concentrations have likely fluctuated (between 10−3 and 1.5 times the present atmospheric level) since the GOE ∼ 2.4 Gyr ago, resulting in a time-varying ozone (O3) layer. Using a three-dimensional (3D) chemistry climate...

Expression status and prognostic value of autophagy-related lncRNAs in prostate cancer

Guo Chen, Xiaoping Qin, Yu Wang, Biyun Gao, Muan Ling, Wenjun Yin, Yutong Li & Bin Pan
LncRNAs involve in the autophagy to regulate prostate cancer (PCA) initiation and progression. Therefore, it urges to explore more significant AR-lncRNAs in PCa. mRNA data and clinical information of PCa were achieved from TCGA database, and ARGs were obtained from the HADb. AR-lncRNAs were identified by correlation analysis of DE ARGs and lncRNAs. Univariate Cox regression, LASSO regression, and multivariate Cox regression were used to identify the prognostic AR-lncRNA signature and constructed a risk model....

Comprehensive comparative analysis and expression profiles and effects on physiological response of DEAD-box RNA helicase genes in Lumnitzera littorea (Jack) Voigt under cold stress

LuLu Hao, Ying Zhang, Yin Li, Linxia Bai, Danfei Yue, Huiyu Zhang & Chunfang Zheng
The DEAD-box family has been shown to play an important role in a variety of abiotic stresses, but little is known in studies of mangrove plants. Here, the effects of cold stress on various physiological changes and the role of the DEAD-box RNA helicase family in response to cold stress were determined. First, we identified 73 DEAD-box RNA helicase family members in L. littorea. Second, the evolutionary relationships between the DEAD family in L. littorea...

Integrative analysis of a novel 5 methylated snoRNA genes prognostic signature in patients with glioma

Bing Zhao, Erbao Bian, Deran Zhang, Zhiwei Wang, Yu Wang, Zhigang Cheng, Zhihao Yang, Lianxin Li, Yinfei Zheng & Xiaoyu Yue
Supplementary Table 1 | Genes associated with risk scores.
Supplementary Table 2 | Expression levels and methylation levels of SNORA71B in gliomas (TCGA Database). Supplementary Table 3 | Fold change values of the 5 methylated snoRNA genes (TCGA Database).
Supplementary Table 4 | Methylation levels of five snoRNAs in gliomas (TCGA Database).
Supplementary Table 5 Clinic-pathological characteristics of 13 glioma patients.

Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng … & Barry Smith
Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.

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