225 Works

Additional file 30 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 30: Table S8. HOGA1 inactivation promotes pancreatic cancer growth through activating LARP7-CDK1 pathway. Table S8A Quantified western blot results of 12 pairs of samples. Table S8B Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 knocked down. Table S8C Proliferation of PANC-1 and BxPC-3 cells associated with HOGA1 overexpressed. Table S8D Proliferation of PANC-1 and BxPC-3 cells associated with metabolic enzyme treatment. Table S8E A list of 773 different proteins detected in PANC-1...

Additional file 26 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 26: Table S4. The Effects of Diabetes on the Proteogenomic Characteristics of PDAC. Table S4A Mutations and arm events information in PDAC patients with or without diabetes history. Table S4B Matrix of differential pathway enrichment in patients with or without diabetes history at mRNA level. Table S4C Matrix of differential pathway enrichment in patients with or without diabetes history at protein level.

Additional file 29 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 29: Table S7. Characterization of Immune Infiltration in PDAC. Table S7A Matrix of xCell signatures significantly altered in 5 immune subgroups. Table S7B Matrix describing the expression of proteins in 5 immune subgroups. Table S7C Matrix of GSVA scores of pathways significantly altered in 5 immune subgroups, transcriptome level. Table S7D Matrix of amplification/deletion events of genes in 5 immune subgroups. Table S7E Matrix describing the expression of proteins involved in TCA cycle.

Additional file 2 of Cross-watershed distribution pattern challenging the elimination of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, in Sichuan province, China

Shen Chen, Ding Lu, Lei Duan, Ben Ma, Chao Lv, Yin-long Li, Shen-ning Lu, Lan-hua Li, Liang Xu, Zi-song Wu, Shang Xia, Jing Xu, Yang Liu & Shan Lv
Additional file 2: Dataset S1. The 130 unique cox1 haplotypes of Oncomelania hupensis from this study including two outgroups

Impact of hepatocyte-specific deletion of staphylococcal nuclease and tudor domain containing 1 (SND1) on liver insulin resistance and acute liver failure of mice

Chunyan Zhao, Xiaoteng Cui, Yan Zhao, Baoxin Qian, Nan Zhang, Lingbiao Xin, Chuanbo Ha, Jie Yang, Xinting Wang & Xingjie Gao
Although our previous research shows an ameliorated high-fat diet (HFD)-induced hepatic steatosis and insulin resistance in global SND1 transgenic mice, the involvement of SND1 loss-of-function in hepatic metabolism remains elusive. Herein, we aim to explore the potential impact of hepatocyte-specific SND1 deletion on insulin-resistant mice. As SND1 is reported to be linked to inflammatory response, the pathobiological feature of acute liver failure (ALF) is also investigated. Hence, we construct the conditional liver knockout (LKO) mice...

Difficulties translating antisense-mediated activation of Frataxin expression from cell culture to mice

Audrius Kilikevicius, Jun Wang, Xiulong Shen, Frank Rigo, Thahza P. Prakash, Marek Napierala & David R. Corey
Friedreich’s ataxia (FA) is an inherited neurodegenerative disorder caused by decreased expression of frataxin (FXN) protein. Previous studies have shown that antisense oligonucleotides (ASOs) and single-stranded silencing RNAs can be used to increase expression of frataxin in cultured patient-derived cells. In this study, we investigate the potential for oligonucleotides to increase frataxin expression in a mouse model for FA. After confirming successful in vivo delivery of oligonucleotides using a benchmark gapmer targeting the nuclear noncoding...

Data from: Phylogenetic, ecological, and allometric correlates of cranial shape in Malagasy lemuriforms

Karen L. Baab, Jonathan M. G. Perry, F. James Rohlf & William L. Jungers
Adaptive radiations provide important insights into many aspects of evolution, including the relationship between ecology and morphological diversification as well as between ecology and speciation. Many such radiations include divergence along a dietary axis, although other ecological variables may also drive diversification, including differences in diel activity patterns. This study examines the role of two key ecological variables, diet and activity patterns, in shaping the radiation of a diverse clade of primates, the Malagasy lemurs....

Data from: Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks

Kevin A. Feldheim, Samuel H. Gruber, Joseph D. DiBattista, Elizabeth A. Babcock, Steven A. Kessel, Andrew P. Hendry, Ellen K. Pikitch, Mary V. Ashley & Demian D. Chapman
Sharks are a globally threatened group of marine fishes that often breed in their natal region of origin. There has even been speculation that female sharks return to their exact birthplace to breed (“natal philopatry”), which would have important conservation implications. Genetic profiling of lemon sharks (Negaprion brevirostris) from 20 consecutive cohorts (1993-2012) at Bimini, Bahamas showed that certain females faithfully gave birth at this site for nearly two decades. At least six females born...

Data from: Measurement, variation, and scaling of osteocyte lacunae: a case study in birds

Michael D. D'Emic, Roger B. J. Benson & Roger B.J. Benson
Basic issues surrounding osteocyte biology are still poorly understood, including the variability of osteocyte morphology within and among bones, individuals, and species. Several studies have suggested that the volume or shape of osteocytes (or their lacunae) are related to bone and/or organismal growth rate or metabolism, but the nature of this relationship, if any, is unclear. Furthermore, several studies have linked osteocyte lacuna volume with genome size or growth rate and suggested that osteocyte lacuna...

Data from: Down-regulation of Rad51 activity during meiosis in yeast prevents competition with Dmc1 for repair of double-strand breaks

Yan Liu, William A. Gaines, Tracy Callender, Valeria Busygina, Ashwini Oke, Patrick Sung, Jennifer C. Fung & Nancy M. Hollingsworth
Interhomolog recombination plays a critical role in promoting proper meiotic chromosome segregation but a mechanistic understanding of this process is far from complete. In vegetative cells, Rad51 is a highly conserved recombinase that exhibits a preference for repairing double strand breaks (DSBs) using sister chromatids, in contrast to the conserved, meiosis-specific recombinase, Dmc1, which preferentially repairs programmed DSBs using homologs. Despite the different preferences for repair templates, both Rad51 and Dmc1 are required for interhomolog...

Data from: Selection for mechanical advantage underlies multiple cranial optima in new world leaf-nosed bats

Elizabeth R. Dumont, Krishna Samadevam, Ian R. Grosse, Omar M. Warsi, Brandon Baird, Liliana M. Davalos & Ian Grosse
Selection for divergent performance optima has been proposed as a central mechanism underlying adaptive radiation. Uncovering multiple optima requires identifying forms associated with different adaptive zones and linking those forms to performance. However, testing and modeling the performance of complex morphologies like the cranium is challenging. We introduce a three-dimensional finite element (FE) model of the cranium that can be morphed into different shapes by varying simple parameters to investigate the relationship between two engineering-based...

Data from: Evolutionary novelties and losses in geometric morphometrics: a practical approach through hominin molar morphology

Aida Gómez-Robles, Anthony Jay Olejniczak, María Martinón-Torres, Leyre Prado-Simón & José María Bermúdez De Castro
Geometric morphometric techniques may offer a promising methodological approach to analyse evolutionary novelties in a quantitative framework. Nevertheless, and despite continuous improvements to this methodology, the inclusion of novel features in these studies presents some difficulties. In the present study, different methods to explicitly include novel traits in geometric morphometric analyses are compared, including homology-free approaches, landmark-based approaches, and combinations of both techniques. The 2D occlusal morphology of the lower second molar in multiple hominin...

Data from: Facultative parthenogenesis in a critically endangered wild vertebrate

Andrew T. Fields, Kevin A. Feldheim, Gregg R. Poulakis & Demian D. Chapman
Facultative parthenogenesis — the ability of sexually reproducing species to sometimes produce offspring asexually — is known from a wide range of ordinarily sexually reproducing vertebrates in captivity, including some birds, reptiles and sharks 1, 2 and 3. Despite this, free-living parthenogens have never been observed in any of these taxa in the wild, although two free-living snakes were recently discovered each gestating a single parthenogen — one copperhead (Agkistrodon contortrix) and one cottonmouth (Agkistrodon...

Data from: Sustained costs of growth and the trajectory of recovery

Kestrel O. Perez & Stephan B. Munch
1. Large body size is associated with many fitness advantages. Despite this, most species do not grow at their physiological maximum, suggesting costs to rapid growth. There are now many empirical examples of trade-offs with growth. 2. Despite the ubiquity of physiological delays, few studies have evaluated the duration over which growth costs occur. To address this question, we measured swimming ability in growth-manipulated Atlantic silversides (Menidia mendia). Fish were manipulated to grow at their...

Data from: Genetic diversity of white sharks, Carcharodon carcharias, in the northwest Atlantic and southern Africa

Shannon J. O'Leary, Kevin A. Feldheim, Andrew T. Fields, Lisa J. Natanson, Sabine Wintner, Nigel Hussey, Mahmood S. Shivji & Demian D. Chapman
The white shark, Carcharodon carcharias, is both one of the largest apex predators in the world and among the most heavily protected marine fish. Population genetic diversity is in part shaped by recent demographic history and can thus provide information complementary to more traditional population assessments, which are difficult to obtain for white sharks and have at times been controversial. Here, we use the mitochondrial control region and 14 nuclear-encoded microsatellite loci to assess white...

Data from: Bayesian hierarchical models suggest oldest known plant-visiting bat was omnivorous

Laurel R. Yohe, Paúl M. Velazco, Danny Rojas, Beth E. Gerstner, Nancy B. Simmons & Liliana M. Dávalos
The earliest record of plant visiting in bats dates to the Middle Miocene of La Venta, the world's most diverse tropical palaeocommunity. Palynephyllum antimaster is known from molars that indicate nectarivory. Skull length, an important indicator of key traits such as body size, bite force and trophic specialization, remains unknown. We developed Bayesian models to infer skull length based on dental measurements. These models account for variation within and between species, variation between clades, and...

Data from: Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

John J. Wiens, Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted M. Townsend, , Tod W. Reeder & J. W. Sites
Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33,717 base pairs), using both concatenated and species-tree methods for the first time. Our...

Data from: Demography, traits, and vulnerability to urbanization: can we make generalizations?

Leone M. Brown & Catherine H. Graham
1. Human-induced land cover change threatens species diversity and ecosystem services. The rapid pace of current change makes predicting species’ declines imperative, but leaves little time for thorough study of all species. One solution is to make generalizations about species’ vulnerability to urbanization based on traits common among studied species in decline. 2. To date, most generalizations about traits associated with species’ declines in response to urbanization are based on presence or abundance, or detailed...

Data from: Integrating remotely sensed fires for predicting deforestation for REDD+

Dolors Armenteras, Cerian Gibbes, Jesús A. Anaya & Liliana M. Dávalos
Fire is an important tool in tropical forest management, as it alters forest composition, structure, and the carbon budget. The United Nations program on Reducing Emissions from Deforestation and Forest Degradation (REDD+) aims to sustainably manage forests, as well as conserve and enhance their carbon stocks. Despite the crucial role of fire management, decision-making on REDD+ interventions fails to systematically include fires. Here, we address this critical knowledge gap in two ways. First, we review...

Data from: Global mammal betadiversity show parallel assemblage structure in similar but isolated environments

Caterina Penone, Ben G. Weinstein, Catherine H. Graham, Thomas M. Brooks, Carlo Rondinini, S. Blair Hedges, Ana D. Davidson & Gabriel C. Costa
The taxonomic, phylogenetic and trait dimensions of betadiversity each provide unique insight into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait betadiversity. Conversely, we expect lower phylogenetic diversity but...

Data from: Novel opsin gene variation in large-bodied, diurnal lemurs

Rachel L. Jacobs, Tammie S. MacFie, Amanda N. Spriggs, Andrea L. Baden, Toni Lyn Morelli, Mitchell T. Irwin, Richard R. Lawler, Jennifer Pastorini, Mireya Mayor, Runhua Lei, Ryan Culligan, Melissa T. R. Hawkins, Peter M. Kappeler, Patricia C. Wright, Edward E. Louis, Nicholas I. Mundy & Brenda J. Bradley
Some primate populations include both trichromatic and dichromatic (red–green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity...

Data from: Evidence for ship noise impacts on humpback whale foraging behaviour

Hannah B. Blair, Nathan D. Merchant, Ari S. Friedlaender, David N. Wiley & Susan E. Parks
Noise from shipping activity in North Atlantic coastal waters has been steadily increasing and is an area of growing conservation concern, as it has the potential to disrupt the behaviour of marine organisms. This study examines the impacts of ship noise on bottom foraging humpback whales (Megaptera novaeangliae) in the western North Atlantic. Data were collected from 10 foraging whales using non-invasive archival tags that simultaneously recorded underwater movements and the acoustic environment at the...

Data from: Ultra-fine scale spatially-integrated mapping of habitat and occupancy using structure-from-motion

Philip McDowall & Heather J. Lynch
Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models...

Data from: Rethinking ‘normal’: the role of stochasticity in the phenology of a synchronously breeding seabird

Casey Youngflesh, Stephanie Jenouvrier, Jefferson T. Hinke, Lauren DuBois, Judy St. Leger, Wayne Z. Trivelpiece, Susan G. Trivelpiece & Heather J. Lynch
1. Phenological changes have been observed in a variety of systems over the past century. There is concern that, as a consequence, ecological interactions are becoming increasingly mismatched in time, with negative consequences for ecological function. 2. Significant spatial heterogeneity (inter-site) and temporal variability (inter-annual) can make it difficult to separate intrinsic, extrinsic, and stochastic drivers of phenological variability. The goal of this study was to understand the timing and variability of breeding phenology of...

Data from: Hovering in the heat: effects of environmental temperature on heat regulation in foraging hummingbirds

Donald R. Powers, Kathleen M. Langland, Susan M. Wethington, Sean D. Powers, Catherine H. Graham & Bret W. Tobalske
At high temperature (>40 ºC) endotherms experience reduced passive heat dissipation (radiation, conduction, and convection) and increased reliance on evaporative heat loss. High temperatures challenge flying birds due to heat produced by wing muscles. Hummingbirds depend on flight for foraging, yet inhabit hot regions. We used infrared thermography to explore how lower passive heat dissipation during flight impacts body-heat management in broad-billed (Cynanthus latirostris, 3.0g), black-chinned (Archilochus alexandri, 3.0g), Rivoli’s (Eugenes fulgens, 7.5g), and blue-throated...

Registration Year

  • 2022
    87
  • 2021
    29
  • 2020
    20
  • 2019
    8
  • 2018
    14
  • 2017
    18
  • 2016
    16
  • 2015
    13
  • 2014
    4
  • 2013
    8

Resource Types

  • Dataset
    225

Affiliations

  • Stony Brook University
    225
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    70
  • Zhejiang University
    65
  • Shanghai Jiao Tong University
    62
  • Capital Medical University
    59
  • University of Chinese Academy of Sciences
    59
  • Sun Yat-sen University
    56
  • Fudan University
    56
  • Chinese Academy of Sciences
    53
  • China Agricultural University
    52