132 Works

Bird predation and landscape context shape arthropod communities on broccoli

Joseph Taylor, Olivia Smith, William Snyder, Jeb Owen, Erin Wilson-Rankin, Max Edworthy, Christina Kennedy, Chris Latimer & William Snyder
Birds increase crop yields via consumption of pests in some contexts but disrupt pest control via intraguild predation in others. Landscape complexity acts as an inconsistent mediator, sometimes increasing, decreasing, or not impacting pest control. Here, we examined how landscape context and seasonal variation mediate the impact of birds on arthropod pests and natural enemies, leaf damage, and yields of broccoli (Brassica oleracea) on highly diversified farms that spanned the USA West Coast. Our study...

Frequency-dependent hybridization contributes to habitat segregation in monkeyflowers

Katherine Toll & David Lowry
Spatial segregation of closely related species is usually attributed to differences in stress tolerance and competitive ability. For both animals and plants, reproductive interactions between close relatives can impose a fitness cost that is more detrimental to the rarer species. Frequency-dependent mating interactions may thus prevent the establishment of immigrants within heterospecific populations, maintaining spatial segregation of species. Despite strong spatial segregation in natural populations, two sympatric California monkeyflowers (Mimulus nudatus and M. guttatus) survive...

Parkinson’s disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), ATXN1, SLC17A6, NR4A2, and PTPRN2 in cortical neurons

Joseph Kochmanski, Nathan Kuhn & Alison Bernstein
Evidence for epigenetic regulation playing a role in Parkinson’s disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell-type or sex in...

Photodegradation of plant litter cuticles enhances microbial decomposition by increasing uptake of non-rainfall moisture

J. Robert Logan, Paul Barnes & Sarah Evans
Litter decomposition plays a central role in carbon cycling in terrestrial ecosystems worldwide. In drylands, which cover 40% of the Earth’s land surface, photodegradation and biotic decomposition driven by non-rainfall moisture are important mechanisms of litter decay, though studies have only recently begun examining interactions between these two processes. We describe a novel priming mechanism in which photodegradation and biotic decay of the cuticle of plant litter increases litter absorption of non-rainfall moisture (fog, dew,...

Additional file 1 of Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma

Guisheng Zhao, Patrick Newbury, Yukitomo Ishi, Eugene Chekalin, Billy Zeng, Benjamin S. Glicksberg, Anita Wen, Shreya Paithankar, Takahiro Sasaki, Amreena Suri, Javad Nazarian, Michael E. Pacold, Daniel J. Brat, Theodore Nicolaides, Bin Chen & Rintaro Hashizume
Additional file 1: Table S1. The list of drugs with predicted reversal predicted reversal gene expression scores (sRGES) and experimental drug efficacy (AC50).

Additional file 7 of Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma

Guisheng Zhao, Patrick Newbury, Yukitomo Ishi, Eugene Chekalin, Billy Zeng, Benjamin S. Glicksberg, Anita Wen, Shreya Paithankar, Takahiro Sasaki, Amreena Suri, Javad Nazarian, Michael E. Pacold, Daniel J. Brat, Theodore Nicolaides, Bin Chen & Rintaro Hashizume
Additional file 7: Table S6. The list of differential expression genes upon drug treament in SF8628 cells.

Data for: Local adaptation of seed and seedling traits along a natural aridity gradient may both predict and constrain adaptive responses to climate change

Kyle Christie, Natalie Pierson, David Lowry & Liza Holeski
Local adaptation of seed and seedling traits along a natural aridity gradient may both predict and constrain adaptive responses to climate change (American Journal of Botany 2022) Premise of study: Variation in seed and seedling traits underlies how plants interact with their environment during establishment, a crucial life history stage. We quantified genetic-based variation in seed and seedling traits in populations of the annual plant Plantago patagonica across a natural aridity gradient, leveraging natural intraspecific...

Additional file 2 of A custom library construction method for super-resolution ribosome profiling in Arabidopsis

Hsin-Yen Larry Wu & Polly Yingshan Hsu
Additional file 2. Code used in this study.

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

Up-regulation of caveolin 1 mediated by chitosan activates Wnt/ β-catenin pathway in chronic refractory wound diabetic rat model

Jie Gao, Jiayuan Zhang, Lianheng Xia, Xuewei Liang, Wukun Ding, Meiyu Song, Linggen Li & Zhen Jia
Diabetes mellitus (DM) can be implicated in the perturbations of vascular integrity and the dysfunction of angiogenesis. Chitosan has the advantage of promoting the vascular endothelial cell proliferation. However, the molecular mechanism of action in the promotion of wound healing by chitosan derivatives is still debated. In the current study, DM with chronic wound (CW) model rats were prepared and treated with chitosan. Vascular endothelial cells isolated from granulation tissues were conducted by RNA sequencing....

Up-regulation of caveolin 1 mediated by chitosan activates Wnt/ β-catenin pathway in chronic refractory wound diabetic rat model

Jie Gao, Jiayuan Zhang, Lianheng Xia, Xuewei Liang, Wukun Ding, Meiyu Song, Linggen Li & Zhen Jia
Diabetes mellitus (DM) can be implicated in the perturbations of vascular integrity and the dysfunction of angiogenesis. Chitosan has the advantage of promoting the vascular endothelial cell proliferation. However, the molecular mechanism of action in the promotion of wound healing by chitosan derivatives is still debated. In the current study, DM with chronic wound (CW) model rats were prepared and treated with chitosan. Vascular endothelial cells isolated from granulation tissues were conducted by RNA sequencing....

Data for: Stronger niche than dispersal effects on α- and β-diversity of stream algae, insects, and fish across latitudes in the US

Joseph Mruzek, William Budnick, Chad Larson, Dinh Luc & Sophia Passy
Aim: Niche and dispersal processes influence biodiversity, but their relative importance along latitude is unclear. We predicted that: i) niche processes would dominate at high latitudes due to increased climatic stress, consistent with the physiological tolerance hypothesis and the Dobzhansky-MacArthur hypothesis and ii) dispersal limitation would prevail at low latitudes due to narrower niches and smaller range sizes, as postulated by the dispersal-ecological specialization tradeoff hypothesis, the latitude-niche breadth hypothesis, and Rapoport’s rule. Location: Central...

Evolutionary effects of nitrogen are not easily predicted from ecological responses

Joseph Waterton, Mark Hammond & Jennifer Lau
Anthropogenic nitrogen (N) addition might alter the evolutionary trajectories of plant populations, in part because it alters the abiotic and biotic environment by increasing aboveground primary productivity, light asymmetry, and herbivory intensity, and reducing plant species diversity. Such evolutionary impacts could be caused by N altering patterns of natural selection (i.e., trait-fitness relationships) and the opportunity for selection (i.e., variance in relative fitness). Because at the community level N addition favors species with light acquisition...

Additional file 2 of Quantifying substantial carcinogenesis of genetic and environmental factors from measurement error in the number of stem cell divisions

Xinhui Liu, Jifeng Yang, Hongkai Li, Qing Wang, Yuanyuan Yu, Xiaoru Sun, Shucheng Si, Lei Hou, Lu Liu, Fan Yang, Ran Yan, Yifan Yu, Zhentao Fu, Zilong Lu, Dejin Li, Hao Xue, Xiaolei Guo, Fuzhong Xue & Xiaokang Ji
Additional file 2: Table S1. Ranked matrix of LCR in global scope and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S2. Ranked matrix of LCR in national-wide of China and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S3. Ranked matrix of LCR in counties of Shandong province, China and the contribution of the genetic and environmental factors on the...

Additional file 6 of m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis

Ling Wang, Haiyan Zhuang, Wenwen Fan, Xia Zhang, Haihong Dong, Hongxing Yang & Jungnam Cho
Additional file 6: Table S5. Sequences of oligonucleotides.

Additional file 2 of m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis

Ling Wang, Haiyan Zhuang, Wenwen Fan, Xia Zhang, Haihong Dong, Hongxing Yang & Jungnam Cho
Additional file 2: Table S1. LVGs identified by different datasets.

Additional file 3 of The effect of SNPs in lncRNA as ceRNA on the risk and prognosis of hepatocellular carcinoma

Han Mo, Xi Wang, Guohua Ji, Xiao Liang, Yi Yang, Wenjing Sun, Xueyuan Jia, Lidan Xu, Yuandong Qiao, Henan Zhou, Wenhui Zhao, Songbin Fu & Xuelong Zhang
Additional file 3:

Additional file 4 of m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis

Ling Wang, Haiyan Zhuang, Wenwen Fan, Xia Zhang, Haihong Dong, Hongxing Yang & Jungnam Cho
Additional file 4: Table S3. Hypermethylated genes in leaves and flowers of 10b-1.

Additional file 1 of Computation and molecular pharmacology to trace the anti-rheumatoid activity of Angelicae Pubescentis Radix

Junhao Zhang, Rui Wang, Xiao Liang, Hao Tian Bai, Ya Lan Li, Shuhui Sun, Qianqian Zhang & Jing Yang
Additional file 1: Figure S1. Original picture of protein expression level.

Data for: A hierarchical framework for unpacking the nitrogen challenge

Weifeng Zhang, Tingyu Li, Xin Zhang, Yuxiu Zhong, Eric Davidson, Zhengxia Dou, Paulo Pavinato, Luiz Martinelli, David Kanter, Jianguo Liu & Fusuo Zhang
To feed the world population while mitigating pressing nitrogen (N) pollution problems, tremendous efforts have been devoted to developing and implementing N-efficient technologies in food production, but limited progress has been made. The N management improvement on a farm does not necessarily translate to N pollution reduction on a broader scale due to complex responses of natural and human systems and lack of coordination among stakeholders. Consequently, it is imperative to develop an N management...

Additional file 3 of A custom library construction method for super-resolution ribosome profiling in Arabidopsis

Hsin-Yen Larry Wu & Polly Yingshan Hsu
Additional file 3. Contaminating sequences from rRNAs, tRNAs, snRNAs, snoRNAs and dominant noncoding RNAs.

Adverse health effects and stresses on offspring due to paternal exposure to harmful substances

Jiaqi Sun, Miaomiao Teng, Fengchang Wu, Xiaoli Zhao, Yunxia Li, Lihui Zhao, Wentian Zhao, Keng Po Lai, Kenneth Mei Yee Leung & John P. Giesy
Recent epidemiological investigations report that environmental factors, such as exposure to harmful substances and stress related to unhealthy lifestyles, can result in health risks to organisms. The involvement of paternal exposure to chemicals and stresses, which leads to a negative impact on physiological responses and developmental processes in descendants, has drawn scientific attention. In this comprehensive review, we systematically describe different exposure sources of intergenerational and transgenerational health effects, including smoking, atmospheric fine particulate matter,...

Additional file 5 of Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma

Guisheng Zhao, Patrick Newbury, Yukitomo Ishi, Eugene Chekalin, Billy Zeng, Benjamin S. Glicksberg, Anita Wen, Shreya Paithankar, Takahiro Sasaki, Amreena Suri, Javad Nazarian, Michael E. Pacold, Daniel J. Brat, Theodore Nicolaides, Bin Chen & Rintaro Hashizume
Additional file 5: Table S4. Top 20 hits of drugs identified by machine-learning aided drug repurposing pipeline in this study.

Additional file 7 of Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma

Guisheng Zhao, Patrick Newbury, Yukitomo Ishi, Eugene Chekalin, Billy Zeng, Benjamin S. Glicksberg, Anita Wen, Shreya Paithankar, Takahiro Sasaki, Amreena Suri, Javad Nazarian, Michael E. Pacold, Daniel J. Brat, Theodore Nicolaides, Bin Chen & Rintaro Hashizume
Additional file 7: Table S6. The list of differential expression genes upon drug treament in SF8628 cells.

Additional file 8 of Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma

Guisheng Zhao, Patrick Newbury, Yukitomo Ishi, Eugene Chekalin, Billy Zeng, Benjamin S. Glicksberg, Anita Wen, Shreya Paithankar, Takahiro Sasaki, Amreena Suri, Javad Nazarian, Michael E. Pacold, Daniel J. Brat, Theodore Nicolaides, Bin Chen & Rintaro Hashizume
Additional file 8: Table S7. The list of differential expression genes upon drug treament in SU-DIPG-IV cells.

Registration Year

  • 2022
    132

Resource Types

  • Dataset
    132

Affiliations

  • Michigan State University
    132
  • Shanghai Jiao Tong University
    37
  • Chinese Academy of Sciences
    33
  • University of Chinese Academy of Sciences
    33
  • Sichuan University
    28
  • Zhejiang University
    27
  • Peking University People's Hospital
    27
  • Southern Medical University
    26
  • Lanzhou University
    24
  • Nanfang Hospital
    23