51 Works

Data for Coco et al. 2022 Oecologia, More phylogenetically diverse polycultures inconsistently suppress insect herbivore populations

A.M. Coco, E.C. Yip, I. Kaplan & J.F. Tooker
Because the diet of many herbivorous insects is restricted to closely related taxa with similar chemistry, intercropping with diverse plant communities may reduce both pest populations and reliance on chemical pesticides in agroecosystems. We tested whether the effectiveness of intercropping against herbivorous insects depends on the phylogenetic relatedness of neighboring crops, using butternut squash (Cucurbita moschata) as a focal crop species in a series of different intercropping combinations. We found that increased phylogenetic divergence of...

Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycusch) ecotypes

Peter Euclide, Andy Jasonowicz, Shawn Sitar, Greg Fischer & Rick Goetz
Genetic evidence of selection for complex and polygenically regulated phenotypes can easily become masked by neutral population genetic structure and phenotypic plasticity. Without direct evidence of genotype-phenotype associations it can be difficult to conclude to what degree a phenotype is heritable or a product of environment. Common garden laboratory studies control for environmental stochasticity and help to determine the mechanism that regulate traits. Here we assess lipid content, growth, weight, and length variation in full...

Additional file 1 of A split influenza vaccine formulated with a combination adjuvant composed of alpha-d-glucan nanoparticles and a STING agonist elicits cross-protective immunity in pigs

V. Patil, J. F. Hernandez-Franco, G. Yadagiri, D. Bugybayeva, S. Dolatyabi, N. Feliciano-Ruiz, J. Schrock, J. Hanson, J. Ngunjiri, H. HogenEsch & G. J. Renukaradhya
Additional file 1: Figure S1. Nano11-SwIAV induced IL-4 and IL-6 cytokine gene expression in TBLN of vaccinated pigs. Five-week-old SPF pigs were administered twice ID/IM with NanoS100-SwIAV, Nano11-SwIAV or control NanoS100 and challenged at post-prime vaccination day 35 with SwIAV H1N1-OH7. TBLN samples collected and stored in RNAlater at DPC6 were analyzed for gene expression using SYBR Green qRT-PCR method. Data represent the mean value of 7-8 pigs ± SEM. Statistical analysis was performed by...

Additional file 2 of A split influenza vaccine formulated with a combination adjuvant composed of alpha-d-glucan nanoparticles and a STING agonist elicits cross-protective immunity in pigs

V. Patil, J. F. Hernandez-Franco, G. Yadagiri, D. Bugybayeva, S. Dolatyabi, N. Feliciano-Ruiz, J. Schrock, J. Hanson, J. Ngunjiri, H. HogenEsch & G. J. Renukaradhya
Additional file 2: Tables S1–S3. Antibody panels used in the flow cytometry analysis. The antibody panels employed for the analysis of T-helper/memory cells, CTLs, and myeloid cells in TBLN MNCs, PBMCs, and BAL cells in Panel#1[Table S1] (Myeloid cells); IL-17A+ lymphocyte subsets in Panel#2 [Table S2]; and IFNγ+ lymphocyte subsets in Panel#3 [Table S3].

Artificial Hotspot Occurrence Inventory (AHOI)

Daniel Park, Yingying Xie, Hanna Thammavong, Rima Tulaiha & Xiao Feng
Aim: Species occurrence records are essential to understanding Earth’s biodiversity and addressing global environmental issues, but do not always reflect actual locations of occurrence. Certain geographic coordinates are assigned repeatedly to thousands of observation/collection records. This may result from imperfect data management and georeferencing practices, and can greatly bias the inferred distribution of biodiversity and associated environmental conditions. Nonetheless, these ‘biodiverse’ coordinates are often overlooked in taxon-centric studies, as they are identifiable only in aggregate...

Additional file 2 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 2.

Additional file 3 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 3.

Additional file 3 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

Yang Yang, Yiqi Wu, Mengting Ji, Xiaoyin Rong, Yanwei Zhang, Shuai Yang, Chang Lu, Chunbo Cai, Pengfei Gao, Xiaohong Guo, Bugao Li & Guoqing Cao
Additional file 3.

Additional file 1 of Proteomic analysis reveals that aging rabbit vocal folds are more vulnerable to changes caused by systemic dehydration

Naila C. do Nascimento, Taylor W. Bailey, Andrea P. Santos, Chenwei Duan, Rodrigo Mohallem, Jackeline Franco, Uma K. Aryal, Jun Xie, Abigail Cox & M. Preeti Sivasankar
Additional file 1.

Additional file 1 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 1: Table S1. Differential promoter coverage genes and GO, KEGG enrichment analysis results of differential genes for all pregnant women with trisomy.

Screening of candidate genes at GLC3B and GLC3C loci in Chinese primary congenital glaucoma patients with targeted next generation sequencing

Yunsheng Qiao, Tingting Shao, Yuhong Chen, Junyi Chen, Xinghuai Sun & Xueli Chen
Primary congenital glaucoma (PCG) is characterized by developmental abnormalities of the anterior chamber angle. Although several genes have been associated with PCG, pathogenic mutations could only be detected in about 20% of Chinese patients. GLC3B (1p36.2–36.1) and GLC3C (14q24.3) loci were previously identified in PCG pedigrees via linkage analysis. However, no causative genes were reported in these loci. This study was designed to search for novel PCG-related genes in these genetic regions. DNA samples from...

Additional file 2 of A split influenza vaccine formulated with a combination adjuvant composed of alpha-d-glucan nanoparticles and a STING agonist elicits cross-protective immunity in pigs

V. Patil, J. F. Hernandez-Franco, G. Yadagiri, D. Bugybayeva, S. Dolatyabi, N. Feliciano-Ruiz, J. Schrock, J. Hanson, J. Ngunjiri, H. HogenEsch & G. J. Renukaradhya
Additional file 2: Tables S1–S3. Antibody panels used in the flow cytometry analysis. The antibody panels employed for the analysis of T-helper/memory cells, CTLs, and myeloid cells in TBLN MNCs, PBMCs, and BAL cells in Panel#1[Table S1] (Myeloid cells); IL-17A+ lymphocyte subsets in Panel#2 [Table S2]; and IFNγ+ lymphocyte subsets in Panel#3 [Table S3].

Additional file 2 of Proteomic analysis reveals that aging rabbit vocal folds are more vulnerable to changes caused by systemic dehydration

Naila C. do Nascimento, Taylor W. Bailey, Andrea P. Santos, Chenwei Duan, Rodrigo Mohallem, Jackeline Franco, Uma K. Aryal, Jun Xie, Abigail Cox & M. Preeti Sivasankar
Additional file 2.

Additional file 2 of Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile

Min Zhang, Kun Li, Shoufang Qu, Zhiwei Guo, Yuanli Wang, Xu Yang, Junhua Zhou, Guojun Ouyang, Rongtao Weng, Fenxia Li, Yingsong Wu & Xuexi Yang
Additional file 2: Table S2. Differential promoter coverage genes and GO, KEGG enrichment analysis results of differential genes for pregnant women with trisomy 21.

Russulaceae of the Pakaraima Mountains of Guyana. IV. New species forming a distinct lineage of Lactarius subg. Plinthogalus

Jorinde Nuytinck, Terry W. Henkel, Lynn Delgat, Katja Milisav, Christina Noordermeer, Annemieke Verbeken & M. Catherine Aime
The Neotropics have recently emerged as an important region for studies of tropical ectomycorrhizal (ECM) fungi. Specific neotropical areas with high ECM host tree densities have ECM fungal diversities rivaling those of higher-latitude forests. Some forests of the Guiana Shield are dominated by endemic ECM trees of the Fabaceae, including species of Dicymbe (subfam. Detarioideae), Aldina (subfam. Papilionoideae), and Pakaraimaea (Cistaceae). One of the most species-rich ECM fungal families present in each of these systems...

Data for: A new GTSeq resource to facilitate multijurisdictional research and management of walleye Sander vitreus

Peter Euclide, Wesley Lason, Matthew Bootsma, Loren Miller, Kim Scribner, Wendylee Stott, Chris Wilson & Emily Latch
Conservation and management professionals often work across jurisdictional boundaries to identify broad ecological patterns. These collaborations help to protect populations whose distributions span political borders. One common limitation to multijurisdictional collaboration is consistency in data recording and reporting. This limitation can impact genetic research which relies on data about specific markers in an organism’s genome. Incomplete overlap of markers between separate studies can prevent direct comparisons of results. Standardized marker panels can reduce the impact...

Supporting data for: Limited genetic differentiation of Mycetomoellerius mikromelanos in Parc National Soberanía, Panama: Implications for queen dispersal

Cody Raul Cardenas, Andrew Mularo, Andreas Chavez & Rachelle Adams
The coevolutionary relationship between fungus-growing ants (Formicidae: Attini: Attina) and their symbionts has been well-studied in the Panamanian rainforests. To further understand the ecological context of these evolutionary relationships, we have examined the population genetic structure of the fungus-growing ant species Mycetomoellerius mikromelanos Cardenas, Schultz, & Adams 2021, in the Panama Canal Zone. We specifically investigated the presence of population structure, the significance of geographic features (i.e., creeks) limiting gene flow, and relatedness between ant...

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.

Additional file 1 of A split influenza vaccine formulated with a combination adjuvant composed of alpha-d-glucan nanoparticles and a STING agonist elicits cross-protective immunity in pigs

V. Patil, J. F. Hernandez-Franco, G. Yadagiri, D. Bugybayeva, S. Dolatyabi, N. Feliciano-Ruiz, J. Schrock, J. Hanson, J. Ngunjiri, H. HogenEsch & G. J. Renukaradhya
Additional file 1: Figure S1. Nano11-SwIAV induced IL-4 and IL-6 cytokine gene expression in TBLN of vaccinated pigs. Five-week-old SPF pigs were administered twice ID/IM with NanoS100-SwIAV, Nano11-SwIAV or control NanoS100 and challenged at post-prime vaccination day 35 with SwIAV H1N1-OH7. TBLN samples collected and stored in RNAlater at DPC6 were analyzed for gene expression using SYBR Green qRT-PCR method. Data represent the mean value of 7-8 pigs ± SEM. Statistical analysis was performed by...

Baltic Sea stable isotope ecology meta-data collection

Elvita Eglite, Clarissa Mohm & Jan Dierking
Stable isotope analysis (SIA) has become a pivotal method in food web and ecological research, leading to the establishment of the research field “stable isotope ecology”. We conducted the first systematic review of stable isotope studies in this field in the Baltic Sea macro-region (Eglite et al. 2022). The meta-data collection provided here includes the information extracted from all 164 studies identified in the systematic review across various dimensions (topic, space, time, taxonomic, and technical...

NLRC5 Restricts Dengue Virus Infection by Promoting the Autophagic Degradation of Viral NS3 through E3 Ligase CUL2 (cullin 2)

Jiawei Hao, Jinqian Li, Zhenzhen Zhang, Yang Yang, Qing Zhou, Tiantian Wu, Tongling Chen, Zhongdao Wu, Ping Zhang, Jun Cui & Yi-Ping Li
NLRC5 has been reported to be involved in antiviral immunity; however, the underlying mechanism remains poorly understood. Here, we investigated the functional role of NLRC5 in the infection of a flavivirus, dengue virus (DENV). We found that expression of NLRC5 was strongly induced by virus infection and IFNB or IFNG stimulation in different cell lines. Overexpression of NLRC5 remarkably suppressed DENV infection, whereas knockout of NLRC5 led to a significant increase in DENV infection. Mechanistic...

Experimental evidence that host species composition alters host-pathogen dynamics in a ranavirus-amphibian assemblage

Paul Snyder, Chloe Ramsay, Carmen Harjoe, Emily Khazan, Cheryl Briggs, Jason Hoverman, Pieter Johnson, Daniel Preston, Jason Rohr & Andrew Blaustein
Losses in biodiversity can alter disease risk through changes in host species composition. Host species vary in pathogen susceptibility and competence. Yet how changes in diversity alter host-pathogen dynamics remains unclear in many systems, particularly with respect to generalist pathogens. Amphibians are experiencing worldwide population declines linked to generalist pathogens, such as ranavirus, and thus represent an ideal group to investigate how host species composition affects disease risk. We conducted experiments where individuals in the...

NLRC5 restricts dengue virus infection by promoting the autophagic degradation of viral NS3 through E3 ligase CUL2 (cullin 2)

Jiawei Hao, Jinqian Li, Zhenzhen Zhang, Yang Yang, Qing Zhou, Tiantian Wu, Tongling Chen, Zhongdao Wu, Ping Zhang, Jun Cui & Yi-Ping Li
NLRC5 has been reported to be involved in antiviral immunity; however, the underlying mechanism remains poorly understood. Here, we investigated the functional role of NLRC5 in the infection of a flavivirus, dengue virus (DENV). We found that the expression of NLRC5 was strongly induced by virus infection and IFNB or IFNG stimulation in different cell lines. Overexpression of NLRC5 remarkably suppressed DENV infection, whereas knockout of NLRC5 led to a significant increase in DENV infection....

Data and supplementary materials from: Large genetic divergence underpins cryptic local adaptation across ecological and evolutionary gradients

Morgan Sparks
Environmentally covarying local adaptation is a form of cryptic local adaptation in which the covariance of the genetic and environmental effects on a phenotype obscures the divergence between locally adapted genotypes. Here, we systematically document the magnitude and drivers of the genetic effect (VG) for two forms of environmentally covarying local adaptation: counter- and cogradient variation. Using a hierarchical Bayesian meta-analysis, we calculated the overall effect size of VG as 1.05 and 2.13 for populations...

Additional file 3 of Interaction of miR-200a-3p with YAP regulates cell proliferation and metastasis differentially in HPV-positive and HPV-negative cervical cancer cells

Hong Chen, Lingling Gu, Min Zhang, Huifen Chen, Hong Liao, Xueping Cao, Lu Yu & Jun Zhang
Additional file 3.

Registration Year

  • 2022
    51

Resource Types

  • Dataset
    51

Affiliations

  • Purdue University West Lafayette
    45
  • Sun Yat-sen University
    25
  • Central South University
    25
  • Sichuan University
    25
  • Shandong University
    24
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    24
  • Chinese Academy of Sciences
    24
  • University of Chinese Academy of Sciences
    22
  • Northwest University
    21
  • Heilongjiang Provincial Academy of Agricultural Sciences
    20