65 Works

Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

Brendan P. Hodkinson, Neil R. Gottel, Christopher W. Schadt & François Lutzoni
Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e., green algal vs. cyanobacterial), mycobiont-types, and large-scale spatial distances (from tropical to arctic latitudes). Amplicons...

Data from: Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

Adrian-Stefan Andrei, Michael S. Robeson, Andreea Baricz, Cristian Coman, Vasile Muntean, Artur Ionescu, Giuseppe Etiope, Mircea Alexe, Cosmin Ionel Sicora, Mircea Podar & Horia Leonard Banciu
Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching...

Data from: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

Hengfu Yin, Hao-Bo Guo, David J. Weston, Anne M. Borland, Priya Ranjan, Paul E. Abraham, Sara S. Jawdy, James Wachira, Gerald A. Tuskan, Timothy J. Tschaplinski, Stan D. Wullschleger, Hong Guo, Robert L. Hettich, Stephen Gross, Zhong Wang, Axel Visel & Xiaohan Yang
Background: Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. However, the genomic basis of evolutionary innovation of CAM in...

Single-chain heteropolymers transport protons selectively and rapidly

Tao Jiang, Aaron Hall, Marco Eres, Zahra Hemmatian, Baofu Qiao, Yun Zhou, Zhiyuan Ruan, Andrew D. Couse, William T. Heller, Haiyan Huang, Monica Olvera De La Cruz, Marco Rolandi & Ting Xu
Precise protein sequencing and folding are believed to generate the natural channel structure and chemical diversity of proteins, both of which are essential to synthetically achieve proton transport performance comparable to that seen in natural systems. Geometrically defined channels have been fabricated using peptides, DNAs, carbon nanotubes, sequence-defined polymers and organic frameworks; however, none of these channels rivals the performance observed in their natural counterparts. Here we show that without forming an atomically structured channel,...

Data from: The Physiological Basis for Estimating Photosynthesis from Chlorophyll a Fluorescence

Jimei Han, Lianhong Gu, Yongjiang Zhang & Ying Sun

Metabolite, qPCR, and metadata for relationships between Sphaerulina musiva infection and the Populus microbiome and metabolome

Nicholas Dove
Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigate the microbiome and metabolome of P....

Data from: Phylogenomic structure and speciation in an emerging model: The Sphagnum magellanicum complex (Bryophyta)

A. Jonathan Shaw, Aaron Duffy, Bryan Piatkowski, Blanka Aguero, Karn Imwattana, Marta Nieto-Lugilde, Adam Healy, David Weston, Megan Patel, Jeremy Schmutz, Joseph Yavitt, Kristian Hassel, Hans Stenøien & Kjell Ivar Flatberg
The moss genus Sphagnum has unparalleled ecological importance because some 30% of the total terrestrial carbon pool is bound up in Sphagnum-dominated peatlands. A major peat-former, S. magellanicum, is one of two species for which a reference-quality genome exists to facilitate research in ecological genomics, but recently published work indicated that S. magellanicum s. str. is restricted to South America and two other species, S. divinum and S. medium occur in North America and Europe....

Additional file 5 of Genotyping and biofilm formation of Mycoplasma hyopneumoniae and their association with virulence

Yuzi Wu, Yanfei Yu, Lizhong Hua, Yanna Wei, Yuan Gan, Hafizah Yousuf Chenia, Yixuan Wang, Xing Xie, Jia Wang, Maojun Liu, Guoqing Shao, Qiyan Xiong & Zhixin Feng
Additional file 5. Correlation of virulence and biofilm.

Additional file 4 of Genotyping and biofilm formation of Mycoplasma hyopneumoniae and their association with virulence

Yuzi Wu, Yanfei Yu, Lizhong Hua, Yanna Wei, Yuan Gan, Hafizah Yousuf Chenia, Yixuan Wang, Xing Xie, Jia Wang, Maojun Liu, Guoqing Shao, Qiyan Xiong & Zhixin Feng
Additional file 4. Results of DNA sequencing based on MLST, P146 gene sequencing and MLVA.

Genotyping and biofilm formation of Mycoplasma hyopneumoniae and their association with virulence

Yuzi Wu, Yanfei Yu, Lizhong Hua, Yanna Wei, Yuan Gan, Hafizah Yousuf Chenia, Yixuan Wang, Xing Xie, Jia Wang, Maojun Liu, Guoqing Shao, Qiyan Xiong & Zhixin Feng
Abstract Mycoplasma hyopneumoniae, the causative agent of swine respiratory disease, demonstrates differences in virulence. However, factors associated with this variation remain unknown. We herein evaluated the association between differences in virulence and genotypes as well as phenotype (i.e., biofilm formation ability). Strains 168 L, RM48, XLW-2, and J show low virulence and strains 232, 7448, 7422, 168, NJ, and LH show high virulence, as determined through animal challenge experiments, complemented with in vitro tracheal mucosa...

CTPS1 suppresses proliferation and migration in colorectal cancer cells

Fahong Wu, Yudong Mao, Tao Ma, Xiaoli Wang, Hangzhi Wei, Tianwei Wang, Jia Wang & Youcheng Zhang
Colorectal cancer (CRC) is now the third most prevalent tumor and one of the deadliest cancers worldwide, with an increasing prevalence every year. Therefore, we urgently need to understand the mechanisms regulating the progression of colorectal cancer and find potential diagnostic biomarkers. In this study, we performed an analysis using the TCGA and GEO databases to find a molecular biomarker for the diagnosis of CRC, namely CTPS1. The results of this analysis revealed that CTPS1...

CTPS1 inhibition suppresses proliferation and migration in colorectal cancer cells

Fahong Wu, Yudong Mao, Tao Ma, Xiaoli Wang, Hangzhi Wei, Tianwei Wang, Jia Wang & Youcheng Zhang
Colorectal cancer (CRC) is now the third most prevalent tumor and one of the deadliest cancers worldwide, with an increasing prevalence every year. Therefore, we urgently need to understand the mechanisms regulating the progression of colorectal cancer and find potential diagnostic biomarkers. In this study, we performed an analysis using the TCGA and GEO databases to find a molecular biomarker for the diagnosis of CRC, namely CTPS1. The results of this analysis revealed that CTPS1...

Data from: A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species

Armando Geraldes, Steve P. DiFazio, Gancho T. Slavov, Priya Ranjan, Wellington Muchero, Jan Hannemann, Lee E. Gunter, Ann M. Wymore, Christopher J. Grassa, Nima Farzaneh, Ilga Porth, Athena D. Mckown, Oleksandr Skyba, Eryang Li, Miki Fujita, Jaroslav Klápště, Joel Martin, Wendy Schackwitz, Christa Pennacchio, Daniel Rokhsar, Michael C. Friedmann, Geoffrey O. Wasteneys, Robert D. Guy, Yousry A. El-Kassaby, Shawn D. Mansfield … & Gerald A. Tuskan
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a...

Data from: Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies

Sagar M. Utturkar, Dawn M. Klingeman, José M. Bruno-Barcena, Mari S. Chinn, Amy M. Grunden, Michael Köpke & Steven D. Brown
During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig...

Data from: Dispersal, niche breadth, and population extinction/colonization ratios predict range size in North American dragonflies

Shannon J. McCauley, Christopher J. Davis, Earl E. Werner, & Michael S. Robeson
1. Species’ range sizes are shaped by fundamental differences in species’ ecological and evolutionary characteristics, and understanding the mechanisms determining range size can shed light on the factors responsible for generating and structuring biological diversity. Moreover, because geographic range size is associated with a species’ risk of extinction and their ability to respond to global changes in climate and land use, understanding these mechanisms has important conservation implications. 2. Despite hypotheses that dispersal behaviour is...

Data from: Interactions among roots, mycorrhizae and free-living microbial communities differentially impact soil carbon processes

Jessica A. M. Moore, Jiang Jiang, Courtney M. Patterson, Gangsheng Wang, Melanie A. Mayes & Aimée T. Classen
Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant–microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon...

Global biogeography of fungal and bacterial biomass carbon in topsoil

Liyuan He, Jorge Rodrigues, Nadejda Soudzilovskaia, Milagros Barceló, Pål Axel Olsson, Changchun Song, Leho Tedersoo, Fenghui Yuan, Fengming Yuan, David Lipson & Xiaofeng Xu
Bacteria and fungi, representing two major soil microorganism groups, play an important role in global nutrient biogeochemistry. Biogeographic patterns of bacterial and fungal biomass are of fundamental importance for mechanistically understanding nutrient cycling. We synthesized 1323 data points of phospholipid fatty acid-derived fungal biomass C (FBC), bacterial biomass C (BBC), and fungi:bacteria (F:B) ratio in topsoil, spanning 11 major biomes. The FBC, BBC, and F:B ratio display clear biogeographic patterns along latitude and environmental gradients...

A Possible Magnetic Structure of the Cluster-Based Haldane Compound Fedotovite K2Cu3O(SO4)3

Masashi Hase, Kirrily C. Rule, James R. Hester, Jaime A. Fernandez-Baca, Takatsugu Masuda & Yukari Matsuo
We carried out neutron powder diffraction experiments on the cluster-based Haldane compound fedotovite K2Cu3O(SO4)3. Weak magnetic reflections caused by a magnetic long-range order appeared below an antiferromagnetic transition temperature TN =3.1 K. We propose a possible magnetic structure that is consistent with the magnetic properties reported in the literature.

Additional file 1 of Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis

Zhangyang Xu, Bo Peng, Reta Birhanu Kitata, Carrie D. Nicora, Karl K. Weitz, Yunqiao Pu, Tujin Shi, John R. Cort, Arthur J. Ragauskas & Bin Yang
Additional file 1: Figure S1. The overall workflow for identifying bacterial lignin degradation pathways. Figure S2. GC–MS analysis of lignin breakdown products. Figure S3. Lignin breakdown products identified by GC–MS. Figure S4. The variation of peaks area of all lignin breakdown products. Figure S5. Main detected lignin linkages. Table S1. Occurrence of putative degradation products of lignin in different treatment conditions. Table S2. Grouped lignin breakdown products among all treatments. Table S3. Main lignin 2D...

Experimental evidence for the recovery of mercury-contaminated fish populations

Lee Hrenchuk, Paul Blanchfield, John Rudd, Marc Amyot, Christopher Babiarz, Ken Beaty, Drew Bodaly, Brian Branfireun, Cynthia Gilmour, Jennifer Graydon, Britt Hall, Reed Harris, Andrew Heyes, Holger Hintelmann, James Hurley, Carol Kelly, David Krabbenhoft, Steve Lindberg, Robert Mason, Michael Paterson, Cheryl Podemski, Ken Sandilands, George Southworth, Vincent St. Louis, Lori Tate … & Michael Tate
Anthropogenic releases of mercury (Hg) are a human health issue because the potent toxicant methylmercury (MeHg), formed primarily by microbial methylation of inorganic Hg in aquatic ecosystems, bioaccumulates to high concentrations in fish consumed by humans. Predicting the efficacy of Hg pollution controls on fish MeHg concentrations is complex because many factors influence the production and bioaccumulation of MeHg. Here we conducted a 15-year whole-ecosystem, single-factor experiment to determine the magnitude and timing of reductions...

Additional file 3 of Genotyping and biofilm formation of Mycoplasma hyopneumoniae and their association with virulence

Yuzi Wu, Yanfei Yu, Lizhong Hua, Yanna Wei, Yuan Gan, Hafizah Yousuf Chenia, Yixuan Wang, Xing Xie, Jia Wang, Maojun Liu, Guoqing Shao, Qiyan Xiong & Zhixin Feng
Additional file 3. Correction of virulence and results of the in vitro tracheal infection.

Quantum supremacy using a programmable superconducting processor

John M. Martinis, Sergio Boixo, Hartmut Neven, Frank Arute, Kunal Arya, Ryan Babbush, Dave Bacon, Joseph C. Bardin, Rami Barends, Rupak Biswas, Fernando G. S. L. Brandao, David A. Buell, Brian Burkett, Yu Chen, Zijun Chen, Ben Chiaro, Roberto Collins, William Courtney, Andrew Dunsworth, Edward Farhi, Brooks Foxen, Austin Fowler, Craig Gidney, Marissa Giustina, Rob Graff … & Adam Zalcman
The tantalizing promise of quantum computers is that certain computational tasks might be executed exponentially faster on a quantum processor than on a classical processor. A fundamental challenge is to build a high-fidelity processor capable of running quantum algorithms in an exponentially large computational space. Here, we report using a processor with programmable superconducting qubits to create quantum states on 53 qubits, corresponding to a computational state-space of dimension 2^53 ∼ 10^16. Measurements from repeated...

Data from: Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem

Allison M. Veach, James C. Stegen, Shawn P. Brown, Walter K. Dodds & Ari Jumpponen
Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third-order stream at Konza Prairie over a 2- to 64-day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations)...

Neutron study of the topological flux model of hydrogen ions in water ice

J.-U. Hoffmann, K. Siemensmeyer, S. Isakov, D. J. P. Morris, B. Klemke, I. Glavatskyi, K. Seiffert, D. A. Tennant, S. Sondhi & R. Moessner
The familiarity of water ice means we often overlook its non-trivial character illustrated, for example, by the many snowflake morphologies resulting from disordered combinations of covalent and hydrogen bonds between hydrogen and oxygen atoms in water ice’s most common phase (Ih) that keep the H_2 O molecular character. Using neutron diffraction on the flat-cone diffractometer E2 at BER-II, Helmholtz-Zentrum Berlin, we probe the atomic scale configuration in the Ih phase of water ice to test...

Registration Year

  • 2022
    39
  • 2021
    3
  • 2020
    5
  • 2019
    1
  • 2018
    4
  • 2017
    2
  • 2016
    1
  • 2015
    3
  • 2014
    2
  • 2013
    3

Resource Types

  • Dataset
    40
  • Text
    19
  • Collection
    6

Affiliations

  • Oak Ridge National Laboratory
    64
  • Zhejiang University
    33
  • Jiangsu Academy of Agricultural Sciences
    25
  • Jilin University
    25
  • Inner Mongolia Agricultural University
    25
  • Southwest University
    25
  • Sun Yat-sen University
    24
  • Peking University
    24
  • Second Hospital of Shanxi Medical University
    24
  • University of KwaZulu-Natal
    24