cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p98uqllw
title: Survival and viral load of chinook salmon, sockeye salmon, and steelhead trout exposed to 4 genogroups of infectious hematopoietic necrosis virus (IHNV)

description: Theory of the evolution of pathogen specialization suggests that a specialist pathogen gains high fitness in one host, but this comes with fitness loss in other hosts. By contrast, a generalist pathogen does not achieve high fitness in any host, but gains ecological fitness by exploiting different hosts, and has higher fitness than specialists in non-specialized hosts. As a result, specialist pathogens are predicted to have greater variation in fitness across hosts, and generalists would have lower fitness variation across hosts. We test these hypotheses by measuring pathogen replicative fitness as within-host viral loads from the onset of infection to the beginning of virus clearance, using the rhabdovirus infectious hematopoietic necrosis virus (IHNV) in salmonid fish. Based on field prevalence and virulence studies, IHNV subgroups UP, MD, and L are specialists, causing infection and mortality in sockeye salmon, steelhead, and Chinook salmon juveniles, respectively. The UC subgroup evolved naturally from a UP ancestor and is a generalist infecting all three host species but without causing severe disease. We show that specialist subgroups had highest peak and mean viral loads in the hosts in which they are specialized, and they had low viral loads in non-specialized hosts, resulting in large variation in viral load across hosts. Viral kinetics show that the mechanisms of specialization involve both the ability to maximize early virus replication and to avoid clearance at later times, with different mechanisms of specialization evident in different host-virus combinations. Additional nuances in the data included different fitness levels for non-specialist interactions, reflecting different trade-offs for specialist viruses in other hosts. The generalist UC subgroup reached intermediate viral loads in all hosts and showed the smallest variation in fitness across hosts. Evolution of the UC generalist from an ancestral UP sockeye specialist was associated with fitness increases in steelhead and Chinook salmon, but only slight decrease in fitness in sockeye salmon, consistent with low- or no-cost generalism. Our results support major elements of specialist-generalist theory, providing evidence of a specialist-generalist continuum in a vertebrate pathogen. These results also quantify within-host replicative fitness tradeoffs resulting from the natural evolution of specialist and generalist virus lineages in multi-host ecosystems.
DOI: 10.5517/ccdc.csd.cc206zrz
title: CCDC 1853761: Experimental Crystal Structure Determination

description: Related Article: Mathato P. Motaung, Jerry O. Adeyemi, Youssef Ben Smida, Hela Ferjani, Mwadham M. Kabanda, Damian C. Onwudiwe, Eric Hosten|2023|J.Mol.Struct.|1271|133988|doi:10.1016/j.molstruc.2022.133988
description: Related Article: Charmaine Arderne, Damian Onwudiwe, Mathatho Motaung|2019|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bmvrl
title: CCDC 2164040: Experimental Crystal Structure Determination

description: Related Article: Ziwei Yu, Shiqi Cao, Yingjie Zhao, Yangwu Guo, Meiqiu Dong, Yue Fu, Jinjin Zhao, Jingrun Yang, Lei Jiang, Yuchen Wu|2022|ACS Applied Materials and Interfaces|14|39451|doi:10.1021/acsami.2c06856
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6069/2r4h-rm14
title: Reduction of MRM protein target list using correlation analysis

description: High mass resolution mass spectrometry provides hundreds to thousands of protein identifications per sample, and quantification is typically performed using label-free quantification. However, the gold standard of quantitative proteomics is multiple reaction monitoring (MRM) using triple quadrupole mass spectrometers and stable isotope reference peptides. This raises the question how to reduce a large data set to a small one without losing essential information. Here we present the reduction of such a data set using correlation analysis of bovine dairy ingredients and derived products. We were able to explain the variance in the proteomics data set using only 9 proteins across all major dairy protein classes: caseins, whey, and milk fat globule membrane proteins. We term this method Trinity-MRM. The reproducibility of the protein extraction and Trinity-MRM methods was shown to be below 5% in independent experiments (multi-day single-user and single-day multi-user) using double cream. Further application of this reductionist approach might include screening of large sample cohorts for biologically interesting samples before analysis by high-resolution mass spectrometry or other omics methodologies.
DOI: 10.20375/0000-000f-73bb-d
title: DocuDataCollection.pdf
DOI: 10.20375/0000-000f-73bc-c
title: original-data.sav
DOI: 10.20375/0000-000f-73bd-b
title: original-data.xlsx
DOI: 10.48320/046fbb44-87c4-41a6-9d99-e33636d19e02
title: Navalny and „smart voting“ in the perception of the Russian population (Public Opinion Polls by the Levada Center)
DOI: 10.6084/m9.figshare.17048165
title: Changes in gene expression levels and chloroplast anatomy induced by <i>Leifsonia xyli</i> subsp. <i>xyli</i> in sugarcane

description: Ratoon stunt caused by <i>Leifsonia xyli</i> subsp. <i>xyli</i> (<i>Lxx</i>) is widely spread across sugarcane planting regions. Here, transcriptomics and cytology were conducted to analyze the changes in gene expression levels and chloroplast ultrastructures after <i>Lxx</i> inoculation. A total of 90.26 Gb clean bases, 156,713 unigenes and 406 differentially expressed genes were obtained. The genes of <i>HSP</i> and <i>ACS</i> were continuously differentially expressed. The photosynthesis-related genes of <i>PsbO</i>, <i>PsbQ</i>, <i>PsaD</i>, <i>PsaE</i>, <i>PsaG</i> and <i>PsaH</i> were up-regulated. <i>PIRH2</i>, <i>WRKY</i>, <i>NCED</i>, <i>AHP</i> and <i>GST</i> were identified as the important specific genes that responded to <i>Lxx</i> inoculation. <i>Lxx</i> inoculation also altered the shape and damaged the membrane of chloroplasts in sugarcane leaves. Sugarcane responds to <i>Lxx</i> infection likely via changing the expression levels of some specific genes and interfered with photosynthesis. A possible molecular regulation network induced by <i>Lxx</i> was speculated. These findings broaden the understanding to the mechanisms of the interaction between sugarcane and <i>Lxx</i>.
DOI: 10.6084/m9.figshare.17048165.v1
title: Changes in gene expression levels and chloroplast anatomy induced by <i>Leifsonia xyli</i> subsp. <i>xyli</i> in sugarcane

description: Ratoon stunt caused by <i>Leifsonia xyli</i> subsp. <i>xyli</i> (<i>Lxx</i>) is widely spread across sugarcane planting regions. Here, transcriptomics and cytology were conducted to analyze the changes in gene expression levels and chloroplast ultrastructures after <i>Lxx</i> inoculation. A total of 90.26 Gb clean bases, 156,713 unigenes and 406 differentially expressed genes were obtained. The genes of <i>HSP</i> and <i>ACS</i> were continuously differentially expressed. The photosynthesis-related genes of <i>PsbO</i>, <i>PsbQ</i>, <i>PsaD</i>, <i>PsaE</i>, <i>PsaG</i> and <i>PsaH</i> were up-regulated. <i>PIRH2</i>, <i>WRKY</i>, <i>NCED</i>, <i>AHP</i> and <i>GST</i> were identified as the important specific genes that responded to <i>Lxx</i> inoculation. <i>Lxx</i> inoculation also altered the shape and damaged the membrane of chloroplasts in sugarcane leaves. Sugarcane responds to <i>Lxx</i> infection likely via changing the expression levels of some specific genes and interfered with photosynthesis. A possible molecular regulation network induced by <i>Lxx</i> was speculated. These findings broaden the understanding to the mechanisms of the interaction between sugarcane and <i>Lxx</i>.
DOI: 10.6084/m9.figshare.17005145
title: Advances in the elucidation of nuclear proteins in the model plant <i>Arabidopsis thaliana</i>: based on protein interactions and bioinformatics analysis

description: Plant protein–protein interaction (PPI) networks provide valuable information for the understanding of plant biological processes. In this study, we summarized and constructed the nuclear-protein interactome of <i>Arabidopsis</i> based on PPIs, and preliminarily analyzed the relationships among the main pathways involving these protein interactions. These proteins are involved mainly in the plant hormone signal transduction and plant-pathogen interaction, and these pathways are linked closely by co-pathway and nodal proteins. The key nodal proteins play important roles in communication among hormonal pathways. Further analysis revealed that all of these key nodal proteins were localized in multiple organelles. High-frequency protein multi-localization analysis suggested that the multi-location proteins may play key roles in organelle communication and plant growth. Thus, the screening and study of multi-location proteins may be an important research direction. Our findings can inform new research based on protein interactions and provide novel directions for plant proteome research.
DOI: 10.6084/m9.figshare.17005145.v1
title: Advances in the elucidation of nuclear proteins in the model plant <i>Arabidopsis thaliana</i>: based on protein interactions and bioinformatics analysis

description: Plant protein–protein interaction (PPI) networks provide valuable information for the understanding of plant biological processes. In this study, we summarized and constructed the nuclear-protein interactome of <i>Arabidopsis</i> based on PPIs, and preliminarily analyzed the relationships among the main pathways involving these protein interactions. These proteins are involved mainly in the plant hormone signal transduction and plant-pathogen interaction, and these pathways are linked closely by co-pathway and nodal proteins. The key nodal proteins play important roles in communication among hormonal pathways. Further analysis revealed that all of these key nodal proteins were localized in multiple organelles. High-frequency protein multi-localization analysis suggested that the multi-location proteins may play key roles in organelle communication and plant growth. Thus, the screening and study of multi-location proteins may be an important research direction. Our findings can inform new research based on protein interactions and provide novel directions for plant proteome research.
DOI: 10.6084/m9.figshare.15168888
title: Foliar application of liquiritin protects Chinese flowering cabbage against cucumber mosaic virus and increases health-promoting compounds

description: Decades of research have revealed notable similarities between the immune systems of the plant and animal kingdoms. Liquiritin has long been used to stimulate the body immunity in animals against an array of diseases. Considering the homology of some induced immune responses between animals and plants, we examined the effects of exogenously applied liquiritin to stimulate defense responses in Chinese flowering cabbage plants against cucumber mosaic virus (CMV) infection under greenhouse and field conditions. Foliar application of liquiritin (200 ppm) effectively suppressed the development of CMV symptoms by not less than 40% compared with the control in cabbage plants in both greenhouse and field trials along with the significant increases in the marketable yield and nutritional quality of cabbage. Liquiritin application enhanced the production of phenolic compounds and different defense-related enzymes in treated plants. Moreover, quantitative real-time PCR analysis revealed that liquiritin significantly up-regulated the expression of different defense-related genes upon pathogen inoculation, indicating an induction of the salicylic acid-mediated defense system. Collectively, the findings of this study indicate that liquiritin can effectively control CMV in cabbage plants.
DOI: 10.6084/m9.figshare.15168888.v1
title: Foliar application of liquiritin protects Chinese flowering cabbage against cucumber mosaic virus and increases health-promoting compounds

description: Decades of research have revealed notable similarities between the immune systems of the plant and animal kingdoms. Liquiritin has long been used to stimulate the body immunity in animals against an array of diseases. Considering the homology of some induced immune responses between animals and plants, we examined the effects of exogenously applied liquiritin to stimulate defense responses in Chinese flowering cabbage plants against cucumber mosaic virus (CMV) infection under greenhouse and field conditions. Foliar application of liquiritin (200 ppm) effectively suppressed the development of CMV symptoms by not less than 40% compared with the control in cabbage plants in both greenhouse and field trials along with the significant increases in the marketable yield and nutritional quality of cabbage. Liquiritin application enhanced the production of phenolic compounds and different defense-related enzymes in treated plants. Moreover, quantitative real-time PCR analysis revealed that liquiritin significantly up-regulated the expression of different defense-related genes upon pathogen inoculation, indicating an induction of the salicylic acid-mediated defense system. Collectively, the findings of this study indicate that liquiritin can effectively control CMV in cabbage plants.
DOI: 10.6084/m9.figshare.16636309
title: Transcriptional regulation of plant sugar transporter genes by beneficial rhizobacteria

description: In their natural environment, plants live in close interaction with complex populations of microorganisms, including rhizobacteria species commonly referred to as ‘Plant Growth Promoting Rhizobacteria’ (PGPR). A growing body of evidence demonstrates the importance of sugar transport in plant pathogen resistance and in plant-microorganism mutualistic symbioses. Using an <i>in vitro</i> experimental system, including the model plant species <i>Arabidopsis thaliana</i>, two PGPR strains (<i>Pseudomonas simiae</i> PICF7 and <i>Burkholderia phytofirmans</i> PsJN) and a non-PGPR strain (<i>Escherichia coli</i>), we conducted a comprehensive set of phenotypic and gene expression analyses to explore the role and regulation of sugar transporter genes in plant-PGPR interactions. In physical contact with the seedling roots, or solely <i>via</i> the emission of bacterial volatile compounds, the two PGPR strains tested improved the growth and development of the Arabidopsis seedlings and altered the expression of several plant sugar transporter genes. Our results also revealed both conserved and strain-specific transcriptional regulation mechanisms.
DOI: 10.6084/m9.figshare.16636309.v1
title: Transcriptional regulation of plant sugar transporter genes by beneficial rhizobacteria

description: In their natural environment, plants live in close interaction with complex populations of microorganisms, including rhizobacteria species commonly referred to as ‘Plant Growth Promoting Rhizobacteria’ (PGPR). A growing body of evidence demonstrates the importance of sugar transport in plant pathogen resistance and in plant-microorganism mutualistic symbioses. Using an <i>in vitro</i> experimental system, including the model plant species <i>Arabidopsis thaliana</i>, two PGPR strains (<i>Pseudomonas simiae</i> PICF7 and <i>Burkholderia phytofirmans</i> PsJN) and a non-PGPR strain (<i>Escherichia coli</i>), we conducted a comprehensive set of phenotypic and gene expression analyses to explore the role and regulation of sugar transporter genes in plant-PGPR interactions. In physical contact with the seedling roots, or solely <i>via</i> the emission of bacterial volatile compounds, the two PGPR strains tested improved the growth and development of the Arabidopsis seedlings and altered the expression of several plant sugar transporter genes. Our results also revealed both conserved and strain-specific transcriptional regulation mechanisms.
DOI: 10.6084/m9.figshare.14169400
title: The cyanobacterium, <i>Nostoc punctiforme</i> can protect against programmed cell death and induce defence genes in <i>Arabidopsis thaliana</i>

description: Cyanobacteria can form nitrogen-fixing symbioses with a broad range of plant species. Unlike other plant-bacteria symbioses, little is understood about the immunological responses induced by plant cyanobionts (symbiotic cyanobacteria). Here, we demonstrated that the model plant-symbiotic cyanobacteria, <i>Nostoc punctiforme</i> is capable of protecting against programmed cell death (PCD) when induced in <i>Arabidopsis thaliana</i> suspension cell cultures. We also profiled the early transcriptomic changes that were induced in response to conditioned medium (CM) from <i>N. punctiforme</i> cell cultures. Interestingly, the reduction in PCD was preceded by the induction of genes associated with defence and immunity, the most striking of which were a number of WRKY-family transcription factors. Down-regulated genes included those involved in the regulation of cell growth and differentiation. This work is the first to show that a cyanobiont can affect plant PCD and provides a useful transcriptome resource for studying early plant cell responses to symbiotic cyanobacteria.
DOI: 10.6084/m9.figshare.14637801
title: Two cerato-platanin proteins FocCP1 interact with MaPR1 and contribute to virulence of <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> to banana

description: <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> tropical race 4 (Foc TR4) causes destructive wilt disease to banana cultivation. However, knowledge of mechanisms in virulence regulation of Foc TR4 is still inadequate. In our previous work, two hypothetical FocCP1 proteins that belong to the cerato-platanin (CP) family were identified in the secretome of Foc TR4. In the present study, knock-out mutants of two FocCP1 were constructed and functions of two proteins were investigated. The results showed that the two FocCP1 play important roles in regulation of full virulence but are not required for vegetative growth or conidiation of the pathogen; besides, there is a functional redundancy between the two FocCP1. Moreover, we found that FocCP1 proteins interact with MaPR1 proteins through yeast two-hybrid and BiFC test. Our results suggest that FocCP1 proteins are important for the virulence of Foc TR4 and might inhibit the antifungal activity of MaPR1 by directly interacting with them.
DOI: 10.6084/m9.figshare.14637801.v1
title: Two cerato-platanin proteins FocCP1 interact with MaPR1 and contribute to virulence of <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> to banana

description: <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> tropical race 4 (Foc TR4) causes destructive wilt disease to banana cultivation. However, knowledge of mechanisms in virulence regulation of Foc TR4 is still inadequate. In our previous work, two hypothetical FocCP1 proteins that belong to the cerato-platanin (CP) family were identified in the secretome of Foc TR4. In the present study, knock-out mutants of two FocCP1 were constructed and functions of two proteins were investigated. The results showed that the two FocCP1 play important roles in regulation of full virulence but are not required for vegetative growth or conidiation of the pathogen; besides, there is a functional redundancy between the two FocCP1. Moreover, we found that FocCP1 proteins interact with MaPR1 proteins through yeast two-hybrid and BiFC test. Our results suggest that FocCP1 proteins are important for the virulence of Foc TR4 and might inhibit the antifungal activity of MaPR1 by directly interacting with them.
DOI: 10.5281/zenodo.7053167
title: camelyon_flamby

description: Features for 4 slides of the Camelyon dataset, produced as described by the FLamby project: https://github.com/owkin/FLamby/tree/1e8023c05814852c23c0b2acb10abba0f7c2c4ee/flamby/datasets/fed_camelyon16
DOI: 10.6084/m9.figshare.14169400.v1
title: The cyanobacterium, <i>Nostoc punctiforme</i> can protect against programmed cell death and induce defence genes in <i>Arabidopsis thaliana</i>

description: Cyanobacteria can form nitrogen-fixing symbioses with a broad range of plant species. Unlike other plant-bacteria symbioses, little is understood about the immunological responses induced by plant cyanobionts (symbiotic cyanobacteria). Here, we demonstrated that the model plant-symbiotic cyanobacteria, <i>Nostoc punctiforme</i> is capable of protecting against programmed cell death (PCD) when induced in <i>Arabidopsis thaliana</i> suspension cell cultures. We also profiled the early transcriptomic changes that were induced in response to conditioned medium (CM) from <i>N. punctiforme</i> cell cultures. Interestingly, the reduction in PCD was preceded by the induction of genes associated with defence and immunity, the most striking of which were a number of WRKY-family transcription factors. Down-regulated genes included those involved in the regulation of cell growth and differentiation. This work is the first to show that a cyanobiont can affect plant PCD and provides a useful transcriptome resource for studying early plant cell responses to symbiotic cyanobacteria.
DOI: 10.6084/m9.figshare.14528433
title: Flower and pod genes involved in soybean sensitivity to drought

description: In soybean, studies on drought-responses are conducted during vegetative season. Information related to genes triggered in response to water-deficit (WD) in flower and pod is lacking. We performed an RNASeq and an agro-physiological characterization at stages R2 and R4 of soybean cultivar BR16, under WD. Physiological results showed a decrease in gas exchange parameters. Agronomical results showed WD impaired yield. Global Gene Ontology analyses indicated that most of the Differential Expressed Genes (DEGs) were down-regulated in flowers but up-regulated in pods. qRT-PCR revealed that WD triggered hormone biosynthesis changes. Mechanisms such as a decrease in glyceollin levels and cell wall instability were observed. This data showed tissue-specific mechanisms correlated with phenotypic responses such as drought escape, early flowering hormone-induced, and loss in grain weight. We presented here a comprehensive expression profile of flowers and pods soybean genes, which could guide researchers in the development of plants more tolerant to drought.
DOI: 10.6084/m9.figshare.14528433.v1
title: Flower and pod genes involved in soybean sensitivity to drought

description: In soybean, studies on drought-responses are conducted during vegetative season. Information related to genes triggered in response to water-deficit (WD) in flower and pod is lacking. We performed an RNASeq and an agro-physiological characterization at stages R2 and R4 of soybean cultivar BR16, under WD. Physiological results showed a decrease in gas exchange parameters. Agronomical results showed WD impaired yield. Global Gene Ontology analyses indicated that most of the Differential Expressed Genes (DEGs) were down-regulated in flowers but up-regulated in pods. qRT-PCR revealed that WD triggered hormone biosynthesis changes. Mechanisms such as a decrease in glyceollin levels and cell wall instability were observed. This data showed tissue-specific mechanisms correlated with phenotypic responses such as drought escape, early flowering hormone-induced, and loss in grain weight. We presented here a comprehensive expression profile of flowers and pods soybean genes, which could guide researchers in the development of plants more tolerant to drought.