AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula

AbstractTrees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer new, elite varieties will benefit from an improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA Sequencing data spanning the secondary phloem, vascular cambium and wood forming tissues. The transcriptome comprised 28,294 expressed, previously annotated genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication were found to have diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. Co-expression network analysis revealed that the regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. The high spatial resolution enabled identification of novel roles for characterised genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the expression profiles and co-expression network.

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Carbon budget estimation of a subarctic catchment using a dynamic ecosystem model at high spatial resolution

Biogeosciences ◽

10.5194/bg-12-2791-2015 ◽

2015 ◽

Vol 12 (9) ◽

pp. 2791-2808 ◽

Cited By ~ 9

Author(s):

J. Tang ◽

P. A. Miller ◽

A. Persson ◽

D. Olefeldt ◽

P. Pilesjö ◽

...

Keyword(s):

Spatial Resolution ◽

Carbon Budget ◽

High Spatial Resolution ◽

Carbon Sink ◽

Carbon Fluxes ◽

Ecosystem Model ◽

Carbon Exchange ◽

Arctic Ecosystems ◽

Flux Dynamics ◽

Ecosystem Responses

Abstract. A large amount of organic carbon is stored in high-latitude soils. A substantial proportion of this carbon stock is vulnerable and may decompose rapidly due to temperature increases that are already greater than the global average. It is therefore crucial to quantify and understand carbon exchange between the atmosphere and subarctic/arctic ecosystems. In this paper, we combine an Arctic-enabled version of the process-based dynamic ecosystem model, LPJ-GUESS (version LPJG-WHyMe-TFM) with comprehensive observations of terrestrial and aquatic carbon fluxes to simulate long-term carbon exchange in a subarctic catchment at 50 m resolution. Integrating the observed carbon fluxes from aquatic systems with the modeled terrestrial carbon fluxes across the whole catchment, we estimate that the area is a carbon sink at present and will become an even stronger carbon sink by 2080, which is mainly a result of a projected densification of birch forest and its encroachment into tundra heath. However, the magnitudes of the modeled sinks are very dependent on future atmospheric CO2 concentrations. Furthermore, comparisons of global warming potentials between two simulations with and without CO2 increase since 1960 reveal that the increased methane emission from the peatland could double the warming effects of the whole catchment by 2080 in the absence of CO2 fertilization of the vegetation. This is the first process-based model study of the temporal evolution of a catchment-level carbon budget at high spatial resolution, including both terrestrial and aquatic carbon. Though this study also highlights some limitations in modeling subarctic ecosystem responses to climate change, such as aquatic system flux dynamics, nutrient limitation, herbivory and other disturbances, and peatland expansion, our study provides one process-based approach to resolve the complexity of carbon cycling in subarctic ecosystems while simultaneously pointing out the key model developments for capturing complex subarctic processes.

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Tissue-specific transcriptome profiling of the Arabidopsis thaliana inflorescence stem reveals local cellular signatures

10.1101/2020.02.10.941492 ◽

2020 ◽

Author(s):

Dongbo Shi ◽

Virginie Jouannet ◽

Javier Agustí ◽

Verena Kaul ◽

Victor Levitsky ◽

...

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Spatial Resolution ◽

High Spatial Resolution ◽

Expression Profiles ◽

Differentially Expressed ◽

Tissue Specific ◽

Inflorescence Stem ◽

Genome Wide ◽

A Genome

AbstractGenome-wide gene expression maps with a high spatial resolution have substantially accelerated molecular plant science. However, the number of characterized tissues and growth stages is still small because of the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next generation RNA sequencing, we characterize transcriptomes of xylem vessels, fibers, the proximal and the distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classify more than 15,000 genes as being differentially expressed among different stem tissues and reveal known and novel tissue-specific cellular signatures. By determining transcription factor binding regions enriched in promoter regions of differentially expressed genes, we furthermore provide candidates for tissue-specific transcriptional regulators. Our datasets predict expression profiles of an exceptional amount of genes and allow generating hypotheses toward the spatial organization of physiological processes. Moreover, we demonstrate that information on gene expression in a broad range of mature plant tissues can be established with high spatial resolution by nuclear mRNA profiling.One sentence summaryA genome-wide high-resolution gene expression map of the Arabidopsis inflorescence stem is established.

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miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data

Cells ◽

10.3390/cells9081752 ◽

2020 ◽

Vol 9 (8) ◽

pp. 1752

Author(s):

Luiz Augusto Bovolenta ◽

Danillo Pinhal ◽

Marcio Luis Acencio ◽

Arthur Casulli de Oliveira ◽

Simon Moxon ◽

...

Keyword(s):

Nile Tilapia ◽

Developmental Stages ◽

Expression Profiles ◽

Interaction Network ◽

Mature Mirnas ◽

Next Generation Sequencing Data ◽

Sequencing Data ◽

Genomic Context ◽

Protein Coding ◽

Post Transcriptional Regulation

Nile tilapia is the third most cultivated fish worldwide and a novel model species for evolutionary studies. Aiming to improve productivity and contribute to the selection of traits of economic impact, biotechnological approaches have been intensively applied to species enhancement. In this sense, recent studies have focused on the multiple roles played by microRNAs (miRNAs) in the post-transcriptional regulation of protein-coding genes involved in the emergence of phenotypes with relevance for aquaculture. However, there is still a growing demand for a reference resource dedicated to integrating Nile Tilapia miRNA information, obtained from both experimental and in silico approaches, and facilitating the analysis and interpretation of RNA sequencing data. Here, we present an open repository dedicated to Nile Tilapia miRNAs: the “miRTil database”. The database stores data on 734 mature miRNAs identified in 11 distinct tissues and five key developmental stages. The database provides detailed information about miRNA structure, genomic context, predicted targets, expression profiles, and relative 5p/3p arm usage. Additionally, miRTil also includes a comprehensive pre-computed miRNA-target interaction network containing 4936 targets and 19,580 interactions.

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Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence

TURKISH JOURNAL OF BIOLOGY ◽

10.3906/biy-2005-21 ◽

2020 ◽

Vol 44 (6) ◽

pp. 356-370

Author(s):

Gökhan KARAKÜLAH ◽

Cihangir YANDIM

Keyword(s):

Cellular Senescence ◽

Noncoding Rna ◽

Expression Profiles ◽

Experimental Studies ◽

Gene Expression Profiles ◽

Sequencing Data ◽

Protein Coding ◽

Repeat Elements ◽

Inflammatory Phenotype ◽

New Perspective

Replicative cellular senescence is the main cause of aging. It is important to note that early senescence is linked to tissue regeneration, whereas late senescence is known to trigger a chronically inflammatory phenotype. Despite the presence of various genome-wide studies, there is a lack of information on distinguishing early and late senescent phenotypes at the transcriptome level. Particularly, the changes in the noncoding RNA portion of the aging cell have not been fully elucidated. By utilising RNA sequencing data of fibroblasts, hereby, we are not only reporting changes in gene expression profiles and relevant biological processes in the early and late senescent phenotypes but also presenting significant differences in the expressions of many unravelled long noncoding RNAs (lncRNAs) and transcripts arisen from repetitive DNA. Our results indicate that, in addition to previously reported L1 elements, various LTR and DNA transposons, as well as members of the classical satellites including HSAT5 and α-satellites (ALR/Alpha), are expressed at higher levels in late senescence. Moreover, we revealed finer links between the expression levels of repeats with the genes located near them and known to be involved in cell cycle and senescence. Noncoding elements reported here provide a new perspective to be explored in further experimental studies.

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Carbon budget estimation of a subarctic catchment using a dynamic ecosystem model at high spatial resolution

Biogeosciences Discussions ◽

10.5194/bgd-12-933-2015 ◽

2015 ◽

Vol 12 (2) ◽

pp. 933-980 ◽

Cited By ~ 2

Author(s):

J. Tang ◽

P. A. Miller ◽

A. Persson ◽

D. Olefeldt ◽

P. Pilesjö ◽

...

Keyword(s):

Spatial Resolution ◽

Carbon Budget ◽

High Spatial Resolution ◽

Carbon Sink ◽

Carbon Fluxes ◽

Ecosystem Model ◽

Birch Forest ◽

Co2 Uptake ◽

Carbon Exchange ◽

Flux Dynamics

Abstract. Large amount of organic carbon is stored in high latitude soils. A substantial proportion of this carbon stock is vulnerable and may decompose rapidly due to temperature increases that are already greater than the global average. It is therefore crucial to quantify and understand carbon exchange between the atmosphere and subarctic/arctic ecosystems. In this paper, we combine an arctic-enabled version of the process-based dynamic ecosystem model, LPJ-GUESS (version LPJG-WHyMe-TFM) with comprehensive observations of terrestrial and aquatic carbon fluxes to simulate long-term carbon exchange in a subarctic catchment comprising both mineral and peatland soils. The model is applied at 50 m resolution and is shown to be able to capture the seasonality and magnitudes of observed fluxes at this fine scale. The modelled magnitudes of CO2 uptake generally follow the descending sequence: birch forest, non-permafrost Eriophorum, Sphagnum and then tundra heath during the observation periods. The catchment-level carbon fluxes from aquatic systems are dominated by CO2 emissions from streams. Integrated across the whole catchment, we estimate that the area is a carbon sink at present, and will become an even stronger carbon sink by 2080, which is mainly a result of a projected densification of birch forest and its encroachment into tundra heath. However, the magnitudes of the modelled sinks are very dependent on future atmospheric CO2 concentrations. Furthermore, comparisons of global warming potentials between two simulations with and without CO2 increase since 1960 reveal that the increased methane emission from the peatland could double the warming effects of the whole catchment by 2080 in the absence of CO2 fertilization of the vegetation. This is the first process-based model study of the temporal evolution of a catchment-level carbon budget at high spatial resolution, integrating comprehensive and diverse fluxes including both terrestrial and aquatic carbon. Though this study also highlights some limitations in modelling subarctic ecosystem responses to climate change including aquatic system flux dynamics, nutrient limitation, herbivory and other disturbances and peatland expansion, our application provides a mechanism to resolve the complexity of carbon cycling in subarctic ecosystems while simultaneously pointing out the key model developments for capturing complex subarctic processes.

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AspWood: High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula

The Plant Cell ◽

10.1105/tpc.17.00153 ◽

2017 ◽

Vol 29 (7) ◽

pp. 1585-1604 ◽

Cited By ~ 75

Author(s):

David Sundell ◽

Nathaniel R. Street ◽

Manoj Kumar ◽

Ewa J. Mellerowicz ◽

Melis Kucukoglu ◽

...

Keyword(s):

Spatial Resolution ◽

High Spatial Resolution ◽

Wood Formation ◽

Populus Tremula

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High spatial resolution AEM observations of yttrium segregation in chromia scales grown on Co-45%Cr

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100144103 ◽

1986 ◽

Vol 44 ◽

pp. 518-519

Author(s):

K. Przybylski ◽

A. J. Garratt-Reed ◽

G. J. Yurek

Keyword(s):

Spatial Resolution ◽

Outer Surface ◽

Maximum Concentration ◽

High Spatial Resolution ◽

Reactive Elements ◽

Chromia Scales

The addition of so-called “reactive” elements such as yttrium to alloys is known to enhance the protective nature of Cr2O3 or Al2O3 scales. However, the mechanism by which this enhancement is achieved remains unclear. An A.E.M. study has been performed of scales grown at 1000°C for 25 hr. in pure O2 on Co-45%Cr implanted at 70 keV with 2x1016 atoms/cm2 of yttrium. In the unoxidized alloys it was calculated that the maximum concentration of Y was 13.9 wt% at a depth of about 17 nm. SIMS results showed that in the scale the yttrium remained near the outer surface.

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Integration of Core-Edge Spectroscopy Methods for the Study of Polymers

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010016323x ◽

1996 ◽

Vol 54 ◽

pp. 154-155

Author(s):

E. G. Rightor

Keyword(s):

Excited State ◽

Polymer Blends ◽

Gas Phase ◽

Spatial Resolution ◽

High Spatial Resolution ◽

Electronic States ◽

Core Electron ◽

Bulk Solids ◽

Development Application

Core edge spectroscopy methods are versatile tools for investigating a wide variety of materials. They can be used to probe the electronic states of materials in bulk solids, on surfaces, or in the gas phase. This family of methods involves promoting an inner shell (core) electron to an excited state and recording either the primary excitation or secondary decay of the excited state. The techniques are complimentary and have different strengths and limitations for studying challenging aspects of materials. The need to identify components in polymers or polymer blends at high spatial resolution has driven development, application, and integration of results from several of these methods.

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