GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties such as soil moisture with root traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.

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GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems

eLife ◽

10.7554/elife.07597 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 109

Author(s):

Rubén Rellán-Álvarez ◽

Guillaume Lobet ◽

Heike Lindner ◽

Pierre-Luc Pradier ◽

Jose Sebastian ◽

...

Keyword(s):

Gene Expression ◽

Imaging System ◽

Expression Patterns ◽

Local Environment ◽

Root Systems ◽

Root System Architecture ◽

Spatial Integration ◽

Adaptive Responses ◽

Physiological Relevance ◽

Great Utility

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.

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Morpho-molecular ex vivo detection and grading of non-muscle-invasive bladder cancer using forward imaging probe based multimodal optical coherence tomography and Raman spectroscopy

The Analyst ◽

10.1039/c9an01911a ◽

2020 ◽

Vol 145 (4) ◽

pp. 1445-1456 ◽

Cited By ~ 1

Author(s):

Fabian Placzek ◽

Eliana Cordero Bautista ◽

Simon Kretschmer ◽

Lara M. Wurster ◽

Florian Knorr ◽

...

Keyword(s):

Raman Spectroscopy ◽

Optical Coherence Tomography ◽

Imaging System ◽

Ex Vivo ◽

Large Field ◽

Optical Coherence ◽

Fiber Optic Probe ◽

Optic Probe ◽

Muscle Invasive

Characterization of bladder biopsies, using a combined fiber optic probe-based optical coherence tomography and Raman spectroscopy imaging system that allows a large field-of-view imaging and detection and grading of cancerous bladder lesions.

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Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

Microorganisms ◽

10.3390/microorganisms9040749 ◽

2021 ◽

Vol 9 (4) ◽

pp. 749

Author(s):

Gülbahar Abaramak ◽

Jaime Ricardo Porras-Domínguez ◽

Henry Christopher Janse van Rensburg ◽

Eveline Lescrinier ◽

Ebru Toksoy Öner ◽

...

Keyword(s):

Molecular Characterization ◽

Phylogenetic Analyses ◽

Halophilic Archaea ◽

Maximum Activity ◽

Physiological Relevance ◽

Health Related ◽

Specific Alternative ◽

Binding Groove ◽

Native Host

Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.

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Characterization of the SIRT genes and their distinct expression patterns in Manila clams (Ruditapes philippinarum) exposed to air

Meta Gene ◽

10.1016/j.mgene.2021.100892 ◽

2021 ◽

Vol 28 ◽

pp. 100892

Author(s):

Jingtian Wang ◽

He Zhang ◽

Shuang Xu ◽

Ze Liu ◽

Lu Yang ◽

...

Keyword(s):

Expression Patterns ◽

Ruditapes Philippinarum

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Identification and Characterization of Abiotic Stress Responsive CBL-CIPK Family Genes in Medicago

International Journal of Molecular Sciences ◽

10.3390/ijms22094634 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4634

Author(s):

Wenxuan Du ◽

Junfeng Yang ◽

Lin Ma ◽

Qian Su ◽

Yongzhen Pang

Keyword(s):

Abiotic Stress ◽

Abiotic Stresses ◽

Expression Patterns ◽

Interacting Protein ◽

Forage Crop ◽

Cis Acting ◽

Protein Motifs ◽

Plant Signal Transduction ◽

Identification And Characterization

The calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) play important roles in plant signal transduction and response to abiotic stress. Plants of Medicago genus contain many important forages, and their growth is often affected by a variety of abiotic stresses. However, studies on the CBL and CIPK family member and their function are rare in Medicago. In this study, a total of 23 CBL and 58 CIPK genes were identified from the genome of Medicago sativa as an important forage crop, and Medicaog truncatula as the model plant. Phylogenetic analysis suggested that these CBL and CIPK genes could be classified into five and seven groups, respectively. Moreover, these genes/proteins showed diverse exon-intron organizations, architectures of conserved protein motifs. Many stress-related cis-acting elements were found in their promoter region. In addition, transcriptional analyses showed that these CBL and CIPK genes exhibited distinct expression patterns in various tissues, and in response to drought, salt, and abscisic acid treatments. In particular, the expression levels of MtCIPK2 (MsCIPK3), MtCIPK17 (MsCIPK11), and MtCIPK18 (MsCIPK12) were significantly increased under PEG, NaCl, and ABA treatments. Collectively, our study suggested that CBL and CIPK genes play crucial roles in response to various abiotic stresses in Medicago.

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Size-based characterization of adalimumab and TNF-α interactions using flow induced dispersion analysis: assessment of avidity-stabilized multiple bound species

Scientific Reports ◽

10.1038/s41598-021-84113-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Morten E. Pedersen ◽

Ragna M. S. Haegebaert ◽

Jesper Østergaard ◽

Henrik Jensen

Keyword(s):

Protein Interactions ◽

Free Ligand ◽

Local Environment ◽

Dispersion Analysis ◽

Surface Immobilization ◽

Covalent Bonds ◽

Essential Information ◽

Tnf Α

AbstractThe understanding and characterization of protein interactions is crucial for elucidation of complicated biomolecular processes as well as for the development of new biopharmaceutical therapies. Often, protein interactions involve multiple binding, avidity, oligomerization, and are dependent on the local environment. Current analytical methodologies are unable to provide a detailed mechanistic characterization considering all these parameters, since they often rely on surface immobilization, cannot measure under biorelevant conditions, or do not feature a structurally-related readout for indicating formation of multiple bound species. In this work, we report the use of flow induced dispersion analysis (FIDA) for in-solution characterization of complex protein interactions under in vivo like conditions. FIDA is an immobilization-free ligand binding methodology employing Taylor dispersion analysis for measuring the hydrodynamic radius (size) of biomolecular complexes. Here, the FIDA technology is utilized for a size-based characterization of the interaction between TNF-α and adalimumab. We report concentration-dependent complex sizes, binding affinities (Kd), kinetics, and higher order stoichiometries, thus providing essential information on the TNF-α–adalimumab binding mechanism. Furthermore, it is shown that the avidity stabilized complexes involving formation of multiple non-covalent bonds are formed on a longer timescale than the primary complexes formed in a simple 1 to 1 binding event.

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