Microrheology reveals microscale viscosity gradients in planktonic systems

AbstractMicrobial activity in planktonic systems creates a dynamic and heterogeneous microscale seascape that harbours a diverse community of microorganisms and ecological interactions of global significance. In recent decades a great effort has been put into understanding this complex system, particularly focusing on the role of chemical patchiness, while overlooking a physical parameter that governs microbial life and is affected by biological activity: viscosity. Here we use microrheological techniques to measure viscosity at length scales relevant to microorganisms. Our results reveal the viscous nature and the spatial extent of the phycosphere, the microenvironment surrounding phytoplankton cells, and show heterogeneity in viscosity at the microscale. Such heterogeneity affects the distribution of chemicals and microorganisms, with pervasive and profound implications for the functioning of the planktonic ecosystem.One Sentence SummaryMicrorheology measurements unveil the existence of layers of increased viscosity surrounding phytoplankton cells and within aggregates.

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Microrheology reveals microscale viscosity gradients in planktonic systems

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2011389118 ◽

2020 ◽

Vol 118 (1) ◽

pp. e2011389118

Author(s):

Òscar Guadayol ◽

Tania Mendonca ◽

Mariona Segura-Noguera ◽

Amanda J. Wright ◽

Manlio Tassieri ◽

...

Keyword(s):

Microbial Activity ◽

Global Scale ◽

Great Effort ◽

Ecological Interactions ◽

Microbial Life ◽

Marine Aggregates ◽

Phytoplankton Cell ◽

Order Of Magnitude ◽

Diverse Community

Microbial activity in planktonic systems creates a dynamic and heterogeneous microscale seascape that harbors a diverse community of microorganisms and ecological interactions of global significance. In recent decades great effort has been put into understanding this complex system, particularly focusing on the role of chemical patchiness, while overlooking a physical parameter that governs microbial life and is affected by biological activity: viscosity. Here we reveal spatial heterogeneity of viscosity in planktonic systems by using microrheological techniques that allow measurement of viscosity at length scales relevant to microorganisms. We show the viscous nature and the spatial extent of the phycosphere, the region surrounding phytoplankton. In ∼45% of the phytoplankton cells analyzed we detected increases in viscosity that extended up to 30 µm away from the cell with up to 40 times the viscosity of seawater. We also show how these gradients of viscosity can be amplified around a lysing phytoplankton cell as its viscous contents leak away. Finally, we report conservative estimates of viscosity inside marine aggregates, hotspots of microbial activity, more than an order of magnitude higher than in seawater. Since the diffusivities of dissolved molecules, particles, and microorganisms are inversely related to viscosity, microheterogeneity in viscosity alters the microscale distribution of microorganisms and their resources, with pervasive implications for the functioning of the planktonic ecosystem. Increasing viscosities impacts ecological interactions and processes, such as nutrient uptake, chemotaxis, and particle encounter, that occur at the microscale but influence carbon and nutrient cycles at a global scale.

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Collection of Ego-Centered Network Data with Computer-Assisted Interviews

Methodology ◽

10.1027/1614-2241.2.1.7 ◽

2006 ◽

Vol 2 (1) ◽

pp. 7-15 ◽

Cited By ~ 10

Author(s):

Joachim Gerich ◽

Roland Lehner

Keyword(s):

Survey Methods ◽

A Priori ◽

Dynamic Structure ◽

Computer Assisted ◽

Network Data ◽

Great Effort ◽

Self Administration ◽

Face To Face ◽

Full Network

Although ego-centered network data provide information that is limited in various ways as compared with full network data, an ego-centered design can be used without the need for a priori and researcher-defined network borders. Moreover, ego-centered network data can be obtained with traditional survey methods. However, due to the dynamic structure of the questionnaires involved, a great effort is required on the part of either respondents (with self-administration) or interviewers (with face-to-face interviews). As an alternative, we will show the advantages of using CASI (computer-assisted self-administered interview) methods for the collection of ego-centered network data as applied in a study on the role of social networks in substance use among college students.

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Biological activity of novel thyroid hormone analogues: role of Na+ taurocholate cotransporting polypeptide in liver selectivity

Endocrine Abstracts ◽

10.1530/endoabs.37.oc6.2 ◽

2015 ◽

Author(s):

Giulia Brigante ◽

Bo Carlsson ◽

Simone Kersseboom ◽

Robin P Peeters ◽

Theo J Visser

Keyword(s):

Biological Activity ◽

Thyroid Hormone

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Studies on the Role of Methylated Bases in the Biological Activity of Soluble Ribonucleic Acid

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)93833-0 ◽

1964 ◽

Vol 239 (9) ◽

pp. 2918-2926

Author(s):

Alan Peterkofsky ◽

Celia Jesensky ◽

Arthur Bank ◽

Alan H. Mehler

Keyword(s):

Biological Activity ◽

Ribonucleic Acid

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Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod

Microorganisms ◽

10.3390/microorganisms9010148 ◽

2021 ◽

Vol 9 (1) ◽

pp. 148

Author(s):

Marius Bredon ◽

Elisabeth Depuydt ◽

Lucas Brisson ◽

Laurent Moulin ◽

Ciriac Charles ◽

...

Keyword(s):

Crucial Role ◽

Structure And Function ◽

Ecological Interactions ◽

Dietary Manipulation ◽

Biotic Factors ◽

Abiotic And Biotic Factors ◽

And Function ◽

Multicellular Organisms ◽

Over Time

The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host’s diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the “eco-holobiont” conceptualization of macroorganisms.

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Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

Microbiome ◽

10.1186/s40168-021-01087-w ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Sharon A. Huws ◽

Joan E. Edwards ◽

Wanchang Lin ◽

Francesco Rubino ◽

Mark Alston ◽

...

Keyword(s):

Energy Harvesting ◽

Perennial Ryegrass ◽

Transcriptional Activity ◽

Ecological Niches ◽

Ecological Interactions ◽

Carbohydrate Degradation ◽

Host Nutrition ◽

Role Based ◽

Insight Into

Abstract Background Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. Results Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be ‘cheating’ in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. Conclusions In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants.

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Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata

International Journal of Molecular Sciences ◽

10.3390/ijms22126557 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6557

Author(s):

Li-Ying Ren ◽

Heng Zhao ◽

Xiao-Ling Liu ◽

Tong-Kai Zong ◽

Min Qiao ◽

...

Keyword(s):

Biological Activity ◽

Abscisic Acid ◽

Lignin Degradation ◽

Molecular Mechanisms ◽

Receptor Protein ◽

Gastrodia Elata ◽

Upregulated Genes ◽

Aba Biosynthesis ◽

Seed Coats

Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.

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Biobanking for Neurodegenerative Diseases: Challenge for Translational Research and Data Privacy

The Neuroscientist ◽

10.1177/10738584211036693 ◽

2021 ◽

pp. 107385842110366

Author(s):

Emilia Giannella ◽

Valentino Notarangelo ◽

Caterina Motta ◽

Giulia Sancesario

Keyword(s):

Neurodegenerative Diseases ◽

Translational Research ◽

Data Protection ◽

Biological Samples ◽

Data Privacy ◽

Neurological Diseases ◽

Great Effort ◽

General Data Protection Regulation ◽

In Silico Studies

Biobanking has emerged as a strategic challenge to promote knowledge on neurological diseases, by the application of translational research. Due to the inaccessibility of the central nervous system, the advent of biobanks, as structure collecting biospecimens and associated data, are essential to turn experimental results into clinical practice. Findings from basic research, omics sciences, and in silico studies, definitely require validation in clinically well-defined cohorts of patients, even more valuable when longitudinal, or including preclinical and asymptomatic individuals. Finally, collecting biological samples requires a great effort to guarantee respect for transparency and protection of sensitive data of patients and donors. Since the European General Data Protection Regulation 2016/679 has been approved, concerns about the use of data in biomedical research have emerged. In this narrative review, we focus on the essential role of biobanking for translational research on neurodegenerative diseases. Moreover, we address considerations for biological samples and data collection, the importance of standardization in the preanalytical phase, data protection (ethical and legal) and the role of donors in improving research in this field.

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Differential Role of Threonine and Tyrosine Phosphorylation in the Activation and Activity of the Yeast MAPK Slt2

International Journal of Molecular Sciences ◽

10.3390/ijms22031110 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1110

Author(s):

Gema González-Rubio ◽

Ángela Sellers-Moya ◽

Humberto Martín ◽

María Molina

Keyword(s):

Cell Wall ◽

Biological Activity ◽

Biological Significance ◽

Mitogen Activated Protein Kinase ◽

Activation Loop ◽

High Increase ◽

Dual Specificity ◽

Mitogen Activated Protein ◽

Full Activation

The Mitogen-Activated Protein Kinase (MAPK) Slt2 is central to signaling through the yeast Cell Wall Integrity (CWI) pathway. MAPKs are regulated by phosphorylation at both the threonine and tyrosine of the conserved TXY motif within the activation loop (T190/Y192 in Slt2). Since phosphorylation at both sites results in the full activation of MAPKs, signaling through MAPK pathways is monitored with antibodies that detect dually phosphorylated forms. However, most of these antibodies also recognize monophosphorylated species, whose relative abundance and functionality are diverse. By using different phosphospecific antibodies and phosphate-affinity (Phos-tag) analysis on distinct Slt2 mutants, we determined that Y192- and T190-monophosphorylated species coexist with biphosphorylated Slt2, although most of the Slt2 pool remains unphosphorylated following stress. Among the monophosphorylated forms, only T190 exhibited biological activity. Upon stimulation, Slt2 is first phosphorylated at Y192, mainly by the MAPKK Mkk1, and this phosphorylation is important for the subsequent T190 phosphorylation. Similarly, dephosphorylation of Slt2 by the Dual Specificity Phosphatase (DSP) Msg5 is ordered, with dephosphorylation of T190 depending on previous Y192 dephosphorylation. Whereas Y192 phosphorylation enhances the Slt2 catalytic activity, T190 is essential for this activity. The conserved T195 residue is also critical for Slt2 functionality. Mutations that abolish the activity of Slt2 result in a high increase in inactive Y192-monophosphorylated Slt2. The coexistence of different Slt2 phosphoforms with diverse biological significance highlights the importance of the precise detection of the Slt2 phosphorylation status.

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