scholarly journals Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties

2018 ◽  
Author(s):  
Steven Boeynaems ◽  
Alex S Holehouse ◽  
Venera Weinhardt ◽  
Denes Kovacs ◽  
Joris Van Lindt ◽  
...  
Keyword(s):  
Material Properties ◽  
Driving Forces ◽  
Coarse Grained ◽  
Biologically Relevant ◽  
Rna Molecules ◽  
Heterotypic Interactions ◽  
Collective Interactions

Collective phase transitions, including phase separation and gelation of multivalent protein and RNA molecules appears to underlie the biogenesis of biomolecular condensates such as membraneless organelles. In vivo, these condensates encompass hundreds of distinct types of molecules that are often organized into multi-layered structures supporting the differential partitioning of molecules into distinct regions with distinct material properties. The interplay between driven (active) versus spontaneous (passive) processes that are required for enabling the formation of condensates with coexisting layers of distinct material properties remains unclear. Here, we investigate the role of spontaneous driving forces as determinants of protein-RNA condensates with complex morphologies and distinct material properties. Through the use of systematic in vitro experiments and simulations based on coarse-grained models we find that that the collective interactions among the simplest, biologically relevant proteins and archetypal RNA molecules are sufficient for driving the spontaneous emergence of multi-layered condensates with distinct material properties. Our results demonstrate that key properties of protein-RNA condensates such as their overall morphologies, internal dynamics, and the selective partitioning of substrates are governed specific amino acid chemistries as well as RNA sequence and secondary structure. Our findings yield a clear set of heuristics regarding homo- and heterotypic interactions that are likely to be relevant for understanding the interplay between active and passive processes that control the formation of functional biomolecular condensates.

scholarly journals Spontaneous driving forces give rise to protein−RNA condensates with coexisting phases and complex material properties

2019 ◽  
Vol 116 (16) ◽  
pp. 7889-7898 ◽  
Author(s):  
Steven Boeynaems ◽  
Alex S. Holehouse ◽  
Venera Weinhardt ◽  
Denes Kovacs ◽  
Joris Van Lindt ◽  
...  
Keyword(s):  
Material Properties ◽  
Driving Forces ◽  
Coarse Grained ◽  
Multilayered Structures ◽  
Biologically Relevant ◽  
Rna Molecules ◽  
Coexisting Phases ◽  
Heterotypic Interactions ◽  
Collective Interactions

Phase separation of multivalent protein and RNA molecules underlies the biogenesis of biomolecular condensates such as membraneless organelles. In vivo, these condensates encompass hundreds of distinct types of molecules that typically organize into multilayered structures supporting the differential partitioning of molecules into distinct regions with distinct material properties. The interplay between driven (active) versus spontaneous (passive) processes that are required for enabling the formation of condensates with coexisting layers of distinct material properties remains unclear. Here, we deploy systematic experiments and simulations based on coarse-grained models to show that the collective interactions among the simplest, biologically relevant proteins and archetypal RNA molecules are sufficient for driving the spontaneous emergence of multilayered condensates with distinct material properties. These studies yield a set of rules regarding homotypic and heterotypic interactions that are likely to be relevant for understanding the interplay between active and passive processes that control the formation of functional biomolecular condensates.

scholarly journals The Ultimate (Mis)match: When DNA Meets RNA

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1433
Author(s):  
Benoit Palancade ◽  
Rodney Rothstein
Keyword(s):  
Dna Polymerases ◽  
Genome Integrity ◽  
Genome Maintenance ◽  
Rna Molecules ◽  
Recombination Proteins ◽  
Repair Enzymes ◽  
Ancestral Function

RNA-containing structures, including ribonucleotide insertions, DNA:RNA hybrids and R-loops, have recently emerged as critical players in the maintenance of genome integrity. Strikingly, different enzymatic activities classically involved in genome maintenance contribute to their generation, their processing into genotoxic or repair intermediates, or their removal. Here we review how this substrate promiscuity can account for the detrimental and beneficial impacts of RNA insertions during genome metabolism. We summarize how in vivo and in vitro experiments support the contribution of DNA polymerases and homologous recombination proteins in the formation of RNA-containing structures, and we discuss the role of DNA repair enzymes in their removal. The diversity of pathways that are thus affected by RNA insertions likely reflects the ancestral function of RNA molecules in genome maintenance and transmission.

scholarly journals Obstacles in Haemocompatibility Testing

Scientifica ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
W. van Oeveren
Keyword(s):  
Material Properties ◽  
Surface Interactions ◽  
Test Results ◽  
Test Models ◽  
Regulatory Purpose ◽  
Biomaterial Surfaces ◽  
Air Interfaces

ISO 10993-4 is an international standard describing the methods of testing of medical devices for interactions with blood for regulatory purpose. The complexity of blood responses to biomaterial surfaces and the variability of blood functions in different individuals and species pose difficulties in standardisation. Moreover,in vivoorin vitrotesting, as well as the clinical relevance of certain findings, is still matter of debate. This review deals with the major remaining problems, including a brief explanation of surface interactions with blood, the current ISO 10993 requirements for testing, and the role ofin vitrotest models. The literature is reviewed on anticoagulation, shear rate, blood-air interfaces, incubation time, and the importance of evaluation of the surface area after blood contact. Two test categories deserve further attention: complement and platelet function, including the effects on platelets from adhesion proteins, venipuncture, and animal derived- blood. The material properties, hydrophilicity, and roughness, as well as reference materials, are discussed. Finally this review calls for completing the acceptance criteria in the ISO standard based on a panel of test results.

scholarly journals SIRNA-MEDIATED INHIBITION OF INTERLEUKINE-13 PRODUCTION IN VITRO

2012 ◽  
Vol 9 (6) ◽  
pp. 24-27
Author(s):  
I P Shilovskiy ◽  
D V Mazurov ◽  
N N Shershakova ◽  
M R Khaitov
Keyword(s):  
Gene Expression ◽  
Protein Product ◽  
Spleen Cells ◽  
Rna Molecules ◽  
In Vitro Methods ◽  
Gene Coding ◽  
Interfering Rna

Background. According to current views, one of the major mediators involved in the development of allergic process is IL-13. The goal of this work was to design small interfering RNA molecules to effectively inhibit il-13 gene expression of mice in experiments in vitro. Methods. For the expression of IL-13 in in vitro gene coding sequence il-13 was amplified using cDNA ConA-stimulated spleen cells from BALE / c mice as a template and cloned into the expression vector pUCHR IRES GFP. Using a computer analysis were designed six variants of siRNA, directed against mRNA-il-13. To test the efficiency of siRNA a co-transfection of 1x 105 cells HEK293T mixture (0,5 mg and 1 mg of plasmid siRNA) coupled with Lipofectamine 2000 reagent was carried out. Twenty-four hours later, the gene expression changes in il-13 recorded by flow cytometry on the fluorescence intensity of GFP+-cells. Gene expression of il-13 mRNA was assessed by quantitative PCR, and the level of the protein product by ELISA. results. As a result, siRNA molecules were obtained and three of them were able to effectively inhibit the gene expression of il-13. Conclusion. Thereby variants of siRNA, which can effectively inhibit the production of mice’s IL-13 in vitro; can be used later in experiments in vivo so to understand the role of IL-13 in the pathogenesis of allergic conditions as to develop new therapy approaches.

scholarly journals Progress in micro RNA focused research in endocrinology

2016 ◽  
Vol 50 (2) ◽  
pp. 83-105 ◽  
Author(s):  
K. Voglova ◽  
J. Bezakova ◽  
Iveta Herichova
Keyword(s):  
Gene Expression ◽  
Physiological Role ◽  
Micro Rna ◽  
Mirna Biogenesis ◽  
Rna Molecules ◽  
Micro Rnas ◽  
Influence Gene Expression

AbstractMicro RNAs (miRNAs) are small regulatory molecules of increasing biologists’ interest. miRNAs, unlikely mRNA, do not encode proteins. It is a class of small double stranded RNA molecules that via their seed sequence interact with mRNA and inhibit its expression. It has been estimated that 30% of human gene expression is regulated by miRNAs. One miRNA usually targets several mRNAs and one mRNA can be regulated by several miRNAs. miRNA biogenesis is realized by key enzymes, Drosha and Dicer. miRNA/mRNA interaction depends on binding to RNA-induced silencing complex. Today, complete commercially available methodical proposals for miRNA investigation are available. There are techniques allowing the identification of new miRNAs and new miRNA targets, validation of predicted targets, measurement of miRNAs and their precursor levels, and validation of physiological role of miRNAs under in vitro and in vivo conditions. miRNAs have been shown to influence gene expression in several endocrine glands, including pancreas, ovary, testes, hypothalamus, and pituitary.

scholarly journals Circ_0001955 facilitates hepatocellular carcinoma (HCC) tumorigenesis by sponging miR-516a-5p to release TRAF6 and MAPK11

2019 ◽  
Vol 10 (12) ◽  
Author(s):  
Zhicheng Yao ◽  
Ruiyun Xu ◽  
Lin Yuan ◽  
Mingxing Xu ◽  
Haiyun Zhuang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Opposite Effect ◽  
Target Genes ◽  
Circular Rnas ◽  
Rna Molecules ◽  
Normal Tissues ◽  
Tumor Tissues

AbstractCircular RNAs (circRNAs) have been increasingly demonstrated to function as novel promising therapeutic RNA molecules for diverse human diseases, including cancer. Although the important role of circRNAs has been well documented in HCC, the complex mechanisms of circRNAs in HCC need to be elucidated. Here, a novel circRNA circ_0001955 was identified from three GSE datasets (GSE7852, GSE94508, and GSE97322) as a differentially expressed circRNA between HCC and normal samples. We revealed that circ_0001955, TRAF6 and MAPK11 levels were increased, while miR-516a-5p levels were decreased in HCC tumor tissues compared to adjacent normal tissues. Knockdown of circ_0001955 repressed HCC tumor growth in vitro and in vivo, while overexpression of circ_0001955 exhibited the opposite effect. Circ_0001955 was identified as a sponge for miR-145-5p and miR-516a-5p, and TRAF6 and MAPK11 were demonstrated to be two target genes of miR-516a-5p. In conclusion, circ_0001955 facilitated HCC tumorigenesis by sponging miR-516a-5p to release TRAF6 and MAPK11 expression.

The Role of Polyphenols in the Modulation of Plasma Non-Enzymatic Antioxidant Capacity (NEAC)

2012 ◽  
Vol 82 (3) ◽  
pp. 228-232 ◽  
Author(s):  
Mauro Serafini ◽  
Giuseppa Morabito
Keyword(s):  
Antioxidant Capacity ◽  
Dietary Intervention ◽  
Ex Vivo ◽  
The Body ◽  
Dietary Polyphenols ◽  
Enzymatic Antioxidant ◽  
Endogenous Antioxidant

Dietary polyphenols have been shown to scavenge free radicals, modulating cellular redox transcription factors in different in vitro and ex vivo models. Dietary intervention studies have shown that consumption of plant foods modulates plasma Non-Enzymatic Antioxidant Capacity (NEAC), a biomarker of the endogenous antioxidant network, in human subjects. However, the identification of the molecules responsible for this effect are yet to be obtained and evidences of an antioxidant in vivo action of polyphenols are conflicting. There is a clear discrepancy between polyphenols (PP) concentration in body fluids and the extent of increase of plasma NEAC. The low degree of absorption and the extensive metabolism of PP within the body have raised questions about their contribution to the endogenous antioxidant network. This work will discuss the role of polyphenols from galenic preparation, food extracts, and selected dietary sources as modulators of plasma NEAC in humans.

Anti-obesity role of Aster glehni extract: in vivo and in vitro effects

Planta Medica ◽  
2012 ◽  
Vol 78 (11) ◽  
Author(s):  
HM Lee ◽  
TG Ahn ◽  
CW Kim ◽  
HJ An
Keyword(s):  
In Vitro Effects

A Molecular Approach to Immunoscintigraphy: A Study of the T-Antigen Conformation on the Surface of Tumors

1987 ◽  
Vol 26 (01) ◽  
pp. 1-6 ◽  
Author(s):  
S. Selvaraj ◽  
M. R. Suresh ◽  
G. McLean ◽  
D. Willans ◽  
C. Turner ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Tumor Cell ◽  
T Antigen ◽  
Human Carcinomas ◽  
Animal Tumor ◽  
Synthetic Antigens

The role of glycoconjugates in tumor cell differentiation has been well documented. We have examined the expression of the two anomers of the Thomsen-Friedenreich antigen on the surface of human, canine and murine tumor cell membranes both in vitro and in vivo. This has been accomplished through the synthesis of the disaccharide terminal residues in both a and ß configuration. Both entities were used to generate murine monoclonal antibodies which recognized the carbohydrate determinants. The determination of fine specificities of these antibodies was effected by means of cellular uptake, immunohistopathology and immunoscintigraphy. Examination of pathological specimens of human and canine tumor tissue indicated that the expressed antigen was in the β configuration. More than 89% of all human carcinomas tested expressed the antigen in the above anomeric form. The combination of synthetic antigens and monoclonal antibodies raised specifically against them provide us with invaluable tools for the study of tumor marker expression in humans and their respective animal tumor models.

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