scholarly journals Thermodynamic aspects of the self-assembly of DsrA, a small noncoding RNA from Escherichia coli.

2014 ◽  
Vol 61 (1) ◽  
Author(s):  
Frédéric Geinguenaud ◽  
Maeva Gesson ◽  
Véronique Arluison
Keyword(s):  
Escherichia Coli ◽  
Self Assembly ◽  
Noncoding Rna ◽  
The Self ◽  
Functional Consequence ◽  
Small Noncoding Rna ◽  
The Difference ◽  
First Time ◽  
Thermodynamic Basis

DsrA is an Escherichia coli small noncoding RNA that acts by base pairing to some mRNAs in order to control their translation and turnover. It was recently shown that DsrA is able to self-associate in a way similar to DNA and to build nanostructures. Although functional consequence of this RNA self-assembly in vivo is not yet understood, the formation of such an assemblage more than likely influences the noncoding RNA function. We report here for the first time the thermodynamic basis of this natural RNA self-assembly. In particular we show that assembling of the ribonucleic acid is enthalpy driven and that the versatility of the RNA molecule is important for the polymerisation; indeed, an equivalent DNA sequence is unable to make a nanoassembly. The origin of the difference is discussed herein.

scholarly journals Influence of High Pressure on the Dimerization of ToxR, a Protein Involved in Bacterial Signal Transduction

2008 ◽  
Vol 74 (24) ◽  
pp. 7821-7823 ◽  
Author(s):  
Kai Linke ◽  
Nagarajan Periasamy ◽  
Matthias Ehrmann ◽  
Roland Winter ◽  
Rudi F. Vogel
Keyword(s):  
Escherichia Coli ◽  
Signal Transduction ◽  
High Pressure ◽  
Structure And Function ◽  
Transmembrane Segments ◽  
Bacterial Signal Transduction ◽  
Reporter Strains ◽  
And Function ◽  
First Time

ABSTRACT High hydrostatic pressure (HHP) is suggested to influence the structure and function of membranes and/or integrated proteins. We demonstrate for the first time HHP-induced dimer dissociation of membrane proteins in vivo with Vibrio cholerae ToxR variants in Escherichia coli reporter strains carrying ctx::lacZ fusions. Dimerization ceased at 20 to 50 MPa depending on the nature of the transmembrane segments rather than on changes in the ToxR lipid bilayer environment.

A dissipative particle dynamics simulation study on phase diagrams for the self-assembly of amphiphilic hyperbranched multiarm copolymers in various solvents

Soft Matter ◽  
2017 ◽  
Vol 13 (36) ◽  
pp. 6178-6188 ◽  
Author(s):  
Haina Tan ◽  
Chunyang Yu ◽  
Zhongyuan Lu ◽  
Yongfeng Zhou ◽  
Deyue Yan
Keyword(s):  
Phase Diagrams ◽  
Simulation Study ◽  
Self Assembly ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
The Self ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
First Time ◽  
Dissipative Particle Dynamics Simulation

This work discloses for the first time the self-assembly phase diagrams of amphiphilic hyperbranched multiarm copolymers in various solvents by dissipative particle dynamics simulations.

A self-assembly based on a hydrogel interface: facile, rapid, and large-scale preparation of colloidal photonic crystals

2020 ◽  
Vol 4 (8) ◽  
pp. 2409-2417
Author(s):  
Mengfan Wu ◽  
Chuyan Zhang ◽  
Fujing Wei ◽  
Huifang An ◽  
Xiaqing Wang ◽  
...  
Keyword(s):  
Photonic Crystals ◽  
Self Assembly ◽  
Large Scale ◽  
The Self ◽  
Colloidal Photonic Crystals ◽  
Large Scale Preparation ◽  
Scale Preparation ◽  
First Time

This is the first time that a hydrogel interface has been used as an assembly interface for the self-assembly of photonic crystals with excellent performances.

scholarly journals Pharmacophore hybridisation and nanoscale assembly to discover self-delivering lysosomotropic new-chemical entities for cancer therapy

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhao Ma ◽  
Jin Li ◽  
Kai Lin ◽  
Mythili Ramachandran ◽  
Dalin Zhang ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Cancer Therapy ◽  
Self Assembly ◽  
The Self ◽  
Single Drug ◽  
Drug Nanoparticles ◽  
Lysosomal Dysfunction ◽  
New Chemical Entities ◽  
Autophagy Inhibition

Abstract Integration of the unique advantages of the fields of drug discovery and drug delivery is invaluable for the advancement of drug development. Here we propose a self-delivering one-component new-chemical-entity nanomedicine (ONN) strategy to improve cancer therapy through incorporation of the self-assembly principle into drug design. A lysosomotropic detergent (MSDH) and an autophagy inhibitor (Lys05) are hybridised to develop bisaminoquinoline derivatives that can intrinsically form nanoassemblies. The selected BAQ12 and BAQ13 ONNs are highly effective in inducing lysosomal disruption, lysosomal dysfunction and autophagy blockade and exhibit 30-fold higher antiproliferative activity than hydroxychloroquine used in clinical trials. These single-drug nanoparticles demonstrate excellent pharmacokinetic and toxicological profiles and dramatic antitumour efficacy in vivo. In addition, they are able to encapsulate and deliver additional drugs to tumour sites and are thus promising agents for autophagy inhibition-based combination therapy. Given their transdisciplinary advantages, these BAQ ONNs have enormous potential to improve cancer therapy.

scholarly journals Contributions of O Island 48 to Adherence of Enterohemorrhagic Escherichia coli O157:H7 to Epithelial Cells In Vitro and in Ligated Pig Ileal Loops

2009 ◽  
Vol 75 (18) ◽  
pp. 5779-5786 ◽  
Author(s):  
Xianhua Yin ◽  
Roger Wheatcroft ◽  
James R. Chambers ◽  
Bianfang Liu ◽  
Jing Zhu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Epithelial Cells ◽  
Cluster Formation ◽  
Gene Clusters ◽  
Enterohemorrhagic Escherichia Coli ◽  
Wild Type ◽  
The Difference ◽  
Large Clusters

ABSTRACT O island 48 (OI-48) of Escherichia coli consists of three functional gene clusters that encode urease, tellurite resistance (Ter), and putative adhesins Iha and AIDA-1. The functions of these clusters in enterohemorrhagic E. coli (EHEC) O157:H7 infection are unknown. Deletion mutants for these three regions were constructed and evaluated for their ability to adhere to epithelial cells in vitro and in ligated pig ileal loops. Deletion of the Ter gene cluster reduced the ability of the organism to adhere to and form large clusters on IPEC-J2 and HEp-2 cells. Complementation of the mutation by introducing the wild-type ter genes restored adherence and large-cluster formation. Tests in ligated pig ileal loops showed a decrease in colonization by the Ter-negative mutant, but the difference was not significant compared to colonization by the wild type (26.4% ± 21.2% versus 40.1% ± 19.1%; P = 0.168). The OI-48 aidA gene deletion had no effect on adherence in vitro or in vivo. Deletion of the iha and ureC genes had no effect on adherence in vitro but significantly reduced the colonization of EHEC O157:H7 in the ligated pig intestine. These data suggest that Ter, Iha, and urease may contribute to EHEC O157:H7 pathogenesis by promoting adherence of the pathogen to the host intestinal epithelium.

scholarly journals Investigation and Identification of let-7a Related Functional Proteins in Gastric Carcinoma by Proteomics

2012 ◽  
Vol 35 (4) ◽  
pp. 285-295 ◽  
Author(s):  
Yimin Zhu ◽  
Xingyuan Xiao ◽  
Lairong Dong ◽  
Zhiming Liu
Keyword(s):  
Gastric Carcinoma ◽  
Noncoding Rna ◽  
Target Genes ◽  
Rho Gtpase ◽  
Two Dimensional Gel Electrophoresis ◽  
Gastric Carcinoma Cell ◽  
Rna Molecules ◽  
Small Noncoding Rna

MicroRNAs are small noncoding RNA molecules that control expression of target genes. Our previous studies show that let-7a decreased in gastric carcinoma and that up-regulation of let-7a by gene augmentation inhibited gastric carcinoma cell growth bothin vitroandin vivo, whereas it remains largely unclear as to how let-7a affects tumor growth. In this study, proteins associated with the function of let-7a were detected by high throughout screening. The cell line of SGC-7901 stablely overexpressing let-7a was successfully established by gene cloning. Two-dimensional gel electrophoresis (2-DEy was used to separate the total proteins of SGC-7901/let-7a, SGC-7901/EV and SGC-7901, and PDQuest software was applied to analyze 2-DE images. Ten different protein spots were identified by MALDI-TOF-MS, and they may be the proteins associated with let-7a function. The overexpressed proteins included Antioxidant protein 2, Insulin–like growth factor binding protein 2, Protein disulfide isomerase A2, C-1-tetrahydrofolate synthase, Cyclin-dependent kinase inhibitor1 (CDKN1) and Rho–GTPase activating protein 4. The underexpressed proteins consisted of S-phase kinase-associated protein 2 (Spk2), Platelet membrane glycoprotein, Fibronectin and Cks1 protein. Furthermore, the different expression levels of the partial proteins (CDKN1, Spk2 and Fibronectin) were confirmed by western blot analysis. The data suggest that these differential proteins are involved in a novel let-7a signal pathway and these findings provide the basis to investigate the functional mechanisms of let-7a in gastric carcinoma.

scholarly journals piRNAs Coordinate poly(UG) Tailing to Prevent Aberrant and Permanent Gene Silencing

2021 ◽  
Author(s):  
Aditi Shukla ◽  
Roberto Perales ◽  
Scott Kennedy
Keyword(s):  
Gene Silencing ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Epigenetic Inheritance ◽  
The Self ◽  
Specific Class ◽  
Transgenerational Epigenetic Inheritance ◽  
Small Noncoding Rna ◽  
C Elegans ◽  
Inheritance System

AbstractNoncoding RNAs have emerged as mediators of transgenerational epigenetic inheritance (TEI) in a number of organisms. A robust example of RNA-directed TEI is the inheritance of gene silencing states following RNA interference (RNAi) in the metazoan C. elegans. During RNAi inheritance, gene silencing is transmitted by a self-perpetuating cascade of siRNA-directed poly(UG) tailing of mRNA fragments (pUGylation), followed by siRNA synthesis from poly(UG)-tailed mRNA templates (termed pUG RNA/siRNA cycling). Despite the self-perpetuating nature of pUG RNA/siRNA cycling, RNAi inheritance is finite, suggesting that systems likely exist to prevent permanent RNAi-triggered gene silencing. Here we show that, in the absence of Piwi-interacting RNAs (piRNAs), an animal-specific class of small noncoding RNA, RNAi-based gene silencing can become essentially permanent, lasting at near 100% penetrance for more than five years and hundreds of generations. This permanent gene silencing is mediated by perpetual activation of the pUG RNA/siRNA TEI pathway. Further, we find that piRNAs coordinate endogenous RNAi pathways to prevent germline-expressed genes, which are not normally subjected to TEI, from entering a state of permanent and irreversible epigenetic silencing also mediated by perpetual activation of pUG RNA/siRNA cycling. Together, our results show that one function of C. elegans piRNAs is to insulate germline-expressed genes from aberrant and runaway inactivation by the pUG RNA/siRNA epigenetic inheritance system.

scholarly journals Construction and Characterizations of Antibacterial Surfaces Based on Self-Assembled Monolayer of Antimicrobial Peptides (Pac-525) Derivatives on Gold

Coatings ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1014
Author(s):  
Zijiao Zhang ◽  
Ni Kou ◽  
Weilong Ye ◽  
Shuo Wang ◽  
Jiaju Lu ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Self Assembly ◽  
The Self ◽  
Self Assembled Monolayer ◽  
E Coli ◽  
Antimicrobial Efficiency ◽  
Gold Substrates ◽  
Self Assembled ◽  
Antibacterial Surfaces

Background: Infection that is related to implanted biomaterials is a serious issue in the clinic. Antimicrobial peptides (AMPs) have been considered as an ideal alternative to traditional antibiotic drugs, for the treatment of infections, while some problems, such as aggregation and protein hydrolysis, are still the dominant concerns that compromise their antimicrobial efficiency in vivo. Methods: In this study, antimicrobial peptides underwent self-assembly on gold substrates, forming good antibacterial surfaces, with stable antibacterial behavior. The antimicrobial ability of AMPs grafted on the surfaces, with or without glycine spaces or a primer layer, was evaluated. Results: Specifically, three Pac-525 derivatives, namely, Ac-CGn-KWRRWVRWI-NH2 (n = 0, 2, or 6) were covalently grafted onto gold substrates via the self-assembling process for inhibiting the growth of Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). Furthermore, the alkanethiols HS(CH)10SH were firstly self-assembled into monolayers, as a primer layer (SAM-SH) for the secondary self-assembly of Pac-525 derivatives, to effectively enhance the bactericidal performance of the grafted AMPs. The -(CH)10-S-S-G6Pac derivative was highly effective against S. aureus and E. coli, and reduced the viable amount of E. coli and S. aureus to 0.4% and 33.2%, respectively, after 24 h of contact. In addition, the immobilized AMPs showed good biocompatibility, promoting bone marrow stem cell proliferation. Conclusion: the self-assembled monolayers of the Pac-525 derivatives have great potential as a novel therapeutic method for the treatment of implanted biomaterial infections.

scholarly journals Human Organ-Specific 3D Cancer Models Produced by the Stromal Self-Assembly Method of Tissue Engineering for the Study of Solid Tumors

2020 ◽  
Vol 2020 ◽  
pp. 1-23 ◽  
Author(s):  
Vincent Roy ◽  
Brice Magne ◽  
Maude Vaillancourt-Audet ◽  
Mathieu Blais ◽  
Stéphane Chabaud ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Tumor Microenvironment ◽  
Self Assembly ◽  
The Self ◽  
Human Organ ◽  
Assembly Method ◽  
Cancer Models ◽  
Organ Specific

Cancer research has considerably progressed with the improvement of in vitro study models, helping to understand the key role of the tumor microenvironment in cancer development and progression. Over the last few years, complex 3D human cell culture systems have gained much popularity over in vivo models, as they accurately mimic the tumor microenvironment and allow high-throughput drug screening. Of particular interest, in vitrohuman 3D tissue constructs, produced by the self-assembly method of tissue engineering, have been successfully used to model the tumor microenvironment and now represent a very promising approach to further develop diverse cancer models. In this review, we describe the importance of the tumor microenvironment and present the existing in vitro cancer models generated through the self-assembly method of tissue engineering. Lastly, we highlight the relevance of this approach to mimic various and complex tumors, including basal cell carcinoma, cutaneous neurofibroma, skin melanoma, bladder cancer, and uveal melanoma.

Directed arrangement of siRNA via polymerization-induced electrostatic self-assembly

2020 ◽  
Vol 56 (16) ◽  
pp. 2411-2414
Author(s):  
Liangliang Shen ◽  
Yahui Li ◽  
Qunzan Lu ◽  
Xiaoliang Qi ◽  
Xuan Wu ◽  
...  
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Short Interfering Rna ◽  
Assembly Behavior ◽  
Interfering Rna ◽  
First Time

Polymerization-induced electrostatic self-assembly (PIESA) is conducted to mediate the self-assembly behavior of short interfering RNA (siRNA) for the first time.

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