Aniline incorporated silica nanobubbles

We report the synthesis of stearate functionalized nanobubbles of SiO2 with a few aniline molecules inside, represented as C6H5NH2@SiO2@stearate, exhibiting fluorescence with red-shifted emission. Stearic acid functionalization allows the materials to be handled just as free molecules, for dissolution, precipitation, storage etc. The methodology adopted involves adsorption of aniline on the surface of gold nanoparticles with subsequent growth of a silica shell through monolayers, followed by the selective removal of the metal core either using sodium cyanide or by a new reaction involving halocarbons. The material is stable and can be stored for extended periods without loss of fluorescence. Spectroscopic and voltammetric properties of the system were studied in order to understand the interaction of aniline with the shell as well as the monolayer, whilst transmission electron microscopy has been used to study the silica shell

Light-stimulable molecules/nanoparticles networks for switchable logical functions and reservoir computing

We report the fabrication and electron transport properties of nanoparticles self-assembled networks (NPSAN) of molecular switches (azobenzene derivatives) interconnected by Au nanoparticles, and we demonstrate optically-driven switchable logical operations associated to the light controlled switching of the molecules. The switching yield is up to 74%. We also demonstrate that these NPSANs are prone for light-stimulable reservoir computing. The complex non-linearity of electron transport and dynamics in these highly connected and recurrent networks of molecular junctions exhibit rich high harmonics generation (HHG) required for reservoir computing (RC) approaches. Logical functions and HHG are controlled by the isomerization of the molecules upon light illumination. These results, without direct analogs in semiconductor devices, open new perspectives to molecular electronics in unconventional computing

Role of Temperature in the Growth of Silver Nanoparticles Through a Synergetic Reduction Approach

This study presents the role of reaction temperature in the formation and growth of silver nanoparticles through a synergetic reduction approach using two or three reducing agents simultaneously. By this approach, the shape-/size-controlled silver nanoparticles (plates and spheres) can be generated under mild conditions. It was found that the reaction temperature could play a key role in particle growth and shape/size control, especially for silver nanoplates. These nanoplates could exhibit an intensive surface plasmon resonance in the wavelength range of 700–1,400 nm in the UV–vis spectrum depending upon their shapes and sizes, which make them useful for optical applications, such as optical probes, ionic sensing, and biochemical sensors. A detailed analysis conducted in this study clearly shows that the reaction temperature can greatly influence reaction rate, and hence the particle characteristics. The findings would be useful for optimization of experimental parameters for shape-controlled synthesis of other metallic nanoparticles (e.g., Au, Cu, Pt, and Pd) with desirable functional properties

Defining the anatomy of the jumbo phage nucleus

Recently, a family of bacteriophages has been found to form a nucleus-like replication compartment, called the phage nucleus, which encapsulates the phage DNA and protects it from bacterial host defense systems. Although we have discovered the general replication with the phage nucleus, it is still poorly understood at the molecular level, especially the macromolecule translocations and the key proteins that play roles in these functions. The aim of this thesis is to identify the phage nucleus and its associated proteins in greater detail to shed light specifically on how DNA and mRNA export occurs, as well as the selective protein transport into this structure.In Chapter 2, we identify a new set of phage nucleus-associated proteins through comprehensive proteomics and biochemistry. Among the identified proteins, now termed ChmB, is further investigated and found to be directly interacting with ChmA, which forms most of the phage nucleus. In addition, it is found to be directly interacting with the portal protein, suggesting that ChmB might be forming pore-like structures to accommodate DNA packaging. This study provides new insights into the composition and functions of the phage nucleus, particularly in protein-protein interactions.In Chapter 3, we focus on another phage nucleus-associated protein, ChmC. We found that ChmC has structural homology to known RNA binding proteins. We confirmed that ChmC binds to mRNA through its surface-exposed positively charged residues and that it also has phase separation properties. Investigating the samples collected during the infection confirmed the phage mRNA binding, particularly in 5’ regions of the transcripts. When ChmC was knocked down via ddCas13d system, microscopy images showed that the phage nucleus could form, but the replication was arrested at an early stage. Correspondingly, we found that the knockdowns cause a significant reduction in phage bouquet formation as well as phage titers. These results show that ChmC has a critical role in the phage nucleus system, possibly being a part of the mRNA export mechanism after the switch to non-virion RNA Polymerase for transcription.Chapter 4 describes the other key proteins for the phage nucleus system, such as the portal protein and its potential docking site of octameric assembly of ChmB. We also investigate the other phage nucleus-associated proteins we found by proximity labeling, gp63 and gp64 of phiPA3. Our observations suggest gp63 has a critical role in selective protein transport to the phage nucleus and that gp64 interacts with it to potentially form a complex. Finally, we identify phage proteins that potentially inhibit host cell division, which is required as the jumbo phages require longer time to complete their replication compared to their hosts. These encoded proteins might provide a more comprehensive understanding of the replication mechanism as it is crucial for phages' ability to propagate in bacterial hosts, while potentially providing underlying mechanisms that could be used in therapeutics and the biotech industry.In conclusion, this thesis provides important insights into the phage nucleus system and the molecular mechanisms behind it. We believe that identifying and characterizing the phage nucleus and its associated proteins can have important implications for developing host-immune system evading phage therapies and allowing broader abilities to prevent severe bacterial infections

Subcellular organization of viral particles during maturation of nucleus-forming jumbo phage.

Many eukaryotic viruses assemble mature particles within distinct subcellular compartments, but bacteriophages are generally assumed to assemble randomly throughout the host cell cytoplasm. Here, we show that viral particles of Pseudomonas nucleus-forming jumbo phage PhiPA3 assemble into a unique structure inside cells we term phage bouquets. We show that after capsids complete DNA packaging at the surface of the phage nucleus, tails assemble and attach to capsids, and these particles accumulate over time in a spherical pattern, with tails oriented inward and the heads outward to form bouquets at specific subcellular locations. Bouquets localize at the same fixed distance from the phage nucleus even when it is mispositioned, suggesting an active mechanism for positioning. These results mark the discovery of a pathway for organizing mature viral particles inside bacteria and demonstrate that nucleus-forming jumbo phages, like most eukaryotic viruses, are highly spatially organized during all stages of their lytic cycle