Genetic Approaches to Study the Interplay Between Transcription and Nucleoid-Associated Proteins in Escherichia coli.

Bacterial nucleoid-associated proteins are important factors in regulation of transcription, in nucleoid structuring, and in homeostasis of DNA supercoiling. Vice versa, transcription influences DNA supercoiling and can affect DNA binding of nucleoid-associated proteins (NAPs) such as H-NS in Escherichia coli. Here we describe genetic tools to study the interplay between transcription and nucleoid-associated proteins in E.

High Abundance of Transcription Regulators Compacts the Nucleoid in Escherichia coli.

In enteric bacteria organization of the circular chromosomal DNA into a highly dynamic and toroidal-shaped nucleoid involves various factors, such as DNA supercoiling, nucleoid-associated proteins (NAPs), the structural maintenance of chromatin (SMC) complex, and macrodomain organizing proteins. Here, we show that ectopic expression of transcription regulators at high levels leads to nucleoid compaction. This serendipitous result was obtained by fluorescence microscopy upon ectopic expression of the transcription regulator and phosphodiesterase PdeL of Escherichia coli.

Deletion of FRT-sites by no-SCAR recombineering in .

Lambda-Red recombineering is the most commonly used method to create point mutations, insertions or deletions in and other bacteria, but usually an Flp recognition target (FRT) scar-site is retained in the genome. Alternative scarless recombineering methods, including CRISPR/Cas9-assisted methods, generally require cloning steps and/or complex PCR schemes for specific targeting of the genome. Here we describe the deletion of FRT scar-sites by the scarless Cas9-assisted recombineering method no-SCAR using an FRT-specific guide RNA, sgRNA, and locus-specific ssDNA oligonucleotides.

The transcription regulator and c-di-GMP phosphodiesterase PdeL represses motility in .

PdeL is a transcription regulator and catalytically active c-di-GMP phosphodiesterases (PDE) in PdeL has been shown to be a transcription autoregulator, while no other target genes have been identified so far. Here, we show that PdeL represses transcription of the flagella class II operon, , and activates encoding an extracellular anchored metalloprotease, among additional loci. DNA-binding studies and expression analyses using plasmidic reporters suggest that regulation of the and promoters by PdeL is direct.

High-Rate Printing of Micro/Nanoscale Patterns Using Interfacial Convective Assembly.

Printing of electronics has been receiving increasing attention from academia and industry over the recent years. However, commonly used printing techniques have limited resolution of micro- or sub-microscale. Here, a directed-assembly-based printing technique, interfacial convective assembly, is reported, which utilizes a substrate-heating-induced solutal Marangoni convective flow to drive particles toward patterned substrates and then uses van der Waals interactions as well as geometrical confinement to trap the particles in the pattern areas.

Directed assembly-based printing of homogeneous and hybrid nanorods using dielectrophoresis.

Printing nano and microscale three-dimensional (3D) structures using directed assembly of nanoparticles has many potential applications in electronics, photonics and biotechnology. This paper presents a reproducible and scalable 3D dielectrophoresis assembly process for printing homogeneous silica and hybrid silica/gold nanorods from silica and gold nanoparticles. The nanoparticles are assembled into patterned vias under a dielectrophoretic force generated by an alternating current (AC) field, and then completely fused in situ to form nanorods.

High-Rate Assembly of Nanomaterials on Insulating Surfaces Using Electro-Fluidic Directed Assembly.

Conductive or semiconducting nanomaterials-based applications such as electronics and sensors often require direct placement of such nanomaterials on insulating surfaces. Most fluidic-based directed assembly techniques on insulating surfaces utilize capillary force and evaporation but are diffusion limited and slow. Electrophoretic-based assembly, on the other hand, is fast but can only be utilized for assembly on a conductive surface.

Novel Nanoprinting for Oral Delivery of Poorly Soluble Drugs.

Many of the newly developed drugs for cancer, and some of those for cardiovascular disease, are poorly soluble in water and cannot be taken orally. This can be overcome by employing a new and effective delivery system utilizing nanotechnology. We present a new method for oral preparation of poorly soluble drugs that entails assembling (printing) drug-loaded polymeric micelles into sub-100 nm orally acceptable nanorods (NRs).

Three-dimensional crystalline and homogeneous metallic nanostructures using directed assembly of nanoparticles.

Directed assembly of nano building blocks offers a versatile route to the creation of complex nanostructures with unique properties. Bottom-up directed assembly of nanoparticles have been considered as one of the best approaches to fabricate such functional and novel nanostructures. However, there is a dearth of studies on making crystalline, solid, and homogeneous nanostructures.

3-D perpendicular assembly of single walled carbon nanotubes for complimentary metal oxide semiconductor interconnects.

Due to their superior electrical properties such as high current density and ballistic transport, carbon nanotubes (CNT) are considered as a potential candidate for future Very Large Scale Integration (VLSI) interconnects. However, direct incorporation of CNTs into Complimentary Metal Oxide Semiconductor (CMOS) architecture by conventional chemical vapor deposition (CVD) growth method is problematic since it requires high temperatures that might damage insulators and doped semiconductors in the underlying CMOS circuits. In this paper, we present a directed assembly method to assemble aligned CNTs into pre-patterned vias and perpendicular to the substrate.

Highly sensitive microscale in vivo sensor enabled by electrophoretic assembly of nanoparticles for multiple biomarker detection.

This paper describes a microscale in vivo sensor platform device for the simultaneous detection of multiple biomarkers. We designed the polymer-based biosensors incorporating multiple active isolated areas, as small as 70 μm × 70 μm, for antigen detection. The fabrication approach involved conventional micro- and nano-fabrication processes followed by site-specific electrophoretic directed assembly of antibody-functionalized nanoparticles.

Size-selective template-assisted electrophoretic assembly of nanoparticles for biosensing applications.

The precise, size-selective assembly of nanoparticles gives rise to many applications where the assembly of nano building blocks with different biological or chemical functionalizations is necessary. We introduce a simple, fast, reproducible-directed assembly technique that enables a complete sorting of nanoparticles with single-particle resolution. Nanoparticles are size-selectively assembled into prefabricated via arrays using a sequential template-directed electrophoretic assembly method.