Characterization of Bimetallic Pd-Fe Nanoparticles Synthesized in .

Biologically mediated nanoparticle (NP) synthesis offers a reliable and sustainable alternative route for metal NP production. Compared with conventional chemical and physical production methods that require hazardous materials and considerable energy expenditure, some microorganisms can reduce metal ions into NPs during standard metabolic processes. However, to be considered a feasible commercial option, the properties and inherent activity of bio-NPs still need to be significantly improved.

Bacterial Envelope Fractionation.

Numerous bioinformatics tools allow predicting the localization of membrane proteins in the outer or inner membrane of Escherichia coli with high precision. Nevertheless, it might be desirable to experimentally verify such predictions or to assay the correct localization of recombinant or mutated variants of membrane proteins. Here we describe two methods (preferential detergent solubilization and sucrose-gradient fractionation) that allow to fractionate Gram-negative bacterial membranes and subsequently to enrich inner or outer membrane proteins.

Recombinant expression of Yersinia ruckeri outer membrane proteins in Escherichia coli extracellular vesicles.

The secretion of extracellular vesicles (EVs) is a common process in Gram-negative bacteria and can be exploited for biotechnological applications. EVs pose a self-adjuvanting, non-replicative vaccine platform, where membrane and antigens are presented to the host immune system in a non-infectious fashion. The secreted quantity of EVs varies between Gram-negative bacterial species and is comparatively high in the model bacterium E.

Aptasensor for the Detection of Adhesin UspA2.

Innovative point-of-care (PoC) diagnostic platforms are desirable to surpass the deficiencies of conventional laboratory diagnostic methods for bacterial infections and to tackle the growing antimicrobial resistance crisis. In this study, a workflow was implemented, comprising the identification of new aptamers with high affinity for the ubiquitous surface protein A2 (UspA2) of the bacterial pathogen and the development of an electrochemical biosensor functionalized with the best-performing aptamer as a bioreceptor to detect UspA2. After cell-systematic evolution of ligands by exponential enrichment (cell-SELEX) was performed, next-generation sequencing was used to sequence the final aptamer pool.

Design of new hydrolyzed collagen-modified magnetic nanoparticles to capture pathogens.

Enrichment and diagnosis tools for pathogens currently available are time consuming, thus the development of fast and highly sensitive alternatives is desirable. In this study, a novel approach was described that enables selective capture of bacteria expressing hydrolyzed collagen-binding adhesins with hydrolyzed collagen-coated magnetic nanoparticles (MNPs). This platform could be useful to shorten the time needed to confirm the presence of a bacterial infection.

The Role of Extracellular Loops in the Folding of Outer Membrane Protein X (OmpX) of .

The outer membrane of Gram-negative bacteria acts as an additional diffusion barrier for solutes and nutrients. It is perforated by outer membrane proteins (OMPs) that function most often as diffusion pores, but sometimes also as parts of larger cellular transport complexes, structural components of the cell wall, or even as enzymes. These OMPs often have large loops that protrude into the extracellular environment, which have promise for biotechnological applications and as therapeutic targets.

Transcriptomic Response Analysis of to Palladium Stress.

Palladium (Pd), due to its unique catalytic properties, is an industrially important heavy metal especially in the form of nanoparticles. It has a wide range of applications from automobile catalytic converters to the pharmaceutical production of morphine. Bacteria have been used to biologically produce Pd nanoparticles as a new environmentally friendly alternative to the currently used energy-intensive and toxic physicochemical methods.

Analysis of O-Antigen-Specific Bacteriophage P22 Inactivation by Outer Membrane Vesicles.

Bacteriophages use a large number of different bacterial cell envelope structures as receptors for surface attachment. As a consequence, bacterial surfaces represent a major control point for the defense against phage attack. One strategy for phage population control is the production of outer membrane vesicles (OMVs).

CbpA is a collagen binding cell surface protein under c-di-GMP control.

Cyclic diguanylate (c-di-GMP) signalling affects several cellular processes in group bacteria including biofilm formation and motility, and CdgF was previously identified as a diguanylate cyclase promoting biofilm formation in C-di-GMP can exert its function as a second messenger via riboswitch binding, and a functional c-di-GMP-responsive riboswitch has been found upstream of in various group strains. Protein signature recognition predicted CbpA to be a cell wall-anchored surface protein with a fibrinogen or collagen binding domain. The aim of this study was to identify the binding ligand of CbpA and the function of CbpA in cellular processes that are part of the group c-di-GMP regulatory network.

The inverse autotransporters of Yersinia ruckeri, YrInv and YrIlm, contribute to biofilm formation and virulence.

Yersinia ruckeri causes enteric redmouth disease (ERM) that mainly affects salmonid fishes and leads to significant economic losses in the aquaculture industry. An increasing number of outbreaks and the lack of effective vaccines against some serotypes necessitates novel measures to control ERM. Importantly, Y.

Type V Secretion Systems: An Overview of Passenger Domain Functions.

Bacteria secrete proteins for different purposes such as communication, virulence functions, adhesion to surfaces, nutrient acquisition, or growth inhibition of competing bacteria. For secretion of proteins, Gram-negative bacteria have evolved different secretion systems, classified as secretion systems I through IX to date. While some of these systems consist of multiple proteins building a complex spanning the cell envelope, the type V secretion system, the subject of this review, is rather minimal.

Assay development for the discovery of small-molecule inhibitors of YadA adhesion to collagen.

We set out to develop scalable assays to measure bacterial adhesion to mammalian extracellular matrix proteins, with the aim to perform high-throughput screening for inhibitors. Our model system is the trimeric autotransporter adhesin YadA from that binds to collagen. Using bacterial cells expressing GFP under an inducible promotor, and co-expressing the adhesin of choice, we were able to establish a 384-well plate-based assay that allowed us to screen 28,000 compounds in 8 days (3520 compounds per day).

Producing Gene Deletions in Escherichia coli by P1 Transduction with Excisable Antibiotic Resistance Cassettes.

A first approach to study the function of an unknown gene in bacteria is to create a knock-out of this gene. Here, we describe a robust and fast protocol for transferring gene deletion mutations from one Escherichia coli strain to another by using generalized transduction with the bacteriophage P1. This method requires that the mutation be selectable (e.

Ribozyme-based transfer RNA switches for post-transcriptional control of amino acid identity in protein synthesis.

Protein mutants are studied in a variety of contexts in the life sciences. However, individual mutations need to be generated in order to transcribe and translate the respective protein variants. Here, we introduce a novel strategy for controlling the incorporation of different amino acids in response to an amber stop codon by utilizing switchable designer transfer RNAs in Escherichia coli .

Thermozymes: Synthetic RNA thermometers based on ribozyme activity.

Synthetic biology approaches often combine natural building blocks to generate new cellular activities. Here, we make use of two RNA elements to design a regulatory device with novel functionality. The system is based on a hammerhead ribozyme (HHR) that cleaves itself to generate a liberated ribosome-binding site and, thus, permits expression of a downstream gene.

Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation.

In cellular systems environmental and metabolic signals are integrated for the conditional control of gene expression. On the other hand, artificial manipulation of gene expression is of high interest for metabolic and genetic engineering. Especially the reprogramming of gene expression patterns to orchestrate cellular responses in a predictable fashion is considered to be of great importance.

In vivo screening of ligand-dependent hammerhead ribozymes.

The development of artificial switches of gene expression is of high importance for future applications in biotechnology and synthetic biology. We have developed a powerful RNA-based system which allows for the ligand-dependent and reprogrammable control of gene expression in Escherichia coli. Our system makes use of the hammerhead ribozyme (HHR) which acts as molecular scaffold for the sequestration of the ribosome binding site (RBS), mimicking expression platforms in naturally occurring riboswitches.

Receptor-mediated targeting of cathepsins in professional antigen presenting cells.

Tag for professionals: A fluorescently tagged clustered mannoside DCG-04 analogue (see structure) is designed and synthesized using a modular approach. Uptake of the probe in professional antigen presenting cells and subsequent labeling of cathepsins proceeded in a mannose-receptor dependent manner.

Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment.

Immobilized lanthanide ions offer the opportunity to refine structures of proteins and the complexes they form by using restraints obtained from paramagnetic NMR experiments. We report the design, synthesis, and spectroscopic evaluation of the lanthanide chelator, Caged Lanthanide NMR Probe 5 (CLaNP-5) readily attachable to a protein surface via two cysteine residues. The probe causes tunable pseudocontact shifts, alignment, paramagnetic relaxation enhancement, and luminescence, by chelating it to the appropriate lanthanide ion.