scholarly journals DNA Aptamers Specific for Legionella Pneumophila: Systematic Evolution of Ligands by Exponential Enrichment in Whole Bacterial Cells

2022 ◽  
Author(s):  
Lina Xiong ◽  
Mingchen Xia ◽  
Qinglin Wang ◽  
Zhen Meng ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Legionella Pneumophila ◽  
Bacterial Species ◽  
Bioinformatic Analysis ◽  
Diagnostic Tools ◽  
Bacterial Cells ◽  
Whole Cells ◽  
Medical Diagnostic ◽  
Systematic Evolution ◽  
Exponential Enrichment

Abstract Legionella pneumophila is the major causative agent of Legionnaires’ disease and Pontiac fever, which pose major public health problems. Rapid detection of L. pneumophila is important for global control of these diseases. Aptamers, short oligonucleotides that bind to targets with high affinity and specificity, have great potential for use in pathogenic bacterium detection, diagnostics, and therapy. Here, we used a whole-cell SELEX (systematic evolution of ligands by exponential enrichment) method to isolate and characterize single-stranded DNA (ssDNA) aptamers against L. pneumophila. A total of 60 ssDNA sequences were identified after 17 rounds of selection. Other bacterial species (Escherichia coli, Bacillus subtilis, Pseudomonas syringae, Staphylococcus aureus, Legionella quateirensis, and Legionella adelaidensis) were used for counterselection to enhance the specificity of ssDNA aptamers against L. pneumophila. Four ssDNA aptamers showed strong affinity and high selectivity for L. pneumophila, with Kd values in the nanomolar range. Bioinformatic analysis of the most specific aptamers revealed predicted conserved secondary structures that might bind to L. pneumophila cell walls. In addition, the binding of these four fluorescently labeled aptamers to the surface of L. pneumophila was observed directly by fluorescence microscopy. This is the first study to use SELEX to target L. pneumophila whole cells. The aptamers identified in this study could be used in the future to develop medical diagnostic tools and public environmental detection assays for L. pneumophila.

Lectinomics I. Relevance of exogenous plant lectins in biomedical diagnostics

Biologia ◽  
2009 ◽  
Vol 64 (1) ◽  
pp. 1-19 ◽  
Author(s):  
Danica Mislovičová ◽  
Peter Gemeiner ◽  
Anna Kozarova ◽  
Tibor Kožár
Keyword(s):  
Biological Samples ◽  
Clinical Microbiology ◽  
Screening Tools ◽  
Diagnostic Tools ◽  
Whole Cells ◽  
Plant Lectins ◽  
Innovative Methods ◽  
Medical Diagnostic ◽  
Biomedical Diagnostics ◽  
Efficient Screening

AbstractThis review focuses on utilization of plant lectins as medical diagnostic reagents and tools. The lectin-related diagnostic is aimed at detection of several diseases connected to alteration of the glycosylation profiles of cells and at identification of microbial and viral agents in clinical microbiology. Certain lectins, proposed for or used as diagnostic tools could even recognize those cellular determinants, which are not detected by available antibodies. Broad information is presented on the lectinomics field, illustrating that lectin diagnostics might become practical alternative to antibody-based diagnostic products. In addition, the rising trend of lectin utilization in biomedical diagnostics might initiate a development of innovative methods based on better analytical technologies. Lectin microarray, a rapid and simple methodology, can be viewed as an example for such initiative. This technology could provide simple and efficient screening tools for analysis of glycosylation patterns in biological samples (cellular extracts, tissues and the whole cells), allowing thus personalized detection of changes associated with carbohydrate-related diseases.

scholarly journals Biophysical and proteomic analyses suggest functions of Pseudomonas syringae pv tomato DC3000 extracellular vesicles in bacterial growth during plant infection

2021 ◽  
Author(s):  
Martin Janda ◽  
Christina Ludwig ◽  
Katarzyna Rybak ◽  
Chen Meng ◽  
Egidio Stigliano ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Extracellular Vesicles ◽  
Membrane Vesicle ◽  
Membrane Vesicles ◽  
Bioinformatic Analysis ◽  
Potential Contribution ◽  
Bacterial Cells ◽  
Bacterial Survival ◽  
In Planta ◽  
Plant Infection

SummaryVesiculation is a process employed by Gram-negative bacteria to release extracellular vesicles (EVs) into the environment. Bacterial EVs contain molecular cargo from the donor bacterium and play important roles in bacterial survival and growth. Here, we describe EV production in plant-pathogenic Pseudomonas syringae pv. tomato DC3000 (Pto DC3000), the causal agent of bacterial speck disease. Cultured Pto DC3000 exhibited EV structures both on the cell surface and in the vicinity of bacterial cells, observed as outer membrane vesicle (OMV) release. We used in-solution trypsin digestion coupled to mass spectrometry to identify 369 proteins enriched in EVs recovered from cultured Pto DC3000. The predicted localization profile of EV proteins supports the production of EVs also in the form of outer-inner-membrane vesicles (OIMVs). EV production varied slightly between bacterial lifestyles and also occurred in planta. The potential contribution of EVs to Pto DC3000 plant infection was assessed using plant treatments and bioinformatic analysis of the EV-enriched proteins. While these results identify immunogenic activities of the EVs, they also point at roles for EVs in bacterial defences and nutrient acquisition by Pto DC3000.

scholarly journals Heterogeneous ice nucleation activity of bacteria: new laboratory experiments at simulated cloud conditions

2008 ◽  
Vol 5 (2) ◽  
pp. 1445-1468 ◽  
Author(s):  
O. Möhler ◽  
D. G. Georgakopoulos ◽  
C. E. Morris ◽  
S. Benz ◽  
V. Ebert ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Cloud Condensation Nuclei ◽  
Bacterial Species ◽  
Ice Nucleation ◽  
Cloud Chamber ◽  
Bacterial Cells ◽  
Spray Formation ◽  
Temperature Range ◽  
Expansion Cooling ◽  
Activation Conditions

Abstract. The ice nucleation activities of five different Pseudomonas syringae, Pseudomonas viridiflava and Erwinia herbicola bacterial species and of SnomaxTM were investigated in the temperature range between −5 and −15°C. Water suspensions of these bacteria were directly spray into the cloud chamber of the AIDA facility of Forschungszentrum Karlsruhe at a temperature of −5.7°. At this temperature, about 1% of the SnomaxTM cells induced freezing of the spray droplets before they evaporated in the cloud chamber. The other suspensions of living cells didn't induce any measurable ice concentration during spray formation at −5.7°. The remaining aerosol was exposed to typical cloud activation conditions in subsequent experiments with expansion cooling to about −11°C. During these experiments, the bacterial cells first acted as cloud condensation nuclei to form cloud droplets and then eventually acted as ice nuclei to freeze the droplets. The results indicate that the bacteria investigated in the present study are mainly ice active in the temperature range between −7 and −11°C with an INA fraction of the order of 10−4. The ice nucleation efficiency of SnomaxTM cells was much larger with an INA fraction of 0.2 at temperatures around −8°C.

scholarly journals Cell-Specific Aptamers as Emerging Therapeutics

2011 ◽  
Vol 2011 ◽  
pp. 1-18 ◽  
Author(s):  
Cindy Meyer ◽  
Ulrich Hahn ◽  
Andrea Rentmeister
Keyword(s):  
Drug Delivery ◽  
Nucleic Acids ◽  
Small Molecules ◽  
Live Cells ◽  
Whole Cells ◽  
High Affinity ◽  
Recent Developments ◽  
Systematic Evolution ◽  
Exponential Enrichment

Aptamers are short nucleic acids that bind to defined targets with high affinity and specificity. The first aptamers have been selected about two decades ago by anin vitroprocess named SELEX (systematic evolution of ligands by exponential enrichment). Since then, numerous aptamers with specificities for a variety of targets from small molecules to proteins or even whole cells have been selected. Their applications range from biosensing and diagnostics to therapy and target-oriented drug delivery. More recently, selections using complex targets such as live cells have become feasible. This paper summarizes progress in cell-SELEX techniques and highlights recent developments, particularly in the field of medically relevant aptamers with a focus on therapeutic and drug-delivery applications.

scholarly journals Heterogeneous ice nucleation activity of bacteria: new laboratory experiments at simulated cloud conditions

2008 ◽  
Vol 5 (5) ◽  
pp. 1425-1435 ◽  
Author(s):  
O. Möhler ◽  
D. G. Georgakopoulos ◽  
C. E. Morris ◽  
S. Benz ◽  
V. Ebert ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Cloud Condensation Nuclei ◽  
Bacterial Species ◽  
Ice Nucleation ◽  
Cloud Chamber ◽  
Bacterial Cells ◽  
Active Fraction ◽  
Temperature Range ◽  
Spray Droplets ◽  
Immersion Freezing

Abstract. The ice nucleation activities of five different Pseudomonas syringae, Pseudomonas viridiflava and Erwinia herbicola bacterial species and of Snomax™ were investigated in the temperature range between −5 and −15°C. Water suspensions of these bacteria were directly sprayed into the cloud chamber of the AIDA facility of Forschungszentrum Karlsruhe at a temperature of −5.7°C. At this temperature, about 1% of the Snomax™ cells induced immersion freezing of the spray droplets before the droplets evaporated in the cloud chamber. The living cells didn't induce any detectable immersion freezing in the spray droplets at −5.7°C. After evaporation of the spray droplets the bacterial cells remained as aerosol particles in the cloud chamber and were exposed to typical cloud formation conditions in experiments with expansion cooling to about −11°C. During these experiments, the bacterial cells first acted as cloud condensation nuclei to form cloud droplets. Then, only a minor fraction of the cells acted as heterogeneous ice nuclei either in the condensation or the immersion mode. The results indicate that the bacteria investigated in the present study are mainly ice active in the temperature range between −7 and −11°C with an ice nucleation (IN) active fraction of the order of 10−4. In agreement to previous literature results, the ice nucleation efficiency of Snomax™ cells was much larger with an IN active fraction of 0.2 at temperatures around −8°C.

scholarly journals Aptamers as Both Drugs and Drug-Carriers

2014 ◽  
Vol 2014 ◽  
pp. 1-21 ◽  
Author(s):  
Md. Ashrafuzzaman
Keyword(s):  
Nucleic Acid ◽  
Specific Binding ◽  
Drug Carriers ◽  
Diagnostic Tools ◽  
Computational Techniques ◽  
Biophysical Properties ◽  
Binding Properties ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Novel Drug

Aptamers are short nucleic acid oligos. They may serve as both drugs and drug-carriers. Their use as diagnostic tools is also evident. They can be generated using various experimental, theoretical, and computational techniques. The systematic evolution of ligands by exponential enrichment which uses iterative screening of nucleic acid libraries is a popular experimental technique. Theory inspired methodology entropy-based seed-and-grow strategy that designs aptamer templates to bind specifically to targets is another one. Aptamers are predicted to be highly useful in producing general drugs and theranostic drugs occasionally for certain diseases like cancer, Alzheimer’s disease, and so on. They bind to various targets like lipids, nucleic acids, proteins, small organic compounds, and even entire organisms. Aptamers may also serve as drug-carriers or nanoparticles helping drugs to get released in specific target regions. Due to better target specific physical binding properties aptamers cause less off-target toxicity effects. Therefore, search for aptamer based drugs, drug-carriers, and even diagnostic tools is expanding fast. The biophysical properties in relation to the target specific binding phenomena of aptamers, energetics behind the aptamer transport of drugs, and the consequent biological implications will be discussed. This review will open up avenues leading to novel drug discovery and drug delivery.

FEATURES OF ORGANOPHOSPHATES IMMOBILIZATION VIA STREPTAVIDIN-BIOTIN SYSTEM FOR EXPERIMENTS ON SELECTION OF APTAMERS

2020 ◽  
pp. 12-20
Author(s):  
D. A. Belinskaya ◽  
Yu. V. Chelusnova ◽  
V. V. Abzianidze ◽  
N. V. Goncharov
Keyword(s):  
Polyethylene Glycol ◽  
Organophosphorus Compounds ◽  
Binding Energies ◽  
Rna Aptamers ◽  
Main Method ◽  
Modeling Methods ◽  
Molecular Dynamics Methods ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Poisoning with organophosphorus compounds occupy one of the leading places in exotoxicosis. At the first stage, the detoxification of organophosphates can be provided with the help of DNA or RNA aptamers that bind the poison in the bloodstream. Currently, the main method of searching for aptamers is the experimental method of systematic evolution of ligands by exponential enrichment (SELEX). In the process of aptamer selection, the target molecule must be immobilized via the streptavidin-biotin complex. Since the poison molecule is small in size, to increase its availability for binding to aptamer, it is necessary to use a spacer between organophosphorus compounds and biotin. The aim of this work was to optimize the selection of aptamers for organophosphorus compounds by increasing the availability of a poison molecule immobilized via the streptavidin-biotin complex on the example of paraoxon. For this purpose, three spacers between organophosphorus compounds and biotin were tested using molecular modeling methods: three links of polyethylene glycol (3-PEG), four links of polyethylene glycol (4-PEG) and aminohexyl. The conformation of the biotinylated paraoxon complex with streptavidin and the interaction of paraoxon with the binding fragment of the aptamer were modeled using molecular docking and molecular dynamics methods. The ability of biotinylated paraoxon to bind to the aptamer has been evaluated by analyzing the surface area of the paraoxon available to the solvent, as well as by calculating the free binding energies. It has been shown that only in the case of aminohexyl immobilized paraoxon can contact the aptamer. At the final stage, the synthesis of paraoxon bound to biotin via aminohexyl was carried out.

Modulation of Gut Microbiota through Dietary Phytochemicals as a Novel Anti-infective Strategy

2020 ◽  
Vol 17 (4) ◽  
pp. 498-506 ◽  
Author(s):  
Pavan K. Mujawdiya ◽  
Suman Kapur
Keyword(s):  
Microbial Community ◽  
Quorum Sensing ◽  
Population Density ◽  
Gut Microbiota ◽  
Biofilm Formation ◽  
Chemical Interaction ◽  
Bacterial Species ◽  
Critical Role ◽  
Bacterial Cells ◽  
Gut Microbes

: Quorum Sensing (QS) is a phenomenon in which bacterial cells communicate with each other with the help of several low molecular weight compounds. QS is largely dependent on population density, and it triggers when the concentration of quorum sensing molecules accumulate in the environment and crosses a particular threshold. Once a certain population density is achieved and the concentration of molecules crosses a threshold, the bacterial cells show a collective behavior in response to various chemical stimuli referred to as “auto-inducers”. The QS signaling is crucial for several phenotypic characteristics responsible for bacterial survival such as motility, virulence, and biofilm formation. Biofilm formation is also responsible for making bacterial cells resistant to antibiotics. : The human gut is home to trillions of bacterial cells collectively called “gut microbiota” or “gut microbes”. Gut microbes are a consortium of more than 15,000 bacterial species and play a very crucial role in several body functions such as metabolism, development and maturation of the immune system, and the synthesis of several essential vitamins. Due to its critical role in shaping human survival and its modulating impact on body metabolisms, the gut microbial community has been referred to as “the forgotten organ” by O`Hara et al. (2006) [1]. Several studies have demonstrated that chemical interaction between the members of bacterial cells in the gut is responsible for shaping the overall microbial community. : Recent advances in phytochemical research have generated a lot of interest in finding new, effective, and safer alternatives to modern chemical-based medicines. In the context of antimicrobial research various plant extracts have been identified with Quorum Sensing Inhibitory (QSI) activities among bacterial cells. This review focuses on the mechanism of quorum sensing and quorum sensing inhibitors isolated from natural sources.

scholarly journals Acetan and Acetan-Like Polysaccharides: Genetics, Biosynthesis, Structure, and Viscoelasticity

Polymers ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 815
Author(s):  
Janja Trček ◽  
Iztok Dogsa ◽  
Tomaž Accetto ◽  
David Stopar
Keyword(s):  
Bacterial Species ◽  
Acetic Acid Bacteria ◽  
Original Description ◽  
Bioinformatic Analysis ◽  
Industrial Sector ◽  
Water Soluble ◽  
Extracellular Polysaccharides ◽  
Genetic Cluster ◽  
Water Release ◽  
Komagataeibacter Xylinus

Bacteria produce a variety of multifunctional polysaccharides, including structural, intracellular, and extracellular polysaccharides. They are attractive for the industrial sector due to their natural origin, sustainability, biodegradability, low toxicity, stability, unique viscoelastic properties, stable cost, and supply. When incorporated into different matrices, they may control emulsification, stabilization, crystallization, water release, and encapsulation. Acetan is an important extracellular water-soluble polysaccharide produced mainly by bacterial species of the genera Komagataeibacter and Acetobacter. Since its original description in Komagataeibacter xylinus, acetan-like polysaccharides have also been described in other species of acetic acid bacteria. Our knowledge on chemical composition of different acetan-like polysaccharides, their viscoelasticity, and the genetic basis for their production has expanded during the last years. Here, we review data on acetan biosynthesis, its molecular structure, genetic organization, and mechanical properties. In addition, we have performed an extended bioinformatic analysis on acetan-like polysaccharide genetic clusters in the genomes of Komagataeibacter and Acetobacter species. The analysis revealed for the first time a second acetan-like polysaccharide genetic cluster, that is widespread in both genera. All species of the Komagataeibacter possess at least one acetan genetic cluster, while it is present in only one third of the Acetobacter species surveyed.

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