Identification of novel genes involved in the biofilm formation process of Avian Pathogenic Escherichia coli (APEC).

Avian pathogenic Escherichia coli (APEC) is the etiological agent of avian colibacillosis, a leading cause of economic loss to the poultry industry worldwide. APEC causes disease using a diverse repertoire of virulence factors and has the ability to form biofilms, which contributes to the survival and persistence of APEC in harsh environments. The objective of this study was to identify genes most widespread and important in APEC that contribute to APEC biofilm formation. Using the characterized APEC O18 as the template strain, a total of 15,660 mutants were randomly generated using signature tagged mutagenesis and evaluated for decreased biofilm formation ability using the crystal violet assay. Biofilm deficient mutants were sequenced, and a total of 547 putative biofilm formation genes were identified. Thirty of these genes were analyzed by PCR for prevalence among 109 APEC isolates and 104 avian fecal E. coli (AFEC) isolates, resulting in nine genes with significantly greater prevalence in APEC than AFEC. The expression of these genes was evaluated in the wild-type APEC O18 strain using quantitative real-time PCR (qPCR) in both the exponential growth phase and the mature biofilm phase. To investigate the role of these genes in biofilm formation, isogenic mutants were constructed and evaluated for their biofilm production and planktonic growth abilities. Four of the mutants (rfaY, rfaI, and two uncharacterized genes) displayed significantly decreased biofilm formation, and of those four, one (rfaI) displayed significantly decreased growth compared to the wild type. Overall, this study identified novel genes that may be important in APEC and its biofilm formation. The data generated from this study will benefit further investigation into the mechanisms of APEC biofilm formation.

Complete Genome Sequence of the Neonatal Meningitis Escherichia coli Serotype O18:K1 Strain NMEC15.

Neonatal meningitis Escherichia coli (NMEC) is the second leading cause of sepsis and meningitis in neonates worldwide. Here, we report the genome sequence of NMEC15, belonging to serotype O18:K1, isolated from the cerebrospinal fluid (CSF) of an infant with neonatal bacterial meningitis (NBM) in the Netherlands.

Characterizing avian pathogenic Escherichia coli (APEC) from colibacillosis cases, 2018.

Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a devastating disease of poultry that results in multi-million-dollar losses annually to the poultry industry. Disease syndromes associated with APEC includes colisepticemia, cellulitis, air sac disease, peritonitis, salpingitis, omphalitis, and osteomyelitis among others. A total of 61 APEC isolates collected during the Fall of 2018 (Aug-Dec) from submitted diagnostic cases of poultry diagnosed with colibacillosis were assessed for the presence of 44 virulence-associated genes, 24 antimicrobial resistance genes and 17 plasmid replicon types. Each isolate was also screened for its ability to form biofilm using the crystal violet assay and antimicrobial susceptibility to 14 antimicrobials using the NARMS panel. Overall, the prevalence of virulence genes ranged from 1.6% to >90% with almost all strains harboring genes that are associated with the ColV plasmid-the defining trait of the APEC pathotype. Overall, 58 strains were able to form biofilms and only three strains formed negligible biofilms. Forty isolates displayed resistance to antimicrobials of the NARMS panel ranging from one to nine agents. This study highlights that current APEC causing disease in poultry possess virulence and resistance traits and form biofilms which could potentially lead to challenges in colibacillosis control.

Characterizing the Type 6 Secretion System (T6SS) and its role in the virulence of avian pathogenic Escherichia coli strain APECO18.

Avian pathogenic E. coli is the causative agent of extra-intestinal infections in birds known as colibacillosis, which can manifest as localized or systemic infections. The disease affects all stages of poultry production, resulting in economic losses that occur due to morbidity, carcass condemnation and increased mortality of the birds. APEC strains have a diverse virulence trait repertoire, which includes virulence factors involved in adherence to and invasion of the host cells, serum resistance factors, and toxins. However, the pathogenesis of APEC infections remains to be fully elucidated. The Type 6 secretion (T6SS) system has recently gained attention due to its role in the infection process and protection of bacteria from host defenses in human and animal pathogens. Previous work has shown that T6SS components are involved in the adherence to and invasion of host cells, as well as in the formation of biofilm, and intramacrophage bacterial replication. Here, we analyzed the frequency of T6SS genes hcp, impK, evpB, vasK and icmF in a collection of APEC strains and their potential role in virulence-associated phenotypes of APECO18. The T6SS genes were found to be significantly more prevalent in APEC than in fecal E. coli isolates from healthy birds. Expression of T6SS genes was analyzed in culture media and upon contact with host cells. Mutants were generated for hcp, impK, evpB, and icmF and characterized for their impact on virulence-associated phenotypes, including adherence to and invasion of host model cells, and resistance to predation by Dictyostelium discoideum. Deletion of the aforementioned genes did not significantly affect adherence and invasion capabilities of APECO18. Deletion of hcp reduced resistance of APECO18 to predation by D. discoideum, suggesting that T6SS is involved in the virulence of APECO18.

Intragenic antimicrobial peptides (IAPs) from human proteins with potent antimicrobial and anti-inflammatory activity.

Following the treads of our previous works on the unveiling of bioactive peptides encrypted in plant proteins from diverse species, the present manuscript reports the occurrence of four proof-of-concept intragenic antimicrobial peptides in human proteins, named Hs IAPs. These IAPs were prospected using the software Kamal, synthesized by solid phase chemistry, and had their interactions with model phospholipid vesicles investigated by differential scanning calorimetry and circular dichroism. Their antimicrobial activity against bacteria, yeasts and filamentous fungi was determined, along with their cytotoxicity towards erythrocytes. Our data demonstrates that Hs IAPs are capable to bind model membranes while attaining α-helical structure, and to inhibit the growth of microorganisms at concentrations as low as 1µM. Hs02, a novel sixteen residue long internal peptide (KWAVRIIRKFIKGFIS-NH2) derived from the unconventional myosin 1h protein, was further investigated in its capacity to inhibit lipopolysaccharide-induced release of TNF-α in murine macrophages. Hs02 presented potent anti-inflammatory activity, inhibiting the release of TNF-α in LPS-primed cells at the lowest assayed concentration, 0.1 µM. A three-dimensional solution structure of Hs02 bound to DPC micelles was determined by Nuclear Magnetic Resonance. Our work exemplifies how the human genome can be mined for molecules with biotechnological potential in human health and demonstrates that IAPs are actual alternatives to antimicrobial peptides as pharmaceutical agents or in their many other putative applications.

Is the formation of N-heterocyclic carbenes (NHCs) a feasible mechanism for the distillation of imidazolium ionic liquids?

We describe the synthesis of two tetrachloroindate ionic liquids used as probes to study the involvement of NHCs (N-heterocyclic carbenes) in the distillation of imidazolium derivatives. Atmospheric-pressure chemical ionization mass spectrometry (APCI-MS), electrospray ionization mass spectrometry (ESI-MS), atmospheric-pressure thermal desorption ion mass spectrometry (APTDI-MS) and laser-induced acoustic desorption (LIAD) were used to depict the possibility of the involvement of NHCs during the distillation process. Each type of imidazolium derivative showed a particular mechanism of distillation, pointing firmly to the dependence of both the cation and the anion natures to distil as ion pairs or NHCs. Ionic liquid 1-n-butyl-3-methylimidazolium tetrachloroindate (1a) exhibited a preference to distil as ion pairs, whereas 3,3'-(ethane-1,2-diyl)bis(1-methyimidazolium)bis-tetrachloroindate (1b) may react with the Lewis acid anion, affording a bidentate NHC complex to distil. Thermodynamics, quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses of the ionic liquid 1a were also conducted and helped understand the preference for ion pairs instead of NHCs. The performed theoretical calculations did not forwent the possibility of NHC formation; however, they clearly indicated the high stability of the anions (Lewis acids in nature) and also indicated that the possible reaction between NHC and the anion is not favoured. The calculated thermodynamic values were in accordance with the features observed by MS and indicated ion pairs as the feasible species for the distillation of imidazolium-based ionic liquids.

Thermoliquefaction of palm oil fiber (Elaeis sp.) using supercritical ethanol.

Thermoliquefaction of palm oil fiber was investigated using supercritical ethanol as solvent. A semi-continuous laboratory scale unit was developed to investigate the effects of temperature (300-500°C), heating rate (10-30°C.min-1) and cracking time (10-30min) on the conversion of biomass in bio-oil. The main advantage of the proposed process is that a pure solvent is pumping through the reactor that contains the biomass, dispensing the use of biomass slurries. The yield of bio-oil ranged from 56% to 84%, depending on the experimental conditions. It was observed that an increase in working temperature led to an increase in the bio-oil production. Cracking time and heating rate variation had not shown a considerable effect on the conversion of biomass. The chemical profiles of bio-oil determined by GC/MS, indicate that at low temperature mainly sugar derivatives are produced, while at higher temperatures alcohols and phenolic are the majority compounds of the bio-oil.

Structural Studies of a Lipid-Binding Peptide from Tunicate Hemocytes with Anti-Biofilm Activity.

Clavanins is a class of peptides (23aa) histidine-rich, free of post-translational modifications. Clavanins have been studied largely for their ability to disrupt bacterial membranes. In the present study, the interaction of clavanin A with membranes was assessed by dynamic light scattering, zeta potential and permeabilization assays. We observed through those assays that clavanin A lysis bacterial cells at concentrations corresponding to its MIC. Further, the structure and function of clavanin A was investigated. To better understand how clavanin interacted with bacteria, its NMR structure was elucidated. The solution state NMR structure of clavanin A in the presence of TFE-d3 indicated an α-helical conformation. Secondary structures, based on circular dichroism measurements in anionic sodium dodecyl sulfate (SDS) and TFE (2,2,2-trifluorethanol), in silico lipid-peptide docking and molecular simulations with lipids DPPC and DOPC revealed that clavanin A can adopt a variety of folds, possibly influencing its different functions. Microcalorimetry assays revealed that clavanin A was capable of discriminating between different lipids. Finally, clavanin A was found to eradicate bacterial biofilms representing a previously unrecognized function.

Synthesis, Structure, Properties, and Bioimaging of a Fluorescent Nitrogen-Linked Bisbenzothiadiazole.

This paper describes the synthesis, structure, photophysical properties, and bioimaging application of a novel 2,1,3-benzothiadiazole (BTD)-based rationally designed fluorophore. The capability of undergoing efficient stabilizing processes from the excited state allowed the novel BTD derivative to be used as a stable probe for bioimaging applications. No notable photobleaching effect or degradation could be observed during the experimental time period. Before the synthesis, the molecular architecture of the novel BTD derivative was evaluated by means of DFT calculations to validate the chosen design. Single-crystal X-ray analysis revealed the nearly flat characteristics of the structure in a syn conformation. The fluorophore was successfully tested as a live-cell-imaging probe and efficiently stained MCF-7 breast cancer cell lineages.

Micelle Bound Structure and Model Membrane Interaction Studies of the Peptide Hylin a1 from the Arboreal South American Frog Hypsiboas albopunctatus.

Antimicrobial peptides (AMPs) appear as a promising therapeutic candidate against multiresistant pathogens, because they are able to kill microorganisms and have low toxicity of resistance cells. Hylin a1 (Hy-a1, IFGAILPLALGALKNLIK-NH2) is a peptide extracted from the skin secretion of the frog Hypsiboas albopunctatus, which displays antimicrobial and hemolytic activities. We report here structural studies of Hy-a1 using different techniques such as fluorescence, CD and NMR. Our data showed that Hy-a1 acquires a well defined amphipathic α-helix when interacting with a membrane-like environment. Furthermore, Hy-a1 presented different affinity when compared to membranes of zwitterionic or anionic lipid composition. Finally, we proposed a molecular interaction model of this peptide with micelles.

An ionically tagged water-soluble artificial enzyme promotes the dephosphorylation reaction with nitroimidazole: enhanced ionic liquid effect and mechanism.

In this paper, we describe a novel synthesized ionically tagged water-soluble artificial enzyme (PI) that can efficiently cleave phosphate esters, with enhanced an ionic liquid effect through cooperative effects for the substrate activation and further nucleophilic reaction. The dephosphorylation reaction with PI was evaluated in the presence and absence of 2-methyl-4(5)-nitroimidazole, showing impressive rate enhancements of up to 2 × 10(6)-fold, ascribed to the imidazolide species known as excellent nucleophiles, and formed favorably at lower pH values in the presence of PI.

Structural insights into Cn-AMP1, a short disulfide-free multifunctional peptide from green coconut water.

Multifunctional and promiscuous antimicrobial peptides (AMPs) can be used as an efficient strategy to control pathogens. However, little is known about the structural properties of plant promiscuous AMPs without disulfide bonds. CD and NMR were used to elucidate the structure of the promiscuous peptide Cn-AMP1, a disulfide-free peptide isolated from green coconut water. Data here reported shows that peptide structure is transitory and could be different according to the micro-environment. In this regard, Cn-AMP1 showed a random coil in a water environment and an α-helical structure in the presence of SDS-d25 micelles. Moreover, deuterium exchange experiments showed that Gly4, Arg5 and Met9 residues are less accessible to solvent, suggesting that flexibility and cationic charges seem to be essential for Cn-AMP1 multiple activities.

Carbon dots (C-dots) from cow manure with impressive subcellular selectivity tuned by simple chemical modification.

Improved cellular selectivity for nucleoli staining was achieved by simple chemical modification of carbon dots (C-dots) synthesized from waste carbon sources such as cow manure (or from glucose). The C-dots were characterized and functionalized (amine-passivated) with ethylenediamine, affording amide bonds that resulted in bright green fluorescence. The new modified C-dots were successfully applied as selective live-cell fluorescence imaging probes with impressive subcellular selectivity and the ability to selectively stain nucleoli in breast cancer cell lineages (MCF-7). The C-dots were also tested in four other cellular models and showed the same cellular selection in live-cell imaging experiments.

Facts, presumptions, and myths on the solvent-free and catalyst-free Biginelli reaction. What is catalysis for?

The current manuscript describes the role and importance of catalysis and solvent effects for the Biginelli multicomponent reaction. The overwhelming number of new catalysts and conditions recently published for the Biginelli synthesis, including in some manuscripts entitled "catalyst-free" and/or "solvent-free" have incentivized controversies and hot debates regarding the importance of developing new catalysts and reaction conditions to perform this very important multicomponent reaction. These so-called "catalyst-free" reports have generated much confusion in the field, requiring urgent elucidations. In this manuscript, we exemplify, demystify, and discuss the crucial role of catalysis, solvent effects, mechanisms, kinetics, facts, presumptions, and myths associated with the Biginelli reaction aiming to avoid current and future confusion and to stimulate new approaches.

Water-soluble Tb3+ and Eu3+ complexes with ionophilic (ionically tagged) ligands as fluorescence imaging probes.

This article describes a straightforward and simple synthesis of ionically tagged water-soluble Eu(3+) and Tb(3+) complexes (with ionophilic ligands) applied for bioimaging of invasive mammal cancer cells (MDA-MB-231). Use of the task-specific ionic liquid 1-methyl-3-carboxymethyl-imidazolium chloride (MAI·Cl) as the ionophilic ligand (ionically tagged) proved to be a simple, elegant, and efficient strategy to obtain highly fluorescent water-soluble Eu(3+) (EuMAI) and Tb(3+) (TbMAI) complexes. TbMAI showed an intense bright green fluorescence emission selectively staining endoplasmic reticulum of MDA-MB-231 cells.

Probing deep into the interaction of a fluorescent chalcone derivative and bovine serum albumin (BSA): an experimental and computational study.

In the present manuscript, a novel fluorescent chalcone derivative is synthesized and its photophysical properties are fully characterized. The designed fluorophore is applied as a probe to study protein-dye interactions with bovine serum albumin. Circular dichroism gave interesting results on the thermodynamics of the interaction. NMR spectroscopy, especially relaxation measurements, revealed the atoms in the chalcone derivative that interacts with the protein upon binding. Molecular docking calculations indicate that the most favourable binding sites are near the two tryptophan residues. Furthermore, ab initio and DFT calculations offer insights into the reactivity and physicochemical properties of this novel fluorophore.

Mechanistic studies on Lewis acid catalyzed Biginelli reactions in ionic liquids: evidence for the reactive intermediates and the role of the reagents.

This paper describes the use of common Lewis acids supported in imidazolium-based ionic liquids as the catalysts to promote the Biginelli reaction. The ionic liquid effect and the reaction mechanism are discussed on the basis of nuclear magnetic resonance (NMR), electrospray ionization mass spectrometry (ESI-MS), and theoretical calculations. Indeed, the results showed that the ionic medium plays a fundamental role in the synthesis of biologically active dihydropyrimidinones due to the stabilization of the charged intermediates proposed in the mechanism. When conducted in an ionic liquid as solvent, the reaction mechanism is more complex than in other Lewis acid catalyzed Biginelli reactions.

The structure of the elicitor Cerato-platanin (CP), the first member of the CP fungal protein family, reveals a double ψß-barrel fold and carbohydrate binding.

Cerato-platanin (CP) is a secretion protein produced by the fungal pathogen Ceratocystis platani, the causal agent of the plane canker disease and the first member of the CP family. CP is considered a pathogen-associated molecular pattern because it induces various defense responses in the host, including production of phytoalexins and cell death. Although much is known about the properties of CP and related proteins as elicitors of plant defense mechanisms, its biochemical activity and host target(s) remain elusive. Here, we present the three-dimensional structure of CP. The protein, which exhibits a remarkable pH and thermal stability, has a double ψß-barrel fold quite similar to those found in expansins, endoglucanases, and the plant defense protein barwin. Interestingly, although CP lacks lytic activity against a variety of carbohydrates, it binds oligosaccharides. We identified the CP region responsible for binding as a shallow surface located at one side of the ß-barrel. Chemical shift perturbation of the protein amide protons, induced by oligo-N-acetylglucosamines of various size, showed that all the residues involved in oligosaccharide binding are conserved among the members of the CP family. Overall, the results suggest that CP might be involved in polysaccharide recognition and that the double ψß-barrel fold is widespread in distantly related organisms, where it is often involved in host-microbe interactions.

Cerato-platanin, a phytotoxic protein from Ceratocystis fimbriata: expression in Pichia pastoris, purification and characterization.

Cerato-platanin (CP) is a phytotoxic protein secreted by the Ascomycete Ceratocystis fimbriata f.sp. platani. This Ascomycete causes canker stain which is a severe disease with a high incidence in the European Platanus acerifolia. CP probably plays a role in the disease, eliciting defence-related responses in the host plants. CP is a 120 amino acid protein, containing 40% hydrophobic residues and two S-S bridges. In the EMBL data bank CP is the first member of a new fungal protein family known as the Cerato-Platanin Family. The N-terminal region of CP shows a high similarity with that of cerato-ulmin, a phytotoxic protein produced by the Ophiostoma species and that belongs to the hydrophobin family. Hydrophobins are hydrophobic proteins secreted by many saprophytic or pathogenic fungi and have a remarkable ability to self-assemble into a rodlet structure takes part in physiological and/or pathological processes. The methyltrophic yeast Pichia pastoris was used to obtain a high-level expression of recombinant CP (rCP) and the pPIC9 vector was chosen to bring about extra-cellular secretion of the protein. The preliminary structural and functional characterization presented here reveals no significant differences between the native and the recombinant protein. We also show that CP self-assembles in solution. The availability of rCP will allow its three-dimensional structure to be determined, facilitating an understanding of the role of CP in the pathogenesis of canker stain. It is also an excellent model for investigating the mechanism of action of the other proteins related to CP.