Comparative genomics of Vibrio toranzoniae strains.

Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade that was originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at the genomic level among six strains (4 isolated from clam and 2 from seawater) and to determine their phylogeny. For this purpose, whole genomes of the six strains were sequenced by different technologies including Illumina and PacBio, and the resulting sequences were corrected. Genomes were annotated and compared using different online tools. Furthermore, the study of core- and pan-genomes were examined, and the phylogeny was inferred. The content of the core genome ranged from 2953 to 2766 genes and that of the pangenome ranged from 6278 to 6132, depending on the tool used. Although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI values higher than 97%, some differences were found related to motility, capsule synthesis, iron acquisition systems or mobile genetic elements. Phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle (commensal or free-living), but that of the pangenome indicated certain geographical isolation in the same growing area. This study led to the reclassification of some isolates formerly described as V. toranzoniae and demonstrated the importance of cured deposited sequences to proper phylogenetic assignment.

Hydrodeoxygenation of anisole over SBA-15-supported Ni, Pd, and Pt mono- and bimetallic catalysts: effect of the metal's nature on catalytic activity and selectivity.

Monometallic Ni, Pd and Pt and bimetallic catalysts formed by combinations of the above metals supported on SBA-15 silica were synthesized, characterized and tested in the hydrodeoxygenation reaction of anisole. The objective of the work was to detect the effect of the nature of metals on the activity of the catalysts at different steps of anisole hydrodeoxygenation: hydrogenation of the aromatic ring of anisole and C-O bond cleavage in the intermediate cyclohexyl methyl ether. The support and the catalysts were characterized by N2 physisorption, X-ray diffraction, UV-vis diffuse reflectance spectroscopy, temperature-programmed reduction, scanning electron microscopy-energy dispersive X-ray spectroscopy, transmission electron microscopy and HAADF-STEM. The catalytic activity tests were carried out in a batch reactor at 280 °C and 7.3 MPa pressure. The activity results show that the NiPd/SBA-15 catalyst had the greatest ability for hydrogenation of the aromatic ring of anisole, while its NiPt/SBA-15 analog resulted in better activity for C-O bond hydrogenolysis. The bimetallic NiPt/SBA-15 catalyst showed the best catalytic performance in the HDO of anisole ascribed to the formation of a Ni-Pt alloy. On the other hand, the combination of Pd and Pt metals in the PdPt/SBA-15 catalyst resulted in the formation of bimetallic particles with Pd-rich and Pt-rich domains, showing high selectivity for the formation of the cyclohexyl methyl ether, which can be useful for the hydrogenation of aromatic rings in O-containing reactants with the formation of saturated O-containing products. According to the characterization results (HAADF-STEM), the different catalytic behavior of NiPd/SBA-15, NiPt/SBA-15, and PdPt/SBA-15 catalysts could be attributed to different characteristics of the bimetallic active phases in them.

Comparative genomics of Vibrio toranzoniae strains.

Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade, originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at genome level among strains, as well as to determine their phylogeny. For this purpose, whole genomes were sequenced by different technologies and the resulting sequences corrected. Genomes were annotated and compared with different online tools. Furthermore, the study of core and pan genome was examined, and the phylogeny was inferred. The content of the core genome ranged from 2,953 to 2,766 genes and that of the pangenome from 6,278 to 6,132, depending on the tool used. The comparison revealed that although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI higher than 97%,notable differences were found related to motility, capsule synthesis, iron acquisition system or mobile genetic elements. The phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle, but that of the pangenome pointed out certain geographical isolation in the same growing area. The study led to a reclassification of some isolates formerly described as V. toranzoniae and manifested the importance of cured deposited sequences to proper phylogenetic assignment.

Experimental High-Resolution Observation of the Truncated Double-Icosahedron Structure: A Stable Twinned Shell in Alloyed Au-Ag Core@Shell Nanoparticles.

Given the binary nature of nanoalloy systems, their properties are dependent on their size, shape, structure, composition, and chemical ordering. When energy and entropic factors for shapes and structure variations are considered in nanoparticle growth, the spectra of shapes become so vast that even metastable arrangements have been reported under ambient conditions. Experimental and theoretical variations of multiply twinned particles have been observed, from the Ino and Marks decahedra to polyicosahedra and polydecahedra with comparable energetic stability among them. Herein, we report the experimental production of a stable doubly truncated double-icosahedron structure (TdIh) in Au-Ag nanoparticles, in which a twinned Ag-rich alloyed shell is reconstructed on a Au-Ag alloyed Ino-decahedral core. The structure, chemical composition, and growth pathway are proposed on the basis of high-angle annular dark-field scanning transmission electron microscopy analysis and excess energy calculations, while its structural stability is estimated by large-scale atomic molecular dynamics simulations. This novel nanostructure differs from other structures previously reported.

Re-evaluation of certain aspects of the EFSA Scientific Opinion of April 2010 on risk assessment of parasites in fishery products, based on new scientific data. Part 1: ToRs1-3.

Surveillance data published since 2010, although limited, showed that there is no evidence of zoonotic parasite infection in market quality Atlantic salmon, marine rainbow trout, gilthead seabream, turbot, meagre, Atlantic halibut, common carp and European catfish. No studies were found for greater amberjack, brown trout, African catfish, European eel and pikeperch. Anisakis pegreffii, A. simplex (s. s.) and Cryptocotyle lingua were found in European seabass, Atlantic bluefin tuna and/or cod, and Pseudamphistomum truncatum and Paracoenogonimus ovatus in tench, produced in open offshore cages or flow-through ponds or tanks. It is almost certain that fish produced in closed recirculating aquaculture systems (RAS) or flow-through facilities with filtered water intake and exclusively fed heat-treated feed are free of zoonotic parasites. Since the last EFSA opinion, the UV-press and artificial digestion methods have been developed into ISO standards to detect parasites in fish, while new UV-scanning, optical, molecular and OMICs technologies and methodologies have been developed for the detection, visualisation, isolation and/or identification of zoonotic parasites in fish. Freezing and heating continue to be the most efficient methods to kill parasites in fishery products. High-pressure processing may be suitable for some specific products. Pulsed electric field is a promising technology although further development is needed. Ultrasound treatments were not effective. Traditional dry salting of anchovies successfully inactivated Anisakis. Studies on other traditional processes - air-drying and double salting (brine salting plus dry salting) - suggest that anisakids are successfully inactivated, but more data covering these and other parasites in more fish species and products is required to determine if these processes are always effective. Marinade combinations with anchovies have not effectively inactivated anisakids. Natural products, essential oils and plant extracts, may kill parasites but safety and organoleptic data are lacking. Advanced processing techniques for intelligent gutting and trimming are being developed to remove parasites from fish.

Surfactant-tail control of CsPbBr3 nanocrystal morphology.

CsPbBr3 nanocrystals (NCs) are promising optoelectronic and catalytic materials. Manipulating their morphology can improve their properties and stability. In this work, an alkene-derived zwitterionic ligand was used to control the morphology of CsPbBr3 NCs to yield the highly unusual rhombicuboctahedron morphology, showcasing the first example of a surfactant-tail controlled growth.

Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages.

Phage satellites are bacterial genetic elements that co-opt phage machinery for their own dissemination. Here we identify a family of satellites, named Phage-Inducible Chromosomal Minimalist Islands (PICMIs), that are broadly distributed in marine bacteria of the family Vibrionaceae. A typical PICMI is characterized by reduced gene content, does not encode genes for capsid remodelling, and packages its DNA as a concatemer. PICMIs integrate in the bacterial host genome next to the fis regulator, and encode three core proteins necessary for excision and replication. PICMIs are dependent on virulent phage particles to spread to other bacteria, and protect their hosts from other competitive phages without interfering with their helper phage. Thus, our work broadens our understanding of phage satellites and narrows down the minimal number of functions necessary to hijack a tailed phage.

Assessment on the efficacy of methods 2 to 5 and method 7 set out in Commission Regulation (EU) No 142/2011 to inactivate relevant pathogens when producing processed animal protein of porcine origin intended to feed poultry and aquaculture animals.

An assessment was conducted on the level of inactivation of relevant pathogens that could be present in processed animal protein of porcine origin intended to feed poultry and aquaculture animals when methods 2 to 5 and method 7, as detailed in Regulation (EU) No 142/2011, are applied. Five approved scenarios were selected for method 7. Salmonella Senftenberg, Enterococcus faecalis, spores of Clostridium perfringens and parvoviruses were shortlisted as target indicators. Inactivation parameters for these indicators were extracted from extensive literature search and a recent EFSA scientific opinion. An adapted Bigelow model was fitted to retrieved data to estimate the probability that methods 2 to 5, in coincidental and consecutive modes, and the five scenarios of method 7 are able to achieve a 5 log10 and a 3 log10 reduction of bacterial indicators and parvoviruses, respectively. Spores of C. perfringens were the indicator with the lowest probability of achieving the target reduction by methods 2 to 5, in coincidental and consecutive mode, and by the five considered scenarios of method 7. An expert knowledge elicitation was conducted to estimate the certainty of achieving a 5 log10 reduction of spores of C. perfringens considering the results of the model and additional evidence. A 5 log10 reduction of C. perfringens spores was judged: 99-100% certain for methods 2 and 3 in coincidental mode; 98-100% certain for method 7 scenario 3; 80-99% certain for method 5 in coincidental mode; 66-100% certain for method 4 in coincidental mode and for method 7 scenarios 4 and 5; 25-75% certain for method 7 scenario 2; and 0-5% certain for method 7 scenario 1. Higher certainty is expected for methods 2 to 5 in consecutive mode compared to coincidental mode.

Perceptions of food environments in the school and at home during Covid-19: An online cross-sectional study of parents, teachers and experts from Latin America.

BACKGROUND: The high prevalence of overweight and obesity in children from Latin America (LA) have been related to obesogenic food environments. Besides, the negative effects of the Covid-19 pandemic should also be considered. The objective of this research was to describe and compare the perceptions of parents, teachers, and experts in LA of food environments at home and school that favor healthy habits in schoolchildren in pre Covid-19 stage and during the pandemic. METHODS: This study used a survey self-reporting regarding conditions at home and the school favoring healthy habits, for three profiles: parents, primary school teachers, and experts. A fisher exact test was used to establish the difference between the response categories between countries and profiles. Logistic regression models were used to determine the probability of response in the levels of importance adjusted for sex and nationality. RESULTS: Information from 954 questionnaires was reported: 48.4% experts, 32.0% teachers, and 19.6% parents. There were differences in the perception of food environments at school between profiles (p<0.001). In multivariate logistic regression models, experts and teachers were 20% more likely to give greater importance to elements of the food environment at school compared to parents (p<0.001). CONCLUSIONS: Our findings showed that parents were less likely to perceive important elements of the school food environment compared to experts and teachers. Interventions are required to improve healthy eating environments that consider children's interpersonal mediators.

Dietary Nitrate Ingestion Does Not Improve Neuromuscular Performance in Male Sport Climbers.

Beetroot juice (BJ) is commonly used as an ergogenic aid in endurance and team sports, however, the effect of this supplement on climbing performance is barely studied. The purpose of the current study was to investigate the effect of acute BJ ingestion on neuromuscular and biochemical variables in amateur male sport climbers. Ten physically active sport climbers (28.8 ± 3.7 years) underwent a battery of neuromuscular tests consisting of the half crimp test, the pull-up to failure test, the isometric handgrip strength test, the countermovement jump (CMJ) and the squat jump (SJ). Participants performed the neuromuscular test battery twice in a cross-over design separated by 10 days, 150 min after having consumed either 70-mL of BJ (6.4 mmol NO3-) or a 70-mL placebo (0.0034 mmol NO3-). In addition, nitrate (NO3-) and nitrite (NO2-) saliva concentrations were analysed, and a side effect questionnaire related to ingestion was administrated. No differences were reported in particular neuromuscular variables measured such as the CMJ (p = 0.960; ES = 0.03), the SJ (p = 0.581; ES = -0.25), isometric handgrip strength (dominant/non dominant) (p = 0.459-0.447; ES = 0.34-0.35), the pull-up failure test (p = 0.272; ES = 0.51) or the maximal isometric half crimp test (p = 0.521-0.824; ES = 0.10-0.28). Salivary NO3- and NO2- increased significantly post BJ supplementation compared to the placebo (p < 0.001), while no side effects associated to ingestion were reported (p = 0.330-1.000) between conditions (BJ/placebo ingestion). Acute dietary nitrate supplementation (70-mL) did not produce any statistically significant improvement in neuromuscular performance or side effects in amateur sport climbers.

PDDA induced step-pyramidal growth of nickel-platinum (Ni-Pt) nanoparticles for enhanced 4-nitrophenol reduction.

Herein, we report the synthesis of novel platinum-based nanoparticles with step-pyramidal growth induced by poly(diallyldimethylammonium chloride) (PDDA). The complex stepped pyramidal shape became the central point for outstanding catalytic reduction of 4-nitrophenol, overcoming the activity of bare Pt nanoparticles. These results are valuable for the catalytic degradation of reactive molecules.

Bimetallic AgPt Nanoalloys as an Electrocatalyst for Ethanol Oxidation Reaction: Synthesis, Structural Analysis, and Electro-Catalytic Activity.

In the present work, the chemical synthesis of AgPt nanoalloys is reported by the polyol method using polyvinylpyrrolidone (PVP) as a surfactant and a heterogeneous nucleation approach. Nanoparticles with different atomic compositions of the Ag and Pt elements (1:1 and 1:3) were synthesized by adjusting the molar ratios of the precursors. The physicochemical and microstructural characterization was initially performed using the UV-Vis technique to determine the presence of nanoparticles in suspension. Then, the morphology, size, and atomic structure were determined using XRD, SEM, and HAADF-STEM techniques, confirming the formation of a well-defined crystalline structure and homogeneous nanoalloy with an average particle size of less than 10 nm. Finally, the cyclic voltammetry technique evaluated the electrochemical activity of bimetallic AgPt nanoparticles supported on Vulcan XC-72 carbon for the ethanol oxidation reaction in an alkaline medium. Chronoamperometry and accelerated electrochemical degradation tests were performed to determine their stability and long-term durability. The synthesized AgPt (1:3)/C electrocatalyst presented significative catalytic activity and superior durability due to the introduction of Ag that weakens the chemisorption of the carbonaceous species. Thus, it could be an attractive candidate for cost-effective ethanol oxidation compared to commercial Pt/C.

Environmental vibrio phage-bacteria interaction networks reflect the genetic structure of host populations.

Phages depend on their bacterial hosts to replicate. The habitat, density and genetic diversity of host populations are therefore key factors in phage ecology, but our ability to explore their biology depends on the isolation of a diverse and representative collection of phages from different sources. Here, we compared two populations of marine bacterial hosts and their phages collected during a time series sampling program in an oyster farm. The population of Vibrio crassostreae, a species associated specifically to oysters, was genetically structured into clades of near clonal strains, leading to the isolation of closely related phages forming large modules in phage-bacterial infection networks. For Vibrio chagasii, which blooms in the water column, a lower number of closely related hosts and a higher diversity of isolated phages resulted in small modules in the phage-bacterial infection network. Over time, phage load was correlated with V. chagasii abundance, indicating a role of host blooms in driving phage abundance. Genetic experiments further demonstrated that these phage blooms can generate epigenetic and genetic variability that can counteract host defence systems. These results highlight the importance of considering both the environmental dynamics and the genetic structure of the host when interpreting phage-bacteria networks.

Spiers Memorial Lecture: Nanoalloys of multiple components; the road to advance the field and experimental and theoretical challenges.

The field of nanoalloys has been advancing at a rapid pace in the last two decades. Many new characterization methods and theoretical advances have produced a substantial knowledge of the nanoalloys' properties and structure. Most of the work has been limited to binary alloys. A path forward for the field will be the study of nanoalloys with three or more metals. Adding new components will produce new properties and possibly more fabrication controls. In this paper, we will discuss the challenges that will arise in multi-metallic nanoalloys. We will show that entropy and twin boundaries play a dominant role in multi-metallic alloys.

Physiological and microbiological hormesis in sedge Eleocharis palustris induced by crude oil in phytoremediation of flooded clay soil.

Soil contamination with petroleum hydrocarbons affects plants and rhizospheric microorganisms. Microbial activity participates in important biochemical processes that stimulate, together with plants, the modification of toxic compounds for organisms. A nine-month experiment was set up to study the effect over time of oil on plant height (cm), formation of new plants, plant matter production (gravimetry), and population of rhizospheric microorganisms (serial dilution) in the sedge Eleocharis palustris. Removal of total petroleum hydrocarbons (soxhlet and gravimetry) from the soil was also evaluated. The means of the evaluated variables registered significant statistical differences (Duncan, p < 0.05) regarding the age of the plant and the amount of crude oil. There was a high correlation between oil and plant height (0.848) and with new plants (0.994). 60 mg oil dose promoted the greatest statistical difference in the amounts of roots and plant biomass (p < 0.05). E. palustris exposed to 60 and 75 mg of oil stimulated high densities of microalgae, actinomycetes, fungi, hydrocarbonoclastic bacteria and Pseudomonas spp; the overall ratio was 2:1 relative to natural attenuation. Plant and microorganism variables evaluated registered physiological and microbiological hormetic indices ≥1, showing a positive linear relationship. Natural attenuation was more efficient in removing crude oil. We conclude that E. palustris is tolerant to oil exposure. It is suggested to combine it with natural attenuation for the optimization of soils contaminated with crude oil.

Photoactivation of a Mechanosensitive Channel.

Optogenetics in the conventional sense, i.e. the use of engineered proteins that gain their light sensitivity from naturally abundant chromophores, represents an exciting means to trigger and control biological activity by light. As an alternate approach, photopharmacology controls biological activity with the help of synthetic photoswitches. Here, we used an azobenzene-derived lipid analogue to optically activate the transmembrane mechanosensitive channel MscL which responds to changes in the lateral pressure of the lipid bilayer. In this work, MscL has been reconstituted in nanodiscs, which provide a native-like environment to the protein and a physical constraint to membrane expansion. We characterized this photomechanical system by FTIR spectroscopy and assigned the vibrational bands of the light-induced FTIR difference spectra of the trans and cis states of the azobenzene photolipid by DFT calculations. Differences in the amide I range indicated reversible conformational changes in MscL as a direct consequence of light switching. With the mediation of nanodiscs, we inserted the transmembrane protein in a free standing photoswitchable lipid bilayer, where electrophysiological recordings confirmed that the ion channel could be set to one of its sub-conducting states upon light illumination. In conclusion, a novel approach is presented to photoactivate and control cellular processes as complex and intricate as gravitropism and turgor sensing in plants, contractility of the heart, as well as sensing pain, hearing, and touch in animals.

Phage-host coevolution in natural populations.

Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.

Pentafluorophosphato-Phenylalanines: Amphiphilic Phosphotyrosine Mimetics Displaying Fluorine-Specific Protein Interactions.

Phosphotyrosine residues are essential functional switches in health and disease. Thus, phosphotyrosine biomimetics are crucial for the development of chemical tools and drug molecules. We report here the discovery and investigation of pentafluorophosphato amino acids as novel phosphotyrosine biomimetics. A mild acidic pentafluorination protocol was developed and two PF5 -amino acids were prepared and employed in peptide synthesis. Their structures, reactivities, and fluorine-specific interactions were studied by NMR and IR spectroscopy, X-ray diffraction, and in bioactivity assays. The mono-anionic PF5 motif displayed an amphiphilic character binding to hydrophobic surfaces, to water molecules, and to protein-binding sites, exploiting charge and H-F-bonding interactions. The novel motifs bind 25- to 30-fold stronger to the phosphotyrosine binding site of the protein tyrosine phosphatase PTP1B than the best current biomimetics, as rationalized by computational methods, including molecular dynamics simulations.

Hydrophobicity of Self-Assembled Monolayers of Alkanes: Fluorination, Density, Roughness, and Lennard-Jones Cutoffs.

The interplay of fluorination and structure of alkane self-assembled monolayers and how these affect hydrophobicity are explored via molecular dynamics simulations, contact angle goniometry, and surface-enhanced infrared absorption spectroscopy. Wetting coefficients are found to grow linearly in the monolayer density for both alkane and perfluoroalkane monolayers. The larger contact angles of monolayers of perfluorinated alkanes are shown to be primarily caused by their larger molecular volume, which leads to a larger nearest-neighbor grafting distance and smaller tilt angle. Increasing the Lennard-Jones force cutoff in simulations is found to increase hydrophilicity. Specifically, wetting coefficients scale like the inverse square of the cutoff, and when extrapolated to the infinite cutoff limit, they yield contact angles that compare favorably to experimental values. Nanoscale roughness is also found to reliably increase monolayer hydrophobicity, mostly via the reduction of the entropic part of the work of adhesion. Analysis of depletion lengths shows that droplets on nanorough surfaces partially penetrate the surface, intermediate between Wenzel and Cassie-Baxter states.

Gold Nanoclusters, Gold Nanoparticles, and Analytical Techniques for Their Characterization.

Many reliable and reproducible methods exist for manufacturing gold nanoparticles with the desired and specific compositions, structures, arrangements, and physicochemical properties. In this report, we review the key principles guiding the formation and growth of nanoclusters, their evolution into nanoparticles, and the role and contribution of coatings. We describe a range of imaging methods for characterization of nanoparticles at atomic resolution and a range of spectroscopy methods for structural and physicochemical characterization of such nanoparticles. This chapter concludes with a short review of the emergent applications of nanoparticles in biosciences.