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This study aimed to investigating the possible interference caused by glass test tubes on the quantification of bacterial adhesion to hydrocarbons by the MATH test. The adhesion of four bacteria to hexadecane and to glass test tubes was evaluated employing different suspending polar phases. The role of the ionic strength of the polar phase regarding adhesion to glassware was investigated. Within the conditions studied, Gram-positive bacteria adhered to both the test tube and the hydrocarbon regardless of the polar phase employed; meanwhile, Escherichia coli ATCC 25922 did not attach to either one. The capacity of the studied microorganisms to adhere to glassware was associated with their electron-donor properties. The ionic strength of the suspending media altered the patterns of adhesion to glass in a strain-specific manner by defining the magnitude of electrostatic repulsion observed between bacteria and the glass surface. This research demonstrated that glass test tubes may interact with suspended bacterial cells during the MATH test under specific conditions, which may lead to overestimating the percentage of adhesion to hydrocarbons and, thus, to erroneous values of cell surface hydrophobicity.

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The number of publications related to the implementation of nanotechnology in the construction industry, and specifically to the application of nanosilica (SiO2), has had a constant increase in recent years. Based on this, in the present work, an analysis was carried out using bibliometric techniques, with the aim at characterizing the development of specialized literature and identifying the largest areas of growth in the field, maintaining hydrophobic nanosilica as the research guideline. This analysis acquired information from the Scopus and Web of Science (WoS) databases to compare bibliometric indicators of the publications. It should be noted that, even though bibliometric analysis is useful to identify the study areas of greatest interest, to complement this work, the implementation of a method that helped in the research process to obtain the most important bibliography was required. This study implemented Methodi Ordinatio, which helped to take a new direction. Therefore, based on this method, a list of articles cataloged and ranked is obtained, which is the basis for integrating the final bibliographic portfolio. •The study applies the Methodi Ordinatio to obtain a portfolio of the most relevant articles to guide the researchers' work.•Insightful information can be obtained using VOSviewer to analyze and visualize metadata of the bibliographic portfolio.•The study demonstrates how the alpha value in the InOrdinatio formula modifies the resulting portfolio.

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BACKGROUND AND OBJECTIVES: Computational biology analyses the theoretical tertiary structure of proteins and identifies the 'topological' differences between RhD and RhCE. Our aim was to identify the theoretical structural differences between the four isoforms of RhCE and RhD using computational biological tools. MATERIALS AND METHODS: Physicochemical profile was determined by hydrophobicity and electrostatic potential analysis. Secondary and tertiary structures were generated using computational biology tools. The structures were evaluated and validated using Ramachandran algorithm, which calculates the single score, p-value and root mean square deviation (RMSD). Structures were overlaid on local refinement of 'RhAG-RhCE-ANK' (PBDID 7uzq) and RhAG to compare their spatial distribution within the membrane. RESULTS: All proteins differed in surface area and electrostatic distance due to variations in hydrophobicity and electrostatic potential. The RMSD between RhD and RhCE was 0.46 ± 0.04 Å, and the comparison within RhCE was 0.57 ± 0.08 Å. The percentage of amino acids in the hydrophobic thickness was 50.24% for RhD while for RhCE it ranged between 73.08% and 76.68%. The RHAG hydrophobic thickness was 34.2 Å, and RhCE's hydrophobic thickness was 33.83 Å. We suggest that the C/c antigens differ exofacially at loops L1 and L2. For the E/e antigens, the difference lies in L6. By contrast, L4 is the same for all proteins except Rhce. CONCLUSION: The physicochemical properties of Rh proteins made them different, although their genes are homologous. Using computational biology, we model structures with sufficient precision, similar to those obtained experimentally. An amino acid variation alters the folding of the tertiary structure and the interactions with other proteins, modifying the electrostatic environment, the spatial conformations and therefore the antigenic recognition.

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The octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was investigated using atomistic molecular dynamics simulations via thermodynamic integration and multistate Bennett acceptance ratio methods. The GAFF and CHARMM36 force fields were used with six water models widely used in molecular dynamics simulations. The OPC4 water model provided the best agreement with the experimental octanol-water partition coefficient of DPPC using the two force fields. However, there is still plenty of room for improvement in water models with correct estimation of surface tension that uses better and suitable non-bonded interaction parameters between water-water and water-DPPC. The Gibbs free energy of transferring DPPC from octanol to water phase was calculated to be 19.8 ± 0.3 and 20.2 ± 0.3 kcal mol-1, giving a partition coefficient of 14.5 ± 0.4 and 14.8 ± 0.3 for the GAFF and CHARMM36 force fields, respectively. This study reinforces the importance of developing new water models that reproduce experimental surface tensions to reconcile the water-water and water-DPPC non-bonded interactions and the existing discrepancy between experimental measurements of amphiphilic molecules that are important in many areas of scientific applications and industry such as biophysics, surfactant, colloids, membranes, medicine, nanotechnology, and food and pharmaceutical industries, and so on. It raises two important open questions: Is the experimental octanol-water partition coefficient of DPPC reliable? Or is its calculation accurate using the OPC4 water model? With respect to the experimental measurements, there may be non-treated aspects such as the formation of aggregates in aqueous phase and limit of detection of the applied method. And, in the calculation, some effects are not possible to be considered in a correct way or viable time such as calculating quantum effects, sampling all conformations, considering phase transitions, and correctly evaluating the intermolecular forces to estimate an accurate surface tension.Communicated by Ramaswamy H. Sarma.

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In this work, we propose a method to harvest liquid water from water vapor using carbon nanocones. The condensation occurs due to the presence of hydrophilic sites at the nanocone entrance. The functionalization, together with the high mobility of water inside nanostructures, leads to a fast water flow through the nanostructure. We show using molecular dynamics simulations that this device is able to collect water if the surface functionalization is properly selected.

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Bacteria persisting in environments contaminated with polycyclic aromatic hydrocarbons (PAHs) have developed physiological mechanisms to counteract environmental stress. Inorganic polyphosphate accumulation represents one of these possible mechanisms. Likewise, properties such as cell-surface hydrophobicity, auto-aggregation, biofilm formation and bioemulsifying activity could facilitate interaction of microorganisms with hydrophobic organic compounds. In this work, these physiological properties were compared in indigenous bacteria from polluted sediments from Argentinian Patagonia, which were cultivated in two culture media (LBm and JPP) as a way to improve in the next future the PAHs removal. The highest hydrophobicity values were obtained in Rhodococcus strains, while Bacillus sp. B18 showed the highest auto-aggregation percentage and emulsion index. The highest numerical values of biofilm formation were determined in Rhodococcus sp. F27, Pseudomonas sp. P26, and Gordonia sp. H19 either on hydrophilic or on hydrophobic support. The qualitative and quantitative polyP determinations confirmed the presence of this biopolymer in the strains evaluated. The highest intracellular phosphate mean values were obtained in Bacillus sp. B18 in LBm and Rhodococcus erythropolis 20 in JPP. The bacteria evaluated belonging to different genera showed significant differences in their cell-surface characteristics, bioemulsifying activity and polyP accumulation. The low-cost JPP culture medium was selected for future contaminant removal studies.

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The sorption of pharmaceuticals on activated sludge during the wastewater treatment process has been widely studied and considered one of the main mechanisms for the removal of these micropollutants from domestic sewage. Understanding the removal mechanism is important to reduce the environmental risk associated with these compounds. To the best of our knowledge, no data are reporting the influence of the aeration rate and, consequently, of the physicochemical properties of the sludge flocs, on the sorption of pharmaceutical compounds. In this context, the influence of the aeration rate (2, 5, and 8 L min-1) on the physical properties of the sludge and the sorption of two emerging pharmaceuticals, 17-alpha-ethynylestradiol (EE2) and diclofenac (DCF), was evaluated. The pharmaceuticals were analyzed by Solid Phase Extraction and Liquid Chromatography, and the sludge by Laser Particle Size Analyzer and Settling Curves. As a result, higher sorption for 17-alpha-ethinylestradiol (78-96%) in comparison to diclofenac (23-43%) was observed, corroborating the greater hydrophobicity of EE2. Higher pharmaceuticals removal rates were observed for the highest aeration (10.02 µgEE2 gSST-1 and 3.99 µgDCF gSST-1) in comparison to the lowest one (7.81 µgEE2 gSST-1 and 2.58 µgDCF gSST-1), what can be attributed to structural and surface changes in flocs. Smaller and more dispersed flocs were observed when aeration was increased (104.4 µm for 8 L min-1 and 63.8 µm for 2 L min-1). The results suggest that the increase in aeration seems to be promising for the removal of pharmaceuticals by sorption in sewage sludge, especially for the hydrophobic ones.

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The consumption of plant proteins is increasing worldwide. These proteins have an important role in human nutrition as well as in the technological properties of foods. Thus, there is a great interest in exploring new sources of plant proteins, such as macauba (Acrocomia aculeata), which is a promising tropical palm tree, native to Brazil, whose fruits are rich in oil, proteins and dietary fiber. Hence, the objective of this work was to obtain and evaluate the physico-chemical and techno-functional properties of the macauba kernel protein isolate (MKPI). Defatted macauba kernel flour was obtained and used to produce the MKPI by isoelectric precipitation. Then, the proximate composition, amino acid profile, and physico-chemical and techno-functional properties of the MKPI were determined. The MKPI stood out for its high protein content (94.9%) and high levels of arginine (16.21%) and glutamate (20.84%). The MKPI average isoelectric point was at pH 4.9 and its proteins showed low solubility in the pH range from 4.0 to 6.0. Moreover, the hydrophobicity of MKPI proteins was higher at pH 3.5 than at pH 7.0, and they had higher oil holding capacity (153.77%) than water holding capacity (97.29%). Regarding the MKPI emulsifying and gelling properties, emulsions with 0.5% and 1.0% of MKPI remained stable during storage and the minimum gelling concentration was 14%. Thus, the MKPI has a great potential to be produced and used by the food industry due to its nutritional and techno-functional properties.

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The therapeutic potential of venom-derived peptides, such as bioactive peptides (BAPs), is determined by specificity, stability, and pharmacokinetics properties. BAPs, including anti-infective or antimicrobial peptides (AMPs) and cell-penetrating peptides (CPPs), share several physicochemical characteristics and are potential alternatives to antibiotic-based therapies and drug delivery systems, respectively. This study used in silico methods to predict AMPs and CPPs derived from natterins from the venomous fish Thalassophryne nattereri. Fifty-seven BAPs (19 AMPs, 8 CPPs, and 30 AMPs/CPPs) were identified using the web servers CAMP, AMPA, AmpGram, C2Pred, and CellPPD. The physicochemical properties were analyzed using ProtParam, PepCalc, and DispHred tools. The membrane-binding potential and cellular location of each peptide were analyzed using the Boman index by APD3, and TMHMM web servers. All CPPs and two AMPs showed high membrane-binding potential. Fifty-four peptides were located in the plasma membrane. Peptide immunogenicity, toxicity, allergenicity, and ADMET parameters were evaluated using several web servers. Sixteen antiviral peptides and 37 anticancer peptides were predicted using the web servers Meta-iAVP and ACPred. Secondary structures and helical wheel projections were predicted using the PEP-FOLD3 and Heliquest web servers. Fifteen peptides are potential lead compounds and were selected to be further synthesized and tested experimentally in vitro to validate the in silico screening. The use of computer-aided design for predicting peptide structure and activity is fast and cost-effective and facilitates the design of potent therapeutic peptides. The results demonstrate that toxins form a natural biotechnological platform in drug discovery, and the presence of CPP and AMP sequences in toxin families opens new possibilities in toxin biochemistry research.

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We have studied the external surface (elytra) of the Sonoran Desert beetle (Eleodes eschscholtzii). Our aim was to assess whether this species has similar traits to some beetles from the Namibian Desert that are known to have hierarchical micropatterns that allow for water harvesting. We have conducted scanning electron microscopy (SEM) and apparent contact angle experiments on specimens collected at two sampling sites with different ambient humidity. The results show that the beetle's external surface microstructure is composed of a compact array of polygons with randomly scattered protuberances. The density of the polygons in the microstructure is different for individuals collected in different sites: the polygon array is denser in the more humid site and less dense in the drier site. The measured contact angles also depend on the sampling site. For individuals collected in the drier site, the average apparent contact angle is 70°, whereas for the more humid site, the average apparent contact angle is 92°. FT-IR experiments are consistent with the presence of hydrophobic wax compounds in the studied surfaces. Our investigation opens new questions that are currently being addressed by experiments that are underway. For instance, it would be interesting to know whether the observed nanopatterns could be used in biomimetic devices for water harvesting purposes.

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We have developed a clean route for the modification of polyvinylchloride surface (PVC) with 4-amino-5-hydrazino-1,2,4-triazole-3-thiol molecule. The modification reaction was investigated through Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Photoelectron Spectroscopy (XPS) analysis. According to our findings, S-H groups are responsible to the molecule attachment and nitrogen atoms are directly involved in metal ion coordination. These results are in agreement with the pseudo-second-order kinetic model, which infers that chemisorption is the main mechanism for metal removal. Adsorption isotherms of Cd(II), Cu(II) and Pb(II) follow the Langmuir model and the results indicated that Ns values are 0.39, 0.52 and 0.15 mmol g-1, respectively. The calculated Ømax values for Cu(II), Pb(II) and Cd(II) were 3.93, 2.95 and 1.13, respectively, indicating that three types of complex are formed depending on the adsorbed species. Therefore, it can be concluded that PVC use as adsorbent is feasible since it requires a simple modification reaction with nontoxic and low-cost solvents.

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Abstract Fluoroquinolones are an important class of antimicrobial agents to manage infectious diseases. However, knowledge about how host bile acids are modified by fluoroquinolones is limited. We investigated and compared the impact of fluoroquinolones on circulating bile acid profiles and gut microbiota from in vivo studies. We administered ciprofloxacin (100 mg/kg/day) or moxifloxacin (40 mg/kg/day) orally to male Wistar rats for seven days. Fifteen bile acids (BAs) from the serum and large intestine were quantified by HPLC-MS/MS. The diversity of gut microbiota after ciprofloxacin and moxifloxacin treatment was analyzed using high-throughput, next-generation sequencing technology. The two fluoroquinolone-treated groups had different BA profiles. Ciprofloxacin significantly reduced the hydrophobicity index of the BA pool, reduced secondary BAs, and increased taurine-conjugated primary BAs in both the serum and large intestine as compared with moxifloxacin. Besides, ciprofloxacin treatment altered intestinal microbiota with a remarkable increase in Firmicutes to Bacteroidetes ratio, while moxifloxacin exerted no effect. What we found suggests that different fluoroquinolones have a distinct effect on the host BAs metabolism and intestinal bacteria, and therefore provide guidance on the selection of fluoroquinolones to treat infectious diseases.

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Bacterial cell surface hydrophobicity is a relevant property in determining the ability of bacteria to adhere to inert surfaces. This property has been measured using the microbial adhesion to hydrocarbon (MATH) test. Several reports in the literature establish the percentage of adhesion to hydrocarbons (PoAtH) value produced by the MATH test for a broad variety of bacteria. Discrepancies in PoAtH values reported for the same strain of a specific microorganism suggest that some method-induced variation may exist, as different research teams employ different versions of the assay. The objective of the present study was to compare the performance of different versions of the MATH test as reported in the literature, to quantify the magnitude of the method-induced variation on PoAtH values. The study demonstrated that PoAtH values are influenced twice as much by variations in the employed assay than by actual differences in cell surface composition or architecture. The two L. reuteri strains studied responded differently to changes in assay conditions showing 40 and 70% method-dependent variation for strain ATCC 53609 and 55730, respectively. These results highlight the need to properly standardize the MATH test to enable comparison of PoAtH values produced by independent research teams.

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The objective of this study was to compare the potential of mono-rhamnolipids (mono-RML) and di-rhamnolipids (di-RML) against biofilm formation on carbon steel coupons submitted to oil produced water for 14 days. The antibiofilm effect of the RML on the coupons was analyzed by scanning electron microscopy (SEM) and by epifluorescence microscopy, and the contact angle was measured using a goniometer. SEM analysis results showed that all RML congeners had effective antibiofilm action, as well as preliminary anticorrosion evaluation confirmed that all RML congeners prevented the metal deterioration. In more detail, epifluorescence microscopy showed that mono-RML were the most efficient congeners in preventing microorganism's adherence on the carbon steel metal. Image analyses indicate the presence of 15.9%, 3.4%, and <0.1% of viable particles in di-RML, mono/di-RML and mono-RML pretreatments, respectively, in comparison to control samples. Contact angle results showed that the crude carbon steel coupon presented hydrophobic character favoring hydrophobic molecules adhesion. We calculated the theoretical polarity of the RML congeners and verified that mono-RML (log P = 3.63) presented the most hydrophobic character. This had perfect correspondence to contact angle results, since mono-RML conditioning (58.2°) more significantly changed the contact angle compared with the conditioning with one of the most common surfactants used on oil industry (29.4°). Based on the results, it was concluded that rhamnolipids are efficient molecules to be used to avoid biofilm on carbon steel metal when submitted to oil produced water and that a higher proportion of mono-rhamnolipids is more indicated for this application.

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Enzymes are highly significant catalysts, essential to biological systems, and a source of inspiration for the design of artificial enzymes. Although many models have been developed describing enzymatic catalysis, a deeper understanding of these biocatalysts remains a major challenge. Herein we detail the formation, characterization, performance, and catalytic mechanisms of a series of bio-inspired supramolecular polymer/surfactant complexes acting as artificial enzymes. The supramolecular complexes were characterized and exhibited exceptional catalytic efficiency for the dephosphorylation of an activated phosphate diester, the reaction rate being highly responsive to: (a) pH, (b) surfactant concentration, and (c) the length of the hydrophobic chain of the surfactant. Under optimal conditions (at pH > 8 for the more hydrophobic systems and at pre-micellar concentrations), enzyme-like rate enhancements of up to 6.0 × 109-fold over the rate of the spontaneous hydrolysis reaction in water were verified. The catalytic performance is a consequence of synergy between the hydrophobicity of the aggregates and the catalytic functionalities of the polymer and the catalytic mechanism is modulated by the nature of the hydrophobic pockets of these catalysts, changing from a general base mechanism to a nucleophilic mechanism as the hydrophobicity increases. Taken as a whole, the present results provide fundamental insights, through an understandable model, which are highly relevant to the design of novel bioinspired enzyme surrogates with multifunctional potentialities for future practical applications.

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The aggregation of Aß42 peptides is considered as one of the main causes for the development of Alzheimer's disease. In this context, Zn2+ and Cu2+ play a significant role in regulating the aggregation mechanism, due to changes in the structural and the solvation free energy of Aß42. In practice, experimental studies are not able to determine the latter properties, since the Aß42-Zn2+ and Aß42-Cu2+ peptide complexes are intrinsically disordered, exhibiting rapid conformational changes in the aqueous environment. Here, we investigate atomic structural variations and the solvation thermodynamics of Aß42, Aß42-Cu2+ , and Aß42-Zn2+ systems in explicit solvent (water) by using quantum chemical structures as templates for a metal binding site and combining extensive all-atom molecular dynamics (MD) simulations with a thorough solvation thermodynamic analysis. Our results show that the zinc and copper coordination results in a significant decrease of the solvation free energy in the C-terminal region (Met35-Val40), which in turn leads to a higher structural disorder. In contrast, the ß-sheet formation at the same C-terminal region indicates a higher solvation free energy in the case of Aß42. The solvation free energy of Aß42 increases upon Zn2+ binding, due to the higher tendency of forming the ß-sheet structure at the Leu17-Ala42 residues, in contrast to the case of binding with Cu2+ . Finally, we find the hydrophobicity of Aß42-Zn2+ in water is greater than in the case of Aß42-Cu2+ .

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Polymicrobial infections are one of the most common reasons for inflammation of surrounding tissues and failure of implanted biomaterials. Because microorganism adhesion is the first step for biofilm formation, physical-chemical modifications of biomaterials have been proposed to reduce the initial microbial attachment. Thus, the use of superhydrophobic coatings has emerged because of their anti-biofilm properties. However, these coatings on the titanium (Ti) surface have been developed mainly by dual-step surface modification techniques and have not been tested using polymicrobial biofilms. Therefore, we developed a one-step superhydrophobic coating on the Ti surface by using a low-pressure plasma technology to create a biocompatible coating that reduces polymicrobial biofilm adhesion and formation. The superhydrophobic coating on Ti was created by the glow discharge plasma using Ar, O2, and hexamethyldisiloxane gases, and after full physical, chemical, and biological characterizations, we evaluated its properties regarding oral biofilm inhibition. The newly developed coating presented an increased surface roughness and, consequently, superhydrophobicity (contact angle over 150°) and enhanced corrosion resistance (p < 0.05) of the Ti surface. Furthermore, proteomic analysis showed a unique pattern of protein adsorption on the superhydrophobic coating without drastically changing the biologic processes mediated by proteins. Additionally, superhydrophobic treatment did not present a cytotoxic effect on fibroblasts or reduction of proliferation; however, it significantly reduced (≈8-fold change) polymicrobial adhesion (bacterial and fungal) and biofilm formation in vitro. Interestingly, superhydrophobic coating shifted the microbiological profile of biofilms formed in situ in the oral cavity, reducing by up to ≈7 fold pathogens associated with the peri-implant disease. Thus, this new superhydrophobic coating developed by a one-step glow discharge plasma technique is a promising biocompatible strategy to drastically reduce microbial adhesion and biofilm formation on Ti-based biomedical implants.

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Bacteria and archaea accumulate cytoplasmic polyhydroxyalkanoate (PHA) granules under nutrient-limited conditions with excess carbon. The transcriptional regulatory (TR) proteins found on the surface of PHA granules act as repressors as well as activators for the expression of major surface proteins called phasins. Until now, detailed information on the evolutionary relationships between these transcription regulators has not been available. Here, we conducted homology searches and analyzed information available for the domains and protein families of the TR proteins through phylogenetic studies. A total of 282 TR proteins were identified and further classified into four distinct subfamilies based upon the presence of conserved motifs: PHB_acc, TetR-like, AbrB-like, and PadR-like. Depending upon the particular family, the DNA-binding domains were located at either the N- or C-terminus. Our results indicated that TR proteins containing the PHB_acc domain are highly conserved within the bacteria, while other TR proteins are present only within archaea (AbrB-like), gram positive bacteria (PadR-like), or the Pseudomonas genera (TetR-like). The repression domains are charged, hydrophobic, and rich in leucine or glutamine. In phylogenetic analyses, many groups of TR proteins were clustered together according to identical domain architectures showing the independent origins of the TR proteins in the PHA reserve storage system. Further analyses revealed that the TR proteins have experienced multiple gene duplications across prokaryotes. Thus, this study investigated the evolutionary framework of TR proteins and has provided a comprehensive catalog of TR proteins for ongoing studies to characterize the functions of these proteins within diverse organisms.

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The emerging opportunistic pathogens comprising the Candida haemulonii complex (C. haemulonii [Ch], C. duobushaemulonii [Cd] and C. haemulonii var. vulnera[Chv]) are notable for their intrinsic antifungal resistance. Different clinical manifestations are associated with these fungal infections; however, little is known about their biology and potential virulence attributes. Herein, we evaluated some surface properties of 12 clinical isolates of Ch (n = 5), Cd (n = 4) and Chv (n = 3) as well as their virulence on murine macrophages and Galleria mellonella larvae. Scanning electron microscopy demonstrated the presence of homogeneous populations among the species of the C. haemulonii complex, represented by oval yeasts with surface irregularities able to form aggregates. Cell surface hydrophobicity was isolate-specific, exhibiting high (16.7%), moderate (25.0%) and low (58.3%) hydrophobicity. The isolates had negative surface charge, except for one. Mannose/glucose- and N-acetylglucosamine-containing glycoconjugates were evidenced in considerable amounts in all isolates; however, the surface expression of sialic acid was poorly detected. Cd isolates presented significantly higher amounts of chitin than Ch and Chv. Membrane sterol and lipid bodies, containing neutral lipids, were quite similar among all fungi studied. All isolates adhered to inert surfaces in the order: polystyrene > poly-L-lysine-coated glass > glass. Likewise, they interacted with murine macrophages in a quite similar way. Regarding in vivo virulence, the C. haemulonii species complex were able to kill at least 80% of the larvae after 120 hours. Our results evidenced the ability of C. haemulonii complex to produce potential surface-related virulence attributes, key components that actively participate in the infection process described in Candida spp.

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