Biogenic Nanosilver against Multidrug-Resistant Bacteria (MDRB)

Multidrug-resistant bacteria (MDRB) are extremely dangerous and bring a serious threat to health care systems as they can survive an attack from almost any drug. The bacteria's adaptive way of living with the use of antimicrobials and antibiotics caused them to modify and prevail in hostile conditions by creating resistance to known antibiotics or their combinations. The emergence of nanomaterials as new antimicrobials introduces a new paradigm for antibiotic use in various fields. For example, silver nanoparticles (AgNPs) are the oldest nanomaterial used for bactericide and bacteriostatic purposes. However, for just a few decades these have been produced in a biogenic or bio-based fashion. This review brings the latest reports on biogenic AgNPs in the combat against MDRB. Some antimicrobial mechanisms and possible silver resistance traits acquired by bacteria are also presented. Hopefully, novel AgNPs-containing products might be designed against MDR bacterial infections.

Bio-based synthesis of silver nanoparticles from orange waste: effects of distinct biomolecule coatings on size, morphology, and antimicrobial activity

Purpose

Despite the numerous reports on biological syntheses of silver nanoparticles (AgNPs), little is known about the composition of their capping agents, protein corona of plant extract-mediated synthesis, and their influence on the properties of AgNPs. Here, orange (Citrus sinensis) waste was utilized as a source of an extract for AgNP synthesis (the protein corona composition of which was elucidated), and also as a starting material for hesperidin and nanocellulose extraction, which were used for bio-based AgNP synthesis. A comparison of the results using the two methods of synthesis is presented.

Methods

AgNPs were synthesized using orange (C. sinensis) peel extract (Or-AgNPs) in a biological route, and using hesperidin (Hsd-AgNPs) and nanocellulose (extracted from oranges) in a green chemical route. Characterization of nanoparticles was carried out using zeta potential and hydrodynamic size measurements, transmission electron microscopy, and X-ray diffraction. Elucidation of proteins from protein corona was performed via ultra performance liquid chromatography-tandem mass spectrometer experiments. Antimicrobial activity was assessed via minimum inhibitory concentration assays against Xanthomonas axonopodis pv. citri (Xac), the bacterium that causes citric canker in oranges.

Results

Or-AgNPs were not completely uniform in morphology, having a size of 48.1±20.5 nm and a zeta potential of −19.0±0.4 mV. Stabilization was performed mainly by three proteins, which were identified by tandem mass spectrometry (MS/MS) experiments. Hsd-AgNPs were smaller (25.4±12.5 nm) and had uniform morphology. Nanocellulose provided a strong steric and electrostatic (−28.2±1.0 mV) stabilization to the nanoparticles. Both AgNPs presented roughly the same activity against Xac, with the minimum inhibitory concentration range between 22 and 24 μg mL⁻¹.

Conclusion

Despite the fact that different capping biomolecules on AgNPs had an influence on morphology, size, and stability of AgNPs, the antibacterial activity against Xac was not sensitive to this parameter. Moreover, three proteins from the protein corona of Or-AgNPs were identified.

Qualitative and Quantitative NMR Approaches in Blood Serum Lipidomics

Nuclear magnetic resonance (NMR) spectroscopy in combination with chemometrics can be applied in the analysis of complex biological samples in many ways. For example, we can analyze lipids, elucidate their structures, determine their nutritional values, and determine their distribution in blood serum. As lipids are not soluble in water, they are transported in blood as lipid-rich self-assembled particles, divided into different density assemblies from high- to very-low-density lipoproteins (HDL to VLDL), or by combining with serum proteins, such as albumins (human serum albumins (HSA)). Therefore, serum lipids can be analyzed as they are using only a 1:1 (v/v) dilution with a buffer or deuterated water prior to analysis by applying ¹H NMR or ¹H NMR edited-by-diffusion techniques. Alternatively, lipids can be extracted from the serum using liquid partition equilibrium and then analyzed using liquid-state NMR techniques. Our chapter describes protocols that are used for extraction of blood serum lipids and their quantitative ¹H NMR (¹H qNMR) analysis in lipid extracts as well as ¹H NMR edited by diffusion for direct blood serum lipid analysis.

A preliminary study of bipolar disorder type I by mass spectrometry-based serum lipidomics

The present study aimed at investigating possible alterations in the serum lipid profile of euthymic patients with bipolar disorder type I (BD) compared to healthy controls (HC). Thirty-five individuals from both genders were recruited, with 14 diagnosed and treated as BD patients (BD group) and 21 healthy subjects (HC group). Clinical assessment was based on the Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), Young Mania Rating Scale (YMRS), and 17-items of Hamilton Depression Rating Scale (HDRS-17) data, which were used to confirm diagnosis, to verify psychiatric comorbidities, and to estimate the severity of manic and depressive symptoms. Ultra-high performance liquid chromatography (UHPLC) coupled to high resolution mass spectrometry (HRMS) was applied to analyze the lipids extracted from all serum samples from both studied groups. In this pioneer and exploratory study, we observed different serum lipid profiles for BD and HC groups, especially regarding glycerophospholipid, glycerolipid, and sphingolipid distribution. Multivariate statistical analyses indicated that 121 lipids were significantly different between BD and HC. Phosphatidylinositols were identified as the most altered lipids in BD patient sera. The results of this preliminary study reinforce the role of lipid abnormalities in BD and offer additional methodological possibilities for investigation in the field.

Analytical approaches for lipidomics and its potential applications in neuropsychiatric disorders

OBJECTIVES

In this review, the authors discuss an overview of lipidomics followed by in-depth discussion of its application to the study of human diseases, including extraction methods of lipids, analytical techniques and clinical research in neuropsychiatric disorders.

METHODS

Lipidomics is a lipid-targeted metabolomics approach aiming at the comprehensive analysis of lipids in biological systems. Recent technological advancements in mass spectrometry and chromatography have greatly enhanced the development and applications of metabolic profiling of diverse lipids in complex biological samples.

RESULTS

An effective evaluation of the clinical course of diseases requires the application of very precise diagnostic and assessment approaches as early as possible. In order to achieve this, "omics" strategies offer new opportunities for biomarker identification and/or discovery in complex diseases and may provide pathological pathways understanding for diseases beyond traditional methodologies.

CONCLUSIONS

This review highlights the importance of lipidomics for the future perspectives as a tool for biomarker identification and discovery and its clinical application.

Metabolomics and lipidomics analyses by 1H nuclear magnetic resonance of schizophrenia patient serum reveal potential peripheral biomarkers for diagnosis

Using ¹H NMR-based metabolomics in association to chemometrics analysis, we analyzed here the metabolic differences between schizophrenia patients (SCZ) compared to healthy controls (HCs). HCs and SCZ patients underwent clinical interview using the Structured Clinical Interview for DSM Disorders (SCID). SCZ patients were further assessed by Positive and Negative Syndrome Scale (PANSS), Calgary Depression Scale, Global Assessment of Functioning Scale (GAF), and Clinical Global Impressions Scale (CGI). Using the principal component analysis (PCA) and supervised partial least-squares discriminate analysis (PLS-DA) in obtained NMR data, a clear group separation between HCs and SCZ patients was achieved. Interestingly, all metabolite compounds identified as exclusively present in the SCZ group, except for the gamma-aminobutyric acid (GABA), were never previously associated with mental disorders. Although the initial perception of an absence of obvious biological link among the different key molecules exclusively observed in each group, and no identification of any specific pathway yet, the present work represents an important contribution for the identification of potential biomarkers to inform diagnosis, as it was possible to completely separate the affected SCZ patients from HCs, with no outliers or exceptions. In addition, the data presented here reinforced the role of the modulation of glycolysis pathway and the loss of GABA interneuron/hyperglutamate hypothesis in SCZ.

1H-NMR, 1H-NMR T2-edited, and 2D-NMR in bipolar disorder metabolic profiling

Background

The objective of this study was to identify molecular alterations in the human blood serum related to bipolar disorder, using nuclear magnetic resonance (NMR) spectroscopy and chemometrics.

Methods

Metabolomic profiling, employing ¹H-NMR, ¹H-NMR T₂-edited, and 2D-NMR spectroscopy and chemometrics of human blood serum samples from patients with bipolar disorder (n = 26) compared with healthy volunteers (n = 50) was performed.

Results

The investigated groups presented distinct metabolic profiles, in which the main differential metabolites found in the serum sample of bipolar disorder patients compared with those from controls were lipids, lipid metabolism-related molecules (choline, myo-inositol), and some amino acids (N-acetyl-l-phenyl alanine, N-acetyl-l-aspartyl-l-glutamic acid, l-glutamine). In addition, amygdalin, α-ketoglutaric acid, and lipoamide, among other compounds, were also present or were significantly altered in the serum of bipolar disorder patients. The data presented herein suggest that some of these metabolites differentially distributed between the groups studied may be directly related to the bipolar disorder pathophysiology.

Conclusions

The strategy employed here showed significant potential for exploring pathophysiological features and molecular pathways involved in bipolar disorder. Thus, our findings may contribute to pave the way for future studies aiming at identifying important potential biomarkers for bipolar disorder diagnosis or progression follow-up.

Electronic supplementary material

The online version of this article (doi:10.1186/s40345-017-0088-2) contains supplementary material, which is available to authorized users.

Discovery of small molecule inhibitors for the snake venom metalloprotease BaP1 using in silico and in vitro tests

Snakebites represent an important public health problem, with a great number of victims with permanent sequelae or fatal outcomes, particularly in rural, agriculturally active areas. The snake venom metalloproteases (SVMPs) are the principal proteins responsible for some clinically-relevant effects, such as local and systemic hemorrhage, dermonecrosis, and myonecrosis. Because of the difficulties in neutralizing them rapidly and locally by antivenoms, the search and design of small molecules as inhibitors of SVMPs are proposed. The Bothrops asper metalloprotease P1 (BaP1) is hereby used as a target protein and by High Throughput Virtual Screening (HTVS) approach, the free access virtual libraries: ZINC, PubChem and ChEMBL, were searched for potent small molecule inhibitors. Results from the aforementioned approaches provided strong evidences on the structural requirements for the efficient BaP1 inhibition such as the presence of the pyrimidine-2,4,6-trione moiety. The two proposed compounds have also shown excellent results in performed in vitro interaction studies against BaP1.

Antimicrobial textiles: Biogenic silver nanoparticles against Candida and Xanthomonas

This paper introduces cotton fibers impregnated with biogenic silver nanoparticles (AgNPs), synthesized from a Fusarium oxysporum fungal filtrate (FF) solution, and open up the possibility for their use in medical environment and agriculture clothing as means to avoid microbial spreading. After thorough AgNPs characterization, regarding their physical, chemical and biochemical properties, Minimum Inhibitory Concentrations (MIC) against some human and orange tree pathogens were determined. We report the strong AgNPs activity against Candida parapsilosis and Xanthomonas axonopodis pv. citri (Xac) that was morphologically characterized, pointing to strong AgNPs effects on microorganisms' membranes. Cotton fibers were then impregnated with AgNPs suspension and these maintained strong antimicrobial activity even after repeated mechanical washing cycles (up to 10). Reported data might point to an application for biogenic AgNPs as potent agrochemicals, as well as, to their application in textiles for antiseptic clothing for medical and agronomic applications.

In vitro Determination of Extracellular Proteins from Xylella fastidiosa

The phytopathogen Xylella fastidiosa causes economic losses in important agricultural crops. Xylem vessel occlusion caused by biofilm formation is the major mechanism underlying the pathogenicity of distinct strains of X. fastidiosa. Here, we provide a detailed in vitro characterization of the extracellular proteins of X. fastidiosa. Based on the results, we performed a comparison with a strain J1a12, which cannot induce citrus variegated chlorosis symptoms when inoculated into citrus plants. We then extend this approach to analyze the extracellular proteins of X. fastidiosa in media supplemented with calcium. We verified increases in extracellular proteins concomitant with the days of growth and, consequently, biofilm development (3-30 days). Outer membrane vesicles carrying toxins were identified beginning at 10 days of growth in the 9a5c strain. In addition, a decrease in extracellular proteins in media supplemented with calcium was observed in both strains. Using mass spectrometry, 71 different proteins were identified during 30 days of X. fastidiosa biofilm development, including proteases, quorum-sensing proteins, biofilm formation proteins, hypothetical proteins, phage-related proteins, chaperones, toxins, antitoxins, and extracellular vesicle membrane components.

Elucidating Protein Involvement in the Stabilization of the Biogenic Silver Nanoparticles

Silver nanoparticles (AgNPs) have been broadly used as antibacterial and antiviral agents. Further, interests for green AgNP synthesis have increased in recent years and several results for AgNP biological synthesis have been reported using bacteria, fungi and plant extracts. The understanding of the role and nature of fungal proteins, their interaction with AgNPs and the subsequent stabilization of nanosilver is yet to be deeply investigated. Therefore, in an attempt to better understand biogenic AgNP stabilization with the extracellular fungal proteins and to describe these supramolecular interactions between proteins and silver nanoparticles, AgNPs, produced extracellularly by Aspergillus tubingensis-isolated as an endophytic fungus from Rizophora mangle-were characterized in order to study their physical characteristics, identify the involved proteins, and shed light into the interactions among protein-NPs by several techniques. AgNPs of around 35 nm in diameter as measured by TEM and a positive zeta potential of +8.48 mV were obtained. These AgNPs exhibited a surface plasmon resonance (SPR) band at 440 nm, indicating the nanoparticles formation, and another band at 280 nm, attributed to the electronic excitations in tryptophan, tyrosine, and/or phenylalanine residues in fungal proteins. Fungal proteins were covalently bounded to the AgNPs, mainly through S-Ag bonds due to cysteine residues (HS-) and with few N-Ag bonds from H2N- groups, as verified by Raman spectroscopy. Observed supramolecular interactions also occur by electrostatic and other protein-protein interactions. Furthermore, proteins that remain free on AgNP surface may perform hydrogen bonds with other proteins or water increasing thus the capping layer around the AgNPs and consequently expanding the hydrodynamic diameter of the particles (~264 nm, measured by DLS). FTIR results enabled us to state that proteins adsorbed to the AgNPs did not suffer relevant secondary structure alteration upon their physical interaction with the AgNPs or when covalently bonded to them. Eight proteins in the AgNP dispersion were identified by mass spectrometry analyses. All these proteins are involved in metabolic pathways of the fungus and are important for carbon, phosphorous and nitrogen uptake, and for the fungal growth. Thereby, important proteins for fungi are also involved in the formation and stabilization of the biogenic AgNPs.

Advances in Chromobacterium violaceum and properties of violacein-Its main secondary metabolite: A review

Chromobacterium violaceum is important in the production of violacein, like other bacteria, such as Alteromonas, Janthinobacterium, Pseudoalteromonas, Duganella, Collimonas and Escherichia. Violacein is a versatile pigment, where it exhibits several biological activities, and every year, it shows increasing commercially interesting uses, especially for industrial applications in cosmetics, medicines and fabrics. This review on violacein focuses mainly on the last five years of research regarding this target compound and describes production and importance of quorum sensing in C. violaceum, mechanistic aspects of its biosynthesis, monitoring processes, genetic perspectives, pathogenic effects, antiparasitic and antimicrobial activities, immunomodulatory potential and uses, antitumor potential and industrial applications.

Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design

The term "agrochemicals" is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, therefore allowing for economically sound and labor efficient agricultural production. A "drug" on the other side is a term that is used for compounds designed for controlling human diseases. Although drugs are subjected to much more severe testing and regulation procedures before reaching the market, they might contain exactly the same active ingredient as certain agrochemicals, what is the case described in present work, showing how a small chemical compound might be used to control pathogenicity of Gram negative bacteria Xylella fastidiosa which devastates citrus plantations, as well as for control of, for example, meningitis in humans. It is also clear that so far the production of new agrochemicals is not benefiting as much from the in silico new chemical compound identification/discovery as pharmaceutical production. Rational drug design crucially depends on detailed knowledge of structural information about the receptor (target protein) and the ligand (drug/agrochemical). The interaction between the two molecules is the subject of analysis that aims to understand relationship between structure and function, mainly deciphering some fundamental elements of the nanoenvironment where the interaction occurs. In this work we will emphasize the role of understanding nanoenvironmental factors that guide recognition and interaction of target protein and its function modifier, an agrochemical or a drug. The repertoire of nanoenvironment descriptors is used for two selected and specific cases we have approached in order to offer a technological solution for some very important problems that needs special attention in agriculture: elimination of pathogenicity of a bacterium which is attacking citrus plants and formulation of a new fungicide. Finally, we also briefly describe a workflow which might be useful when research requires that model structures of target proteins are firstly generated (starting from genome sequences), followed by identification of ligand-target sites at the surface of those modeled structures, then application of procedures that adequately prepare both protein and ligand structures (the latter also involving filtration that satisfies acceptable adsorption/desorption/metabolism/excretion/toxicity [ADMET] parameters) for virtual high throughput screening (involving docking of ligands to indicated sites) and terminating by ranking of best pairs: target protein with selected ligand.

VapD in Xylella fastidiosa Is a Thermostable Protein with Ribonuclease Activity

Xylella fastidiosa strain 9a5c is a gram-negative phytopathogen that is the causal agent of citrus variegated chlorosis (CVC), a disease that is responsible for economic losses in Brazilian agriculture. The most well-known mechanism of pathogenicity for this bacterial pathogen is xylem vessel occlusion, which results from bacterial movement and the formation of biofilms. The molecular mechanisms underlying the virulence caused by biofilm formation are unknown. Here, we provide evidence showing that virulence-associated protein D in X. fastidiosa (Xf-VapD) is a thermostable protein with ribonuclease activity. Moreover, protein expression analyses in two X. fastidiosa strains, including virulent (Xf9a5c) and nonpathogenic (XfJ1a12) strains, showed that Xf-VapD was expressed during all phases of development in both strains and that increased expression was observed in Xf9a5c during biofilm growth. This study is an important step toward characterizing and improving our understanding of the biological significance of Xf-VapD and its potential functions in the CVC pathosystem.

Enhanced materials from nature: nanocellulose from citrus waste

Nanocellulose is a relatively inexpensive, highly versatile bio-based renewable material with advantageous properties, including biodegradability and nontoxicity. Numerous potential applications of nanocellulose, such as its use for the preparation of high-performance composites, have attracted much attention from industry. Owing to the low energy consumption and the addition of significant value, nanocellulose extraction from agricultural waste is one of the best alternatives for waste treatment. Different techniques for the isolation and purification of nanocellulose have been reported, and combining these techniques influences the morphology of the resultant fibers. Herein, some of the extraction routes for obtaining nanocellulose from citrus waste are addressed. The morphology of nanocellulose was determined by Scanning Electron Microscopy (SEM) and Field Emission Scanning Electron Microscopy (FESEM), while cellulose crystallinity indexes (CI) from lyophilized samples were determined using solid-state Nuclear Magnetic Resonance (NMR) and X-Ray Diffraction (XRD) measurements. The resultant nanofibers had 55% crystallinity, an average diameter of 10 nm and a length of 458 nm.