Showing papers by "Enzo A. Palombo published in 2016"

A review of analytical techniques and their application in disease diagnosis in breathomics and salivaomics research

Abstract: The application of metabolomics to biological samples has been a key focus in systems biology research, which is aimed at the development of rapid diagnostic methods and the creation of personalized medicine. More recently, there has been a strong focus towards this approach applied to non-invasively acquired samples, such as saliva and exhaled breath. The analysis of these biological samples, in conjunction with other sample types and traditional diagnostic tests, has resulted in faster and more reliable characterization of a range of health disorders and diseases. As the sampling process involved in collecting exhaled breath and saliva is non-intrusive as well as comparatively low-cost and uses a series of widely accepted methods, it provides researchers with easy access to the metabolites secreted by the human body. Owing to its accuracy and rapid nature, metabolomic analysis of saliva and breath (known as salivaomics and breathomics, respectively) is a rapidly growing field and has shown potential to be effective in detecting and diagnosing the early stages of numerous diseases and infections in preclinical studies. This review discusses the various collection and analyses methods currently applied in two of the least used non-invasive sample types in metabolomics, specifically their application in salivaomics and breathomics research. Some of the salient research completed in this field to date is also assessed and discussed in order to provide a basis to advocate their use and possible future scientific directions.

Archetypal tryptophan-rich antimicrobial peptides: properties and applications.

Abstract: Drug-resistant microorganisms ('superbugs') present a serious challenge to the success of antimicrobial treatments. Subsequently, there is a crucial need for novel bio-control agents. Many antimicrobial peptides (AMPs) show a broad-spectrum activity against bacteria, fungi or viruses and are strong candidates to complement or substitute current antimicrobial agents. Some AMPs are also effective against protozoa or cancer cells. The tryptophan (Trp)-rich peptides (TRPs) are a subset of AMPs that display potent antimicrobial activity, credited to the unique biochemical properties of tryptophan that allow it to insert into biological membranes. Further, many Trp-rich AMPs cross bacterial membranes without compromising their integrity and act intracellularly, suggesting interactions with nucleic acids and enzymes. In this work, we overview some archetypal TRPs derived from natural sources, i.e., indolicidin, tritrpticin and lactoferricin, summarising their biochemical properties, structures, antimicrobial activities, mechanistic studies and potential applications.

Anthelmintic activity of selected ethno-medicinal plant extracts on parasitic stages of Haemonchus contortus.

Abstract: Background Parasitic roundworms (nematodes) cause substantial morbidity and mortality in livestock animals globally, and considerable productivity losses to farmers. The control of these nematodes has relied largely on the use of a limited number of anthelmintics. However, resistance to many of these these anthelmintics is now widespread, and, therefore, there is a need to find new drugs to ensure sustained and effective treatment and control into the future.

Fecal microbiota and metabolome in a mouse model of spontaneous chronic colitis: Relevance to human inflammatory bowel disease

Abstract: Background: Dysbiosis of the gut microbiota may be involved in the pathogenesis of inflammatory bowel disease (IBD). However, the mechanisms underlying the role of the intestinal microbiome and metabolome in IBD onset and its alteration during active treatment and recovery remain unknown. Animal models of chronic intestinal inflammation with similar microbial and metabolomic profiles would enable investigation of these mechanisms and development of more effective treatments. Recently, the Winnie mouse model of colitis closely representing the clinical symptoms and characteristics of human IBD has been developed. In this study, we have analyzed fecal microbial and metabolomic profiles in Winnie mice and discussed their relevance to human IBD. Methods: The 16S rRNA gene was sequenced from fecal DNA of Winnie and C57BL/6 mice to define operational taxonomic units at ≥97% similarity threshold. Metabolomic profiling of the same fecal samples was performed by gas chromatography-mass spectrometry. Results: Composition of the dominant microbiota was disturbed, and prominent differences were evident at all levels of the intestinal microbiome in fecal samples from Winnie mice, similar to observations in patients with IBD. Metabolomic profiling revealed that chronic colitis in Winnie mice upregulated production of metabolites and altered several metabolic pathways, mostly affecting amino acid synthesis and breakdown of monosaccharides to short chain fatty acids. Conclusions: Significant dysbiosis in the Winnie mouse gut replicates many changes observed in patients with IBD. These results provide justification for the suitability of this model to investigate mechanisms underlying the role of intestinal microbiota and metabolome in the pathophysiology of IBD.

Omics-based approaches and their use in the assessment of microbial-influenced corrosion of metals

Abstract: Abstract Microbial-influenced corrosion (MIC) has been known to have economic, environmental, and social implications to offshore oil and gas pipelines, concrete structures, and piped water assets. While corrosion itself is a relatively simple process, the localised manner of corrosion makes in situ assessments difficult. Furthermore, corrosion assessments tend to be measured as part of a forensic investigation. Compounding the issue further is the impact of microbiological/biofilm processes, where corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. While traditional microbiological culture-dependent techniques and electrochemical/physical assessments provide some insight into corrosion activity, the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments are scarce. One avenue to explore MIC and MIC inhibition is through the application of omics-based techniques, where insight into the bacterial population in terms of diversification and their metabolism can be further understood. As such, this paper discusses the recent progresses made in a number of fields that have used omics-based applications to improve the fundamental understanding of biofilms and MIC processes.

Metabolic profiling and in vitro assessment of anthelmintic fractions of Picria fel-terrae Lour.

Abstract: Anthelmintic resistance is widespread in gastrointestinal nematode populations, such that there is a consistent need to search for new anthelmintics. However, the cost of screening for new compounds is high and has a very low success rate. Using the knowledge of traditional healers from Borneo Rainforests (Sarawak, Malaysia), we have previously shown that some traditional medicinal plants are a rich source of potential new anthelmintic drug candidates. In this study, Picria fel-terrae Lour. plant extract, which has previously shown promising anthelmintic activities, was fractionated via the use of a solid phase extraction cartridge and each isolated fraction was then tested on free-living nematode Caenorhabditis elegans and the parasitic nematode Haemonchus contortus. We found that a single fraction was enriched for nematocidal activity, killing ≥90% of C. elegans adults and inhibiting the motility of exsheathed L3 of H. contortus, while having minimal cytotoxic activity in mammalian cell culture. Metabolic profiling and chemometric analysis of the effective fraction indicated medium chained fatty acids and phenolic acids were highly represented.

Structure of solid lipid nanoparticles produced by a microwave-assisted microemulsion technique

Abstract: We have recently reported a novel microwave-assisted microemulsion technique for the production of solid lipid nanoparticles (SLNs). SLNs are colloidal carriers made from physiologically well-tolerated lipids that are normally solid at room and body temperature. These microwave-produced SLNs have small size, moderate zeta potential, high encapsulation efficiency and low crystallinity. The drug release studies conducted on drug-loaded SLNs are consistent with a core–shell structure for the microwave-produced SLNs, but with significantly different release profiles depending on the drug used. We further employed multi-angle static and dynamic light scattering (SLS/DLS) and small angle X-ray scattering (SAXS) techniques to help elucidate the structure of microwave-produced SLNs. The SLS/DLS data for the SLNs prepared in this study are consistent with a core–shell structure with a shell thickness of ∼13 nm. SAXS data suggest that the SLNs have a lipid lamellar structure with a repeat spacing of 41.0 ± 0.1 A.

Anti-biofilm and sporicidal activity of peptides based on wheat puroindoline and barley hordoindoline proteins

Abstract: The broad-spectrum activity of antimicrobial peptides (AMPs) and low probability of development of host resistance make them excellent candidates as novel bio-control agents. A number of AMPs are found to be cationic, and a small proportion of these are tryptophan-rich. The puroindolines (PIN) are small, basic proteins found in wheat grains with proposed roles in biotic defence of seeds and seedlings. Synthetic peptides based on their unique tryptophan-rich domain (TRD) display antimicrobial properties. Bacterial endospores and biofilms are highly resistant cells, with significant implications in both medical and food industries. In this study, the cationic PIN TRD-based peptides PuroA (FPVTWRWWKWWKG-NH2 ) and Pina-M (FSVTWRWWKWWKG-NH2 ) and the related barley hordoindoline (HIN) based Hina (FPVTWRWWTWWKG-NH2 ) were tested for effects on planktonic cells and biofilms of the common human pathogens including Pseudomonas aeruginosa, Listeria monocytogenes and the non-pathogenic Listeria innocua. All peptides showed significant bactericidal activity. Further, PuroA and Pina-M at 2 × MIC prevented initial biomass attachment by 85-90% and inhibited >90% of 6-h preformed biofilms of all three organisms. However Hina, with a substitution of Lys-9 with uncharged Thr, particularly inhibited Listeria biofilms. The PIN based peptides were also tested against vegetative cells and endospores of Bacillus subtilis. The results provided evidence that these tryptophan-rich peptides could kill B. subtilis even in sporulated state, reducing the number of viable spores by 4 log units. The treated spores appeared withered under scanning electron microscopy. The results establish the potential of these tryptophan-rich peptides in controlling persistent pathogens of relevance to food industries and human health. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Determination of Ancylostoma caninum ova viability using metabolic profiling.

Abstract: Differentiation between viable and non-viable hookworm ova in environmental samples is necessary in order to implement strategies to mitigate re-infections in endemic regions. In this study, an untargeted metabolic profiling method was developed that utilised gas chromatography-mass spectrometry (GC-MS) in order to investigate hookworm ova viability. Ancylostoma caninum was used to investigate the metabolites within viable and non-viable ova. Univariate and multivariate statistical analyses of the data resulted in the identification of 53 significant metabolites across all hookworm ova samples. The major compounds observed in viable and non-viable hookworm ova were tetradecanoic acid, commonly known as myristic acid [fold change (FC) = 0.4], and dodecanoic acid, commonly known as lauric acid (FC = 0.388). Additionally, the viable ova had self-protecting metabolites such as prostaglandins, a typical feature absent in non-viable ova. The results of this study demonstrate that metabolic profiling using GC-MS methods can be used to determine the viability of canine hookworm ova. Further studies are needed to assess the applicability of metabolic profiling using GC-MS to detect viable hookworm ova in the mixed (viable and non-viable) populations from environmental samples and identify the metabolites specific to human hookworm species.

Untargeted metabolic profiling of winery‐derived biomass waste degradation by Aspergillus niger

Abstract: BACKGROUND: Ascomycetes are capable of considerable lignocellulose degradation. However, there is limited knowledge on the metabolic profile of their biomass degradation. Metabolomic studies are capable of providing important biochemical information to understand and characterise fungal biomass degradation mechanisms. RESULTS: Winery biomass waste of Vitis vinifera var. Shiraz was subjected to Aspergillus niger mediated solid state fermentation for 8 days in 2H2O supplemented medium. Samples were collected every 24h, freeze-dried and derivatized before GC-MS analysis. Covariance-inverse multivariate statistics were used to classify the most significant metabolites. Metabolite-flux profiling classified 37 unique metabolites in 18 different pathways leading to or from glycolysis-tricarboxylic acid pathways. The majority of the sugars were consumed during the first 4 days; this was in order to synthesize fatty acids, amino acids and secondary metabolites. Inhibition started at day 5, as indicated by the accumulation of sugars and the plateauing of N-acetyl glucosamine (a major fungal cell wall component). CONCLUSIONS: A 4-day continuous yeast or mixed fungal fermentation will not only prevent product inhibition, but it will also aid in generating bio-ethanol. Inducing 2-keto-acid decarboxylases followed alcohol dehydrogenases at the onset of inhibition is predicted to aid in the generation of butanol isomers, which are considered valuable sources of fuel.

Direct Measurement of Pore Dynamics and Leakage Induced by a Model Antimicrobial Peptide in Single Vesicles and Cells

Abstract: Antimicrobial peptides are promising therapeutic alternatives to counter growing antimicrobial resistance. Their precise mechanism of action remains elusive, however, particularly with respect to live bacterial cells. We investigated the interaction of a fluorescent melittin analogue with single giant unilamellar vesicles, giant multilamellar vesicles, and bilamellar Gram-negative Escherichia coli (E. coli) bacteria. Time-lapse fluorescence lifetime imaging microscopy was employed to determine the population distribution of the fluorescent melittin analogue between pore state and membrane surface state, and simultaneously measure the leakage of entrapped fluorescent species from the vesicle (or bacterium) interior. In giant unilamellar vesicles, leakage from vesicle interior was correlated with an increase in level of pore states, consistent with a stable pore formation mechanism. In giant multilamellar vesicles, vesicle leakage occurred more gradually and did not appear to correlate with increased pore s...

Current therapeutics and prophylactic approaches to treat pneumonia

Abstract: Bacterial pneumonia caused by Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Mycoplasma pneumoniae, and Klebsiella pneumoniae represents a frequent cause of mortality worldwide. The increased incidence of pneumococcal diseases in both developed and developing countries is alarmingly high, affecting infants and aged adult populations. The growing rate of antibiotic resistance and biofilm formation on medical device surfaces poses a greater challenge for treating respiratory infections. Over recent years, a better understanding of bacterial growth, metabolism, and virulence has offered several potential targets for developing therapeutics against bacterial pneumonia. This chapter will discuss the current and developing trends in treating bacterial pneumonia.

Microbial Metabolomics in Biomass Waste Management

Abstract: Agricultural processes, especially harvesting and post-harvesting, generate considerable amounts of biomass waste every year, the majority of which is incinerated or ends up in landfill. However, this biomass has, instead, the potential to be utilised for various applications including the production of biofuels and numerous medicinal and important industrial metabolites. Numerous bacteria, especially thermophilic species, and fungi have the ability to degrade complex biomass substrates to simpler, useful products which have wide commercial applications. The wide variability in biomass composition and the low degradation capability of individual microbes, however, has limited the utilisation of these wastes. In recent years, the field of metabolomics has been successfully applied to identify the many limiting factors of bioconversion processes. Metabolic profiling has also helped to identify the critical points in microbial metabolic pathways to not only overcome these limiting factors, but also increase the production of valuable by-products products. This chapter reviews the application of microbial metabolomics to increase the efficiency of biomass degradation. It will describe recent advances and future aspects of microbial metabolite profiling and metabolic engineering processes to optimise the production of various compounds of medicinal and industrial interest.