Proteomic and lipidomic biomarkers in the diagnosis and progression of inflammatory bowel disease - a review.

PURPOSE: There is an increasing prevalence of inflammatory bowel disease (IBD) and to date, no effective treatment has been developed and the exact etiology of this disease remains unknown. Nevertheless, a growing number of proteomic and lipidomic studies have identified certain proteins and lipids which can be used successfully in patients to improve diagnoses and monitoring of treatment. EXPERIMENTAL DESIGN: We have focused on the applications of proteins and lipids for IBD diagnostics, including differentiation of Crohn's disease (CD) and ulcerative colitis (UC), treatment monitoring, monitoring of clinical state, likelihood of relapse, and their potential for novel targeted treatments. RESULTS: Analysis of protein and lipid profiles can: improve the availability and use of diagnostic markers; improve understanding of the pathomechanisms of IBD, for example, several studies have implicated platelet dysfunction (PF4), autoimmune responses (granzyme B, perforin), and abnormal metabolism (arachidonic acid pathways); aid in monitoring patient health; and improve therapeutics (experimental phosphatidylcholine therapy has been shown to result in an improvement in intestinal condition). CONCLUSIONS: Despite the enormous progress of proteomics and lipidomics in recent years and the development of new technologies, further research is needed to select some of the most sensitive and specific markers applicable in diagnosing and treating IBD.

PhageScore-based analysis of Acinetobacter baumannii infecting phages antibiotic interaction in liquid medium.

The growing interest in bacteriophages and antibiotics' combined use poses new challenges regarding this phenomenon's accurate description. This study aimed to apply the PhageScore methodology to assess the phage-antibiotic combination activity in liquid bacterial culture. For this purpose, previously described Acinetobacter infecting phages vB_AbaP_AGC01, Aba-1, and Aba-4 and antibiotics (gentamicin, ciprofloxacin, meropenem, norfloxacin, and fosfomycin) were used to obtain a lysis curve of bacteriophages under antibiotic pressure. The experimental data were analyzed using the Fractional Inhibitory Concentration Index (FICI) and PhageScore methodology. The results obtained by this method clearly show differences between phage lytic activity after antibiotic addition. Thus, we present the potential use of the PhageScore method as a tool for characterizing the phage antibiotic synergy in liquid culture. Further, the optimization of the PhageScore for this purpose can help compare antibiotics and their outcome on bacteriophage lytic activity.

Rotating Magnetic Field-Assisted Reactor Enhances Mechanisms of Phage Adsorption on Bacterial Cell Surface.

Growing interest in bacteriophage research and use, especially as an alternative treatment option for multidrug-resistant bacterial infection, requires rapid development of production methods and strengthening of bacteriophage activities. Bacteriophage adsorption to host cells initiates the process of infection. The rotating magnetic field (RMF) is a promising biotechnological method for process intensification, especially for the intensification of micromixing and mass transfer. This study evaluates the use of RMF to enhance the infection process by influencing bacteriophage adsorption rate. The RMF exposition decreased the t50 and t75 of bacteriophages T4 on Escherichia coli cells and vb_SauM_A phages on Staphylococcus aureus cells. The T4 phage adsorption rate increased from 3.13 × 10-9 mL × min-1 to 1.64 × 10-8 mL × min-1. The adsorption rate of vb_SauM_A phages exposed to RMF increased from 4.94 × 10-9 mL × min-1 to 7.34 × 10-9 mL × min-1. Additionally, the phage T4 zeta potential changed under RMF from -11.1 ± 0.49 mV to -7.66 ± 0.29 for unexposed and RMF-exposed bacteriophages, respectively.

Bacteriophage-Ciprofloxacin Combination Effectiveness Depends on Staphylococcus aureus-Candida albicans Dual-Species Communities' Growth Model.

Alternative therapies against multidrug-resistant bacteria are widely investigated in the postantibiotic era. Polymicrobial biofilms formed by two or more species of bacteria or fungi pose an additional threat. The removal of such complex communities requires more effort and a multidirectional approach. In this study, the effectiveness of two bacteriophages vB_SauM-A (A) and vB_SauM-D (D) combined with ciprofloxacin was used to combat Staphylococcus aureus in the presence of Candida albicans both in liquid culture and biofilm. The results showed that phage-antibiotic synergy (PAS) led to the complete removal of S. aureus in liquid culture without bacterial population regrowth after 24 hours, and C. albicans enhanced this therapeutic effect. In a biofilm assay, C. albicans presence caused a decrease of bacterial eradication and a reduction of biofilm-specific activity (BSA). However, the strong effect of PAS was observed both in mono- and dual-species biofilm. Usage of phages and ciprofloxacin (1 mg/L) caused a 90% reduction of BSA of mono-species biofilm and 69% of dual-species biofilm. Phages alone resulted in a decrease of 71% and 48%, and ciprofloxacin (1 mg/L) alone resulted in 45% and 23% reduction, respectively. The influence of C. albicans on the PAS effect against S. aureus presented in this study was not previously investigated.

Comparative Assessment of Bacteriophage and Antibiotic Activity against Multidrug-Resistant Staphylococcus aureus Biofilms.

Problems connected with biofilm-related infections and antibiotic resistance necessitate the investigation and development of novel treatment strategies. Given their unique characteristics, one of the most promising alternatives to conventional antibiotics are bacteriophages. In the in vitro and in vivo larva model study, we demonstrate that phages vB_SauM-A, vB_SauM-C, and vB_SauM-D are effective antibiofilm agents. The exposure of biofilm to phages vB_SauM-A and vB_SauM-D led to 2-3 log reductions in the colony-forming unit number in most of the multidrug-resistant S. aureus strains. It was found that phage application reduced the formed biofilms independently of the used titer. Moreover, the study demonstrated that bacteriophages are more efficient in biofilm biomass removal and reduction in staphylococci count when compared to the antibiotics used. The scanning electron microscopy analysis results are in line with colony forming unit (CFU) counting but not entirely consistent with crystal violet (CV) staining. Additionally, phages vB_SauM-A, vB_SauM-C, and vB_SauM-D can significantly increase the survival rate and extend the survival time of Galleria mellonella larvae.

Renal and Inflammation Markers-Renalase, Cystatin C, and NGAL Levels in Asymptomatic and Symptomatic SARS-CoV-2 Infection in a One-Month Follow-Up Study.

The aim of our study was to evaluate the influence of asymptomatic infection and the occurrence of symptomatic COVID-19 on specific biochemical, renal, and immune parameters-renalase, neutrophil gelatinase-associated lipocalin (NGAL) cystatin C (CysC), and creatinine-and their weekly fluctuations during a one-month observation period in COVID-19 patients admitted to hospital. The study involved 86 individuals: 30 patients with diagnosed COVID-19, 28 people with asymptomatic infection confirmed with IgG antibodies-the IG(+) group-and 28 individuals without any (IgG, IgE) anti-SARS-CoV-2 antibodies-the IG(-) group. In the COVID-19 group, blood was drawn four times: (1) on day 0/1 after admission to hospital (C1 group), (2) 7 days later (C7 group), (3) 14 days later (C14 group), and (4) 28 days later (C28 group). In the IG(-) and IG(+) groups, blood was drawn once. There were no significant differences in creatinine, Cys C, and uric acid between any of the analyzed groups. NGAL levels were significantly higher in IG(+) and at all time-points in the COVID-19 groups than in controls. A similar observation was made for renalase at the C7, C14, and C28 time-points. Plasma renalase, NGAL, and CysC are unrelated to kidney function in non-critically ill COVID-19 patients and those with asymptomatic infection. Renalase and NGAL are most likely related to the activation of the immune system rather than kidney function. Asymptomatic SARS-CoV-2 infection causes a rise in plasma NGAL levels similar to those observed in symptomatic COVID-19 patients. Therefore, more attention should be paid to tracking and monitoring the health of these people.

Adiponectin is unrelated to kidney function or injury markers in renal transplant recipients: A one-year follow-up study.

BACKGROUND: Adiponectin (ADPN) is a biologically active cytokine produced by adipose tissue. This protein exhibits anti-inflammatory, antioxidant, antifibrotic, and insulin-sensitizing properties. As ADPN is primarily eliminated by the kidneys, it is a potential biomarker of chronic kidney disease progression. This study aimed to analyze the fluctuations in ADPN levels after kidney transplantation during a one-year follow-up and to compare them to significant renal (eGFR, NGAL) and metabolic (insulin, glucose, lipids, HOMA-IR) markers. METHODS: Insulin, ADPN, NGAL, and basic biochemical parameters were evaluated in 51 healthy controls and 39 patients right before kidney transplantation and at five time points following transplantation (5-7 days, one month, three months, six months, and twelve months). RESULTS: Mean ADPN levels dropped significantly right after transplantation (from 35.449 to 30.920 µg/mL, p = 0.001) and decreased gradually over a year. From the third month after the transplantation, ADPN levels were comparable to healthy individuals. At the pre-transplant time point, ADPN correlated only with insulin (r = -0.60, p < 0.001) and HOMA-IR (r = -0.55, p < 0.001). At the timepoints after transplantation, ADPN correlated only with NGAL at three months (r = -0.70, p = 0.048). The correlation of ADPN with HOMA-IR found at pre-transplant was not significant at any post-transplant time point, but at one and three months after transplant, the correlations reached a borderline significance (p = 0.07 and p = 0.08, respectively). CONCLUSIONS: Successful kidney transplantation is followed by a gradual and significant ADPN decrease. In pre- and post-transplant patients, ADPN is unrelated to kidney function defined by GFR, but to glucose metabolism. Most of the analyzed metabolic and kidney parameters, apart from NGAL, stabilize within three months after transplantation.

Importance of oxidative stress in the pathogenesis, diagnosis, and monitoring of patients with neuropsychiatric disorders, a review.

Oxidative stress is defined as the persistent imbalance between the activity of toxic reactive forms of both oxygen and nitrogen and the antioxidant defense. In low concentrations, they are essential for the proper functioning of the body. Still, their excessive amount contributes to the damage of the biomolecules, consequently leading to various pathologies of the organism. Due to the lipid-rich brain structure, enormous oxygen consumption, and the lack of a sufficient antioxidant barrier make it highly susceptible to oxidative imbalance. Hence, oxidative stress has been linked to various psychiatric disorders. These diseases include all behavioral, emotional, and cognitive abnormalities associated with a significant impediment to social life. Each of the diseases in question: Alzheimer's disease, schizophrenia, depression, and bipolar disorder, is characterized by excessive oxidative stress. Considerable damages to DNA, RNA, proteins, lipids, and mitochondrial dysfunction, are observed. All conditions show increased lipid peroxidation, which appears to be typical of psychiatric disorders because the brain contains large amounts of these types of molecules. In addition, numerous abnormalities in the antioxidant defense are noted, but the results of studies on the activity of antioxidant enzymes differ significantly. The most promising biomarkers seem to be GSH in Alzheimer's disease as an early-stage marker of the disease and thioredoxin in schizophrenia as a marker for therapy monitoring. Data from the literature are consistent with the decrease in antioxidants such as vitamin C, E, uric acid, albumin, etc. Despite these numerous inconsistencies, it seems that oxidative stress is present in the course of psychiatric diseases. Still, it cannot be conclusively determined whether it is the direct cause of development, a consequence of other abnormalities at the biochemical or molecular level, or the result of the disease itself.

Applications of the regenerative capacity of platelets in modern medicine.

Platelets produce platelet growth factors such as PDGF, IGF-1, EGF-, HGF, TGFß, bFGF, and VEGF, which are crucial in regulating all stages of the wound healing process. The source of these substances is platelet-rich plasma (PRP). Over the past five decades, the interest and use of the regenerative properties of platelets have increased significantly in many different fields of medicine around the world. PRP and PRF plate preparations are used in: 1. Dentistry (they reduce bleeding, facilitate and accelerate soft tissue healing and bone regeneration - FGF 2, IGF-1, IGF-2, TGF-ß1, and PDGF); 2. Sports medicine - IGF-1, IGF-2, TGF-ß, VEGF, PDGF and bFGF, EGF); 3. dermatology and cosmetology (treatment of alopecia, hair reconstruction - FGF-7, HGF, acne scars, skin rejuvenation and regeneration, treatment of chronic and poorly healing wounds, burns, and acquired vitiligo); 4. Gynecology and reproductive medicine (treatment of infertility, erectile dysfunction - PDGF-ß, TGF-ß, IGF-1, in sexual dysfunction - PDGF, in vaginal atrophy); 5 Ophthalmology (in the healing of corneal epithelial wounds, in the treatment of dormant corneal ulcers, dry eye syndrome and the reconstruction of the corneal surface; 6. Neurology (regeneration of neurons, pain alleviation, and clinical symptoms - TGF-ß 1, IGF-1, PDGF, VEGF) and FGF). Platelet-rich plasma therapy is a very interesting alternative and complement to traditional methods of treatment. However, the potential for using platelets is still not fully understood. The composition of platelet-rich plasma depends on many factors that may affect its use's efficacy and clinical benefits. Further research is necessary to standardize PRP delivery's preparation procedures and methods for a specific disease entity or clinical case.

Development of an Autochthonous Microbial Consortium for Enhanced Bioremediation of PAH-Contaminated Soil.

The main objectives of this study were to isolate bacteria from soil chronically contaminated with polycyclic aromatic hydrocarbons (PAHs), develop an autochthonous microbial consortium, and evaluate its ability to degrade PAHs in their native contaminated soil. Strains with the best bioremediation potential were selected during the multi-stage isolation process. Moreover, to choose bacteria with the highest bioremediation potential, the presence of PAH-degrading genes (pahE) was confirmed and the following tests were performed: tolerance to heavy metals, antagonistic behavior, phytotoxicity, and antimicrobial susceptibility. In vitro degradation of hydrocarbons led to the reduction of the total PAH content by 93.5% after the first day of incubation and by 99.22% after the eighth day. Bioremediation experiment conducted in situ in the contaminated area resulted in the average reduction of the total PAH concentration by 33.3% after 5 months and by over 72% after 13 months, compared to the concentration recorded before the intervention. Therefore, this study implicates that the development of an autochthonous microbial consortium isolated from long-term PAH-contaminated soil has the potential to enhance the bioremediation process.

Double-Layer Agar (DLA) Modifications for the First Step of the Phage-Antibiotic Synergy (PAS) Identification.

The research carried out so far for phage-antibiotic synergy (PAS) differs as regards the technique of modifying the double-layer agar (DLA) method to show the PAS effect on Petri plates, which may contribute to non-uniform research results. Therefore, there is a need to unify the method to effectively detect the PAS effect, at its most basic in vitro test. In this study, bacteriophage T45 and 43 antibiotics belonging to different antibiotic classes were used. Seven different DLA method modifications were tested, in terms of antibiotic addition placement and presence or absence of the base agar. The overall number of phage plaques per plate mainly depended on the antibiotic used. Differences in plaque quantity depended on the type of the DLA method modification. The largest total number of plaques was obtained by the addition of an antibiotic to a bottom agar with the presence of a top agar. This indicates that even though an antibiotic could manifest the PAS effect by a standard disk method, it would be worth examining if the effect is equally satisfactory when applying antibiotics directly into the agar, with regards to using the same bacteriophage and bacterial host.

Environmental Phage-Based Cocktail and Antibiotic Combination Effects on Acinetobacter baumannii Biofilm in a Human Urine Model.

The emergence of multidrug-resistant (MDR) bacterial infections poses a catastrophic threat to medicine. The development of phage-based therapy combined with antibiotics might be an advantageous weapon in the arms race between human and MDR bacteria. A cocktail composed of the MDR Acinetobacter baumannii infecting bacteriophages with high lytic activity was used in combination with antibiotics to destroy a bacterial biofilm in human urine. A. baumannii exhibited varying susceptibility to the host range of bacteriophages used in this study, ranging from 56% to 84%. This study demonstrated that bacteriophages could reduce biofilm biomass in a human urine model, and some of the antibiotics commonly used in the treatment of urinary tract infection (UTI) act synergistically with phage cocktails. Additionally, the combined treatment showed a significantly greater reduction of biofilm biomass and clearance of persister cells.

Antibiotics Act with vB_AbaP_AGC01 Phage against Acinetobacter baumannii in Human Heat-Inactivated Plasma Blood and Galleria mellonella Models.

Increasing multidrug resistance has led to renewed interest in phage-based therapy. A combination of the bacteriophages and antibiotics presents a promising approach enhancing the phage therapy effectiveness. First, phage candidates for therapy should be deeply characterized. Here we characterize the bacteriophage vB_AbaP_AGC01 that poses antibacterial activity against clinical Acinetobacter baumannii strains. Moreover, besides genomic and phenotypic analysis our study aims to analyze phage-antibiotic combination effectiveness with the use of ex vivo and in vivo models. The phage AGC01 efficiently adsorbs to A. baumannii cells and possesses a bacteriolytic lifecycle resulting in high production of progeny phages (317 ± 20 PFU × cell-1). The broad host range (50.27%, 93 out of 185 strains) against A. baumannii isolates and the inability of AGC01 to infect other bacterial species show its high specificity. Genomic analysis revealed a high similarity of the AGC01 genome sequence with that of the Friunavirus genus from a subfamily of Autographivirinae. The AGC01 is able to significantly reduce the A. baumannii cell count in a human heat-inactivated plasma blood model (HIP-B), both alone and in combination with antibiotics (gentamicin (GEN), ciprofloxacin (CIP), and meropenem (MER)). The synergistic action was observed when a combination of phage treatment with CIP or MER was used. The antimicrobial activity of AGC01 and phage-antibiotic combinations was confirmed using an in vivo larva model. This study shows the greatest increase in survival of G. mellonella larvae when the combination of phage (MOI = 1) and MER was used, which increased larval survival from 35% to 77%. Hence, AGC01 represents a novel candidate for phage therapy. Additionally, our study suggests that phages and antibiotics can act synergistically for greater antimicrobial effect when used as combination therapy.