Exploring the virome: An integral part of human health and disease.

The human microbiome is a complex network of microorganisms that includes viruses, bacteria, and fungi. The gut virome is an essential component of the immune system, which is responsible for regulating the growth and responses of the host's immune system. The virome maintains a crucial role in the development of numerous diseases, including inflammatory bowel disease (IBD), Crohn's disease, and neurodegenerative disorders. The human virome has emerged as a promising biomarker and therapeutic target. This comprehensive review summarizes the present understanding of the virome and its implications in matters of health and disease, with a focus on the Human Microbiome Project.

15N metabolic labeling-TMT multiplexing approach to facilitate the quantitation of glycopeptides derived from cell lines.

The study of glycoproteomics presents a set of unique challenges, primarily due to the low abundance of glycopeptides and their intricate heterogeneity, which is specific to each site. Glycoproteins play a crucial role in numerous biological functions, including cell signaling, adhesion, and intercellular communication, and are increasingly recognized as vital markers in the diagnosis and study of various diseases. Consequently, a quantitative approach to glycopeptide research is essential. One effective strategy to address this need is the use of multiplex glycopeptide labeling. By harnessing the synergies of 15N metabolic labeling via the isotopic detection of amino sugars with glutamine (IDAWG) technique for glycan parts and tandem mass tag (TMT)pro labeling for peptide backbones, we have developed a method that allows for the accurate quantification and comparison of multiple samples simultaneously. The adoption of the liquid chromatography-synchronous precursor selection (LC-SPS-MS3) technique minimizes fragmentation interference, enhancing data reliability, as shown by a 97% TMT labeling efficiency. This method allows for detailed, high-throughput analysis of 32 diverse samples from 231BR cell lines, using both 14N and 15N glycopeptides at a 1:1 ratio. A key component of our methodology was the precise correction for isotope and TMTpro distortions, significantly improving quantification accuracy to less than 5% distortion. This breakthrough enhances the efficiency and accuracy of glycoproteomic studies, increasing our understanding of glycoproteins in health and disease. Its applicability to various cancer cell types sets a new standard in quantitative glycoproteomics, enabling deeper investigation into glycopeptide profiles.

Tolerogenic probiotics Lactobacillus delbrueckii and Lactobacillus rhamnosus promote anti-inflammatory profile of macrophages-derived monocytes of newly diagnosed patients with systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is known as an autoimmune disorder that is characterized by the breakdown of self-tolerance, resulting in disease onset and progression. Macrophages have been implicated as a factor in the development of SLE through faulty phagocytosis of dead cells or an imbalanced M1/M2 ratio. The study aimed to investigate the immunomodulatory effects of Lactobacillus delbrueckii and Lactobacillus rhamnosus on M1 and M2 macrophages in new case lupus patients. For this purpose, blood monocytes were collected from lupus patients and healthy people and were cultured for 5 days to produce macrophages. For 48 h, the macrophages were then cocultured with either probiotics or lipopolysaccharides (LPS). Flow cytometry and real-time polymerase chain reaction were then used to analyze the expression of cluster of differentiation (CD) 14, CD80, and human leukocyte antigen - DR (HLADR) markers, as well as cytokine expression (interleukin [IL]1-ß, IL-12, tumor necrosis factor α [TNF-α], IL-10, and transforming growth factor beta [TGF-ß]). The results indicated three distinct macrophage populations, M0, M1, and M2. In both control and patient-derived macrophage-derived monocytes (MDMs), the probiotic groups showed a decrease in CD14, CD80, and HLADR expression compared to the LPS group. This decrease was particularly evident in M0 and M2 macrophages from lupus patients and M1 macrophages from healthy subjects. In addition, the probiotic groups showed increased levels of IL-10 and TGF-ß and decreased levels of IL-12, IL1-ß, and TNF-α in MDMs from both healthy and lupus subjects compared to the LPS groups. Although there was a higher expression of pro-inflammatory cytokines in lupus patients, there was a higher expression of anti-inflammatory cytokines in healthy subjects. In general, L. delbrueckii and L. rhamnosus could induce anti-inflammatory effects on MDMs from both healthy and lupus subjects.

Targeted Glycoproteomics Analysis Using MRM/PRM Approaches.

MS-target analyses are frequently utilized to analyze and validate structural changes of biomolecules across diverse fields of study such as proteomics, glycoproteomics, glycomics, lipidomics, and metabolomics. Targeted studies are commonly conducted using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) techniques. A reliable glycoproteomics analysis in intricate biological matrices is possible with these techniques, which streamline the analytical workflow, lower background interference, and enhance selectivity and specificity.

Targeted Analysis of Permethylated N-Glycans Using MRM/PRM Approaches.

Targeted mass spectrometric analysis is widely employed across various omics fields as a validation strategy due to its high sensitivity and accuracy. The approach has been successfully employed for the structural analysis of proteins, glycans, lipids, and metabolites. Multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) have been the methods of choice for targeted structural studies of biomolecules. These target analyses simplify the analytical workflow, reduce background interference, and increase selectivity/specificity, allowing for a reliable quantification of permethylated N-glycans in complex biological matrices.

Characterization of acorn oil and its application on carnauba wax-based oleogel and chocolate spread.

This study aimed to characterize acorn oil (AO) and carnauba wax-based acorn oil oleogel (AOG) and the effect of AOG replacement on the textural and sensorial properties of chocolate spread. Oil yields from cold-pressing (Quercus longipes) were around 14%wt with a nice nutty smell. The main fatty acids of AO were included oleic, linoleic, and palmitic acid (44, 38, and 10%wt) respectively. The prepared AOG using 6%wt of carnauba wax (CW) showed high strength (G' > 100 mPa) and oil binding capacity ∼87 %. Based on microstructure assays platelet-like and ß' polymorphic triglyceride crystalline networks were formed in AOG. The Pickering AOG/water emulsions in the volumetric ratio of from 90:10 up to 40:60 were stable due to the placement of CW-based AOG particles at the interface of water/oil as Pickering stabilizer. The high physical stability of the emulgel against phase separation is considered an important advantage for using oleogel in chocolate spread formulations instead of vegetable oils, which usually have a high percentage of oil release. The spreads prepared by replacing 50%wt AOG with butter showed acceptable textural and sensorial properties.

Lipid-lowering drugs and cancer: an updated perspective.

Statins and non-statin medications used for the management of dyslipidemia have been shown to possess antitumor properties. Since the use of these drugs has steadily increased over the past decades, more knowledge is required about their relationship with cancer. Lipid-lowering agents are heterogeneous compounds; therefore, it remains to be revealed whether anticancer potential is a class effect or related to them all. Here, we reviewed the literature on the influence of lipid-lowering medications on various types of cancer during development or metastasis. We also elaborated on the underlying mechanisms associated with the anticancer effects of antihyperlipidemic agents by linking the reported in vivo and in vitro studies.

Agrobacterium tumefaciens-Mediated Genetic Engineering of Green Microalgae, Chlorella vulgaris.

Agrobacterium tumefaciens-mediated transformation (AMT) serves as a widely employed tool for manipulating plant genomes. However, A. tumefaciens exhibit the capacity for gene transfer to a diverse array of species. Numerous microalgae species lack well-established methods for reliably integrating genes of interest into their nuclear genome. To harness the potential benefits of microalgal biotechnology, simple and efficient genome manipulation tools are crucial. Herein, an optimized AMT protocol is presented for the industrial microalgae species Chlorella vulgaris, utilizing the reporter green fluorescent protein (mGFP5) and the antibiotic resistance marker for Hygromycin B. Mutants are selected through plating on Tris-Acetate-Phosphate (TAP) media containing Hygromycin B and cefotaxime. Expression of mGFP5 is quantified via fluorescence after over ten generations of subculturing, indicating the stable transformation of the T-DNA cassette. This protocol allows for the reliable generation of multiple transgenic C. vulgaris colonies in under two weeks, employing the commercially available pCAMBIA1302 plant expression vector.

LC-MS/MS Quantitation of HILIC-Enriched N-glycopeptides Derived from Low-Abundance Serum Glycoproteins in Patients with Narcolepsy Type 1.

Glycoproteomic analysis is always challenging because of low abundance and complex site-specific heterogeneity. Glycoproteins are involved in various biological processes such as cell signaling, adhesion, and cell-cell communication and may serve as potential biomarkers when analyzing different diseases. Here, we investigate glycoproteins in narcolepsy type 1 (NT1) disease, a form of narcolepsy characterized by cataplexy-the sudden onset of muscle paralysis that is typically triggered by intense emotions. In this study, 27 human blood serum samples were analyzed, 16 from NT1 patients and 11 from healthy individuals serving as controls. We quantified hydrophilic interaction liquid chromatography (HILIC)-enriched glycopeptides from low-abundance serum samples of controls and NT1 patients via LC-MS/MS. Twenty-eight unique N-glycopeptides showed significant changes between the two studied groups. The sialylated N-glycopeptide structures LPTQNITFQTESSVAEQEAEFQSPK HexNAc6, Hex3, Neu5Ac2 (derived from the ITIH4 protein) and the structure IVLDPSGSMNIYLVLDGSDSIGASNFTGAK HexNAc5, Hex4, Fuc1 (derived from the CFB protein), with p values of 0.008 and 0.01, respectively, were elevated in NT1 samples compared with controls. In addition, the N-glycopeptide protein sources Ceruloplasmin, Complement factor B, and ITH4 were observed to play an important role in the complement activation and acute-phase response signaling pathways. This may explain the possible association between the biomarkers and pathophysiological effects.

N-Glycome Profile of the Spike Protein S1: Systemic and Comparative Analysis from Eleven Variants of SARS-CoV-2.

The SARS-CoV-2 virus rapidly spread worldwide, threatening public health. Since it emerged, the scientific community has been engaged in the development of effective therapeutics and vaccines. The subunit S1 in the spike protein of SARS-CoV-2 mediates the viral entry into the host and is therefore one of the major research targets. The S1 protein is extensively glycosylated, and there is compelling evidence that glycans protect the virus' active site from the human defense system. Therefore, investigation of the S1 protein glycome alterations in the different virus variants will provide a view of the glycan evolution and its relationship with the virus pathogenesis. In this study, we explored the N-glycosylation expression of the S1 protein for eleven SARS-CoV-2 variants: five variants of concern (VOC), including alpha, beta, gamma, delta, and omicron, and six variants of interest (VOI), including epsilon, eta, iota, lambda, kappa, and mu. The results showed significant differences in the N-glycome abundance of all variants. The N-glycome of the VOC showed a large increase in the abundance of sialofucosylated glycans, with the greatest abundance in the omicron variant. In contrast, the results showed a large abundance of fucosylated glycans for most of the VOI. Two glycan compositions, GlcNAc4,Hex5,Fuc,NeuAc (4-5-1-1) and GlcNAc6,Hex8,Fuc,NeuAc (6-8-1-1), were the most abundant structures across all variants. We believe that our data will contribute to understanding the S1 protein's structural differences between SARS-CoV-2 mutations.

Impacts of Porphyromonas gingivalis periodontitis on rheumatoid arthritis autoimmunity.

In RA patients' synovial sites, citrullinated RA-related antigens such as type II collagens, fibrin (ogen), vimentin, and α-enolase could be targeted by ACCPAs. Since ACCPA production can be initiated a long time before RA sign appearance, primary auto-immunization against these citrullinated proteins can be originated from extra-articular sites. It has been shown that there is a significant association between P. gingivalis periodontitis, anti- P. gingivalis antibodies, and RA. P. gingivalis gingipains (Rgp, Kgp) can degrade proteins such as fibrin and α-enolase into some peptides in the form of Arg in the C-terminal which is converted to citrulline by PPAD. Also, PPAD can citrullinate type II collagen and vimentins (SA antigen). P. gingivalis induces inflammation and chemoattraction of immune cells such as neutrophils and macrophages through the increase of C5a (gingipain C5 convertase-like activity) and SCFA secretion. Besides, this microorganism stimulates anoikis, a special type of apoptosis, and NETosis, an antimicrobial form of neutrophil death, leading to the release of PAD1-4, α-enolase, and vimentin from apoptotic cells into the periodontal site. In addition, gingipains can degrade macrophages CD14 and decrease their ability in apoptotic cell removal. Gingipains also can cleave IgGs in the Fc region and transform them into rheumatoid factor (RF) antigens. In the present study, the effects of P. gingivalis on rheumatoid arthritis autoimmune response have been reviewed, which could attract practical insight both in bench and clinic.

Mass spectrometry based biomarkers for early detection of HCC using a glycoproteomic approach.

Hepatocellular carcinoma (HCC) is the fourth most common cause of cancer-related mortality worldwide and 80%-90% of HCC develops in patients that have underlying cirrhosis. Better methods of surveillance are needed to increase early detection of HCC and the proportion of patients that can be offered curative therapies. Recent work in novel mass spec-based methods for glycomic and glycopeptide analysis for discovery and confirmation of markers for early detection of HCC versus cirrhosis is reviewed in this chapter. Results from recent work in these fields by several groups and the progress made in developing markers of early HCC which can outperform the current serum-based markers are described and discussed. Also, recent developments in isoform analysis of glycans and glycopeptides and in various mass spec fragmentation methods will be described and discussed.

Encapsulation of Vitamins Using Nanoliposome: Recent Advances and Perspectives.

Nowadays the importance of vitamins is clear for everyone. However, many patients are suffering from insufficient intake of vitamins. Incomplete intake of different vitamins from food sources due to their destruction during food processing or decrease in their bioavailability when mixing with other food materials, are factors resulting in vitamin deficiency in the body. Therefore, various lipid based nanocarriers such as nanoliposomes were developed to increase the bioavailability of bioactive compounds. Since the function of nanoliposomes containing vitamins on the body has a direct relationship with the quality of produced nanoliposomes, this review study was planned to investigate the several aspects of liposomal characteristics such as size, polydispersity index, zeta potential, and encapsulation efficiency on the quality of synthesized vitamin-loaded nanoliposomes.

Recent advances in electrospun protein fibers/nanofibers for the food and biomedical applications.

Electrospinning (ES) is one of the most investigated processes for the convenient, adaptive, and scalable manufacturing of nano/micro/macro-fibers. With this technique, virgin and composite fibers may be made in different designs using a wide range of polymers (both natural and synthetic). Electrospun protein fibers (EPF) shave desirable capabilities such as biocompatibility, low toxicity, degradability, and solvolysis. However, issues with the proteins' processibility have limited their widespread utilization. This paper gives an overview of the features of protein-based biomaterials, which are already being employed and has the potential to be exploited for ES. State-of-the-art examples showcasing the usefulness of EPFs in the food and biomedical industries, including tissue engineering, wound dressings, and drug delivery, provided in the applications. The EPFs' future perspective and the challenge they pose are presented at the end. It is believed that protein and biopolymeric nanofibers will soon be manufactured on an industrial scale owing to the limitations of employing synthetic materials, as well as enormous potential of nanofibers in other fields, such as active food packaging, regenerative medicine, drug delivery, cosmetic, and filtration.

Preparation and characterization of polyurethane/chitosan/CNT nanofibrous scaffold for cardiac tissue engineering.

Myocardial infarction of cardiomyocytes is a leading cause of heart failure (HF) worldwide. Since heart has very limited regeneration capacity, cardiac tissue engineering (TE) to produce a bioactive scaffold is considered. In this study, a series of polyurethane solutions (5-7%wt) in aqueous acetic acid were prepared using electrospinning. A variety of Polyurethane (PU)/Chitosan (Cs)/carbon nanotubes (CNT) composite nanofibrous scaffolds with random and aligned orientation were fabricated to structurally mimic the extracellular matrix (ECM). Electrospun nanofibers were then characterized using field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), water contact angle, degradation studies, tensile tests, electrical resistance measurement and cell viability assay. The biocompatibility of electrospun random and aligned nanofibrous scaffolds with H9C2 Cells was confirmed. The results revealed that fabricated PU/Cs/CNT composite nanofibrous scaffolds were electro-conductive and aligned nanofibers could be considered as promising scaffolds with nano-scale features for regeneration of infarcted myocardium.

Functional biocompatible nanocomposite films consisting of selenium and zinc oxide nanoparticles embedded in gelatin/cellulose nanofiber matrices.

In recent decades, environmental concerns and increasing consumer demand for healthy and nutritious food products with prolonged shelf life have made the food packaging industry pay more attention to the preparation of multifunctional biodegradable packaging films based on biopolymers containing active components such as antioxidant and antimicrobial agents. In this study, bio-nanocomposite films were fabricated from gelatin (G) and cellulose nanofibers (CNFs), and different concentrations of zinc oxide (ZnO) and/or Selenium (Se) nanoparticles (NPs) by the casting method. The mechanical, barrier, optical, and structural (FTIR, XRD, and SEM) properties of the films were investigated along with their antibacterial and antioxidant features. The incorporation of ZnO and Se NPs improved the physicomechanical and water resistance of G/CNF films. In this regard, the maximum tensile strength value was obtained for the G/CNF containing 5% w/w ZnO NPs (G/CNF/ZnO3) and G/CNF containing 0.1% w/w Se NPs (G/CNF/Se2) films (~2.20-fold and ~2.13-fold higher than the G/CNF film, respectively). Also, G/CNF with 3% w/w ZnO NPs (G/CNF/ZnO2) film had the lowest water vapor permeability and water solubility among all films. Results of the disc diffusion assay showed a stronger antibacterial effect of ZnO NPs compared with Se NPs. The bacterial susceptibility to the antibacterial films was as follows: Listeria monocytogenes > Escherichia coli > Staphylococcus aureus > Pseudomonas fluorescens. The G/CNF films incorporated with Se nanoparticles possessed the higher property of scavenging free radicals in comparison films containing ZnO nanoparticles. Also, the combination of Se NPs and ZnO NPs enhanced the antioxidant effect of the films. In conclusion, gelatin-based edible films containing CNFs, ZnO NPs, and Se NPs can be used in the development of active food packaging products.

Development of an active packaging system containing zinc oxide nanoparticles for the extension of chicken fillet shelf life.

The casting method was employed to prepare gelatin-based nanocomposite films containing different concentrations of cellulose nanofiber (CNF) as a reinforcement filler (2.5%, 5%, and 7.5% w/w of gelatin) as well as zinc oxide nanoparticles (ZnO NPs) as an antimicrobial agent (1%, 3%, 5%, and 7% w/w of gelatin). The results showed that the incorporation of 5% CNFs (optimum concentration) significantly boosted the films' stiffness (YM; by 47%) and strength (TS; by 72%) but decreased its flexibility (EAB; by 28%), water vapor permeability, and moisture absorption. The best G/CNF film antibacterial activity was provided by the 5% concentration of ZnO NPs according to the disk diffusion assay; Gram-positive bacteria were inhibited significantly more than Gram-negative bacteria. The antimicrobial efficacy of the G/CNF/ZnO NPs film as a food packaging material was assessed via counts of Staphylococcus aureus and Pseudomonas fluorescens inoculated on chicken fillets (as a food model) in the treatment (G/5% CNF/5% ZnO) and control groups (plastic bag). The antibacterial film led to a significant reduction in the bacterial load of the chicken fillets (p < .05), especially against the Gram-positive strain. This study illustrated that G/CNF/ZnO NPs films can be utilized as active packaging to prolong the shelf life of different perishable foods such as meat.

Development of behenic acid-ethyl cellulose oleogel stabilized Pickering emulsions as low calorie fat replacer.

This study investigated the optimization of thermal, functional and rheological properties of Ethyl Cellulose (EC)-based oleogel considering different concentrations of Behenic Acid (BA) and stability of water in oleogel (w/og) emulsions. The results showed that the combination of EC and BA improved the oleogel properties at specific ratios (2:4 and 1:5 wt%). High strength (G' > 1000 mPa) with good thermo-responsive and viscoelastic behavior in the range of 45-60 °C and low loss of oil (<0.2%) were observed in these oleogel formulations. Polarized light microscopy images and XRD results showed the presence of crystals and high proportion of crystalline regions in the mentioned formulations. There were no significant differences among solid fat content (SFC) of EC contained oleogels. The FTIR results indicated new hydrogen bonds formation. The w/og stabilized emulsions with EC: BA (1:5 wt%) oleogel showed high physical stability even at high ratios of disperse phase (5 to 45 wt% of water). The particle size and polydispersity index (PDI) of emulsions were reduced significantly to 250 nm and 0.19, respectively by increasing the ratio of water phase to 45:55 w/og. The oleogel and developed Pickering w/og emulsion has good potential in the formulation of low calorie food products.

The Relationship Between HIV Antibody Titer, HIV Viral Load, HIV p24 Antigen, and CD4 T-cell Count Among Iranian HIV-positive Patients.

OBJECTIVE: This study aimed to simultaneously measure and assess the correlation between the available HIV infection parameters including HIV antibody, p24 Antigen, CD4 cell count, and viral load at the different stages of HIV disease among HIV-positive individuals in Iran. MATERIALS AND METHODS: Fifty HIV-positive individuals were classified into three stages (1, 2, and 3) according to the HIV disease stages classification, available in Control of Disease and Prevention (CDC) guideline. 10 ml of the venous blood sample was collected to run the tests for HIV antibody and p24 Ag levels, CD4 cell counts, and viral load. Pearson's correlation test was employed to calculate the coefficients for the in-between correlation of different HIV parameters in each stage. RESULTS: Of 50 participants, 17 (34%), 25 (50%), and 8 (16%) patients belonged to stages 1, 2, and 3, respectively. Sexual relationship was the main route of HIV transmission among the patients (36%); however, injecting drug use (20%) was also reported frequently. There was no significant correlation between the parameters of HIV disease in different stages in the present study. CONCLUSION: The findings showed no correlation between HIV parameters in the present study. Considering the fact that the association of HIV antibodies with HIV disease progression in infected individuals is independent of HIV-1 RNA levels, combined measurement of HIV-1 RNA and CD4 cell counts should be routinely carried out in HIV infected patients follow up.

An investigation on patient attitudes toward package inserts and their accessibility in Iran.

BACKGROUND: Package inserts (PIs) can be a source of information for patients, especially when clinicians do not provide adequate consultations to the patients. Therefore, for the first time, we investigated the state of PIs in Iran and evaluated patients' attitude toward PI. MATERIALS AND METHODS: In this descriptive study, conducted in a major teaching pharmacy in Isfahan, Iran, in 2016, 100 patients who presented a prescription were interviewed randomly and all medications in their medication bags were examined. The main outcome measures were whether or not the dispensed medications were accompanied by a PI and the behavior of patients in reading these PIs. RESULTS: From the 237 medication items investigated, 129 (54.4%) were dispensed with a PI. Eighty-four percent of patients read the PIs and only 19% stated reading a non-Farsi PI. The level of education was the only significant factor related to reading the PI (P = 0.02). Reading the side effects was the main reason for reading the PI (64%). PIs were considered useful by 83% while 25% kept PIs as a source of drug information. Experience of fear to take the medication after reading the PI was reported by 47%. CONCLUSION: About half of medications were dispensed along with the PI. Although the majority of patients report reading the PIs and consider them useful, confidence in using the medicine may be diminished after reading the PI. Patients with higher education read the PIs the most.