Infectious diseases are one of the core biological complications for public health. It is important to recognize the pathogen-specific mechanisms to improve our understanding of infectious diseases. Differentiations between bacterial- and viral-targeted human proteins are important for improving both prognosis and treatment for the patient. Here, we introduce machine learning-based classifiers to discriminate between the two groups of human proteins. We used the sequence, network, and gene ontology features of human proteins. Among different classifiers and features, the deep neural network (DNN) classifier with amino acid composition (AAC), dipeptide composition (DC), and pseudo-amino acid composition (PAAC) (445 features) achieved the best area under the curve (AUC) value (0.939), F1-score (94.9%), and Matthews correlation coefficient (MCC) value (0.81). We found that each of the selected top 100 of the bacteria- and virus-targeted human proteins from a candidate pool of 1618 and 391... [more]

Cross-flow microfiltration and membrane plate filtration are the main filtration processes used in wineries. However, the inherent compositional variability of red wines could affect the impact of these two filtration techniques on the final wine quality. Thus, this work aims to study, under winery-scale conditions, the impact of these two filtration processes on the turbidity level, phenolic composition, chromatic characteristics and sensory profile of red wine. For this purpose, three different Portuguese red wines with different initial phenolic contents were used. In this context, several methodologies were used to quantify the total phenolic composition, chromatic characteristics, individual anthocyanins and proanthocyanidins before and after filtration. The sensory profiles of the different red wines were also considered. The results indicated that each filtration process produced a substantial reduction in turbidity values and, consequently, an increase in wine clarification. In... [more]

Nowadays, plant-based proteins are gaining momentum due to their wide availability, good amino acid content, and their market appeal. Unfortunately, these molecules usually have low water solubility, affecting other functional characteristics, such as foaming and emulsification, opening technological opportunities for research. Some plant-based protein applications rely on adjustments to final formulations and changing these chemical structures to produce new protein ingredients is also a path widely used in recent research. These modifications can be classified as physical or chemical, the latter being the most popular, and hydrolysis is one of the more widely reported modifications. This review explores the application of chemical modifications to plant-based proteins to improve techno-functional properties, when applied as part of food formulations. In addition, acetylation and succinylation, as the second and third most used processes, are discussed, including a deep analysis of th... [more]

A novel endo-β-1,4-mannanase gene was cloned from a novel actinomycetes, Nonomuraea jabiensis ID06-379, isolated from soil, overexpressed as an extracellular protein (47.8 kDa) in Streptomyces lividans 1326. This new endo-1,4-β-mannanase gene (manNj6-379) is encoded by 445-amino acids. The ManNj6-379 consists of a 28-residue signal peptide and a carbohydrate-binding module of family 2 belonging to the glycoside hydrolase (GH) family 5, with 59−77% identity to GH5 mannan endo-1,4-β-mannanase. The recombinant ManNj6-379 displayed an optimal pH of 6.5 with pH stability ranging between 5.5 and 7.0 and was stable for 120 min at 50 °C and lower temperatures. The optimal temperature for activity was 70 °C. An enzymatic hydrolysis assay revealed that ManNj6-379 could hydrolyze commercial β-mannan and biomass containing mannan.

The goal of this study was to determine the concentrations of 16 PAHs (PAH16) naphthalene—Nap, acenaphthylene—Anl, acenaphthene—Ane, fluorene—Flu, phenanthrene—Phen, anthracene—Ant, fluoranthene—Flt, pyrene—Pyr, benz[a]anthracene—BaA, chrysene—Chry, benzo[b]fluoranthene—BbF, benzo[k]fluoranthene—BkF, benzo[a]pyrene—BaP, indeno[1,2,3-cd]pyrene—InP, dibenz[a,h]anthracene—DahA and benzo[g,h,i]perylene—BghiP) in Slavonska slanina traditionally smoked bacon over open fire and industrially smoked on a smoke generator with a heated plate. In the samples of Slavoska slanina smoked in a traditional manner, the presence of 11 out of 16 analyzed PAHs was determined (Nap, Anl, Ane, Fln, Ant, Phen, Flt, BaA, Pyr, BbF, BkF). In the samples smoked in industrial conditions, only 2 out of 16 (Nap, Anl) were quantified. In the samples smoked with open fire (the traditional method), PAH4 (BaA, BaP BbF, Chry) concentations were as follows: 14.84 μg kg−1 in the middle, 10.60 μg kg−1 on the surface and 17.3... [more]

SUMOylation is a reversible covalent process between a small ubiquitin-like modifier (SUMO) and its target protein and has become a crucial regulator of protein functions. Here, we report that Bombyx mori nucleopolyhedrovirus (BmNPV) may take advantage of the host SUMOylation system to enhance its own replication, similar to many other viruses. Both the knockdown of BmSUMO by RNAi and chemical blocking by ginkgolic acid both impaired BmNPV replication. Using site mutation and pull-down assays, we found that lysine K70 of the protein kinase-interacting protein (PKIP), which is conserved in all Alphabaculoviruses, was modified by SUMO. Mutation of K70 in PKIP led to its translocation from the cytoplasm to the nucleus. Knockout and rescue experiments showed that the rescue of PKIP mutant virus with wild-type PKIP restored BmNPV replication to the normal level, but this was not true for the K70R mutation. Altogether, these results show that SUMOylation of PKIP plays a key role in BmNPV rep... [more]

Banana peel, a little-used waste, contains a high amount of biologically active compounds. The aim of the study is to demonstrate in vitro, the antioxidant, cytotoxic, and antimicrobial effects of hydroalcoholic extracts from yellow (BP) and red (BPR) banana peels. The analysis of the extracts by Capillary Zone Electrophoresis (CZE) has confirmed the presence of several bioactive compounds. BPR has a higher in vitro antioxidant activity than BP, which correlates with a significant cytotoxic, antimicrobial effect, with a UVA/UVB rate of 0.9. In the case of BPR, the results confirm the presence of isoquercitrin and kaempferol in a 1:3 ratio. The bioactive compounds from the extracts have shown a different interaction with HCT-8 cell lines and with tested bacterial strains with pathogenic properties. The HCA analysis proved the biological value of BPR to reduce oxidative stress and its potential use in natural products.

The current study aimed to develop carbomer based hydrogel dressings, incorporating ethanolic extracts of Rosmarinus officinalis aerial parts, Achillea millefolium and Calendula officinalis flowers. The pharmaceutical properties of the obtained hydrogels, as well as their texture and antimicrobial activity, were further evaluated. Five wound dressing formulations based on carbopol were prepared. The addition of the ethanolic extracts to the formulation slightly lowered the pH of the hydrogels, as expected. The Rosmarinus officinalis aerial parts extract loaded hydrogel proved to be the firmest one. In terms of consistency and viscosity, the behavior of the five hydrogels was relatively similar. Based on the texture analysis, the texture of the hydrogels has been affected to some extent by the addition of the ethanolic extracts, decreasing their consistency, firmness, and adhesiveness. The hydrogel loaded with Rosmarinus officinalis aerial parts extract and the one incorporating the ble... [more]

The rapid advancement of genetically modified (GM) technology over the years has raised concerns about the safety of GM crops and foods for human health and the environment. Gene flow from GM crops may be a threat to the environment. Therefore, it is critical to develop reliable, rapid, and low-cost technologies for detecting and monitoring the presence of GM crops and crop products. Here, we used visible near-infrared (Vis-NIR) spectroscopy to distinguish between GM and non-GM Brassica napus, B. juncea, and F1 hybrids (B. juncea X GM B. napus). The Vis-NIR spectra were preprocessed with different preprocessing methods, namely normalization, standard normal variate, and Savitzky−Golay. Both raw and preprocessed spectra were used in combination with eight different chemometric methods for the effective discrimination of GM and non-GM plants. The standard normal variate and support vector machine combination was determined to be the most accurate model in the discrimination of GM, non-GM... [more]

Thermal ablation of tumors is a minimally invasive technique more and more employed in cancer treatments. The main shortcomings of this technique are, on the one hand, the risk of an incomplete ablation, and on the other hand, the destruction of the surrounding healthy tissue. In this work, thermal ablation of a spherical hepatocellular carcinoma tumor (HCC) surrounded by healthy tissue is modeled. A modified porous media-based bioheat model is employed, including porosity variability from tumor core to healthy tissue, following experimental in vivo measures. Moreover, three different protocols are investigated: a constant heating protocol, a pulsating protocol, and a new developed damage-controlled protocol. The proposed damage-controlled protocol changes the heating source from constant to pulsating according to the thermal damage probability on the tumor rim. The equations are numerically solved by means of the commercial software COMSOL Multiphysics, and the outcomes show that the... [more]

Combinations of indigenous ingredients lacking in certain essential amino acids could be used to obtain a protein isolate with a better amino acid profile that can be used as a functional food ingredient and suitable raw material for the food industry. Functional properties and amino acid profile of Bambara groundnut and Moringa oleifera leaf protein complex and its precursors (Bambara groundnut protein isolates (BGNPI) and Moringa oleifera leaf protein isolate (MOLPI)) were evaluated. The protein, fat, ash, carbohydrate, and moisture content of the protein isolates and complex ranged from 39.42 to 63.51%, 2.19 to 11.52%, 1.60 to 7.09%, 24.07 to 51.29%, and 2.61 to 9.57%, respectively, and differed significantly (p < 0.05) from one another. The total amino acids of the protein isolates and complex were 75.11, 50.00, and 71.83 g/100 g, respectively. The protein complex is higher in threonine, phenylalanine, lysine, and leucine when compared to the FAO/WHO reference pattern. The oil a... [more]

Chronic Helicobacter pylori infection produces several lesions in the human stomach, which can progress to chronic atrophic gastritis and gastric cancer. To date, there is very little information on gene expression in chronic atrophic gastritis and its relationship with progression to gastric cancer. In this study, we performed a gene expression analysis during chronic atrophic gastritis in order to identify possible biomarkers that allow an early diagnosis of gastric cancer. We studied biopsies from patients with chronic atrophic gastritis and gastric cancer. The biopsies were analyzed by a gene expression microarray and corroborated by qPCR and validated through immunohistochemistry. Our results revealed that gene expression profiles in patients with chronic atrophic gastritis showed molecular changes of the gastric mucosa, leading to gastric cancer. The gene expression profiles of CLDN1, CLDN7, OLFM4, C-MYC and MMP9 were more notable from the chronic atrophic gastritis. The gene exp... [more]

Known for its high nutritional and medicinal value, okra (Abelmoschus esculentus) is commonly used for replacing plasma and expanding blood volume in humans. It is a major economic crop cultivated in tropical and subtropical regions worldwide. The present study aimed to investigate and evaluate the nutritional properties and prospective applications of the consumable parts of okra. The total ash content (mineral content), carbohydrate, crude fiber, fat, protein, and moisture fractions of okra pod aqueous extract were determined. The results show that okra aqueous extract contained 84.670−87.650% moisture, 1.514−1.197% ash, 7.857−8.261% carbohydrate, 2.367−3.410% crude protein, and 6.781−8.314% crude fiber. Okra was determined to have high nutritional value, with γ-tocopherol and α-tocopherol contents about 2.67 mg/100 g and 1.62 mg/100 g, respectively. High-performance liquid chromatography (HPLC) was performed to determine the sugars present in okra aqueous extract. The water-soluble... [more]

White cocoon is developed and used as a natural fiber, and different silkworm strains have different cocoon colors. Natural-colored cocoons are preferred by people, however, the cocoon color mainly settles on sericin and it basically falls off after reeling. Currently, there are no varieties applied to production due to the formation mechanism of cocoon color is not clear. The formation of cocoon color involves multiple gene regulations. Previous studies have shown that the main genes regulating cocoon traits are the yellow blood (Y) gene, yellow blood inhibitor (I) gene, and yellow cocoon (C) gene. Among them, the products of the Y gene and C gene have been studied, but the I gene is still unclear. In this study, the midgut tissues of the yellow (NB) and the white (306) cocoon silkworm were analyzed by whole transcriptome sequencing. The results showed that there are 1639 DE-circRNAs, 70 DE-miRNAs, and 3225 DE-mRNAs, including 1785 up-regulated genes and 1440 down-regulated genes. GO... [more]

Gut microbiota has strong connections with health. Regulating and enhancing gut microbiota and increasing the population of beneficial microorganisms constitutes a new approach to increasing the efficiency of health status. Although it has been shown that Lactococcus can adjust gut microbiota and be beneficial for the host, little is known about whether strains of Lactococcus petauri can improve the gut microbiota. This study focused on the influence of Lactococcus petauri CF11 on the gut microbiome composition and the levels of short-chain fatty acids (SCFAs) in vivo in healthy Sprague Dawley rats. The present results showed that strain CF11 was able to induce a higher amount of fecal acetic acid and propionic acid and enhance species richness. Moreover, strain CF11 improved the gut microbiota community structure. In the experimental group, the genera Oscillospira, Coprococcus, and Ruminococcus, which are reported to be able to produce SCFAs, are significantly increased when compared... [more]

(canola) seed is a rich source of phytosterols, tocopherols and carotenoids, which all have recognized health benefits, although these are reduced or lost during crude oil refinement. Many studies are now outdated, so new research to monitor bioactive retention through current processing techniques is warranted. In this work, canola seed, in-process seed, and oil samples were collected from the major stages of five commercial canola oil processes. Analysis of phytosterols, tocopherols and carotenoids indicated seed pre-treatment enhanced bioactive concentrations in the crude oil. Although the bleaching step in each process eliminated all carotenoids, high concentrations of phytosterols and tocopherols remained in the refined oil across all processes, with losses notably lower than those found in previous reports. Moreover, crude oil samples from a two-stage cold pressing process showed greatly enriched concentrations of tocopherols (+122%), sterols (+140%) and carotenoids (+217%). The... [more]

Grapes’ infection with the fungi Botrytis cinerea is one of the major causes of economic loss in the winemaking sector worldwide. The laccase activity of grapes is considered an appropriate indicator of this type of fungal infection, and enzymatic activity higher than 3 U/mL indicates a high risk of irreversibly damaged grape must due to enzymatic browning. This work describes a fast test for the measurement of laccase activity based on a dual optical and electrochemical detection method. A paper sensor impregnated with the enzymatic substrate dye 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) provides a semi-quantitative optical measurement. While the paper sensor can be used independently, when combined with a screen-printed electrode and amperometry measurements, it enables the quantitative detection of laccase activities down to 0.4 U/mL in only 5 min. The method was applied for monitoring the artificial infection of white, rosé, and red grapes with different strains... [more]

The agricultural sector is responsible for about 30% of greenhouse gas emissions, and thus there is a need to develop new plant-based proteins with lower climate impact. Rapeseed press cake, a by-product from rapeseed oil production, contains 30% high-quality protein. The purpose of this study was to recover protein from cold-pressed rapeseed press cakes on a pilot scale using a decanter and investigate the effect of recirculation of the spent solids fraction on protein yield. Proteins were extracted under alkaline conditions (pH 10.5) followed by precipitation at pH 3.5. Recirculating the spent solids fraction once increased the accumulated protein yield from 70% to 83%. The efficiency of the recovery process was highest in the first and second cycles. The additional yield after the third and fourth cycles was only 2%. The amino acid composition showed high levels of essential amino acids and was not reduced throughout the recovery process. The glucosinolate and phytate content was re... [more]

Rapamycin, also known as sirolimus, inhibits the mTOR pathway in complex diseases such as cancer, and its downstream targets are ribosomal S6 kinases (RPS6K). Sirolimus is involved in regulating cell growth and cell survival through roles such as the mediation of epidermal growth factor signaling. However, the systemic efficacy of sirolimus in pathway regulation is unclear. The purpose of this study is to determine systemic drug efficacy using computational methods and drug-induced datasets. We suggest a computational method using gene expression datasets induced by sirolimus and an inverse algorithm that simultaneously identifies parameters referring to gene−gene interactions. We downloaded two sirolimus-induced microarray gene expression datasets and used a computational method to obtain the most enriched pathway, then adopted an inverse algorithm to discover the gene−gene interactions of that pathway. In the results, RPS6KB1 was a target gene of sirolimus and was associated with gen... [more]

Electro-fermentation is a novel process that consists in coupling a microbial fermentative metabolism with an electrochemical system. In such a process, the electrodes act either as the electron sinks or sources modifying the fermentation balance of a microbial fermentative metabolism and provide new options for the control of microbial activity. A theoretical framework for the analysis and control of fermentations using electro-fermentation is currently lacking. In this paper, we propose a simple electro-fermentation model in which a population of fermentative bacteria switch between two metabolic behaviors in response to different electrode potentials. We then mathematically analyze optimal strategies to maximize the production of one of the rising products in a batch fermentation using Pontryagin’s Maximum Principle. The obtained results show that, in some experimental configurations, a dynamic control of the electrode potential is required for the maximization of the desired produc... [more]

The effect of ultrasound in combination of heat on the extraction yield and technological properties of chia seed mucilage was investigated. Chia seeds were mixed with distilled water at a seed-to-water ratio of 1:30. The dispersion was adjusted to pH 9 and treated either with heat extraction by water bath or with heat/ultrasound extraction by probe-type sonication at 50 °C and 80 °C for 30 and 60 min. The yield and technological properties of mucilage samples were evaluated. The heat/ultrasound extraction gave a greater yield of mucilage (6.92−10.52%) as compared to the heat extraction (1.03−1.86%). Images obtained from Scanning Electron Microscope (SEM) have shown that during heat/ultrasound extraction, the amount of mucilage fibers on the surface of chia seed decreased with the increased extraction time. Thus, the yield of mucilage prepared with heat/ultrasound extraction for 60 min was significantly higher than that of mucilage extracted for 30 min. However, the difference between... [more]

Trastuzumab is a target-based recombinant humanized IgG1 monoclonal antibody (mAbs), extensively employed for treatment of metastatic breast cancer with human epidermal growth receptor 2 (HER2) overexpression. Studies around the world have reported that mAbs have substantial inter-patient unpredictable absorption, distribution, metabolism, and excretion (ADME-pharmacokinetics) because of multiple elements manipulating the concentration of mAbs in plasma. Herein, we have established a bioanalytical technique using UPLC-MS/MS with an easy sample workup method and in-solution digestion protocol to assay the trastuzumab plasma samples from breast cancer patients in clinical studies. Surrogated proteolytic peptides were used for accurate quantification of trastuzumab (CanMab) with a trastuzumab signature peptide with [13C6, 15N4]-arginine and [13C6, 15N2]-lysine stable isotope-labeled (SIL) peptide. Experiments to validate the method were accurately carried out according to the guidelines m... [more]

Studies have proven that alkaline water has a protective effect on gastric diseases. However, the underlying mechanism is not clear. Moreover, in some countries, especially in China, purified water (distilled water) is also an important form of drinking water, while its protective effect on gastric diseases is still unknown. This study aimed to compare the effects of distilled water (pH = 5.6 ± 0.3) and alkaline natural mineral water (pH = 9.3 ± 0.6) on ethanol-induced gastric ulcers in mice and to further clarify the underlying mechanisms. Pepsin activity, prostaglandin E-2 (PGE2) and heat shock protein 70 (HSP70), superoxide dismutase (SOD), reduced glutathione (GSH), and malondialdehyde (MDA), as well as the oxidative stress pathway related proteins such as nuclear factor erythroid-2 related factor 2 (Nrf2), heme oxygenase-1 (HO-1), and NADH quinone oxidoreductase 1 (NQO1) were measured. After alkaline natural mineral water treatment, the levels of PGE2 and HSP70 were significantly... [more]

Two options, in regard to applying microbial fuel cells (MFCs) in water treatment, are under discussion, namely the conversion of the chemical energy of organic substrates to electricity, as well as the use their potential to reduce different species, such as the ionic form of copper (Cu2+ converted to metal copper) and iron (Fe3+ converted to Fe2+). The high reduction potential of Cu2+ and Fe3+ makes the processes of electricity production and metal reduction, to be performed simultaneously in MFC, achievable. The electrical yield measurement during the experiments of anodic organic matter degradation by MFC in treating an artificial wastewater with chemical oxygen demand (COD) 0.6 and 1.6 g O2·dm−3, as initial COD, are given. It is demonstrated that the higher organic load is associated with better electrical yield. A comparison of MFC and conventional anaerobic digestion performance is discussed, as well. Experimental proofs of copper removal and phosphate mobilization, following th... [more]

Polycaprolactone (PCL) and polycaprolactone-hydroxyapatite (PCL-HA) scaffolds were produced by foaming in supercritical carbon dioxide (scCO2) at 20 MPa, as well as in one-step foaming and impregnation process using carvacrol as an antibacterial agent with proven activity against Gram-positive and Gram-negative bacteria. The experimental design was developed to study the influence of temperature (40 °C and 50 °C), HA content (10 and 20 wt.%), and depressurization rate (one and two-step decompression) on the foams’ morphology, porosity, pore size distribution, and carvacrol impregnation yield. The characterization of the foams was carried out using scanning electron microscopy (SEM, SEM-FIB), Gay-Lussac density bottle measurements, and Fourier−transform infrared (FTIR) analyses. The obtained results demonstrate that processing PCL and PCL-HA scaffolds by means of scCO2 foaming enables preparing foams with porosity in the range of 65.55−74.39% and 61.98−67.13%, at 40 °C and 50 °C, respec... [more]