Aqueous two-phase systems (ATPS) based on ionic liquids (IL) and deep eutectic solvents (DES) are ecofriendly choices and can be used to selectively separate compounds of interest, such as bioactive compounds. Bioactive compounds are nutrients and nonnutrients of animal, plant, and microbial origin that benefit the human body in addition to their classic nutritional properties. They can also be used for technical purposes in food and as active components in the chemical and pharmaceutical industries. Because they are usually present in complex matrices and low concentrations, it is necessary to separate them in order to increase their availability and stability, and ATPS is a highlighted technique for this purpose. This review demonstrates the application of ATPS based on IL and DES as a tool for recovering nonprotein bioactive compounds, considering critical factors, results and the most recent advances in this field. In addition, the review emphasizes the perspectives for expanding t... [more]

Wound healing continues to pose a challenge in clinical settings. Moreover, wound management must be performed properly and efficiently. Acute wound healing involves multiple cell divisions, a new extracellular matrix, and the process of formation, such as growth factors and cytokines, which are released at the site of the wound to regulate the process. Any changes that disrupt the healing process could cause tissue damage and prolong the healing process. Various factors, such as microbial infection, oxidation, and inflammation, can delay wound healing. In order to counter these problems, utilizing natural products with wound-healing effects has been reported to promote this process. Several natural products have been associated with wound healing, most of which are from medicinal plants. However, secondary microbial metabolites have not been extensively studied for their wound-healing properties. Further, investigations on the wound-healing control of natural microbial products are re... [more]

Global warming is one of the most serious problems leading to changes in the distribution areas of species and biodiversity. Rhodiola quadrifida is a rare plant with adaptogenic properties and grows in the highlands in a narrow temperature range of 2−15 °C. The aim of our work was to study the growth and content of the main metabolites in two in vitro cultures of Rhodiola quadrifida at temperatures of 5, 15 and 25 °C. Hairy roots and calli were cultivated on agar medium for 28 days. The maximum values of the growth index were observed at 25 °C (2.32 and 2.12 for calli and hairy roots, respectively). HPLC-MS showed the absence of tyrosol and rosarin in both cultures, and rosin in the root culture. The content of salidroside changed slightly in calli and roots. Cultivation at 5 °C significantly stimulated the formation of rosin in calli. Only a residual amount of rosavin was noted in the roots, regardless of temperature. The content of rosin was higher in calli at 15 °C with a maximum co... [more]

The use of photogrammetry provides an inexpensive, alternative method that can simplify the processes traditionally carried out in the orthotics workshop. The objectives of this study are to develop a method based on photogrammetry to obtain 3D-printed positive foot casts for fabricating thermoconformed orthoses from a negative cast in phenolic foam. Using a basic Smartphone, a photo capture protocol for feet, free software and a 3D printer, we tested the suitability of the positive cast obtained to fabricate custom foot orthoses using thermoconformed 3 mm polypropylene in the orthotics laboratory. The results show that digitally fabricated casts provide a very close replicate of the positive casts obtained traditionally through plaster casting (maximum dimension discrepancy between casts of 2 mm in length and 0.4 mm in forefoot, midfoot and rearfoot measurements). They are also suitable for the process of fabricating 2- and 3-mm polypropylene thermoconformed plantar orthoses. Photogra... [more]

In the upcoming years, the world will face societal challenges arising, in particular, from the impact of climate change and the inefficient use of natural resources, in addition to an exponential growth of the world population, which according to the United Nations (UN) estimations will be 9.8 billion in 2050. This increasing trend requires optimized management of natural resources with the use of value-added waste and a significant reduction in food loss and food waste. Moreover, the recent pandemic situation, COVID-19, has contributed indisputably. Along with the agri-food supply chain, several amounts of waste or by-products are generated. In most cases, these biomass wastes cause serious environmental concerns and high costs to enterprises. The valorisation of the agri-food loss and food industry wastes emerged as a useful strategy to produce certain value-added compounds with several potential applications, namely in the food, health, pharmaceutical, cosmetic, and environmental f... [more]

This is the source code for the STORE (STochasic Omentum REsponse) model. The model is used to simulate how naive T-cells in the omentum will prime and multiply during the expansion period (8 days) after a T-cell vaccination in a mouse.

This is the matlab source code used in the following paper:

Christian DA, Adams TA II, Smith TA, Shallberg LA, Theisen DJ, Phan AT, Abraha M, Perry J, Ruthel G, Clark JT, Murphy KM, Kedl, RM, Hunter CA. cDC1 coordinate innate and adaptive responses in the omentum required for T cell priming and memory. Science Immunology 7, eabq7432 (2022).

This is fixed legacy code used for the paper for scientific auditing and reproduction purposes. See paper for documentation.

Proprotein Convertase Subtilisin Kexin type 9 (PCSK9), comprises 12 exons, encoded for an enzyme which plays a critical role in the regulation of circulating low density lipoprotein. The gain-of-function (GOF) mutations aggravate the degradation of LDL receptors, resulting in familial hypercholesterolemia (FH), while loss-of-function (LOF) mutations lead to higher levels of the LDL receptors, lower the levels of LDL cholesterol, and preventing from cardiovascular diseases. It is noted that, previous publications related to the mutations of PCSK9 were not always unification. Therefore, this study aims to present the spectrum and distribution of PCSK9 gene mutations by a meta-analysis. A systematic literature analysis was conducted based on previous studies published by using different keywords. The weighted average frequency of PCSK9 mutation was calculated and accessed by MedCalc®. A total of 32 cohort studies, that included 19,725 familial hypercholesterolemia blood samples, were enro... [more]

Emerging evidence highlights the relevance of extracellular vesicles (EVs) in modulating human diseases including but not limited to cancer, inflammation, and neurological disorders. EVs can be found in almost all types of human body fluids, suggesting that their trafficking may allow for their targeting to remote recipient cells. While molecular processes underlying EV biogenesis and secretion are increasingly elucidated, mechanisms governing EV transportation, target finding and binding, as well as uptake into recipient cells remain to be characterized. Understanding the specificity of EV transport and uptake is critical to facilitating the development of EVs as valuable diagnostics and therapeutics. In this mini review, we focus on EV uptake mechanisms and specificities, as well as their implications in human diseases.

Recent years have witnessed a growing interest in the use of biocatalysts in flow reactors. This merging combines the high selectivity and mild operation conditions typical of biocatalysis with enhanced mass transfer and resource efficiency associated to flow chemistry. Additionally, it provides a sound environment to emulate Nature by mimicking metabolic pathways in living cells and to produce goods through the systematic organization of enzymes towards efficient cascade reactions. Moreover, by enabling the combination of enzymes from different hosts, this approach paves the way for novel pathways. The present review aims to present recent developments within the scope of flow chemistry involving multi-enzymatic cascade reactions. The types of reactors used are briefly addressed. Immobilization methodologies and strategies for the application of the immobilized biocatalysts are presented and discussed. Key aspects related to the use of whole cells in flow chemistry are presented. The... [more]

We previously reported that macropinocytosis (accompanied by actin reorganization, ruffling of the plasma membrane, and engulfment of large volumes of extracellular fluid) is an important process for the cellular uptake of extracellular vesicles, exosomes. Accordingly, we developed techniques to induce macropinocytosis by the modification of biofunctional peptides on exosomal membranes, thereby enhancing their cellular uptake. Arginine-rich cell-penetrating peptides have been shown to induce macropinocytosis via proteoglycans; accordingly, we developed peptide-modified exosomes that could actively induce macropinocytotic uptake by cells. In addition, the activation of EGFR induces macropinocytosis; based on this knowledge, we developed artificial leucine-zipper peptide (K4)-modified exosomes. These exosomes can recognize E3 sequence-fused EGFR (E3-EGFR), leading to the clustering and activation of E3-EGFR by coiled-coil formation (E3/K4), which induces cellular exosome uptake by macrop... [more]

A liposome-based artificial cell (LBAC) consists of a liposome encapsulating a cell-free protein expression system (CFPES) and protein-encoding DNA. It is surrounded by a lipid bilayer membrane and synthesizes proteins that resemble actual cells. Hence, they have been one of the most studied artificial cells. According to recent studies, they have been able to sense bio-functional molecules by synthesizing fluorescent proteins in response to target molecules. Therefore, they are expected to be used as biosensors. However, previously reported LBACs encapsulated the CFPES derived from Escherichia coli, resulting in the most productive protein expression at 20−40 °C. To broaden the range of their working temperatures to lower temperatures, in this study, we constructed LBACs using a CFPES derived from Pseudomonas fluorescens that grows at a temperature range of 4 °C to 30 °C. We then demonstrated that the constructed LBAC expressed proteins at 8 °C and that, the protein expression capabil... [more]

Nonalcoholic fatty liver disease (NAFLD) generally co-occurs with metabolic disorders, but it is unclear which genes have a pleiotripic effect on NAFLD and metabolic traits. We performed a large-scale cross-trait association analysis to identify the overlapping genes between NAFLD and nine metabolic traits. Among all the metabolic traits, we found that obesity and type II diabetes are associated with NAFLD. Then, a multitrait association analysis among NAFLD, obesity and type II diabetes was conducted to improve the overall statistical power. We identified 792 significant variants by a cross-trait meta-analysis involving 100 pleiotripic genes. Moreover, we detected another two common genes by a genome-wide gene test. The results from the pathway enrichment analysis show that the 102 shared risk genes are enriched in cancer, diabetes, insulin secretion, and other related pathways. This study can help us understand the molecular mechanisms underlying comorbid NAFLD and metabolic disorder... [more]

We present the centrifugal microfluidic implementation of a four-plex digital droplet polymerase chain reaction (ddPCR). The platform features 12 identical ddPCR units on a LabDisk cartridge, each capable of generating droplets with a diameter of 82.7 ± 9 µm. By investigating different oil−surfactant concentrations, we identified a robust process for droplet generation and stabilization. We observed high droplet stability during thermocycling and endpoint fluorescence imaging, as is required for ddPCRs. Furthermore, we introduce an automated process for four-color fluorescence imaging using a commercial cell analysis microscope, including a customized software pipeline for ddPCR image evaluation. The applicability of ddPCRs is demonstrated by the quantification of three cancer-associated KRAS point mutations (G12D, G12V and G12A) in a diagnostically relevant wild type DNA background. The four-plex assay showed high sensitivity (3.5−35 mutant DNA copies in 15,000 wild type DNA copies) a... [more]

Fructan sucrase is a kind of biological enzyme that catalyzes the synthesis of fructan, and fructan is a polysaccharide product with important industrial application value. In this study, the Fructan sucrase gene of Bacillus subtilis was cloned to plasmid PET-28A-ACMA-Z, and three clones were obtained after the transformation of Escherichia coli BL21, namely BS-FF, BSO, and BS. The clones BS-FF and BSO secreted the recombinant enzymes outside the cells, while the clone BS expressed them inside the cells. The induction experiment results showed that the optimum IPTG concentration in the medium was 0.5 mM and 1.0 mM for clones BS-FF and BSO, respectively, while the incubation conditions were at 28 °C for 8 h. The recombinant fructan sucrase was purified one step using a material called GEM particles. The results indicated that 95.25% of fructan sucrase expressed by the clone BS-FF could be secreted into the extracellular area, and even 98.78% by the clone BSO. With the above purification... [more]

A set membership estimator (SME) based on limited number of measurements is proposed for estimating metabolite concentrations using dynamic flux balance models (DFBMs). To deal with multiplicity of solutions of the DFBM, a weighted primal dual method is used to find solutions that best fit the data. Multiparametric nonlinear programming is applied to propagate uncertainty in initial concentrations along a batch/fed-batch operation. The proposed method has been applied to E. coli batch and fed-batch fermentation without noise.

Autism Spectrum Disorders (ASD) are a group of neurological disorders that present with limited social communication/interaction and restricted, repetitive behaviors/interests. The current estimate is that approximately 1.9% of children in the US are diagnosed with ASD. While this is a high prevalence and the economic burden by ASD is significant, there is still considerable debate regarding the underlying pathophysiology of ASD. Because of this lack of biological knowledge, autism diagnoses are restricted to observational behavioral and psychometric tools. This work takes a step towards the goal of incorporating bio-chemical data into ASD diagnosis by analyzing measurements of metabolite concentrations of the folate-dependent one-carbon metabolism and transulfuration pathways. Unlike traditional approaches that are based upon comparing differences in individual metabolite concentrations between children with and without an ASD diagnosis, we made use of multivariate classification via... [more]

In our previous work, a mathematical, agent-based dynamic model was developed which simulates the response of the mammalian omentum to a T cell vaccine injection during the expansion phase. The model tracks how each individual naïve T cell interacts with antigen presenting cells, and subsequently primes and divides over an 8-day period following vaccine injection. The model works from first principles; individual phenomena based on experimental observation and theory are incorporated into the model, and the collection of many such phenomena together create a nuanced model of the system as a whole. In this work, we show that the model works well in other relevant tissues, such as the spleen.

The rapid spread of the COVID-19 worldwide pandemic at the beginning of 2020 has significantly affect-ed the global economy with severe human and economic losses. Despite the shortage of personal protective equipment, the facemask serves as a fundamental means to protect health care professionals' and re-strict the spread of the coronavirus. However, due to the limited stock of facemasks, many sterilization methods were developed to eliminate the infection and established strategies for fast and repeated reuse without affecting the filtration efficiency. The current study extrapolates the effective utilization of the ozonic sterilization of the N95 mask. First, we demonstrated the potential of ozone as a disinfectant that successfully destructs the organic food colour compounds deposited on the N95 mask; In the quantitative part of this research, the N95 facemask pieces were soaked in diphenylamine solution and later oxidized with ozone under the different intervals of time. Finally,... [more]

Amongst different living organisms studied as potential candidates for the green synthesis of copper nanoparticles, algal biomass is presented as a novel and easy-to-handle method. However, the role of specific biomolecules and their contribution as reductant and capping agents has not yet been described. This contribution reports a green synthesis method to obtain copper oxide nanoparticles (CuO-NPs) using separated protein fractions from an aqueous extract of brown algae Macrocystis pyrifera through size exclusion chromatography (HPLC-SEC). Proteins were detected by a UV/VIS diode array, time-based fraction collection was carried out, and each collected fraction was used to evaluate the synthesis of CuO-NPs. The characterization of CuO-NPs was evaluated by Dynamic Light Scattering (DLS), Z-potential, Fourier Transform Infrared (FTIR), Transmission Electron Microscope (TEM) equipped with Energy Dispersive X-ray Spectroscopy (EDS) detector. Low Molecular Weight (LMW) and High Molecular... [more]

The particles from gas saturated solutions (PGSS) process were performed to encapsulate lactofer-rin, an iron-binding milk glycoprotein, using supercritical carbon dioxide (scCO2). A natural en-teric polymer, shellac, was used as a coating material of lactoferrin carried out by the PGSS pro-cess. Conditions were optimized by applying different temperatures (20−50 °C) and pressures (8−10 MPa) and the particles were evaluated for particle shape and size, lactoferrin encapsulation ef-ficiency, Fourier transform infrared (FTIR) spectroscopy to confirm lactoferrin entrapment and in vitro dissolution studies at different pH values. Particles with an average diameter of 75.5 ± 7 μm were produced with encapsulation efficiency up to 71 ± 2%. Furthermore, particles that showed high stability in low pH (pH 1.2) and a sustained release over time (t2h = 75%) in higher pH (pH 7.4) suggested an effective encapsulation process for the protection of lactoferrin from gastric di-gestion.

Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels a... [more]

Evaluation of pH-dependent reactivity of drugs is an essential component in the pharmaceutical industry. Thus, the stability of three antihistaminic drugs, i.e., ketotifen, epinastine and emedastine, was tested, in solutions of five pH values, i.e., 1.0, 3.0, 7.0, 10.0 and 13.0, at high temperature (70 °C). LC-UV isocratic methods were developed to estimate percentage degradation as well as the kinetics of degradation. Generally, epinastine was shown to be the most stable compound with degradation below 14%. Emedastine was labile in all pH conditions, with degradation in the range 29.26−51.88%. Ketotifen was moderately stable at pH 1−7 (degradation ≤ 14.04%). However, at pH ≥ 10, its degradation exceeded 30%. The kinetics of degradation of ketotifen, epinastine and emedastine was shown as a pseudo-first-order reaction with the rate constants in the range 10−4−10−3 min−1 Finally, the UPLC-MS/MS method was applied to identify the main degradants and suggest degradation pathways. Degradat... [more]

In this research work, Polydimethylsiloxane (PDMS) has been used for the fabrication of microchannels for biomedical application. Under the internet of things (IoT)-based controlled environment, the authors have simulated and fabricated bio-endurable, biocompatible and bioengineered PDMS-based microchannels for varicose veins implantation exclusively to avoid tissue damaging. Five curved ascending curvilinear micro-channel (5CACMC) and five curved descending curvilinear micro-channels (5CDCMC) are simulated by MATLAB (The Math-Works, Natick, MA, USA) and ANSYS (ANSYS, The University of Lahore, Pakistan) with actual environments and confirmed experimentally. The total length of each channel is 1.6 cm. The diameter of both channels is 400 µm. In the ascending channel, the first to fifth curve cycles have the radii of 2.5 mm, 5 mm, 7.5 mm, 10 mm, and 2.5 mm respectively. In the descending channel, the first and second curve cycles have the radii of 12.5 mm and 10 mm respectively. The thir... [more]

The gene encoding a thermostable β-1,3-glucanase was cloned from Thermobifida fusca and expressed constitutively by Yarrowia lipolytica using plasmid pYLSC1. The expression level of the recombinant β-1,3-glucanase reached up to 270 U/mL in the culture medium. After a treatment with endo-β-N-acetyl-glucosaminidase H, the recombinant protein appeared as a single protein band, with a molecular size of approximately 66 kDa on the SDS-polyacrylamide gel. The molecular weight was consistent with the size predicted from the nucleotide sequence. The optimum temperature and pH of the transformant β-1,3-glucanase were 60 °C and pH 8.0, respectively. This β-1,3-glucanase was tolerant to 10% methanol, ethanol, and DMSO, retaining 70% activity. The enzyme markedly hydrolyzed Wolfiporia cocos and Pycnoporus sanguineus glucans. The DPPH and ABTS scavenging potential, reducing power and total phenolic contents of these two Polyporaceae hydrolysates, were significantly increased after 18 h of the enzym... [more]

In this paper, we present a simple, versatile method that creates patterns for cell migration studies using thermoplastic elastomer (TPE). The TPE material used here can be robustly, but reversibly, bonded to a variety of plastic substrates, allowing patterning of cultured cells in a microenvironment. We first examine the bonding strength of TPE to glass and polystyrene substrates and com-pare it to thermoset silicone-based PDMS under various conditions and demonstrate that the TPE can be strongly and reversibly bonded on commercially available polystyrene culture plates. In cell migration studies, cell patterns are templated around TPE features cored from a thin TPE film. We show that the significance of fibroblast cell growth with fetal bovine serum (FBS)-cell culture media compared to the cells cultured without FBS, analyzed over two days of cell culture. This simple approach allows us to generate cell patterns without harsh manipulations like scratch assays and to avoid damaging th... [more]