Functional-preserving predictor-corrector multiderivative schemes

In this work, we develop a class of high-order multiderivative time integration methods that is able to preserve certain functionals discretely. Important ingredients are the recently developed Hermite-Birkhoff-Predictor-Corrector methods and the technique of relaxation for numerical methods of ODEs. We explain the algorithm in detail and show numerical results for two- and three-derivative methods, comparing relaxed and unrelaxed methods. The numerical results demonstrate that, at the slight cost of the relaxation, an improved scheme is obtained.Comment: Submitted to the Proceedings in Applied Mathematics and Mechanic (GAMM Annual Meeting 2023

Metabolic network capacity of Escherichia coli for Krebs cycle-dependent proline hydroxylation

Figure S1. Physiology of recombinant E. coli BL21(DE3)(pLysS) strains bearing pET-24a. Panel A and B show biomass formation (circles), glucose consumption (squares), acetate formation (triangles), and proline consumption (diamonds) during batch cultivation of wildtype (closed symbols) and ΔputA (open symbols) strains at 30°C in M9 medium supplemented with 5 g L−1 glucose in the absence (A) or presence (B) of 5 mM proline, respectively. Figure S2. SDS-PAGE analysis of recombinant E. coli BL21(DE3)(pLysS) (pET_p4h1of) and E. coli BL21 ΔputA (DE3) (pLysS) (pET_p4h1of) at different time points during growth in M9 medium with 5 g L−1 glucose (glc) only or with addition of 5 mM proline (pro) at 30°C. M: protein size marker. Figure S3. Physiology of recombinant E. coli BL21(DE3)(pLysS) strains bearing pET_p4h1of. Biomass formation (circles), glucose consumption (squares), acetate formation (triangles), hyp formation (stars), and proline consumption (diamonds) during batch cultivation of wildtype (closed symbols) and ΔputA (open symbols) strains are shown. Cultivation was performed at 30°C in M9 medium supplemented with 5 g L−1 glucose in the absence (panel A) or presence of 5 mM proline (panels B and C). Table S4. Mass isotopomer distribution of alanine for the wt_pET strain at 30°C in M9 medium supplemented with 5 g L−1 U-13C labeled glucose in the absence or presence of 5 mM proline. Table S5. Reactions of the central carbon metabolism generating or consuming NTP and/or redox equivalents. Table S6. Bacterial strains and plasmids used in this study. Table S7. Correlation factors between OD600 1 and cell dry weight concentration (gCDW L−1) of the strains used in this study

Novel concepts for the biocatalytic synthesis of second-generation biodiesel

Biodiesel is synthesized by the transesterification of triglycerides of oils with short-chain alcohols, such as methanol and ethanol. According to the Renewable Energy Directive guidelines (RED II 2018/2001/EU) the contribution of advanced biofuels, which do not include edible oils, towards the overall EU target, is at 1% in 2025 and at least 3.5% in 2030. Bioprocesses that valorize non-edible oils for the production of second-generation biodiesel could play a critical role in achieving this goal. Immobilized lipases, as well as other enzyme classes, such as cutinases and acyltransferases, are utilized as biocatalysts for this process. For the sustainability of the process, renewable materials can be used as immobilization matrices, or even enzymes anchored on the cells as whole-cell biocatalysts. Membrane reactors can also be employed to facilitate the enzymatic transesterification by conducting a continuous enzymatic reaction and simultaneously separate the products in a single operation. The advances on the aforementioned fast-pacing fields are presented in this work

Iron oxide nanoflowers encapsulated in thermosensitive fluorescent liposomes for hyperthermia treatment of lung adenocarcinoma

Magnetic hyperthermia (MHT) is in the spotlight of nanomedical research for the treatment of cancer employing magnetic iron oxide nanoparticles and their intrinsic capability for heat dissipation under an alternating magnetic field (AMF). Herein we focus on the synthesis of iron oxide nanoflowers (Nfs) of different sizes (15 and 35 nm) and coatings (bare, citrate, and Rhodamine B) while comparing their physicochemical and magnetothermal properties. We encapsulated colloidally stable citrate coated Nfs, of both sizes, in thermosensitive liposomes via extrusion, and RhB was loaded in the lipid bilayer. All formulations proved hemocompatible and cytocompatible. We found that 35 nm Nfs, at lower concentrations than 15 nm Nfs, served better as nanoheaters for magnetic hyperthermia applications. In vitro, magnetic hyperthermia results showed promising therapeutic and imaging potential for RhB loaded magnetoliposomes containing 35 nm Nfs against LLC and CULA cell lines of lung adenocarcinoma

Radiolabeled iron oxide nanoparticles functionalized with PSMA/BN ligands for dual-targeting of prostate cancer

IntroductionProstate cancer (PCa) is the second most frequent cancer diagnosis in men and the fifth leading cause of death worldwide. Prostate Specific Membrane Antigen (PSMA) and Gastrin Releasing Peptide (GRP) receptors are overexpressed in PCa. In this study, we have developed iron oxide nanoparticles (IONs) functionalized with the Prostate Specific Membrane Antigen (PSMA) and Gastrin Releasing Peptide (GRP) ligands for dual targeting of Prostate cancer.MethodsIONs were developed with a thin silica layer on their surface with MPTES (carrying -SH groups, IONs-SH), and they were coupled either with a pharmacophore targeting PSMA (IONs-PSMA) or with bombesin peptide (IONs-BN), targeting GRP receptors, or with both (IONs-PSMA/BN). The functionalized IONs were characterized for their size, zeta potential, and efficiency of functionalization using dynamic light scattering (DLS) and Fourier-Transform Infrared Spectroscopy (FT-IR). All the aforementioned types of IONs were radiolabeled directly with Technetium-99m (99mTc) and evaluated for their radiolabeling efficiency, stability, and binding ability on two different PCa cell lines (PC3 and LNCaP).Results and DiscussionThe MTT assay demonstrated low toxicity of the IONs against PC3 and LNCaP cells, while the performed wound-healing assay further proved that these nanostructures did not affect cellular growth mechanisms. The observed hemolysis ratio after co-incubation with red blood cells was extremely low. Furthermore, the 99mTc-radiolabeled IONs showed good stability in human serum, DTPA, and histidine, and high specific binding rates in cancer cells, supporting their future utilization as potential diagnostic tools for PCa with Single Photon Emission Computed Tomography (SPECT) imaging

Strategies for the biocatalytic modification of natural compounds

The present thesis deals with the enzymatic modification of selective antioxidant compounds of plant origin (silybin and rutin) with simple fatty acids, esters of fatty acids and dicarboxylic acids by lipase CALB (Novozym®435) in organic solvents, in order to increase their lipophilic nature and modify their biological action. Several parameters were studied concerning their impact on the performance of the enzymatic process. Acetone was the most suitable medium for the studied enzymatic processes, since its use lead to the highest conversion of silybin. Using simple fatty acids for the enzymatic acylation of silybin, it was found that the conversion increased by increasing the fatty chain length from 8 to 16 carbon atoms. Increasing the number of carbon atoms from 16 to 18, resulted in lower performance. The highest conversion was determined when butyric acid was used as acyl donor, a short chain fatty acid with 4 carbon atoms, in the presence of lipase Novozym®435 in acetone after 96 h at 50°C. In all cases, higher conversion yields were determined when fatty acids esters were used as acyl donors, instead of their corresponding fatty acids. Regardless of the acyl donor nature, increase of its concentration led to higher silybin conversion as well as higher reaction initial velocity, due to thermodynamic equilibrium shift towards synthesis. Using acetone as reaction medium, increase of silybin concentration led to higher process productivity. Of the organic solvents studied, acetone and acetonitrile were those that led to high conversion yields for the synthesis of mono-and di- acylated silybin derivatives, irrespectively of the dicarboxylic acid used. Lipase Novozym®435 exhibited higher selectivity for dicarboxylic acids with long carbon chain length (16 carbon atoms). In all cases, increasing of dicarboxylic acid concentration resulted in increased silybin conversion until the amount of the acyl donor exceeded the maximum solubility capacity of the solvent. Increasing silybin concentration led to increased monoester synthesis and reduced formation of corresponding diester. When rutin was used, only mono acylated derivatives were detected, unlike silybin for which both mono-and di-esters were detected. The aim of this study was also to introduce a lipase or esterase capable of catalyzing adequately the acylation of flavonoids (rutin and narigin) and anthocyanins (cyanin), and to investigate the feasibility of improving the catalytic performance by using "directed evolution" methodology. The reaction between nargin and vinyl butyrate in tertiary alcohol was chosen as model reaction. The reaction leads to the formation of narigin butyrate accompanied by vinyl alcohol release, which is automatically tautomerized into acetaldehyde. Acetaldehyde reacts with NBD-H, which is added to the system, and the complex formed can be fast and with sufficient sensitivity determined photometrically. Finally, the effect of the new compounds on cell proliferation, secretion of vascular endothelial growth factor (VEGF) and induction of apoptosis in human leukemia K562 cells was investigated. Additionally, their ability to induce the proteasome activity, a protein complex with important role in maintaining cellular homeostasis and cellular aging, was estimated in order to assess their anti-aging action. It was found that the antiproliferative effect of the new silybin esters with simple fatty acids on human leukemia K562 cells, was significantly retained compared to the parental compound (silybin). Silybin esters with dicarboxylic acids maintained the antiproliferative and anti-angiogenic effect of the parental compound and in some cases the effect was strengthened (ester of silybin with hexadecanedioic acid). The esters of silybin with dicarboxylic acids, did not induce the apoptosis of human leukemia K562 cells in contrast to silybin. In this study, the effect of silybin and its esters with simple fatty and dicarboxylic acids on the proteolytic activity of the proteasome was evaluated, in order to determine whether these substances inhibit the aging phenomenon in vitro. The ester with hexadecanedioic acid led to proteasome induction for all the studied concentrations and the determined proteasome proteolytic activity was higher than the parental compound.Στην παρούσα διατριβή μελετήθηκε η καταλυόμενη από λιπάση CALB (Novozym®435) εκλεκτική ακυλίωση αντιοξειδωτικών ενώσεων φυτικής προέλευσης (σιλυμπίνη και ρουτίνη) με απλά λιπαρά οξέα, εστέρες λιπαρών οξέων και δικαρβοξυλικά οξέα σε οργανικούς διαλύτες, με στόχο την αύξηση του λιπόφιλου χαρακτήρα τους και την τροποποίηση της βιολογικής τους δράσης. Η ακετόνη επιλέχθηκε ως ο καταλληλότερος διαλύτης ως μέσο για τις ενζυμικές διεργασίες υπό μελέτη, αφού οδήγησε στις υψηλότερες αποδόσεις μετατροπής των φυσικών αντιοξειδωτικών. Αναφορικά με τη χρήση απλών λιπαρών οξέων για την ενζυμική ακυλίωση της σιλυμπίνης, διαπιστώθηκε ότι η ποσοστιαία απόδοση μετατροπής αυξήθηκε με αύξηση του μήκους της ανθρακικής αλυσίδας από 8 σε 16 άτομα άνθρακα, ενώ αύξηση του αριθμού των ατόμων άνθρακα από 16 σε 18, οδήγησε σε μείωση της απόδοσης. Η υψηλότερη απόδοση μετατροπής προσδιορίστηκε όταν χρησιμοποιήθηκε ως ακυλοδότης βουτυρικό οξύ. Σε όλες τις περιπτώσεις ενζυμικής ακυλίωσης της σιλυμπίνης, υψηλότερες αποδόσεις προσδιορίστηκαν όταν ως ακυλοδότες χρησιμοποιήθηκαν εστέρες λιπαρών οξέων αντί για τα αντίστοιχα απλά λιπαρά οξέα. Ανεξάρτητα από τον τύπο του ακυλοδότη, η αύξηση της συγκέντρωσής του οδήγησε σε αύξηση της απόδοσης μετατροπής καθώς επίσης και σε αύξηση της αρχικής ταχύτητας των αντιδράσεων. Από τους οργανικούς διαλύτες που μελετήθηκαν, η ακετόνη και το ακετονιτρίλιο ήταν εκείνοι που οδήγησαν στην υψηλότερη απόδοση μετατροπής για τη σύνθεση μόνο- και δι-ακυλιωμένων παραγώγων σιλυμπίνης με όλα τα δικαρβοξυλικά οξέα. Διαπιστώθηκε εκλεκτικότητα της λιπάσης Novozym®435 για μεγάλης ανθρακικής αλυσίδας δικαρβοξυλικά οξέα (16 άτομα άνθρακα). Σε όλες τις περιπτώσεις, η αύξηση της συγκέντρωσης του δικαρβοξυλικού οξέος οδήγησε σε αύξηση της απόδοσης της αντίδρασης ακυλίωσης της σιλυμπίνης. Η χρήση ρουτίνης δεν οδήγησε σε σύνθεση διεστέρων και σε όλες τις περιπτώσεις η απόδοση μετατροπής ήταν χαμηλότερη συγκριτικά με τη σιλυμπίνη. Στόχο της συγκεκριμένης μελέτης αποτέλεσε επίσης, η εύρεση λιπάσης ή εστεράσης ικανής να καταλύει με επάρκεια την ακυλίωση φλαβονοειδών (ρουτίνη και ναριγκίνη) και ανθοκυανινών (κυανίνη), και η διερεύνηση της δυνατότητας βελτίωσης της καταλυτικής συμπεριφοράς με την αξιοποίηση των μεθόδων «κατευθυνόμενης εξέλιξης». Η αντίδραση μεταξύ ναριγκίνης και βινυλεστέρα του βουτυρικού οξέος σε τριτοταγή αλκοόλη ήταν εκείνη που επιλέχθηκε για μελέτη. Η συνθετική δάση του ενζύμου υπό τις συγκεκριμένες συνθήκες, οδηγεί σε σχηματισμό εστέρα ναριγκίνης με βουτυρικό οξύ και απελευθέρωση βινυλικής αλκοόλης η οποία αυτόματα μετασχηματίζεται σε ακεταλδεΰδη. Στη συνέχεια η ακεταλδεΰδη σχηματίζει σύμπλοκο με την ένωση NBD-H που έχει προστεθεί στο σύστημα και το οποίο μπορεί να προσδιοριστεί φωτομετρικά. Δεν εντοπίστηκε κλώνος ικανός να καταλύει την αντίδραση σύνθεσης υπό μελέτη. Τέλος, ελέγχθηκε η δράση των νέων ενώσεων στον κυτταρικό πολλαπλασιασμό, την έκκριση του αγγειακού ενδοθηλιακού αυξητικού παράγοντα (VEGF) και την επαγωγή της απόπτωσης στην καρκινική σειρά ανθρώπινων λευχαιμικών κυττάρων Κ562. Επίσης, μελετήθηκε η ικανότητά τους να ενεργοποιούν το πρωτεάσωμα. Διαπιστώθηκε ότι η παρεμποδιστική δράση των νέων εστέρων σιλυμπίνης με απλά λιπαρά οξέα στον πολλαπλασιασμό ανθρώπινων λευχαιμικών κυττάρων Κ562, διατηρήθηκε σε σημαντικό βαθμό συγκρινόμενη με τη μητρική ένωση (σιλυμπίνη). Οι εστέρες σιλυμπίνης με δικαρβοξυλικά οξέα διατήρησαν την παρεμποδιστική δράση της μητρικής ένωσης στον πολλαπλασιασμό καθώς και την έκκριση του αγγειακού ενδοθηλιακού παράγοντα ανάπτυξης (VEGF) από ανθρώπινα λευχαιμικά κύτταρα Κ562 και σε ορισμένες περιπτώσεις η δράση ενισχύθηκε. Τέλος, τα νέα ανάλογα της σιλυμπίνης μετά από ενζυμική ακυλίωση με δικαρβοξυλικά οξέα, βρέθηκε ότι σε αντίθεση με τη σιλυμπίνη δεν προκαλούν επαγωγή της απόπτωση σε ανθρώπινα λευχαιμικά κύτταρα Κ562. Ο εστέρας της σιλυμπίνης με δεκαεξανοδιοϊκό οξύ ήταν εκείνος που οδήγησε σε επαγωγή της δράσης του πρωτεασώματος αφού για όλες τις υπό μελέτη συγκεντρώσεις προσδιορίστηκε πρωτεολυτική δράση πρωτεασώματος υψηλότερη από εκείνη της μητρική ένωσης

Simulation of Colloidal Stability and Aggregation Tendency of Magnetic Nanoflowers in Biofluids

A population balance model for the aggregation of iron oxide nanoflowers (IONfs) is presented. The model is based on the fixed pivot technique and is validated successfully for four kinds of aggregation kernels. The extended Derjaguin, Landau, Verwey, and Overbeek (xDLVO) theory is also employed for assessing the collision efficiency of the particles, which is pertinent to the total energy of the interaction. Colloidal stability experiments were conducted on IONfs for two dispersant cases—aqueous phosphate buffered saline solution (PBS) and simulated body fluid (SBF). Dynamic light scattering (DLS) measurements after 24-h of incubation show a significant size increase in plain PBS, whereas the presence of proteins in SBF prevents aggregation by protein corona formation on the IONfs. Subsequent simulations tend to overpredict the aggregation rate, and this can be attributed to the flower-like shape of IONfs, thus allowing patchiness on the surface of the particles that promotes an uneven energy potential and aggregation hindering. In silico parametric study on the effects of the ionic strength shows a prominent dependency of the aggregation rate on the salinity of the dispersant underlying the effect of repulsion forces, which are almost absent in the PBS case, promoting aggregation. In addition, the parametric study on the van der Waals potential energy effect—within common Hamaker-constant values for iron oxides—shows that this is almost absent for high salinity dispersants, whereas low salinity gives a wide range of results, thus underlying the high sensitivity of the model on the potential energy parameters

Additional file 1: of Metabolic network capacity of Escherichia coli for Krebs cycle-dependent proline hydroxylation

Figure S1. Physiology of recombinant E. coli BL21(DE3)(pLysS) strains bearing pET-24a. Panel A and B show biomass formation (circles), glucose consumption (squares), acetate formation (triangles), and proline consumption (diamonds) during batch cultivation of wildtype (closed symbols) and ΔputA (open symbols) strains at 30°C in M9 medium supplemented with 5 g L−1 glucose in the absence (A) or presence (B) of 5 mM proline, respectively. Figure S2. SDS-PAGE analysis of recombinant E. coli BL21(DE3)(pLysS) (pET_p4h1of) and E. coli BL21 ΔputA (DE3) (pLysS) (pET_p4h1of) at different time points during growth in M9 medium with 5 g L−1 glucose (glc) only or with addition of 5 mM proline (pro) at 30°C. M: protein size marker. Figure S3. Physiology of recombinant E. coli BL21(DE3)(pLysS) strains bearing pET_p4h1of. Biomass formation (circles), glucose consumption (squares), acetate formation (triangles), hyp formation (stars), and proline consumption (diamonds) during batch cultivation of wildtype (closed symbols) and ΔputA (open symbols) strains are shown. Cultivation was performed at 30°C in M9 medium supplemented with 5 g L−1 glucose in the absence (panel A) or presence of 5 mM proline (panels B and C). Table S4. Mass isotopomer distribution of alanine for the wt_pET strain at 30°C in M9 medium supplemented with 5 g L−1 U-13C labeled glucose in the absence or presence of 5 mM proline. Table S5. Reactions of the central carbon metabolism generating or consuming NTP and/or redox equivalents. Table S6. Bacterial strains and plasmids used in this study. Table S7. Correlation factors between OD600 1 and cell dry weight concentration (gCDW L−1) of the strains used in this study

Vulnerability assessment of an innovative precast concrete sandwich panel subjected to the ISO 834 fire

Development and use of preconstruction have been exhibited for several decades. Numerous modules, ranging from the simplest to the most advanced concepts, have been suggested to ameliorate the layout of building structures, with respect to a broad spectrum of needs. This study aims to unfold the fire defensiveness of an innovative precast concrete sandwich wall-system subjected to the ISO 834 fire, such as this is provided for in EN1991-1-2. In light of a rapidly evolving environment that should shield structures against fire, this investigation emphasises on the vulnerability of precast panels with a varying thickness of insulation by means of a numerical methodology and a versatile heat transfer-model. A finite-element analysis is carried out with COMSOL Multiphysics® simulation software. In a following step, as fire risk should be vigorously tackled, the research is extended to validate numerical predictions of the model by means of an experimental setup for wall specimens arranged in the laboratory. Therefore, an additional goal of this research is to assess temperature discrepancies for both addressed cases. Despite various approximations of the model, an excellent agreement between numerical and experimental results is shown, confirming the rationality of computational simulations in terms of temperatures’ precision. It has been revealed that for all examined cases, the insulation ability (I) has been maintained for more than 3 h regardless of the positioning of the insulation. Further evidence though suggested that is not the case for the loadbearing capacity (R), as the installation of a fire exposed insulation layer resulted in lower stability systems. Also, the effect of the insulation thickness is not that dominant as on average and maximum temperature deviations among marginal assemblies (d EPS  = 2 cm and d EPS  = 10 cm) did not exceed 5 °C and 10 °C at t fire  ≈ 100 min

CHD2 pathogenic nonsense variant in a three-generation family with variable phenotype and a paracentric inversion 16: Case report

Chromosomal inversions are usually balanced structural chromosomal rearrangements that do not have an impact on the clinical phenotype of a carrier. The main clinical consequence of inversions is the risk for unbalanced gametes and offspring with severe phenotypes. Rarely though, inversions are associated with a phenotype, mainly due to submicroscopic Copy Number Variants (CNVs) or disruption at the breakpoints of a functionally important gene and/or genomic elements. In this study, a paracentric inversion of chromosome 16 [inv(16)(q22.3q24.1)] was identified in a three-generation family with discordant phenotypes with/without epilepsy and/or intellectual impairment, as well as with an unaffected carrier. This finding was confirmed by fluorescence in situ hybridization (FISH). Genetic investigation, initially with chromosomal microarray (CMA), did not reveal any copy number variants. Finally, Clinical Exome Sequencing (CES), detected the presence of a pathogenic nonsense variant (rs797044912) in the Chromodomain Helicase DNA-binding protein 2 (CHD2) gene [NM_001271.4:c.5035C>T p.(Arg1679Ter)]. CHD2 pathogenic variants have been associated with Developmental and Epileptic Encephalopathy-94 (DEE-94), a rare yet severe condition, characterized by developmental delay, seizures with an early onset, intellectual impairment, autism spectrum disorder, and sometimes behavioral issues. Family testing showed that the variant segregated with phenotypic heterogeneity in the affected individuals and appears to be causative. To the best of our knowledge, this is the first CHD2 pathogenic variant segregating in a three-generation family and the fourth familial case reported. These results further support our previous findings that familial, balanced rearrangements with discordant phenotypes in the same family are, in the vast majority, coincidental