DeepFRAP: Fast fluorescence recovery after photobleaching data analysis using deep neural networks

Conventional analysis of fluorescence recovery after photobleaching (FRAP) data for diffusion coefficient estimation typically involves fitting an analytical or numerical FRAP model to the recovery curve data using non-linear least squares. Depending on the model this can be time-consuming, especially for batch analysis of large numbers of data sets and if multiple initial guesses for the parameter vector are used to ensure convergence. In this work, we develop a completely new approach, DeepFRAP, utilizing machine learning for parameter estimation in FRAP. From a numerical FRAP model developed in previous work, we generate a very large set of simulated recovery curve data with realistic noise levels. The data is used for training different deep neural network regression models for prediction of several parameters, most importantly the diffusion coefficient. The neural networks are extremely fast and can estimate the parameters orders of magnitude faster than least squares. The performance of the neural network estimation framework is compared to conventional least squares estimation on simulated data, and found to be strikingly similar. Also, a simple experimental validation is performed, demonstrating excellent agreement between the two methods. We make the data and code used publicly available to facilitate further 34development of machine learning-based estimation in FRAP

Bioprocessed Brewers’ Spent Grain Improves Nutritional and Antioxidant Properties of Pasta

Brewers’ spent grain (BSG), the by-product of brewing, was subjected to a xylanase treatment followed by fermentation with Lactiplantibacillus plantarum PU1. Bioprocessed BSG has been used as ingredient to obtain a fortified semolina pasta which can be labeled as “high fiber” and “source of protein” according to the European Community Regulation No. 1924/2006. Compared to native BSG, the use of bioprocessed BSG led to higher protein digestibility and quality indices (essential amino acid index, biological value, protein efficiency ratio, nutritional index), as well as lower predicted glycemic index. Bioprocessing also improved the technological properties of fortified pasta. Indeed, brightfield and confocal laser scanning microscopy revealed the formation of a more homogeneous protein network, resulting from the degradation of the arabinoxylan structure of BSG, and the release of the components entrapped into the cellular compartments. The extensive cell wall disruption contributed to the release of phenols, and conferred enhanced antioxidant activity to the fortified pasta. The persistence of the activity was demonstrated after in vitro-mimicked digestion, evaluating the protective effects of the digested pasta towards induced oxidative stress in Caco-2 cells cultures. The fortified pasta showed a peculiar sensory profile, markedly improved by the pre-treatment, thus confirming the great potential of bioprocessed BSG as health-promoting food ingredient

Bioprocessing of Brewers’ Spent Grain Enhances Its Antioxidant Activity: Characterization of Phenolic Compounds and Bioactive Peptides

Brewers' spent grain (BSG) is the major by-product of the brewing industry which remain largely unutilized despite its nutritional quality. In this study, the effects of fermentation on BSG antioxidant potential were analyzed. A biotechnological protocol including the use of xylanase followed by fermentation withLactiplantibacillus plantarum (Lactobacillus plantarum)PU1, PRO17, and H46 was used. Bioprocessed BSG exhibited enhanced antioxidant potential, characterized by high radical scavenging activity, long-term inhibition of linoleic acid oxidation and protective effect toward oxidative stress on human keratinocytes NCTC 2544. Immunolabelling and confocal laser microscopy showed that xylanase caused an extensive cell wall arabinoxylan disruption, contributing to the release of bound phenols molecules, thus available to further conversion through lactic acid bacteria metabolism. To clarify the role of fermentation on the antioxidant BSG potential, phenols were selectively extracted and characterized through HPLC-MS techniques. Novel antioxidant peptides were purified and identified in the most active bioprocessed BSG.Peer reviewe

Bioprocessed Brewers’ Spent Grain Improves Nutritional and Antioxidant Properties of Pasta

Brewers’ spent grain (BSG), the by-product of brewing, was subjected to a xylanase treatment followed by fermentation with Lactiplantibacillus plantarum PU1. Bioprocessed BSG has been used as ingredient to obtain a fortified semolina pasta which can be labeled as “high fiber” and “source of protein” according to the European Community Regulation No. 1924/2006. Compared to native BSG, the use of bioprocessed BSG led to higher protein digestibility and quality indices (essential amino acid index, biological value, protein efficiency ratio, nutritional index), as well as lower predicted glycemic index. Bioprocessing also improved the technological properties of fortified pasta. Indeed, brightfield and confocal laser scanning microscopy revealed the formation of a more homogeneous protein network, resulting from the degradation of the arabinoxylan structure of BSG, and the release of the components entrapped into the cellular compartments. The extensive cell wall disruption contributed to the release of phenols, and conferred enhanced antioxidant activity to the fortified pasta. The persistence of the activity was demonstrated after in vitro-mimicked digestion, evaluating the protective effects of the digested pasta towards induced oxidative stress in Caco-2 cells cultures. The fortified pasta showed a peculiar sensory profile, markedly improved by the pre-treatment, thus confirming the great potential of bioprocessed BSG as health-promoting food ingredient

ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours

Background: Neuroblastoma (NB) tumours are commonly divided into three cytogenetic subgroups. However, by unsupervised principal components analysis of gene expression profiles we recently identified four distinct subgroups, r1-r4. In the current study we characterized these different subgroups in more detail, with a specific focus on the fourth divergent tumour subgroup (r4). Methods: Expression microarray data from four international studies corresponding to 148 neuroblastic tumour cases were subject to division into four expression subgroups using a previously described 6-gene signature. Differentially expressed genes between groups were identified using Significance Analysis of Microarray (SAM). Next, gene expression network modelling was performed to map signalling pathways and cellular processes representing each subgroup. Findings were validated at the protein level by immunohistochemistry and immunoblot analyses. Results: We identified several significantly up-regulated genes in the r4 subgroup of which the tyrosine kinase receptor ERBB3 was most prominent (fold change: 132–240). By gene set enrichment analysis (GSEA) the constructed gene network of ERBB3 (n = 38 network partners) was significantly enriched in the r4 subgroup in all four independent data sets. ERBB3 was also positively correlated to the ErbB family members EGFR and ERBB2 in all data sets, and a concurrent overexpression was seen in the r4 subgroup. Further studies of histopathology categories using a fifth data set of 110 neuroblastic tumours, showed a striking similarity between the expression profile of r4 to ganglioneuroblastoma (GNB) and ganglioneuroma (GN) tumours. In contrast, the NB histopathological subtype was dominated by mitotic regulating genes, characterizing unfavourable NB subgroups in particular. The high ErbB3 expression in GN tumour types was verified at the protein level, and showed mainly expression in the mature ganglion cells. Conclusions: Conclusively, this study demonstrates the importance of performing unsupervised clustering and subtype discovery of data sets prior to analyses to avoid a mixture of tumour subtypes, which may otherwise give distorted results and lead to incorrect conclusions. The current study identifies ERBB3 as a clear-cut marker of a GNB/GN-like expression profile, and we suggest a 7-gene expression signature (including ERBB3) as a complement to histopathology analysis of neuroblastic tumours. Further studies of ErbB3 and other ErbB family members and their role in neuroblastic differentiation and pathogenesis are warranted

Gene expression studies in human astrocytoma, with emphasis on oncostatin M induced effects

Brain tumors comprise about one percent of all cancers and astrocytoma is the most common primary brain malignancy. According to the World Health Organization system, the astrocytomas are divided into four grades according to degree of malignancy. Grade I, pilocytic astrocytoma (PA), is the least malignant form and most often affects children. Grade IV, glioblastoma multiforme (GBM), is the most malignant astrocytoma and has very poor prognosis, with an average survival of 9 - 11 months despite current therapies. This project started as a screening project, in which RT-PCR was used to search for over-expressed cytokines in human brain tumors. In our first paper, we discovered that members of the IL-6 cytokine family were highly expressed in different types of brain tumors. One of them was oncostatin M (OSM), a multifunctional cytokine, produced in the central nervous system after injury, inflammation and various diseases. Immunohistochemistry analysis showed that the tumor cells contained OSM in their cytoplasm, suggesting they produce this factor. The expression of OSM in non-tumor brain tissue was found to be very low or below detection limit. The function of OSM are unclear with conflicting reports of growth stimulatory or inhibitory effects in various cell types. OSM is known to signal through gp130 and the JAK/STAT pathway. In our second paper, we investigated the effects of OSM in vitro by stimulating glioblastoma cell cultures with OSM. STAT1 and STAT3 were immediately phosphorylated, indicating presence of a functional JAK/STAT pathway. We however, could not detect any changes in proliferation or in apoptosis after addition of OSM to cell cultures.In our third paper gene expression were examined by microarray in a glioblastoma cell line before and after addition of OSM. Twelve up-regulated and six down-regulated genes were identified in the U1242MG after stimulation with OSM. Among the up-regulated genes were: CH3L1 and PLAU which both affect cell migration, degradation and remodeling of extracellular matrix. MT2A was also induced and it has a function in metal ion binding and is known to be implicated in the regulation of cell proliferation and as an inhibitor of apoptosis. Another up-regulated gene was EPAS1, which is important for tumor adaptation to hypoxia and induces the expression of VEGF. These are all cancer promoting properties and therefore, we conclude that OSM may function as a master switch for several genes that contribute to the invasive nature of GBM.In the fourth paper, microarray were used to search for differentially expressed genes in PA and GBM. We hoped to find genes that could help explain the malignant behavior of GBM. Fourteen differentially expressed genes were identified and further tested in an extended tumor panel. SLC1A2, HNT, PLEKHB1 and STOM were low expressed in the GBM group. SLC1A2 expression has been shown to decrease glioma cell proliferation; HNT may promote cell adhesion; PLEKHB1 encodes a signal transduction protein with unknown function and STOM is a mediator of ion transport. Loss of these genes and their functions may be important for the highly malignant growth of this tumor group

Increased release of carotenoids and delayed in vitro lipid digestion of high pressure homogenized tomato and pepper emulsions

Carotenoids are lipophilic compounds that are digested and absorbed along with lipids. Emulsions based on a mixture of plum tomato and red sweet pepper, with 5% or 10% rapeseed oil, were obtained by high pressure homogenization, and the concentration of carotenoids in the emulsion oil droplets was quantified. The fraction of lycopene and beta-carotene released from the plant matrix into the oil droplets was highest in the 10% emulsion, which had larger oil droplets than the 5% emulsion. Xanthophylls were easily released into oil droplets in both 5% and 10% emulsions. The results suggest that the release of carotenoids made available for intestinal absorption depends on carotenoid type and can be significantly improved by increasing the homogenization pressure and oil content. However, in vitro gastrointestinal digestion indicated the presence of constituents or structures in the emulsions, originating from tomato, that reduced pancreatic activity, which may delay micellarization and uptake of carotenoids.acceptedVersio

Relationship between hemolysis and lipid oxidation in red blood cell-spiked fish muscle; dependance on pH and blood plasma

The relationship between hemolysis and lipid oxidation was explored in red blood cell (RBCs)-spiked washed cod mince (WCM). At pH 6.8 and 3 ± 1 °C, intact RBCs (71 µM Hb) delayed lipid oxidation by 1 day compared to WCM with partly or fully lysed RBCs which oxidized immediately. Intact RBCs also lowered peak peroxide value (PV) and thiobarbituric acid reactive substances (TBARS) with up to 59.5% and 48.1%, respectively. Adding 3% (v/w) blood plasma to RBC-spiked WCM delayed the lipid oxidation onset from 1 to 3–4 days without delaying hemolysis. At pH 6.4 the oxidation onset in RBC-WCM was the same as for pH 6.8 while at pH 7.2–7.6 lipid oxidation was suppressed for 7 days. Micrographs revealed RBC-lysis from day 2 at pH 6.4 but at pH 7.6, RBC stayed intact for ≥ 7 days. Thus, assuring presence of plasma-derived antioxidants and/or elevating muscle pH to avoid hemolysis can aid valorization of blood rich underutilized fish raw materials. This work was supported by the Swedish research council for sustainable development (FORMAS) Grant no. 2016-01181. This project has also received funding from Region Västra Götaland (project RUN 2019-00345) and the Bio Based Industries Joint Undertaking (JU) under grant agreement (No 837726). The JU receives support from the European Union’s Horizon 2020 research and innovation programme and the Bio Based Industries Consortium</p