Comparison of Properties of Breads Enriched with Omega-3 Oil Encapsulated in β-Glucan and Saccharomyces cerevisiae Yeast Cells

  Background and objective: Flaxseed oil, as a potential source of polyunsaturated fatty acids, is susceptible to oxidation. Yeast cells of Saccharomyces cerevisiae and β-glucan can be used as biocompatible and biodegradable matrices for the protection of this nutritious oil from oxidation in foods enriched with omega-3 fatty acids. The aim of this study was to investigate quality properties of breads containing encapsulated and free flaxseed oils. Materials and methods: Flaxseed oil was encapsulated in either yeast cells or β-glucan. Functional wheat bread samples were prepared using unencapsulated and encapsulated flaxseed oils. These were compared with control samples in terms of dough rheological and bread quality parameters. Results and conclusion: Encapsulation significantly increased dough rheological properties (G′ and G″ values), firmness and density and decreased lightness, compared to control samples. Breads, containing flaxseed oil encapsulated in yeast cells, showed a lower peroxide index and a higher α-linolenic acid value, compared to two other samples containing oil samples. This showed a better protection of unsaturated fatty acids against deleterious oxidation reactions. Results of this study indicate that addition of microencapsulated flaxseed oil into breads helps preserve sensory properties of the control sample, compared to breads fortified with free flaxseed oil. Conflict of interest: The authors declare no conflict of interest

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

Iron is essential for most living organisms. In addition, its biogeochemical cycling influences important processes in the geosphere (e.g., the mobilization or immobilization of trace elements and contaminants). The reduction of Fe(III) to Fe(II) can be catalysed microbially, particularly by metal-respiring bacteria utilizing Fe(III) as a terminal electron acceptor. Furthermore, Grampositive fermentative iron reducers are known to reduce Fe(III) by using it as a sink for excess reducing equivalents, as a form of enhanced fermentation. Here, we use the Gram-positive fermentative bacterium Clostridium acetobutylicum as a model system due to its ability to reduce heavy metals.We investigated the reduction of soluble and solid iron during fermentation. We found that exogenous (resazurin, resorufin, anthraquinone-2,- 6-disulfonate) aswell as endogenous (riboflavin) electron mediators enhance solid iron reduction. In addition, iron reduction buffers the pH, and elicits a shift in the carbon and electron flow to less reduced products relative to fermentation. This study underscores the role fermentative bacteria can play in iron cycling and provides insights into the metabolic profile of coupled fermentation and iron reduction with laboratory experiments and metabolic network modellin

Oncogenic role of connective tissue growth factor is associated with canonical TGF-β cascade in colorectal cancer

TGF-β signaling pathways promote tumour development and control several downstream genes such as CTGF and MMPs. This study aimed to investigate the association between CTGF and MMP-1 mRNA expressions with clinicopathological status and survival rate in colorectal cancer patients. We investigated expression levels of CTGF and MMP-1 genes in paraffin-embedded tumours and adjacent normal tissue blocks (ADJ) by Real Time-PCR. Then, the expression of Smad2 and Smad4 proteins in the TGF-β canonical pathway was evaluated by immunohistochemistry. Finally, the correlation between CTGF, MMP-1, and the canonical TGF-β-signalling pathway with the clinicopathological features was investigated. Expression levels of MMP-1and CTGF were higher in tumours compared with adjacent normal tissues. Overexpression levels of MMP-1 and CTGF were associated with lymph node metastasis, distant metastasis, tumour histopathological grading, advanced stage, and poor survival (p 0.05). Additionally, a significant association between the upregulation of MMP-1 and tumour location was noted. Upregulation of Smad2 and Smad4 proteins were also significantly correlated with lymph node metastasis, distant metastasis, advanced stage, and poor survival (p 0.0001). This study showed that canonical TGF-β signalling regulates both CTGF and MMP-1 expression and CRC progression. Moreover, TGF-β signalling and its downstream genes could be used as novel biomarkers and novel approaches for targeted therapy in CRC

Age-associated B cells predict impaired humoral immunity after COVID-19 vaccination in patients receiving immune checkpoint blockade

Age-associated B cells (ABC) accumulate with age and in individuals with different immunological disorders, including cancer patients treated with immune checkpoint blockade and those with inborn errors of immunity. Here, we investigate whether ABCs from different conditions are similar and how they impact the longitudinal level of the COVID-19 vaccine response. Single-cell RNA sequencing indicates that ABCs with distinct aetiologies have common transcriptional profiles and can be categorised according to their expression of immune genes, such as the autoimmune regulator (AIRE). Furthermore, higher baseline ABC frequency correlates with decreased levels of antigen-specific memory B cells and reduced neutralising capacity against SARS-CoV-2. ABCs express high levels of the inhibitory FcγRIIB receptor and are distinctive in their ability to bind immune complexes, which could contribute to diminish vaccine responses either directly, or indirectly via enhanced clearance of immune complexed-antigen. Expansion of ABCs may, therefore, serve as a biomarker identifying individuals at risk of suboptimal responses to vaccination

Optimization methods and objective functions for analysis of metabolic network models

Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichiometric balances while taking into account gene-protein-reaction associations. Several methods have already been developed for the analysis of these models. These methods are mainly used to optimize a single or combination of objective functions subject to different constraints. In this thesis, we have summarized the optimization methods and objective functions by classifying them based on biological and mathematical features. Particularly, we suggest reformulations to convert some of the complex optimization classes to simpler ones. One of the reformulations is the conversion of mixed-integer linear fractional programming (MILFP) to mixed-integer linear programming (MILP). We show that this conversion is useful in studying coupling relationships in thermodynamically constrained metabolic network models. Coupling determines how different components of the network such as metabolites or reactions are interrelated. Particularly, flux Coupling Analysis (FCA) is a method for evaluating the dependencies between metabolic reactions. In FCA, two reactions are considered as coupled if the activity of one, constrains the activity of the other. So far, FCA has been used for analyzing metabolic reactions in flux-balanced models. In this work, we developed a new formulation, Thermodynamic Flux Coupling Analysis (TFCA), which calculates flux couplings of metabolic models that are subjected to thermodynamic constraints. With TFCA, we show that adding thermodynamic constraints can significantly change the coupling relationship of reactions of the network. Moreover, we show that calculating coupling relations helps in reducing the number of combinations of bidirectional reactions (BDRs), which in turn will facilitate the analysis of the metabolic network. In addition to proposing several mathematical reformulations to gain global optimality, we also addressed the issue of finding the proper cellular objective function in different conditions of cellular metabolism. This is not always straight-forward, since the metabolic activities of some organisms are not well-characterized, e.g., metabolism of dormancy phase in some bacteria and parasites. In this thesis, we studied the metabolic behaviour of dormant malaria parasite using genome-scale model of Plasmodium falciparum. We examined known and novel objective functions and scored them based on the modelâs consistency with experimental gene expression data. Our results suggested that minimizing energy dissipation can best describe the metabolic activities of the malaria parasites in the dormancy phase. In the last chapter, we focus on studying another poorly characterized metabolic system that is the process of iron reduction in Clostridium acetobutylicum. Research has shown that this organism can reduce Fe(III), but the mechanism behind this reduction is yet to be identified. In this thesis, we analyzed the metabolism of C. acetobutylicum using its reconstructed genome-scale metabolic network model and experimental transcriptomics data in the presence or absence of Fe(III). By performing several computational studies, we suggested that NAD(P) is involved in the reduction of iron and is the potential physiological electron donor to Fe(III)

Oncogenic Role of Connective Tissue Growth Factor Is Associated with Canonical TGF-β Cascade in Colorectal Cancer

TGF-β signaling pathways promote tumour development and control several downstream genes such as CTGF and MMPs. This study aimed to investigate the association between CTGF and MMP-1 mRNA expressions with clinicopathological status and survival rate in colorectal cancer patients. We investigated expression levels of CTGF and MMP-1 genes in paraffin-embedded tumours and adjacent normal tissue blocks (ADJ) by Real Time-PCR. Then, the expression of Smad2 and Smad4 proteins in the TGF-β canonical pathway was evaluated by immunohistochemistry. Finally, the correlation between CTGF, MMP-1, and the canonical TGF-β-signalling pathway with the clinicopathological features was investigated. Expression levels of MMP-1and CTGF were higher in tumours compared with adjacent normal tissues. Overexpression levels of MMP-1 and CTGF were associated with lymph node metastasis, distant metastasis, tumour histopathological grading, advanced stage, and poor survival (p p < 0.0001). This study showed that canonical TGF-β signalling regulates both CTGF and MMP-1 expression and CRC progression. Moreover, TGF-β signalling and its downstream genes could be used as novel biomarkers and novel approaches for targeted therapy in CRC

Age-associated B cells predict impaired humoral immunity after COVID-19 vaccination in patients receiving immune checkpoint blockade

Acknowledgements: This work was funded by the UK Medical Research Council (project number MC_UU_00025/12), the Medical Research Foundation (MRF-057-0002-RG-THAV-C0798) and The Evelyn Trust (grant number 20/40) to J.E.D.T. N.J.M. was supported by the MRC (TSF ref. MR/T032413/1), NHSBT (grant ref. WPA15-02) and Addenbrooke’s Charitable Trust (grant ref. 900239). M.A.C. was supported by the Medical Research Council (project number MC_UU_00025/10). K.R.P. was supported by the Medical Research Council (project number MC_UU_00025/11). K.F. held an MRC studentship with support from the Cambridge European Trust and St. John’s College. K.W. has received funding by the Deutsche Forschungsgemeinschaft (WA 1597/6-1 and WA 1597/7-1). K.W. and B.K. received support by the German Federal Ministry of Education and Research (BMBF) through a grant to the German genetic multi-organ Auto-Immunity Network (GAIN), grant code 01GM2206A. F.H. is an ERC Advanced Investigator (695669). We thank Carola G. Vinuesa for helpful discussion. The authors also thank the Flow Cytometry Facilities at the MRC-Toxicology Unit, University of Cambridge; Katarzyna Kania from CRUK-CI-Genomics, Cambridge UK for advice on single cell RNA sequencing experiments; and Rosalind Kieran from the Department of Oncology, Cambridge University NHS Hospitals Foundation Trust, Cambridge UK, for contributions for patient recruitment and data collection.Age-associated B cells (ABC) accumulate with age and in individuals with different immunological disorders, including cancer patients treated with immune checkpoint blockade and those with inborn errors of immunity. Here, we investigate whether ABCs from different conditions are similar and how they impact the longitudinal level of the COVID-19 vaccine response. Single-cell RNA sequencing indicates that ABCs with distinct aetiologies have common transcriptional profiles and can be categorised according to their expression of immune genes, such as the autoimmune regulator (AIRE). Furthermore, higher baseline ABC frequency correlates with decreased levels of antigen-specific memory B cells and reduced neutralising capacity against SARS-CoV-2. ABCs express high levels of the inhibitory FcγRIIB receptor and are distinctive in their ability to bind immune complexes, which could contribute to diminish vaccine responses either directly, or indirectly via enhanced clearance of immune complexed-antigen. Expansion of ABCs may, therefore, serve as a biomarker identifying individuals at risk of suboptimal responses to vaccination