​Department of Biotechnology and Biosciences

Macrophages and dendritic cells (DCs) differently contribute to the generation of coordinated immune system responses against infectious agents. They interact with microbes through germline-encoded pattern-recognition receptors (PRRs), which recognize molecular patterns expressed by various microorganisms. Upon antigen binding, PRRs instruct DCs for the appropriate priming of natural killer cells, followed by specific T-cell responses. Once completed the effector phase, DCs reach the terminal differentiation stage and eventually die by apoptosis. By contrast, following antigen recognition, macrophages initiate first the inflammatory process and then switch to an anti-inflammatory phenotype for the restoration of tissue homeostasis. Following lipopolysaccharide (LPS)-stimulation the initiation of the apoptotic pathway in DCs is due the activation of NFAT proteins. DC stimulation with lipopolysaccharide (LPS) induces Src-family kinase and phospholipase C (PLC)γ2 activation, influx of extracellular Ca2+ and calcineurin-dependent nuclear NFAT translocation. The initiation of this pathway is independent of TLR4 engagement, and dependent exclusively on CD14. We asked whether macrophage survival after LPS encounter was due to their inability to activate the Ca2+ pathway. As matter of fact, bone marrow-derived macrophages were unable to mobilize Ca2+ and to translocate NFAT to the. To further investigate whether the Ca2+-NFAT pathway played any role in LPS-stimulated macrophages, we performed a comparative kinetic microarray analysis in conditions allowing or inhibiting NFAT activation. We show here that no modulation of gene expression can be attributed to NFAT. Gene expression analyses were performed using Affymetrix GeneChips in the following groups of murine macrophaghes: 1) CD14-deficient macrophages stimulated with LPS; 2) wt macrophages stimulated with LPS in presence of EGTA; 3) wt macrophages stimulated with LPS. The following kinetic time points were examined: 0, 6 and 24 hours following LPS activation. This experimental setting allowed us to select for effects due to Ca2+ fluxes and exclude the effects due to other causes, particularly the block of TRIF recruitment in CD14-deficient cells and the EGTA effects unrelated to Ca2+ chelation.

Neurodegenerative diseases include a significant number of pathologies affecting the nervous system. Generally, the primary cause of each disease is specific; however, recently, it was shown that they may be correlated at molecular level. This aspect, together with the exhibition of similar symptoms, renders the diagnosis of these disorders difficult. Amyotrophic lateral sclerosis is one of these pathologies. Herein, we report several cases of amyotrophic lateral sclerosis misdiagnosed as a consequence of features that are common to several neurodegenerative diseases, such as Parkinson's, Huntington's and Alzheimer's disease, spinal muscular atrophy, progressive bulbar palsy, spastic paraplegia and frontotemporal dementia, and mostly with the lysosomal storage disorder GM2 gangliosidosis. Overall reports highlight that the differential diagnosis for amyotrophic lateral sclerosis should include correlated mechanisms.

Abstract Background The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO2). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO2-fixation yield compared to sugars. Recently, we described an engineered Saccharomyces cerevisiae strain which allowed SA production in synthetic glycerol medium with a maximum yield of 0.23 Cmol Cmol−1. The results of that previous study suggested that the glyoxylate cycle considerably contributed to SA accumulation in the respective strain. The current study aimed at improving the flux into the rTCA pathway accompanied by a higher CO2-fixation and SA yield. Results By changing the design of the expression cassettes for the rTCA pathway, overexpressing PYC2, and adding CaCO3 to the batch fermentations, an SA yield on glycerol of 0.63 Cmol Cmol−1 was achieved (i.e. 47.1% of the theoretical maximum). The modifications in this 2nd-generation SA producer improved the maximum biomass-specific glycerol consumption rate by a factor of nearly four compared to the isogenic baseline strain solely equipped with the dihydroxyacetone (DHA) pathway for glycerol catabolism. The data also suggest that the glyoxylate cycle did not contribute to the SA production in the new strain. Cultivation conditions which directly or indirectly increased the concentration of bicarbonate, led to an accumulation of malate in addition to the predominant product SA (ca. 0.1 Cmol Cmol−1 at the time point when SA yield was highest). Off-gas analysis in controlled bioreactors with CO2-enriched gas-phase indicated that CO2 was fixed during the SA production phase. Conclusions The data strongly suggest that a major part of dicarboxylic acids in our 2nd-generation SA-producer was formed via the rTCA pathway enabling a net fixation of CO2. The greatly increased capacity of the rTCA pathway obviously allowed successful competition with other pathways for the common precursor pyruvate. The overexpression of PYC2 and the increased availability of bicarbonate, the co-substrate for the PYC reaction, further strengthened this capacity. The achievements are encouraging to invest in future efforts establishing a process for SA production from (crude) glycerol and CO2.

of A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the ÎąB-Crystallin case study

Additional file 2: Figure S2. Second derivatives of FTIR absorption spectra of S. cerevisiae BY4741 strain in the absence and in the presence of lactic acid. Cells were grown in shake flasks in minimal (YNB) medium with 2 % w/v glucose in the absence and in the presence of different concentration of lactic acid: pH3, 40 g/L and 46 g/L lactic acid (LA) at pH3. FTIR analysis was performed at 18 h after the inoculation, corresponding the exponential phase of growth. a: amide I band; b: vibrational modes mainly due to lipid CH2/CH3 and to phosphate groups. Derivative spectra have been normalized to the tyrosine band at ~ 1516 cm−1.

Abstract Background Saccharomyces cerevisiae and Pichia pastoris are two of the most relevant microbial eukaryotic platforms for the production of recombinant proteins. Their known genome sequences enabled several transcriptomic profiling studies under many different environmental conditions, thus mimicking not only perturbations and adaptations which occur in their natural surroundings, but also in industrial processes. Notably, the majority of such transcriptome analyses were performed using non-engineered strains. In this comparative study, the gene expression profiles of S. cerevisiae and P. pastoris, a Crabtree positive and Crabtree negative yeast, respectively, were analyzed for three different oxygenation conditions (normoxic, oxygen-limited and hypoxic) under recombinant protein producing conditions in chemostat cultivations. Results The major differences in the transcriptomes of S. cerevisiae and P. pastoris were observed between hypoxic and normoxic conditions, where the availability of oxygen strongly affected ergosterol biosynthesis, central carbon metabolism and stress responses, particularly the unfolded protein response. Steady state conditions under low oxygen set-points seemed to perturb the transcriptome of S. cerevisiae to a much lesser extent than the one of P. pastoris, reflecting the major tolerance of the baker's yeast towards oxygen limitation, and a higher fermentative capacity. Further important differences were related to Fab production, which was not significantly affected by oxygen availability in S. cerevisiae, while a clear productivity increase had been previously reported for hypoxically grown P. pastoris. Conclusions The effect of three different levels of oxygen availability on the physiology of P. pastoris and S. cerevisiae revealed a very distinct remodelling of the transcriptional program, leading to novel insights into the different adaptive responses of Crabtree negative and positive yeasts to oxygen availability. Moreover, the application of such comparative genomic studies to recombinant hosts grown in different environments might lead to the identification of key factors for efficient protein production.

Spermatocytes expressing YFP-Rab1 during telophase. Red arrows show YFP-Rab1 localizing to the cleavage furrow. Left panel shows a phase-contrast image of telophase spermatocytes, right panel the corresponding fluorescence image. Scale bar, 10 μm.

(a) Interphase spermatocytes from wild type and omt/Df stained for Garz, Tubulin and DNA. (N=32 wild type spermatocytes, N=36 omt/Df mutant spermatocytes; the cells examined were from four independent experiments). Scale bar, 10 μm. (b) Co-IP of Garz with RFP-Rab1. Protein extracts from testes expressing either RFP-Rab1 or RFP (as a control) proteins were immunoprecipitated with anti-RFP (i.e RFP-trap beads) and immunoblotted for RFP and Garz. 2% of the total lysates (Input), and 1/3 of the immunoprecipitates were loaded and probed with the indicated antibody. Molecular masses are in kilodalton. (c) Quantification of Garz protein Co-immunoprecipitated from testis protein extracts expressing either RFP, or RFP-Rab1. The protein band intensities were obtained from three independent experiments.

Neural stem cells appear to be best suited for regenerative therapy in neurological diseases. However, the effects of high levels of potentially toxic substances such as sulfatides – which accumulate in metachromatic leukodystrophy (MLD) – on this regenerative ability are still largely unclear. To start addressing this question, in vitro and in vivo experiments were used to examine the behavior of multipotential neural precursors exposed to abnormally high levels of sulfatides. Following transplantation of dissociated neurospheres into the brain of presymptomatic MLD pups, the majority of donor-derived cells were distributed in a caudal to rostral direction, with higher numbers in the cortex. Most if not all of the donor cells acquired an astroglial phenotype. We found no evidence of oligodendrocyte or neuronal commitment of transplanted cells in long-term-treated MLD mice (e.g. up to 1.5 years of age). This was in line with our in vitro findings of sulfatides blocking oligodendrocyte formation after induction of differentiation in sulfatide-treated epidermal growth factor/fibroblast growth factor responsive neurospheres. Transplanted MLD mice showed an improved arylsulfatase A (ARSA) activity and a significant amelioration of sulfatide metabolism, neurodegeneration and motor-learning/memory deficits. Furthermore, transplanted cells were shown to act as a source of ARSA enzyme that accumulated in endogenous brain cells, indicating the occurrence of enzyme cross-correction between transplanted and host cells. These results provide a first insight into the effect of sulfatides on the stemness properties of neural stem cells and on the effects of the MLD environment on the in vivo expectations of using neural stem cells in cell therapy.

of A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the ÎąB-Crystallin case study