In silico constraint-based strain optimization methods: the quest for optimal cell factories

Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production yields is of paramount importance for this leap to happen. Constraint-based models of metabolism, together with in silico strain design algorithms, promise to reveal insights into the best genetic design strategies, a step further toward achieving that goal. In this work, a thorough analysis of the main in silico constraint-based strain design strategies and algorithms is presented, their application in real-world case studies is analyzed, and a path for the future is discussed.

Mechanical fatigue performance of PCL-chondroprogenitor constructs after cell culture under bioreactor mechanical stimulus

In tissue engineering of cartilage, polymeric scaffolds are implanted in the damaged tissue and subjected to repeated compression loading cycles. The possibility of failure due to mechanical fatigue has not been properly addressed in these scaffolds. Nevertheless, the macroporous scaffold is susceptible to failure after repeated loading-unloading cycles. This is related to inherent discontinuities in the material due to the micropore structure of the macro-pore walls that act as stress concentration points. In this work, chondrogenic precursor cells have been seeded in Poly-ε-caprolactone (PCL) scaffolds with fibrin and some were submitted to free swelling culture and others to cyclic loading in a bioreactor. After cell culture, all the samples were analyzed for fatigue behavior under repeated loading-unloading cycles. Moreover, some components of the extracellular matrix (ECM) were identified. No differences were observed between samples undergoing free swelling or bioreactor loading conditions, neither respect to matrix components nor to mechanical performance to fatigue. The ECM did not achieve the desired preponderance of collagen type II over collagen type I which is considered the main characteristic of hyaline cartilage ECM. However, prediction in PCL with ECM constructs was possible up to 600 cycles, an enhanced performance when compared to previous works. PCL after cell culture presents an improved fatigue resistance, despite the fact that the measured elastic modulus at the first cycle was similar to PCL with poly(vinyl alcohol) samples. This finding suggests that fatigue analysis in tissue engineering constructs can provide additional information missed with traditional mechanical measurements.

Biochemical and physical surface functionalization of polycaprolactone as a key mediator of osteogenic differentiation and vascularized tissue morphogenesis

Tese de Doutoramento em Engenharia de Tecidos, Medicina Regenerativa e Células Estaminais.

Human and murine clonal CD8+ T cell expansions arise during tuberculosis because of TCR selection

The immune system can recognize virtually any antigen, yet T cell responses against several pathogens, including Mycobacterium tuberculosis, are restricted to a limited number of immunodominant epitopes. The host factors that affect immunodominance are incompletely understood. Whether immunodominant epitopes elicit protective CD8+ T cell responses or instead act as decoys to subvert immunity and allow pathogens to establish chronic infection is unknown. Here we show that anatomically distinct human granulomas contain clonally expanded CD8+ T cells with overlapping T cell receptor (TCR) repertoires. Similarly, the murine CD8+ T cell response against M. tuberculosis is dominated by TB10.44-11-specific T cells with extreme TCRß bias. Using a retro genic model of TB10.44-11-specific CD8+ Tcells, we show that TCR dominance can arise because of competition between clonotypes driven by differences in affinity. Finally, we demonstrate that TB10.4-specific CD8+ T cells mediate protection against tuberculosis, which requires interferon-? production and TAP1-dependent antigen presentation in vivo. Our study of how immunodominance, biased TCR repertoires, and protection are inter-related, provides a new way to measure the quality of T cell immunity, which if applied to vaccine evaluation, could enhance our understanding of how to elicit protective T cell immunity.

Clear cell adenocarcinoma of the cervix in a young woman: a diagnostic challenge

Clear cell adenocarcinoma of the cervix is a rare tumor, classically related with in utero diethylstilbestrol (DES) exposure. The authors report a rare case of clear cell adenocarcinoma of the cervix in a 21-yearold woman who had no history of in utero DES exposure, presenting with intermittent vaginal bleeding. It stresses the relevance to always clarify the etiology of abnormal genital bleeding and consider the possibility of cervicovaginal tumors.

Study of the tightness of the metallization used on top of a thin film capacitor cell

Dissertação de mestrado integrado em Engenharia de Materiais

Development of hyaluronic acid, dextrin and extracellular matrix hydrogels for cell expansion

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Engenharia Clínica)

Production of secondary metabolites in cell suspension cultures of Ocimum sanctum L.

Dissertação de mestrado em Plant Molecular Biology, Biotechnology and Bioentrepreneurship

Exploring the role of O-Mannosylation in the modulation of E-Cadherin function in Gastric Cancer cell line models

Dissertação de mestrado em Bioquímica Aplicada – Biomedicina

Goblet cell density association with tear function and ocular surface physiology

Purpose: To determine the relationship of goblet cell density (GCD) with tear function and ocular surface physiology. Methods: This was a cross-sectional study conducted in 35 asymptomatic subjects with mean age 23.8±3.6 years. Tear film assessment, conjunctiva and cornea examination were done in each subject. Conjunctival impression cytology was performed by applying Nitrocellulose Millipore MFTM-Membrane filter over the superior bulbar conjunctiva. The filter paper was than fixed with 96% ethanol and stained with Periodic Acid Schiff, Hematoxylin and Eosin. GCD was determined by optical microscopy. Relation between GCD and Schirmer score, tear break-up time (TBUT), bulbar redness, limbal redness and corneal staining was determined. Results: The mean GCD was 151±122 cells/mm2. GCD was found higher in eyes with higher Schirmer score but it was not significant (p = 0.75). There was a significant relationship ofGCDwith TBUT (p = 0.042). GCD was not correlated with bulbar redness (p = 0.126), and limbal redness (p = 0.054) as well as corneal staining (p = 0.079). No relationship of GCD with age and gender of the subjects (p > 0.05) was observed. Conclusion: GCD was found correlated with TBUT but no significant correlation was found with the aqueous portion of the tear, limbal as well as bulbar redness and corneal staining.

Regulation of human mesenchymal stem cell osteogenesis by specific surface density of fibronectin: a gradient study

 The success of synthetic bone implants requires good interface between the material and the host tissue. To study the biological relevance of fi bronectin (FN) density on the osteogenic commitment of human bone marrow mesenchymal stem cells (hBMMSCs), human FN was adsorbed in a linear density gradient on the surface of PCL. The evolution of the osteogenic markers alkaline phosphatase and collagen 1 alpha 1 was monitored by immunohistochemistry, and the cytoskeletal organization and the cell-derived FN were assessed. The functional analysis of the gradient revealed that the lower FN-density elicited stronger osteogenic expression and higher cytoskeleton spreading, hallmarks of the stem cell commitment to the osteoblastic lineage. The identifi cation of the optimal FN density regime for the osteogenic commitment of hBM-MSCs presents a simple and versatile strategy to signifi cantly enhance the surface properties of polycaprolactone as a paradigm for other synthetic polymers intended for bone-related applications.

Gellan gum-coated gold nanorods: an intracellular nanosystem for bone tissue engineering

Gold nanorods (AuNRs) have emerged as an exceptional nanotool for a myriad of applications ranging from cancer therapy to tissue engineering. However, their surface modification with biocompatible and stabilizing biomaterials is crucial to allow their use in a biological environment. Herein, low-acyl gellan gum (GG) was used to coat AuNRs surface, taking advantage of its stabilizing, biocompatible and gelling features. The layer-by-layer based strategy implied the successive deposition of poly(acrylic acid), poly(allylamine hydrochloride) and GG, which allowed the formation of a GG hydrogel-like shell with 7 nm thickness around individual AuNRs. Stability studies in a wide range of pH and salt concentrations showed that the polysaccharide coating can prevent AuNRs aggregation. Moreover, a reversible pH-responsive feature of the nanoparticles was observed. Cytocompatibility and osteogenic ability of GG-coated AuNRs was also addressed. After 14 days of culturing within SaOS-2, an osteoblast-like cell line, in vitro studies revealed that AuNRs-GG exhibit no cytotoxicity, were internalized by the cells and localized inside lysosomes. AuNRs-GG combined with osteogenic media enhanced the mineralization capacity two-fold, as compared to cells exposed to osteogenic media alone. The proposed system has shown interesting features for osteogenesis, and further insights might be relevant for drug delivery, tissue engineering and regenerative medicine.

Light responsive multilayer surfaces with controlled spatial extinction capability

Multilayer systems obtained using the Layer-by-Layer (LbL) technology have been proposed for a variety of biomedical applications in tissue engineering and regenerative medicine. LbL assembly is a simple and highly versatile method to modify surfaces and fabricate robust and highly-ordered nanostructured coatings over almost any type of substrates and with a wide range of substances. The incorporation of polyoxometalate (POM) inorganic salts as constituents of the layers presents a possibility of promoting light-stimuli responses in LbL substrates. We propose the design of a biocompatible photo-responsive multilayer system based on a Preyssler-type POM ([NaP5W30O110]14â ) and a natural origin polymer, chitosan, using the LbL methodology. The photo-reduction properties of the POM allow the spatially controlled disruption of the assembled layers due to the weakening of the electrostatic interactions between the layers. This system has found applicability in detaching devices, such as the cell sheet technology, which may solve the drawbacks actually found in other cell treatment proposals.

Adipogenic cell sheets to recreate in vitro adipose tissue microenvironments

Cell sheet (CS) engineering, taking advantage of cellular self-matrix organized as in native tissue, has been largely explored, including by us, for different purposes [1â 3]. Herein we propose for the ï¬ rst time, the use of human adipose stem cells (hASCs)-derived CS to create adipose tissue analogues with different levels of maturation. hASCs were cultured on UpCellTM thermo-responsive dishes for 1, 3 and 5 days under basal conditions previously established by us [3]. The inï¬ uence of pre-differentiation time and respective cell number, over CS stability and differentiation was assessed. Mechanically robust CS were only obtained with 5 days pre-differentiation period. Adipogenesis was followed along the culture assessing the variation of expression of mesenchymal (CD73, CD105 but not CD90) and adipogenic (PPARg, FABP4 and LPL) markers by ï¬ ow cytometry, immunocytochemistry and RT-PCR. Increased ratio of differentiated cells was achieved for longer pre-differentiation periods, while maturation degree was modulated by the maintenance medium. Independently of the overall CS differentiation/maturation level, 3D constructs were fabricated by stacking and further culturing 3 CS. Thus, by varying the culture conditions, different 3D adipose tissue-like microenvironments were recreated, enabling future development of new tissue engineering strategies, as well as further study of adipose tissue role in the regeneration of different tissues.

Topography of aligned PNIPAm nanogels determines cell motility and cytoskeleton architecture

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Engenharia Clínica)