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

Homer1a is a core brain molecular correlate of sleep loss.

Sleep is regulated by a homeostatic process that determines its need and by a circadian process that determines its timing. By using sleep deprivation and transcriptome profiling in inbred mouse strains, we show that genetic background affects susceptibility to sleep loss at the transcriptional level in a tissue-dependent manner. In the brain, Homer1a expression best reflects the response to sleep loss. Time-course gene expression analysis suggests that 2,032 brain transcripts are under circadian control. However, only 391 remain rhythmic when mice are sleep-deprived at four time points around the clock, suggesting that most diurnal changes in gene transcription are, in fact, sleep-wake-dependent. By generating a transgenic mouse line, we show that in Homer1-expressing cells specifically, apart from Homer1a, three other activity-induced genes (Ptgs2, Jph3, and Nptx2) are overexpressed after sleep loss. All four genes play a role in recovery from glutamate-induced neuronal hyperactivity. The consistent activation of Homer1a suggests a role for sleep in intracellular calcium homeostasis for protecting and recovering from the neuronal activation imposed by wakefulness.

Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance

The 2009 pandemic influenza A virus outbreak led to the systematic use of the neuraminidase (NA) inhibitor oseltamivir (OST). Consequently, OST-resistant strains, carrying the mutation H275Y, emerged in the years after the pandemics, with a prevalence of 1-2%. Currently, OST-resistant strains have been found in community settings, in untreated individuals. To spread in community settings, H275Y mutants must contain additional mutations, collectively called permissive mutations. We display the permissive mutations in NA of OST-resistant A(H1N1)pdm09 virus found in Brazilian community settings. The NAs from 2013 are phylogenetically distinct from those of 2012, indicating a tendency of positive selection of NAs with better fitness. Some previously predicted permissive mutations, such as V241I and N369K, found in different countries, were also detected in Brazil. Importantly, the change D344N, also predicted to compensate loss of fitness imposed by H275Y mutation, was found in Brazil, but not in other countries in 2013. Our results reinforce the notion that OST-resistant A(H1N1)pdm09 strains with compensatory mutations may arise in an independent fashion, with samples being identified in different states of Brazil and in different countries. Systematic circulation of these viral strains may jeopardise the use of the first line of anti-influenza drugs in the future.

Long-term effectiveness of first-line antiretroviral theraphy in a cohort of HIV-1 infected patients.

Eligibility criteria might explain differences in viral response to combined antiretroviral treatment (cART) between clinical trials and routine care setting. Prospective analysis including HIV-1 infected patients starting cART between January 2004 and December 2009, at Hospital Universitari Vall d’Hebron. Effectiveness evaluated as time to treatment failure (TF), defined as virologic failure, loss to follow-up, death or treatment discontinuation whatever the reason other than switching. Effectiveness month 12, 24 and 36 was 82.9%, 78.5% and 76%, respectively. 57 (24.6%) patients presented TF, mainly due to intolerance or toxicity. Higher risk in patients starting before 2006 and those with protease inhibitor based regimen.

Effects of mineralocorticoid and K+ concentration on K+ secretion and ROMK channel expression in a mouse cortical collecting duct cell line.

The cortical collecting duct (CCD) plays a key role in regulated K(+) secretion, which is mediated mainly through renal outer medullary K(+) (ROMK) channels located in the apical membrane. However, the mechanisms of the regulation of urinary K(+) excretion with regard to K(+) balance are not well known. We took advantage of a recently established mouse CCD cell line (mCCD(cl1)) to investigate the regulation of K(+) secretion by mineralocorticoid and K(+) concentration. We show that this cell line expresses ROMK mRNA and a barium-sensitive K(+) conductance in its apical membrane. As this conductance is sensitive to tertiapin-Q, with an apparent affinity of 6 nM, and to intracellular acidification, it is probably mediated by ROMK. Overnight exposure to 100 nM aldosterone did not significantly change the K(+) conductance, while it increased the amiloride-sensitive Na(+) transport. Overnight exposure to a high K(+) (7 mM) concentration produced a small but significant increase in the apical membrane barium-sensitive K(+) conductance. The mRNA levels of all ROMK isoforms measured by qRT-PCR were not changed by altering the basolateral K(+) concentration but were decreased by 15-45% upon treatment with aldosterone (0.3 or 300 nM for 1 and 3 h). The paradoxical response of ROMK expression to aldosterone could possibly work as a preventative mechanism to avoid excessive K(+) loss which would otherwise result from the increased electrogenic Na(+) transport and associated depolarization of the apical membrane in the CCD. In conclusion, mCCD(cl1) cells demonstrate a significant K(+) secretion, probably mediated by ROMK, which is not stimulated by aldosterone but increased by overnight exposure to a high K(+) concentration.

Worst-case bounds for the logarithmic loss of predictors

We investigate on-line prediction of individual sequences. Given a class of predictors, the goal is to predict as well as the best predictor in the class, where the loss is measured by the self information (logarithmic) loss function. The excess loss (regret) is closely related to the redundancy of the associated lossless universal code. Using Shtarkov's theorem and tools from empirical process theory, we prove a general upper bound on the best possible (minimax) regret. The bound depends on certain metric properties of the class of predictors. We apply the bound to both parametric and nonparametric classes ofpredictors. Finally, we point out a suboptimal behavior of the popular Bayesian weighted average algorithm.

Autosomal Recessive Posterior Microphthalmos/Nanophthalmos is Caused by Loss-of-function Mutations in LOC646960, a Novel Gene Encoding a Trypsin-like Serine Protease

Purpose: Posterior microphthalmos (MCOP)/nanophthalmos (NNO) is a developmental anomaly characterized by extreme hyperopia due to short axial length. The population of the Faroe Islands shows a high prevalence of an autosomal recessive form (arMCOP). The gene mutated in arMCOP is not yet known.Methods: Genetic mapping by linkage analysis using microsatellite and single nucleotide polymorphisms, mutation analysis by PCR and sequencing, molecular modellingResults: Having refined the position of the disease locus (MCOP6) in an interval of 250 kb in chromosome 2q37.1 in Faroese families, we detected 3 mutations in a novel gene, LOC646960: Patients of 10 different Faroese families were either homozygous (n=22) for c.926G>C (p.Trp309Ser) or compound heterozygous (n=6) for c.926G>C and c.526C>G (p.Arg176Gly), whereas a homozygous 1 bp duplication (c.1066dupC) was identified in patients with arNNO from a Tunisian family. In two unrelated patients with MCOP, no LOC646960 mutation was found. LOC646960 is expressed in the human adult retina and RPE. The expression of the mouse homologue in the eye can be first detected at E17 and is highest in adults. The predicted protein is a 603 amino acid long secreted trypsin-like serine peptidase. c.1066dupC should result in a functional null allele. Molecular modelling of the p.Trp309Ser mutant suggests that both affinity and reactivity of the enzyme towards in vivo substrates are substantially reduced.Conclusions: Postnatal growth of the eye is important for proper development of the refractive components (emmetropization), and is mainly due to elongation of the posterior segment from 10-11 mm at birth to 15-16 mm at the age of 13 years. Optical defocus leads to changes in axial length by moving the retina towards the image plane. arMCOP may theoretically be explained, in line with the expression pattern of LOC646960, by a postnatal growth retardation of the posterior segment.

Sweet taste loss in myasthenia gravis: more than a coincidence?

Sweet dysgeusia, a rare taste disorder, may be encountered in severe anti-acetylcholine receptor antibody (AChRAb)-myasthenia gravis (MG). A 42 year-old man reported progressive loss of sweet taste evolving for almost 10 weeks, revealing an AChRAb-positive MG with thymoma. Improvement of sweet perception paralleled reduction of the MG composite score during the 15 months follow up period, with immunosuppressive and surgical treatments. We suggest that sweet dysgeusia is a non-motor manifestation of MG that may result from a thymoma-dependent autoimmune mechanism targeting gustducin-positive G-protein-coupled taste receptor cells, in line with recent data from MRL/MpJ-Fas lpr/ (MRL/lpr) transgenic mice with autoimmune disease.

NITROGEN LOSS BY EROSION FROM MECHANICALLY TILLED AND UNTILLED SOIL UNDER SUCCESSIVE SIMULATED RAINFALLS

The description of the fate of fertilizer-derived nitrogen (N) in agricultural systems is an essential tool to enhance management practices that maximize nutrient use by crops and minimize losses. Soil erosion causes loss of nutrients such as N, causing negative effects on surface and ground water quality, aside from losses in agricultural productivity by soil depletion. Studies correlating the percentage of fertilizer-derived N (FDN) with soil erosion rates and the factors involved in this process are scarce. The losses of soil and fertilizer-derived N by water erosion in soil under conventional tillage and no tillage under different rainfall intensities were quantified, identifying the intervening factors that increase loss. The experiment was carried out on plots (3.5 × 11 m) with two treatments and three replications, under simulated rainfall. The treatments consisted of soil with and soil without tillage. Three successive rainfalls were applied in intervals of 24 h, at intensities of 30 mm/h, 30 mm/h and 70 mm/h. The applied N fertilizer was isotopically labeled (15N) and incorporated into the soil in a line perpendicular to the plot length. Tillage absence resulted in higher soil losses and higher total nitrogen losses (TN) by erosion induced by the rainfalls. The FDN losses followed another pattern, since FDN contributions were highest from tilled plots, even when soil and TN losses were lowest, i.e., the smaller the amount of eroded sediment, the greater the percentage of FDN associated with these. Rain intensity did not affect the FDN loss, and losses were greatest after less intense rainfalls in both treatments.

Study of inner ear and lateral line hair cell regeneration

Death of sensory hair cells in the inner ear results in two global health problems that millions of people around the world suffer: hearing loss and balance disorders. Hair cells convert sound vibrations and head movements into electrical signals that are conveyed to the brain, and as a result of aging, exposure to noise, modern drugs or genetic predisposition, hair cells die. In mammals, the great majority of hair cells are produced during embryogenesis, and hair cells that are lost after birth are not replaceable. However, in the last decades, researches have shown some model organisms that retain the ability to regenerate hair cells damaged after embryogenesis, such as Zebrafish and chicken, providing clues as to the cellular and molecular mechanisms that may block hair cell regeneration in mammals. This discovery initiated a search for methods to stimulate regeneration or replacement of hair cells in mammals, a search that, if fruitful, will revolutionize the treatment of hearing loss and balance disorders. One aim of my project is to study the role of retinoic acid in adult Zebrafish and in mice, which is a metabolite of vitamin A known as an essential molecule to activate hair cell regeneration after cells damaged in Zebrafish embryo. We want to study important genes involved in retinoic acid pathway, such as Aldh1a3 and RARs genes, to check what their role is in the inner ear of adult Zebrafish and compare result obtained in the inner ear of mice. On the other hand, Zebrafish lateral line contains neuromast, which are formed by the same structure than the inner ear: hair cells surrounded by supporting cells and neurons. The lateral line is a structure below the skin's surface that makes easier to damage hair cells to study their regeneration. For that reason, another aim of my project is to study how Sox2 and Atoh1, essential genes during the inner ear development, change their expression during hair cell regeneration in the lateral line. In my project, the most important concepts related to Zebrafish world are explained in order to understand why we have studied this animal and these essential genes. Then, techniques that we used are explained, with their protocol attached in the annexes. Finally, results of my project are shown, but many of them were not expected and they would be needed to follow studying.

Loss of insulin synthesis and beta cell survival induced by oxidized LDL require activation of reticulum endoplasmic stress: a mechanism countered by HDL

Elevated circulating concentrations in modified LDL-cholesterol particles (e.g. oxidised LDL) and low levels in HDL increase not only the risk for diabetic patients to develop cardiovascular diseases but also may contribute to development and progression of diabetes by directly having adverse effects on β-cells. Chronic exposure of β-cells to 2 mM human oxidised LDL-cholesterol (oxLDL) increases the rate of apoptosis, reduce insulin biosynthesis and the secretory capacity of the cells in response to nutrients. In line with the protective role, HDL efficiently antagonised the harmful effects of ox- LDL, suggesting that low levels of HDL would be inefficient to protect β-cells against oxLDL attack in patients. Activation of endoplasmic reticulum (ER) stress is pointed out to contribute to β-cell dysfunction elicited by environmental stressors. In this study we investigated whether activation of ER stress is required for oxLDL to mediate detrimental effects on β-cells and we tested the potential antagonist properties of HDL: The mouse MIN6 insulin-secreting cells were cultured with 2 mM of LDL-cholesterol preparation (native or in vitro oxidized) in the presence or absence of 1 mM of HDL-cholesterol or the ER stress inhibitor 4-phenylbutyrate (4-PBA): Prolonged exposure of MIN6 cells to 2 mM oxLDL-cholesterol for 48 hours led to an increase in expression of ER stress markers such as ATF4, CHOP and p58 and stimulated the splicing of XBP-1 whereas, induction of these markers was not observable in the cells cultured with native LDL. Treatment of the cells with the 4-PBA chemical chaperone molecule efficiently blocked activation of the ER stress markers induced by oxLDL. The latter mediates β-cell dysfunction and apoptosis by diminishing the expression of islet brain 1 (IB1) and Bcl2. The levels of these two proteins were preserved in the cells that were co-treated with oxLDL and the 4-PBA. Consistent with this result we found that blockade of ER stress activation alleviated the loss of insulin synthesis and abolished apoptosis evoked by oxLDL. However incubation of the cells with 4-PBA did not prevent impairment of insulin secretion elicited by oxLDL, indicating that ER stress is not responsible for the oxLDL-mediated defect of insulin secretion. Co-incubation of the cells with HDL mimicked the effects of 4-PBA on the expression of IB1 and Blc2 and thereby counteracted oxLDL attacks on insulin synthesis and cell survivals. We found that HDL efficiently inhibited activation of the ER stress mediated by oxLDL: These data highlight the contribution of the ER stress in the defects of insulin synthesis and cell survivals induced by oxLDL and emphasize the potent role of HDL to counter activation of the oxLDL-mediated ER-stress activation:

Improvement of Operational Efficiency effectiveness (OEE) using Six Sigma DMAIC Methodology — Case Bottomer line AD2378

Overall Equipment Effectiveness (OEE) is the key metric of operational excellence. OEE monitors the actual performance of equipment relative to its performance capabilities under optimal manufacturing conditions. It looks at the entire manufacturing environment measuring, in addition to the equipment availability, the production efficiency while the equipment is available to run products, as well as the efficiency loss that results from scrap, rework, and yield losses. The analysis of the OEE provides improvement opportunities for the operation. One of the tools used for OEE improvement is Six Sigma DMAIC methodology which is a set of practices originally developed to improve processes by eliminating defects. It asserts the continuous efforts to reduce variation in process outputs as key to business success, as well as the possibility of measurement, analysis, improvement and control of manufacturing and business processes. In the case of the Bottomer line AD2378 in Papsac Maghreb Casablanca plant, the OEE figures reached 48.65 %, which is below the accepted OEE group performance. This required immediate actions to achieve OEE improvement. This Master thesis focuses on the application of Six Sigma DMAIC methodology in the OEE improvement on the Bottomer Line AD2378 in Papsac Maghreb Casablanca plant. First, the Six Sigma DMAIC and OEE usage in operation measurement will be discussed. Afterwards, the different DMAIC phases will allow the identification of improvement focus, the identification of OEE low performance causes and the design of improvement solutions. These will be implemented to allow further tracking of improvement impact on the plant operations.

Flow analysis by using solenoid valves for As(III) determination in natural waters by an on-line separation and pre-concentration system coupled to a tungsten coil atomizer

A flow system coupled to a tungsten coil atomizer in an atomic absorption spectrometer (TCA-AAS) was developed for As(III) determination in waters, by extraction with sodium diethyldithiocarbamate (NaDDTC) as complexing agent, and by sorption of the As(III)-DDTC complex in a micro-column filled with 5 mg C18 reversed phase (10 µL dry sorbent), followed by elution with ethanol. A complete pre-concentration/elution cycle took 208 s, with 30 s sample load time (1.7 mL) and 4 s elution time (71 µL). The interface and software for the synchronous control of two peristaltic pumps (RUN/ STOP), an autosampler arm, seven solenoid valves, one injection valve, the electrothermal atomizer and the spectrometer Read function were constructed. The system was characterized and validated by analytical recovery studies performed both in synthetic solutions and in natural waters. Using a 30 s pre-concentration period, the working curve was linear between 0.25 and 6.0 µg L-1 (r = 0.9976), the retention efficiency was 94±1% (6.0 µg L-1), and the pre-concentration coefficient was 28.9. The characteristic mass was 58 pg, the mean repeatability (expressed as the variation coefficient) was 3.4% (n=5), the detection limit was 0.058 µg L-1 (4.1 pg in 71 µL of eluate injected into the coil), and the mean analytical recovery in natural waters was 92.6 ± 9.5 % (n=15). The procedure is simple, economic, less prone to sample loss and contamination and the useful lifetime of the micro-column was between 200-300 pre-concentration cycles.

Coverage mobilization in the sowing line and its influence on temperature and water content and on maize emergence

Straw on sowing line modifies seed germination environment regarding temperature and water content. Given these considerations, the aim of this study was to evaluate different mechanisms for coverage mobilization on the sowing line and their effect on germination environment of maize seeds, mainly in relation to the dynamics of straw in the seedbed, water content and soil temperature. Treatments consisted on the combination of two mechanisms at front of furrow opener, composed of cutting disc and row cleaners, with three mechanisms behind the seed furrower for returning the soil, consisting of three covering mechanisms, commercial and prototype models. It was found that straw presence on the surface of sowing line contributed to germination of maize seeds, maintenance of temperature and soil water content. The cutting disc treatment, associated with prototype, introduced percentages of water content near the ones in bottom layer, and this soil water content was 29.7% with 93.75% of straw coverage and deeper seeding depth, granting better conditions for seed germination. However, the straw coverage removal on soil by the row cleaners and its low sowing depth caused water loss in the lines resulting in great reduction of the emergence speed index in maize seedlings.

Modelling head loss along emitting pipes using dimensional analysis

Local head losses must be considered in estimating properly the maximum length of drip irrigation laterals. The aim of this work was to develop a model based on dimensional analysis for calculating head loss along laterals accounting for in-line drippers. Several measurements were performed with 12 models of emitters to obtain the experimental data required for developing and assessing the model. Based on the Camargo & Sentelhas coefficient, the model presented an excellent result in terms of precision and accuracy on estimating head loss. The deviation between estimated and observed values of head loss increased according to the head loss and the maximum deviation reached 0.17 m. The maximum relative error was 33.75% and only 15% of the data set presented relative errors higher than 20%. Neglecting local head losses incurred a higher than estimated maximum lateral length of 19.48% for pressure-compensating drippers and 16.48% for non pressure-compensating drippers.