Recoding: reprogrammed genetic decoding with an emphasis on antizyme regulatory frameshifting

Recoding embraces mechanisms that augment the rules of standard genetic decoding. The deviations from standard decoding are often purposeful and their realisation provides diverse and flexible regulatory mechanisms. Recoding events such as programed ribosomal frameshifting are especially plentiful in viruses. In most organisms only a few cellular genes are known to employ programed ribosomal frameshifting in their expression. By far the most prominent and therefore well-studied case of cellular +1 frameshifting is in expression of antizyme mRNAs. The protein antizyme is a key regulator of polyamine levels in most eukaryotes with some exceptions such as plants. A +1 frameshifting event is required for the full length protein to be synthesized and this requirement is a conserved feature of antizyme mRNAs from yeast to mammals. The efficiency of the frameshifting event is dependent on the free polyamine levels in the cell. cis-acting elements in antizyme mRNAs such as specific RNA structures are required to stimulate the frameshifting efficiency. Here I describe a novel stimulator of antizyme +1 frameshifting in the Agaricomycotina class of Basidiomycete fungi. It is a nascent peptide that acts from within the ribosome exit tunnel to stimulate frameshifting efficiency in response to polyamines. The interactions of the nascent peptide with components of the peptidyl transferase centre and the protein exit tunnel emerge in our understanding as powerful means which the cell employs for monitoring and tuning the translational process. These interactions can modulate the rate of translation, protein cotranslational folding and localization. Some nascent peptides act in concert with small molecules such as polyamines or antibiotics to stall the ribosome. To these known nascent peptide effects we have added that of a stimulatory effect on the +1 frameshifting in antizyme mRNAs. It is becoming evident that nascent peptide involvement in regulation of translation is a much more general phenomenon than previously anticipated.

Chemoprevention in BRCA1 Mutation Carriers—A Proof-of-Concept Study

Background: Women with germline BRCA1 mutations have a high lifetime risk of breast cancer, with the only available risk-reduction strategies being risk-reducing surgery or chemoprevention. These women predominantly develop triple-negative breast cancers; hence, it is unlikely that selective estrogen receptor modulators (serms) will reduce the risk of developing cancer, as these have not been shown to reduce the incidence of estrogen receptor–negative breast cancers. Preclinical data from our laboratory suggest that exposure to estrogen and its metabolites is capable of causing dna double-strand breaks (dsbs) and thus driving genomic instability, an early hallmark of BRCA1-related breast cancer. Therefore, an approach that lowers circulating estrogen levels and reduces estrogen metabolite exposure may prove a successful chemopreventive strategy.

Aims: To provide proof of concept of the hypothesis that the combination of luteinizing-hormone releasing-hormone agonists (lhrha) and aromatase inhibitors (ais) can suppress circulating levels of estrogen and its metabolites in BRCA1 mutation carriers, thus reducing estrogen metabolite levels in breast cells, reducing dna dsbs, and potentially reducing the incidence of breast cancer.

Methods: 12 Premenopausal BRCA1 mutation carriers will undergo baseline ultrasound-guided breast core biopsy and plasma and urine sampling. Half the women will be treated for 3 months with combination goserelin (lhrha) plus anastrazole (ai), and the remainder with tamoxifen (serm) before repeat tissue, plasma, and urine sampling. After a 1-month washout period, groups will cross over for a further 3 months treatment before final biologic sample collection. Tissue, plasma, and urine samples will be examined using a combination of immunohistochemistry, comet assays, and ultrahigh performance liquid chromatography tandem mass spectrometry to assess the impact of lhrha plus ai compared with serm on levels of dna damage, estrogens, and genotoxic estrogen metabolites. Quality of life will also be assessed during the study.

Results: This trial is currently ongoing.

Charge migration induced by attosecond pulses in bio-relevant molecules

After sudden ionization of a large molecule, the positive charge can migrate throughout the system on a sub-femtosecond time scale, purely guided by electronic coherences. The possibility to actively explore the role of the electron dynamics in the photo-chemistry of bio-relevant molecules is of fundamental interest for understanding, and perhaps ultimately controlling, the processes leading to damage, mutation and, more generally, to the alteration of the biological functions of the macromolecule. Attosecond laser sources can provide the extreme time resolution required to follow this ultrafast charge flow. In this review we will present recent advances in attosecond molecular science: after a brief description of the results obtained for small molecules, recent experimental and theoretical findings on charge migration in bio-relevant molecules will be discussed.

Eficiência, gestão e meio ambiente na carcinicultura do Rio Grande do Norte

SILVA, J. L. M. da; SAMPAIO, L. M. . Eficiência, Gestão e Meio Ambiente na Carcinicultura do Rio Grande do Norte. In: Congresso da Sociendade Brasileira de Economia, Administração e Sociologia Rural - SOBER, 40., 2007, Londrina. Conhecimentos para a Agricultura do Futuro, 2007.

Feature-based camera pose estimation

The estimating of the relative orientation and position of a camera is one of the integral topics in the field of computer vision. The accuracy of a certain Finnish technology company’s traffic sign inventory and localization process can be improved by utilizing the aforementioned concept. The company’s localization process uses video data produced by a vehicle installed camera. The accuracy of estimated traffic sign locations depends on the relative orientation between the camera and the vehicle. This thesis proposes a computer vision based software solution which can estimate a camera’s orientation relative to the movement direction of the vehicle by utilizing video data. The task was solved by using feature-based methods and open source software. When using simulated data sets, the camera orientation estimates had an absolute error of 0.31 degrees on average. The software solution can be integrated to be a part of the traffic sign localization pipeline of the company in question.

Factors affecting the prognosis of Albanian adult patients with generalized tetanus

Background. Despite systematic vaccination of the population, tetanus continues to be a health problem in Albania, as in some other developing countries. In this study, our intent was to evaluate prognostic factors relating to death in adult patients with generalized tetanus. Methodology and patients. All the patients (60) included in the study were hospitalized at the regional hospitals of Shkodra and Korça, and the University Hospital Centre “Mother Theresa” of Tirana, Albania, during the period of 1984-2004. They had a mean age of 49.1+14.4 years, 43 (71.7%) were males and 40 (66.6%) of them lived in rural areas. The mean incubation period was 12 days and the case-fatality rate (CFR) was 38.3%. Results. The CFR in patients with an onset period ≥2 days was 21.7% and in those with <2 days was 48.6%, OR=0.29 (p<0.05). Patients >50 years old had a CFR=60.87% (OR=7, p<0.05). We found the high CFR to be significantly associated with urban residency, male gender, complicated wound, head localization, fever ≥ 38.4 °C, tachycardia > 120 beats/min, and hypertension. Discussion. The main prognostic factor of those analyzed in our study appeared to be the onset period and the age of the patients. We didn’t find significant differences in CFR in patients with different incubation periods. Clinicians must take into account that wound complication and localization, tachycardia and hypertension, high fever, male gender and urban residency significantly influence the prognoses of adults with generalized tetanus.

Assessment of the quality of sample labelling for clinical research

Objective: To assess the quality of the labels for clinical trial samples through current regulations, and to analyze its potential correlation with the specific characteristics of each sample. Method: A transversal multicenter study where the clinical trial samples from two third level hospitals were analyzed. The eleven items from Directive 2003/94/EC, as well as the name of the clinical trial and the dose on the label cover, were considered variables for labelling quality. The influence of the characteristics of each sample on labelling quality was also analyzed. Outcome: The study included 503 samples from 220 clinical trials. The mean quality of labelling, understood as the proportion of items from Appendix 13, was of 91.9%. Out of these, 6.6% did not include the name of the sample in the outer face of the label, while in 9.7% the dose was missing. The samples with clinical trial-type samples presented a higher quality (p < 0.049), blinding reduced their quality (p = 0.017), and identification by kit number or by patient increased it (p < 0.01). The promoter was the variable which introduced the highest variability into the analysis. Conclusions: The mean quality of labelling is adequate in the majority of clinical trial samples. The lack of essential information in some samples, such as the clinical trial code and the period of validity, is alarming and might be the potential source for dispensing or administration errors.

Eficiência, gestão e meio ambiente na carcinicultura do Rio Grande do Norte

SILVA, J. L. M. da; SAMPAIO, L. M. . Eficiência, Gestão e Meio Ambiente na Carcinicultura do Rio Grande do Norte. In: Congresso da Sociendade Brasileira de Economia, Administração e Sociologia Rural - SOBER, 40., 2007, Londrina. Conhecimentos para a Agricultura do Futuro, 2007.

Characterization of sea water ageing effects on mechanical properties of carbon/epoxy composites for tidal turbine blades

In recent years, many tidal turbine projects have been developed using composites blades. Tidal turbine blades are subject to ocean forces and sea water aggressions, and the reliability of these components is crucial to the profitability of ocean energy recovery systems. The majority of tidal turbine developers have preferred carbon/epoxy blades, so there is a need to understand how prolonged immersion in the ocean affects these composites. In this study the long term behaviour of different carbon/epoxy composites has been studied using accelerated ageing tests. A significant reduction of composite strengths has been observed after saturation of water in the material. For longer immersions only small further changes in these properties occur. No significant changes have been observed for moduli nor for composite toughness. The effect of sea water ageing on damage thresholds and kinetics has been studied and modelled. After saturation, the damage threshold is modified while kinetics of damage development remain the same.

Homogalactanas sulfatadas da alga Codium isthmocladum com atividade anticoagulante

Since the first description of sulfated polysaccharides from seaweeds, the biological activities of these compounds have been evaluated under different aspects and experimental procedures. Among the broad biological activities presented by seaweed polysaccharides, anticoagulant action appears as a promising function. In this present study we have obtained sulfated polysaccharides from the green seaweed Codium isthmocladium by proteolytic digestion, followed by separation into five fractions (0.3, 0.5, 0.7, 0.9 and 1.2) by sequential acetone precipitation. The chemical analyses have demonstrated that all fractions are composed mainly by sulfated polysaccharides. The anticoagulant activity of these fractions was determined by activated partial thromboplastin time (aPTT) and prothrombin time test (PT) using citrate normal human plasma. None fraction has shown anticoagulant activity by PT test. Furthermore, all of them have shown anticoagulant activity by aPTT test. These results indicated that the molecular targets of these sulfated polysaccharides are mainly in the intrinsic via of the coagulation cascade. Agarose gel electrophoresis in 1,3-diaminopropane acetate buffer, pH 9.0, stained with 0.1% toluidine blue showed the presence of two or three bands in several fractions while the fraction 0.9 showed a single spot. By anion exchange chromatography, the acid polysaccharides from the 0.9 acetone fraction were separated into two new fractions eluted respectively with 2.0 and 3.0 M NaCl. These compounds showed a molecular weight of 6.4 and 7.4 kDa respectively. Chemical analyses and infrared spectroscopy showed that Gal 1 and Gal 2 are sulfated homogalactans and differ one from the other in degree and localization of sulfate groups. aPPT test demonstrated that fractions 2,0 and 3,0M (Gal1 and Gal 2, respectively) have anticoagulant activity. This is the first time that anticoagulant sulfated homogalatans have been isolated from green algae. To prolong the coagulation time to double the baseline value in the aPTT, the required amount of sulfated galactan 1 (6,3mg) was similar to low molecular heparin Clexane®, whereas only 0,7mg of sulfated galactan 2 was needed to obtain the same effect. Sulfated galactan 2 in high doses (250mg) induces platelet aggregation. These results suggest that these galactans from C. isthmocladum have a potential application as an anticoagulant drug

Stoichiometry dependence of the evolution of the irradiated-induced defect clusters in lanthanum-doped ceria

To study the stoichiometry dependence of irradiation e ects in fluorite-type mixed oxide nuclear fuel (UPuO2), ion implantation in La doped ceria was used. Cerium dioxide single crystals with 0 mol%, 5 mol% and 25 mol% La concentration were irradiated with 1 MeV Kr ions at 800 C. In-situ transmission electron microscope (TEM) was utilized to observe the the damage process and defects created by the ion beam irradiation. Dislocation loops were observed after irradiation and were determined to be on {111} planes, but not on {220} or {200} planes. Ab substantial difference in the average size of dislocation loops for 0 %, 5% and 25% cases was observed at several doses.The growth rate of dislocation loops and the oxygen vacancy di usivity were found to be inversely correlated.

Modulação da expressão da proteína XPA em resposta ao tratamento com azul de metileno fotossensibilizado

Reactive oxygen species (ROS) are produced by aerobic metabolism and react with biomolecules, such as lipids, proteins and DNA. In high concentration, they lead to oxidative stress. Among ROS, singlet oxygen (1O2) is one of the main ROS involved in oxidative stress and is one of the most reactive forms of molecular oxygen. The exposure of some dyes, such as methylene blue (MB) to light (MB+VL), is able to generate 1O2 and it is the principle involved in photodynamic therapy (PDT). 1O2 e other ROS have caused toxic and carcinogenic effects and have been associated with ageing, neurodegenerative diseases and cancer. Oxidative DNA damage is mainly repaired by base excision repair (BER) pathway. However, recent studies have observed the involvement of nucleotide excision repair (NER) factors in the repair of this type of injury. One of these factors is the Xeroderma Pigmentosum Complementation Group A (XPA) protein, which acts with other proteins in DNA damage recognition and in the recruitment of other repair factors. Moreover, oxidative agents such as 1O2 can induce gene expression. In this context, this study aimed at evaluating the response of XPA-deficient cells after treatment with photosensitized MB. For this purpose, we analyzed the cell viability and occurrence of oxidative DNA damage in cells lines proficient and deficient in XPA after treatment with MB+VL, and evaluated the expression of this enzyme in proficient and complemented cells. Our results indicate an increased resistance to treatment of complemented cells and a higher level of oxidative damage in the deficient cell lines. Furthermore, the treatment was able to modulate the XPA expression up to 24 hours later. These results indicate a direct evidence for the involvement of NER enzymes in the repair of oxidative damage. Besides, a better understanding of the effects of PDT on the induction of gene expression could be provided

Testicular arteries systematization based on different levels of scrotal configuration in caprines

O objetivo deste trabalho foi analisar a distribuição dos vasos arteriais nos testículos em caprinos com diferentes graus de divisão escrotal. A configuração escrotal foi classificada da seguinte forma: Grupo I: constituído por caprinos com escroto único, Grupo II: com escroto separado até a metade do testículo e Grupo III: com separação escrotal estendendo-se além da metade do testículos. As artérias foram injetadas e coradas com solução de acetado de vinil, sendo os orgãos (30 pares) submetidos à corrossão para obtenção dos moldes vasculares. As artérias testiculares emergem da aorta abdominal, com trajeto retilíneo, atravessam o canal inguinal, apresentam-se espiraladas e envolvidas parcialmente pelo plexo pampiniforme. Próximo à extremidade caudada do testículo, dividem-se mais freqüentemente nos ramos cranial e caudal, os quais emitem vasos colaterais, de onde emergem ramos penetrantes. Os testículos dos animais com nível intermediário de divisão escrotal (Grupo II) apresentam menor quantidade destes ramos, sendo os quadrantes mais povoados o ventrolateral e o dorsolateral. Conclui-se que a origem, o trajeto e a distribuição das artérias testiculares não apresentam variações relacionadas ao grau de divisão escrotal em caprinos.

A three-dimensional representation method for noisy point clouds based on growing self-organizing maps accelerated on GPUs

The research described in this thesis was motivated by the need of a robust model capable of representing 3D data obtained with 3D sensors, which are inherently noisy. In addition, time constraints have to be considered as these sensors are capable of providing a 3D data stream in real time. This thesis proposed the use of Self-Organizing Maps (SOMs) as a 3D representation model. In particular, we proposed the use of the Growing Neural Gas (GNG) network, which has been successfully used for clustering, pattern recognition and topology representation of multi-dimensional data. Until now, Self-Organizing Maps have been primarily computed offline and their application in 3D data has mainly focused on free noise models, without considering time constraints. It is proposed a hardware implementation leveraging the computing power of modern GPUs, which takes advantage of a new paradigm coined as General-Purpose Computing on Graphics Processing Units (GPGPU). The proposed methods were applied to different problem and applications in the area of computer vision such as the recognition and localization of objects, visual surveillance or 3D reconstruction.

How to optimize operational shipping processes of non-production materials? The Volkswagen Autoeuropa case study

Field lab: Entrepreneurial and innovative ventures