Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

NGS y Metagenómica

The Next Generation Sequencing (NGS) allows to sequence the whole genome of an organism, compared to Maxam and Gilbert and Sanger sequencing that only allow to sequence, hardly, a single gene. Removing the separation of DNA fragments by electrophoresis, and the development of techniques that let the parallelization (analysing simultaneously several DNA fragments) have been crucial for the improvements of this process. The new companies in this ambit, Roche and Illumina, bet for different protocols to achieve these goals. Illumina bets for the sequencing by synthesis (SBS), requiring the library preparation and the use of adapters. Likewise, Illumina has replaced Roche because its lower rate of misincorporation, making it ideal for studies of genetic variability, transcriptomic, epigenomic, and metagenomic, in which this study will focus. However, it is noteworthy that the last progress in sequencing is carried out by the third generation sequencing, using nanotechnology to design small sequencers that sequence the whole genome of an organism quickly and inexpensively. Moreover, they provide more reliable data than current systems because they sequence a single molecule, solving the problem of synchronisation. In this way, PacBio and Nanopore allow a great progress in diagnostic and personalized medicine. Metagenomics provide to make a qualitative and quantitative analysis of the various species present in a sample. The main advantage of this technique is the no necessary isolation and growth of the species, allowing the analysis of nonculturable species. The Illumina protocol studies the variable regions of the 16S rRNA gene, which contains variable and not variables regions providing a phylogenetic classification. Therefore, metagenomics is a topic of interest to know the biodiversity of complex ecosystems and to study the microbiome of patients given the high involvement with certain microbial profiles on the condition of certain metabolic diseases.

Estudio in vitro de la resistencia adhesiva en la interfaz de resina entre la base del pad y el resinoso utilizado en cementación indirecta de la técnica lingual

Con el fin de aminorar retrasos por descementación de cualquier accesorio durante el tratamiento de Ortodoncia Lingual, se ha considerado que la fuerza de adhesión es muy importante, especialmente cuando está ubicada en las diferentes interfaces presentes entre el bracket y la resina del PAD; entre la resina del PAD y el cemento resinoso fotopolimerizable y entre este cemento y el esmalte dental. Por lo que este estudio se ha enfocado en determinar la resistencia adhesiva en la interfaz localizada entre la resina de la base del PAD y el cemento resinoso fotopolimerizable utilizando ácido fluorhídrico y óxido de aluminio como tratamiento de superficie previo a la cementación indirecta de la técnica lingual. MATERIALES Y METODOS: El tipo de estudio fue experimental "in vitro", con una muestra de 30 cuerpos de prueba hechos con resina Transbond XT, utilizando para su confección un blíster de brackets, se siguieron tres protocolos diferentes; G1 o grupo control sin ninguna preparación, G2 con aplicación de óxido de aluminio, 50 micrones durante 10 segundos en la superficie del cuerpo de prueba, G3 con aplicación de ácido fluorhídrico al 9% en la superficie del cuerpo de prueba durante 10 minutos. Previo al test de resistencia adhesiva, se realizó los cortes de precisión en cada cuerpo de prueba, obteniendo así 45 tiras de prueba, cada una de las muestras fue adherida a un porta muestra para la prueba de micro tracción, la misma que fue realizada con la máquina universal Mini-Instron modelo 5942, a una velocidad de deformación constante de 0.5 mm/min. Los datos fueron sometidos al test de Normalidad de residuos de Shapiro Wilk (p>0,05) y de LEVENE para el análisis de homogeneidad de las varianzas. La resistencia adhesiva fue comparada entre los grupos por medio del Análisis de Varianza (ANOVA) como factor único para el procesamiento de los datos. Para todos los análisis el nivel de significancia fue del 5% (p< 0,05) con un nivel de confianza del 95% (IC95%). Se consideró estadísticamente significativo valores por debajo de 0,05. RESULTADOS Y CONCLUSIONES: El resultado del test de ANOVA, reveló que el factor de tratamiento de superficie F(2,12)=2,52;p=0,12 no es significante, por lo tanto los diferentes tratamientos de superficie (óxido de aluminio y ácido fluorhídrico) utilizados son equivalentes al grupo control, indicando que no ejercen influencia de manera significativa en los valores de Resistencia Adhesiva (RA) en la preparación de la interfaz localizada entre la resina de la base del PAD y el cemento resinoso fotopolimerizable; concluyendo que se puede utilizar cualquier protocolo de tratamiento de superficie indicado en la presente investigación.

Estudo da implementação de rotinas de controlo reprodutivo em fêmeas bovinas Holstein frísia para optimização de alguns índices reprodutivos numa exploração leiteira da Ilha Terceira (Açores)

Dissertação de Mestrado Integrado em Medicina Veterinária

Establishment of a protocol for the cryopreservation of cell sheets of adipose tissue stem cells

Dissertação de Mestrado, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2016

Metacromasia para identificação de basófilos sanguíneos em surubim híbrido: contribuição metodológica

Padua S.B. & Ishikawa M.M. [Metachromasia for blood basophils identification in hybrid surubim catfish: methodological contribution]. Metacromasia para identificacao de basofilos sanguineos em surubim hibrido: contribuicao metodologica. Revista Brasileira de Medicina Veterinaria, 33(3):147-150, 2011. Centro de Aquicultura da Unesp/Jaboticabal Rod. Paulo Donato Castellane, s/n Bairro Rural, Jaboticabal, 14884-900, SP. Brasil. E-mail: santiagopadua@live.comDifferent protocols of fixation and hydrolysis of blood smears of hybrid surubim catfish for metachromasia to marking blood basophils were evaluated. For this reason, methanol, acid-alcohol and formalin vapor were tested as fixatives. For hydrolysis of blood smears, HCl, citric acid and 2-Mercaptoethanol + Urea + NaCl solutions was evaluated. After procedures, the blood smears was stained with toluidine blue (0.025%) diluted in McIlvaine buffer (pH 4). The different protocols for fixation and hydrolysis of blood smears for metachromasia influenced the quality of the reaction. Hydrolysis with 2-Mercaptoethanol + Urea + NaCl solutions provided negative results when using methanol and acid-alcohol as fixatives. The fixation with acid-alcohol associated with citric acid hydrolysis provides highest quality reason.

Acidentes com hipoclorito de sódio

O objectivo deste trabalho consistiu em definir, com base na evidência científica mais recente sobre Acidentes com hipoclorito de sódio, diferentes protocolos para a prevenção e tratamento dos acidentes causados no âmbito da endodontia. O Hipoclorito de Sódio é o irrigante frequentemente mais utilizado durante o Tratamento Endodôntico, devido às suas excelentes propriedades, capacidade de dissolver tecidos e capacidade bactericida. Há diversos factores que podem influenciar o modo de atuação do NaOCl, tais como: a concentração, a temperatura, o pH, o tempo/volume de irrigação, a agitação do irrigante, os métodos de introdução do irrigante, a conicidade apical e a profundidade de colocação da agulha. A pesquisa bibliográfica deste trabalho foi realizada nas bibliotecas da Universidade Fernando Pessoa e Faculdade de Medicina Dentária da Universidade do Porto e nos motores de internet Pubmed, Science Direct, Scielo e B-On, entre Junho de 2016 a Outubro de 2016. As palavras utilizadas para a pesquisa foram as seguintes: “desinfection endodontics”, “endodontics”, “endodontic treatment”, “sodium hypochlorite”, “irrigants endodontics”, “sodium hypochlorite accidents”, “irrigation methods”, “root canal irrigant”, “management NaOCL accidents”.

Expansão rápida da maxila

O presente trabalho tem como objetivo estudar a técnica da Expansão Rápida da Maxila, comparando os tipos de aparelhos recomendados consoante as diferentes propriedades, vantagens e desvantagens associadas. Quando pensamos em um padrão normal para a oclusão temos em mente uma correta relação entre as bases apicais em que a arcada maxilar deverá englobar a arcada mandibular permitindo o equilíbrio entre ambas. Quando ocorre uma redução das dimensões transversais da maxila nos vemos diante de atresias, entre elas uma anomalia de má oclusão bastante frequente na nossa clínica, a mordida cruzada posterior. Quando isto acontece o profissional precisa buscar uma correção da conformação do arco através da expansão rápida da maxila abrindo a sutura palatina mediana por meio de aparelhos expansores fixos tais como o de Haas (dento-muco-suportado) ou os classificados como dento-suportados como o Hyrax ou o disjuntor de McNamara, na dentição decídua, mista ou permanente e até mesmo em pacientes adultos com protocolos diferenciados para cada faixa etária. Caso o indivíduo apresente uma calcificação óssea avançada da sutura mediana deve ser encaminhado para a expansão rápida da maxila cirurgicamente assistida.

Assessment of a best practise approach for the attribution and authentication of paintings

The ever-growing interest in scientific techniques, able to characterise the materials and rediscover the steps behind the execution of a painting, makes them widely accepted in its investigation. This research discusses issues emerging from attribution and authentication studies and proposes best practise for the characterisation of materials and techniques, favouring the contextualisation of the results in an integrated approach; the work aims to systematically classify paintings in categories that aid the examination of objects. A first grouping of paintings is based on the information initially available on them, identifying four categories. A focus of this study is the examination of case studies, spanning from the 16th to the 20th century, to evaluate and validate different protocols associated to each category, to show problems arising from paintings and explain advantages and limits of the approach. The research methodology incorporates a combined set of scientific techniques (non-invasive, such as technical imaging and XRF, micro-invasive, such as optical microscopy, SEM-EDS, FTIR, Raman microscopy and in one case radiocarbon dating) to answer the questions and, if necessary for the classification, exhaustively characterise the materials of the paintings, as the creation and contribution of shared technical databases related to various artists and their evolution over time is an objective tool that benefits this kind of study. The reliability of a close collaboration among different professionals is an essential aspect of this research to comprehensively study a painting, as the integration of stylistic, documentary and provenance studies corroborates the scientific findings and helps in the successful contextualisation of the results and the reconstruction of the history of the object.

Impact of retransmissions in IEEE 802.11bd

The main goal of this thesis is to study the impact of retransmissions in the upcoming IEEE 802.11bd standard and to determine an algorithm which can, on a vehicle to vehicle basis, activate them or not depending on the channel state, using the channel busy rate (CBR) as the leading metric. The study was based on simulations performed with the WiLabV2Xsim, which is an open source discrete event simulator that can be used to simulate communication between vehicles under the rules of different protocols.

Non perturbative aspects of non equilibrium physics in two dimensional models

The present manuscript focuses on out of equilibrium physics in two dimensional models. It has the purpose of presenting some results obtained as part of out of equilibrium dynamics in its non perturbative aspects. This can be understood in two different ways: the former is related to integrability, which is non perturbative by nature; the latter is related to emergence of phenomena in the out of equilibirum dynamics of non integrable models that are not accessible by standard perturbative techniques. In the study of out of equilibirum dynamics, two different protocols are used througout this work: the bipartitioning protocol, within the Generalised Hydrodynamics (GHD) framework, and the quantum quench protocol. With GHD machinery we study the Staircase Model, highlighting how the hydrodynamic picture sheds new light into the physics of Integrable Quantum Field Theories; with quench protocols we analyse different setups where a non-perturbative description is needed and various dynamical phenomena emerge, such as the manifistation of a dynamical Gibbs effect, confinement and the emergence of Bloch oscillations preventing thermalisation.

Niobium-based heterogeneous catalysts synthesised in supercritical carbon dioxide for selective olefin epoxidation

In this work, two different protocols for the synthesis of Nb2O5-SiO2 with a sol-gel route in which supercritical carbon dioxide was used as solvent have been developed. The tailored design of the reactor allowed the reactants to come into contact only when supercritical CO2 is present, and the high-throughput experimentation scCO2 unit allowed the screening of synthetic parameters, that led to a Nb2O5 incorporation into the silica matrix of 2.5 wt%. N2-physisorption revealed high surface areas and the presence of meso- and micropores. XRD allowed to demonstrate the amorphous character of these materials. SEM-EDX proved the excellent dispersion of Nb2O5 into the silica matrix. These materials were tested in the epoxidation of cyclooctene with hydrogen peroxide, which is considered an environmentally friendly oxidant. The catalysts were virtually inactive in an organic, polar, aprotic solvent (1,4-dioxane). However, the most active scCO2 Nb2O5-SiO2 catalyst achieved a cyclooctene conversion of 44% with a selectivity of 88% towards the epoxide when tested in ethanol. Catalytic tests on cyclohexene revealed the presence of the epoxide, which is remarkable, considering that this substrate is easily oxidised to the diol. The behaviour in protic and aprotic solvents is compared to that of TS-1.

RED-Bridge: A Multiprotocol Tool Prototype for IoT Sensors

The IoT is growing more and more each year and is becoming so ubiquitous that it includes heterogeneous devices with different hardware and software constraints leading to an highly fragmented ecosystem. Devices are using different protocols with different paradigms and they are not compatible with each other; some devices use request-response protocols like HTTP or CoAP while others use publish-subscribe protocols like MQTT. Integration in IoT is still an open research topic. When handling and testing IoT sensors there are some common task that people may be interested in: reading and visualizing the current value of the sensor; doing some aggregations on a set of values in order to compute statistical features; saving the history of the data to a time-series database; forecasting the future values to react in advance to a future condition; bridging the protocol of the sensor in order to integrate the device with other tools. In this work we will show the working implementation of a low-code and flow-based tool prototype which supports the common operations mentioned above, based on Node-RED and Python. Since this system is just a prototype, it has some issues and limitations that will be discussed in this work.

A Microleakage Study Of Gutta-percha/ah Plus And Resilon/real Self-etch Systems After Different Irrigation Protocols.

The development and maintenance of the sealing of the root canal system is the key to the success of root canal treatment. The resin-based adhesive material has the potential to reduce the microleakage of the root canal because of its adhesive properties and penetration into dentinal walls. Moreover, the irrigation protocols may have an influence on the adhesiveness of resin-based sealers to root dentin. The objective of the present study was to evaluate the effect of different irrigant protocols on coronal bacterial microleakage of gutta-percha/AH Plus and Resilon/Real Seal Self-etch systems. One hundred ninety pre-molars were used. The teeth were divided into 18 experimental groups according to the irrigation protocols and filling materials used. The protocols used were: distilled water; sodium hypochlorite (NaOCl)+eDTA; NaOCl+H3PO4; NaOCl+eDTA+chlorhexidine (CHX); NaOCl+H3PO4+CHX; CHX+eDTA; CHX+ H3PO4; CHX+eDTA+CHX and CHX+H3PO4+CHX. Gutta-percha/AH Plus or Resilon/Real Seal Se were used as root-filling materials. The coronal microleakage was evaluated for 90 days against Enterococcus faecalis. Data were statistically analyzed using Kaplan-Meier survival test, Kruskal-Wallis and Mann-Whitney tests. No significant difference was verified in the groups using chlorhexidine or sodium hypochlorite during the chemo-mechanical preparation followed by eDTA or phosphoric acid for smear layer removal. The same results were found for filling materials. However, the statistical analyses revealed that a final flush with 2% chlorhexidine reduced significantly the coronal microleakage. A final flush with 2% chlorhexidine after smear layer removal reduces coronal microleakage of teeth filled with gutta-percha/AH Plus or Resilon/Real Seal SE.

Effectiveness of different final irrigation protocols in removing debris in flattened root canals

This study evaluated in vitro the capacity of debris removal from the apical third of flattened root canals, using different final irrigation protocols. Thirty human mandibular central incisors with a mesiodistal flattened root were prepared using rotary instrumentation by Endo-Flare 25.12 and Hero 642 30.06, 35.02, 40.02 files, irrigated with 2 mL of 1% NaOCl after each file. The specimens were randomly distributed into 5 groups according to the final irrigation of root canals: Group I: 10 mL of distilled water (control), Group II: 10 mL of 1% NaOCl for 8 min, Group III: 2 mL of 1% NaOCl for 2 min (repeated 4 times), Group IV: 10 mL of 2.5% NaOCl for 8 min, and Group V: 10 mL of 2.5% NaOCl for 2 min (repeated 4 times). The apical thirds of the specimens were subjected to histological processing and 6-μm cross-sections were obtained and stained with hematoxylin-eosin. The specimens were examined under optical microscopy at ×40 magnification and the images were subjected to morphometric analysis using the Scion image-analysis software. The total area of root canal and the area with debris were measured in square millimeters. Analysis of variance showed no statistically significant difference (p>0.05) among the groups GI (2.39 ± 3.59), GII (2.91 ± 2.21), GIII (0.73 ± 1.36), GIV (0.95 ± 0.84) and GV (0.51 ± 0.22). In conclusion, the final irrigation protocols evaluated in this study using the Luer syringe presented similar performance in the removal of debris from the apical third of flattened root canals.