Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens.

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales.

Feather mercury levels in seabirds at South Georgia: Influences of trophic position, sex and age

We studied the mercury contamination of 13 species of seabirds breeding on Bird Island, South Georgia, in 1998. Total mercury concentrations in body feather samples of birds caught at their breeding colonies were determined. Among the species, grey-headed albatross (8933 ng g-1) and southern giant petrel (7774 ng g-1) showed the highest, and gentoo penguin (948 ng g-1) the lowest body feather mercury concentrations. Mercury levels were negatively correlated with the proportion of crustaceans (mainly krill) in the species¹ diets, suggesting that the trophic level is the most important factor in explaining the variation of mercury concentrations in Antarctic seabirds. In 4 species studied for age effects among adult birds (grey-headed and black-browed albatross, northern and southern giant petrel), no age-dependent variation in mercury levels was found. Sex differences were also assessed: female gentoo penguins had lower mercury levels than males, which may be related to the elimination of part of the mercury body burden by females into eggs. In contrast, northern giant petrel males had lower levels than females, which may be related to a higher consumption by males of carrion from Antarctic fur seals. In grey-headed albatrosses, mercury levels were 113% higher than in 1989, when this species was investigated at the same site, indicating a possible increase in mercury pollution of the Southern Ocean during the last decade.

Combining Advanced Forecasting Methods with System Dynamics - the Case of Finnish Seaports

Seaports play an important part in the wellbeing of a nation. Many nations are highly dependent on foreign trade and most trade is done using sea vessels. This study is part of a larger research project, where a simulation model is required in order to create further analyses on Finnish macro logistical networks. The objective of this study is to create a system dynamic simulation model, which gives an accurate forecast for the development of demand of Finnish seaports up to 2030. The emphasis on this study is to show how it is possible to create a detailed harbor demand System Dynamic model with the help of statistical methods. The used forecasting methods were ARIMA (autoregressive integrated moving average) and regression models. The created simulation model gives a forecast with confidence intervals and allows studying different scenarios. The building process was found to be a useful one and the built model can be expanded to be more detailed. Required capacity for other parts of the Finnish logistical system could easily be included in the model.

Distribuição de metais pesados em sedimentos do sistema estuarino da Ilha de Vitória-ES

Heavy-metal concentration in sediment is an important parameter for identifying pollution sources and assessing pollution levels in aquatic ecosystems. In this context, the present study aimed at determining concentrations of heavy metals in sediments from the Vitória estuarine system, Brazil. Twenty nine stations were surveyed to assess the spatial distribution of heavy metals. The metals for silt-clay fractions (<63 µm) were analyzed through atomic absorption spectrometry. A discriminant analysis segregated the stations in four groups representing four areas within the estuarine system. The Espírito Santo Bay showed the lowest metal concentrations, while the Vitória harbor canal showed the highest. We concluded that concentrations of heavy metals reflect natural conditions and the contribution of human activities from sewage and industrial effluents. It was not possible to directly associate metal concentrations to specific pollution sources.

Fourier-based registration for robust forward-looking sonar mosaicing in low-visibility underwater environments

Vehicle operations in underwater environments are often compromised by poor visibility conditions. For instance, the perception range of optical devices is heavily constrained in turbid waters, thus complicating navigation and mapping tasks in environments such as harbors, bays, or rivers. A new generation of high-definition forward-looking sonars providing acoustic imagery at high frame rates has recently emerged as a promising alternative for working under these challenging conditions. However, the characteristics of the sonar data introduce difficulties in image registration, a key step in mosaicing and motion estimation applications. In this work, we propose the use of a Fourier-based registration technique capable of handling the low resolution, noise, and artifacts associated with sonar image formation. When compared to a state-of-the art region-based technique, our approach shows superior performance in the alignment of both consecutive and nonconsecutive views as well as higher robustness in featureless environments. The method is used to compute pose constraints between sonar frames that, integrated inside a global alignment framework, enable the rendering of consistent acoustic mosaics with high detail and increased resolution. An extensive experimental section is reported showing results in relevant field applications, such as ship hull inspection and harbor mapping

Características ópticas e morfológicas de nanoestruturas de ouro

The present study describes a new procedure to obtain gold nanoparticles, directly in the pores of polycarbonate membranes commonly used in ultrafiltration. The dimensions of the particles may be controlled through the reduction time of the ions in the channels of the harbor matrix. The dissolution of the metallized polymer enables an investigation of the optical and morphologic properties of these elements.

Genotypic diversity among brazilian isolates of Macrophomina phaseolina revealed by RAPD

Macrophomina phaseolina has been considered one of the most prevalent soybean (Glycine max) pathogens in Brazil. No genetic resistance has been determined in soybean and very little is known about the genetic diversity of this pathogen in tropical and sub-tropical regions. Fifty-five isolates from soybean roots were collected in different regions and analyzed through RAPD for genetic diversity. The UPGMA cluster analysis for 74 loci scored permitted identification of three divergent groups with an average similarity of 99%, 92% and 88%, respectively. The three groups corresponded to 5.45%, 59.95% and 34.6%, respectively of all isolates used. A single plant had three different haplotypes, while 10.9% of the analyzed plants had two different haplotypes. In another study the genetic similarity was evaluated among isolates from different hosts [soybean, sorghum (Sorghum bicolor), sunflower (Helianthus annuus), cowpea (Vigna unguiculata), corn (Zea mays) and wheat (Triticum aestivum)] as well as two soil samples from native areas. Results showed that more divergent isolates originated from areas with a single crop. Isolates from areas with crop rotation were less divergent, showing high similarity values and consequently formed the largest group. Amplification of the ITS region using primers ITS1 and ITS4 produced only one DNA fragment of 620 bp. None of the isolates were differentiated through PCR-RFLP. Our results demonstrated genetic variability among Brazilian isolates of M. phaseolina and showed that one single root can harbor more than one haplotype. Moreover, cultivation with crop rotation tends to induce less specialization of the pathogen isolates. Knowledge of this variation may be useful in screening soybean genotypes for resistance to charcoal rot.

Epidemiological analysis of clones and cultivars of potato in soil naturally infested with Ralstonia solanacearum biovar 2

The objectives of this study were to evaluate the progress of Ralstonia solanacearum bacterial potato wilt biovar 2 (race 3) in 14 potato (Solanum tuberosum L.) cultivars or clones, the resistance of potato clone MB 03 (selected in Brasília, Brazil) to race 1 of R. solanacearum, and the occurrence of the pathogen in tubers harvested from asymptomatic potato plants. During the spring (September to the end of November in the southern hemisphere) of 1999 and 2000, 14 cultivars or clones were grown in a field naturally infested with R. solanacearum biovar 2, in Caxias do Sul, RS. The number of wilted potato plants was recorded each week and a disease progress curve plotted, the resistance of the potato genotypes to bacterial wilt being evaluated by determining the area under the curve. Various models were evaluated to fit the curves, with the logistic model being the best fit. At the end of each growing season tubers produced by asymptomatic plants were harvested and stored until budding and then tested for the presence of R. solanacearum. Cultivar Cruza 148 and clone MB 03 were the most resistant but both showed tubers with latent infections. The epidemiological implications of the incidence of R. solanacearum biovar 2 (race 3) in potato crops, as well as the resistance of certain genotypes that may harbor latent infections, are important aspects to be considered in the integrated management of bacterial wilt.

Operatiivisen toiminnan liikevaihdon seurantajärjestelmä

Tämä työ tehdään Steveco Oy:lle sataman operatiivisen toiminnan aiheuttamien kulujen ja tuottojen seurantaan. Työssä käsitellään automaattisen liikevaihdon laskennan ongelmia ja ratkaisuja. Työssä sivutaan myös työajanseurannan sosiaalisia vaikutuksia työntekijöihin, sekä esitetään keinoja ongelmatilanteiden välttämiseksi. Työn tuottavuuden mittaamiseksi on kehitetty matemaattisia malleja, joita voidaan soveltaa organisaatiossa työtehojen mittaamiseksi. Työssä esitellään näitä malleja sekä pohditaan niiden soveltamista. Työssä esitetään malli automaattiseen liikevaihdon ja kulujen laskentaan sekä siihen liittyviä teknisiä ratkaisuja. Työn lopussa todetaan että automaattinen liikevaihdon ja kulujen seurantajärjestelmä on mahdollista rakentaa ja tuloksessa päästään hyvin tarkkaan arvioon lopullisesta liikevaihdosta. Arvion tarkkuus riippuu operatiivisten järjestelmien käyttötavoista sekä työnohjauksen menettelytavoista.

Esôfago de Barrett: aspectos fisiopatológicos e moleculares da seqüência metaplasia-displasia-adenocarcinoma - artigo de revisão

The Barrett's esophagus (BE) is defined as endoscopically visible columnar mucosa at the distal esophagus, of any extension, proved to harbor intestinal metaplasia on biopsy, highlighted by the presence of goblet cells. BE denotes long-standing gastroesophageal reflux disease (GERD) and is an important risk factor for the development of esophageal adenocarcinoma (EAC). Therefore, these patients must be on follow-up, in order to diagnose cancer early. BE patients have frequent alterations in esophageal physiologyc studies. Alkaline duodenogastroesophageal reflux seems to have important role. The development BE occurs in steps, initially with formation of cardiac type mucosa subsequent intestinalization. Futher progression can follow a sequence, from low grade dysplasia, to high grade dysplasia and esophageal adenocarcinoma. Current follow-up is based on the presence of dysplasia. It has limitations, grouping patients heterogeneously. Different steps of carcinogenesis have been studied looking for an ideal prognostic marker. Uncontrolled proliferative activity, apoptosis inhibition, angiogenesis, tissue invasion and metastases formation are all implicated in cancer origin. Some cycle cell molecules have been studied in BE, such as retinoblastoma protein, ciclins, kinase dependent ciclins and cell cycle inhibitors. The P53 protein is one of the most investigated in the metaplasia-adenocarcinoma progression. Growth Factors, apoptotic proteins, telomers and DNA ploidy have also been searched. Increased proliferative activity has been implicated in Barrett's carcinogenesis and the Ki-67 antigen, through imunohistochemical analysis, has become the the method of choice. Present in the nucleus, it is found in proliferative cells only. Some studies suport association between Ki-67 activity and the metaplasia-dysplasia-adenocarcinoma sequence.The results, however, are inconclusive and research should follow this way.

The Roots of Neurofibromas in Neurofibromatosis 1 — A Question of Multipotency, Differentiation and Hiding

Neurofibromatosis type 1 (NF1) is an autosomal dominant cancer predisposition syndrome that affects about 1 in 3500 individuals worldwide. NF1 is caused by mutations in the NF1 gene that encodes the tumor suppressor protein neurofibromin, an inactivator of the Ras oncogene. The hallmarks of NF1 include pigmentary lesions of the skin, Lisch nodules of the iris and cutaneous neurofibromas. Cutaneous neurofibromas are benign tumors composed of all the cell types of normal peripheral nerve. The traditional view of neurofibroma development has been that cutaneous neurofibromas arise from the disruption of the small nerve tributaries of the skin and subsequent proliferation of the resident cells. The second hit mutation in the NF1 gene has been considered as a prerequisite for neurofibroma development. The second hit is detectable in a subpopulation of primary Schwann cells cultured from neurofibromas. This thesis challenges the traditional concept of neurofibroma development. The results show that cutaneous neurofibromas are intimately associated with hair follicular structures and contain multipotent precursor cells (NFPs), suggesting that neurofibromas may arise from the multipotent cells which reside in hair follicles. Furthermore, this study presents that neurofibroma-derived Schwann cells that harbor bi-allelic inactivation in the NF1 gene express HLA class II genes and may act as nonprofessional antigen presenting cells. The CD4- and FoxP3-positive cells detected in cutaneous neurofibromas suggest that these cells may represent regulatory T cells (Tregs) which interact with HLA II –positive cells and aid the tumor cells in hiding from the immune system and are thus mediators of immune tolerance. This thesis also investigated neurofibroma development in the oral cavity and the use of different biomarkers to characterize cellular differentiation in neurofibromas. The results revealed that oral neurofibromas are not rare, but they usually appear as solitary lesions contrary to multiple cutaneous neurofibromas and present high heterogeneity within and between tumors. The use of class III beta-tubulin as a marker for neuronal differentiation led to an unexpected finding showing that multiple cell types express class III beta-tubulin during mitosis. The increased understanding of the multipotency of tumor cells, cellular differentiation and ability to hide from immune system will aid in the development of future treatments. Specifically, targeting Tregs in NF1 patients could provide a novel therapeutic approach to interfere with the development of neurofibromas.

SISÄPIIRIN KAUPANKÄYNTI OMIA OSAKKEITAAN OSTAVISSA PÖRSSIYHTIÖISSÄ - Toiminta-analyyttinen tarkastelu Helsingin Pörssin markkina-arvoltaan pienistä yhtiöistä

Tässä tutkielmassa tarkastellaan sisäpiirin kaupankäyntiä suomalaisten, markkina-arvoltaan pienten, pörssiyritysten omien osakkeiden ostojen ympärillä. Huolimatta aiheen herättämistä mielenkiintoisista kysymyksistä, sisäpiirin kaupankäynnistä omien osakkeiden ympärillä on verraten vähän akateemista tutkimusta. Suomessa aihepiiriä ei ole tiettävästi tutkittu lainkaan. Tätä tutkielmaa innoittivat erityisesti havainnot reaalimaailmasta, jotka antoivat impulssin induktiiviselle lähestymistavalle ja uusien teorioiden kehittämiselle. Kriitikot ovat esittäneet kysymyksen, pitäisikö takaisinostoja toteuttavien yritysten johdon ostaa osakkeita myös omaan lukuunsa. Mutta entä jos sisäpiiri myykin omia omistuksiaan samaan aikaan, kun yhtiö suorittaa omien osakkeiden takaisinostoja? Lainsäädäntö ei aseta rajoitteita tällaiselle toiminnalle. Takaisinostoja on siis mahdollista yrittää käyttää myös opportunistiseen osakekurssin tai likviditeetin nostamiseen, mutta mikäli takaisinostot suoritetaan Euroopan unionin komission asetuksen (N:o 2273/2003) mukaisesti, saavuttaa yritys nykylainsäädännön mukaisen turvasataman (safe harbor) syytteiltä osakekurssin manipulointia vastaan. Tilanteissa, jossa takaisinostoja toteutetaan samanaikaisesti kun sisäpiiri myy omia omistuksiaan, on kiistatta päämiehen ja agentin välinen eturistiriita. Tutkielmassa analysoitiin 992 sisäpiirikauppaa aikavälillä 11.7.2006–31.7.2009. Aineistosta havaittiin kolmen suomalaisen pörssiyrityksen sisäpiirin myyneen omistuksiaan merkittävästi takaisinostojen aikana. Kun analyysi tarkennettiin kaupankäyntipäiville, havaittiin, että sekä sisäpiirimyynnit että takaisinostot voivat olla jopa 100% osakkeen päivävaihdosta. Tämä antaa vahvan signaalin siitä, että sisäpiiri pyrkii hyödyntämään takaisinostojen kasvattamaa likviditeettiä ajoittaessaan henkilökohtaisten osakkeidensa myyntiä.

Analysis of Escherichia coli isolated from bovine mastitic milk

Mastitis has been recognized for some time as the most costly disease in dairy herds. From February to November 2004, 670 samples of bovine mastitic milk from which 231 Escherichia coli strains were isolated, were collected from two Brazilian states. The strains were screened for the presence of Shiga toxin-producing (stx 1 and stx 2) and intimin (eae) genes. Twenty (8.6%) strains were detected by PCR to harbor the Shiga toxin genes (8 the stx 1 gene, 12 the stx 2 gene and none both of them). Two (0.8%) of the Escherichia coli strains studied were eae positive non Shiga toxin-producing. The strains were also examined for resistance to 12 antimicrobial agents. The predominantly observed resistance was to tetracycline (92.2%), streptomycin (90.4%), nalidixic acid (88.3%), amikacin (86.5%) and cephalothin (84.8%). Multidrug resistance was found among 152 isolates (65.8%).

Occurrence of enterotoxin-encoding genes in Staphylococcus aureus causing mastitis in lactating goats

Staphylococcal enterotoxins are the leading cause of human food poisoning worldwide. Staphylococcus spp. are the main mastitis-causing agents in goats and frequently found in high counts in goat milk. This study aimed to investigate the occurrence of enterotoxin-encoding genes in Staphylococcus aureus associated with mastitis in lactating goats in Paraiba State, Brazil. Milk samples (n=2024) were collected from 393 farms. Staphylococcus aureus was isolated in 55 milk samples. Classical (sea, seb, sec, sed, see) and novel (seg, seh, sei) enterotoxin-encoding genes were investigated by means of polymerase chain reaction (PCR). From thirty-six tested isolates, enterotoxin-encoding genes were detected in 7 (19.5%) S. aureus. The gene encoding enterotoxin C (seC) was identified in six isolates, while seiwas observed in only one isolate. The genes sea, seb, sed, see, seg and seh were not observed amongst the S. aureus investigated in this study. In summary, S. aureus causing mastitis in goats can harbor enterotoxin-encoding genes and seC was the most frequent gene observed amongst the investigated isolates. This finding is important for surveillance purposes, since enterotoxin C should be investigated in human staphylococcal food poisoning outbreaks caused by consumption of goat milk and dairy products.