Evaluation of the In Situ Ichthyoplankton Imaging System (ISIIS): comparison with the traditional (bongo net) sampler

Plankton and larval fish sampling programs often are limited by a balance between sampling frequency (for precision) and costs. Advancements in sampling techniques hold the potential to add considerable efficiency and, therefore, add sampling frequency to improve precision. We compare a newly developed plankton imaging system, In Situ Ichthyoplankton Imaging System (ISIIS), with a bongo sampler, which is a traditional plankton sampling gear developed in the 1960s. Comparative sampling was conducted along 2 transects ~30–40 km long. Over 2 days, we completed 36 ISIIS tow-yo undulations and 11 bongo oblique tows, each from the surface to within 10 m of the seafloor. Overall, the 2 gears detected comparable numbers of larval fishes, representing similar taxonomic compositions, although larvae captured with the bongo were capable of being identified to lower taxonomic levels, especially larvae in the small (<5 mm), preflexion stages. Size distributions of the sampled larval fishes differed considerably between these 2 sampling methods, with the size range and mean size of larval fishes larger with ISIIS than with the bongo sampler. The high frequency and fine spatial scale of ISIIS allow it to add considerable sampling precision (i.e., more vertical sections) to plankton surveys. Improvements in the ISIIS technology (including greater depth of field and image resolution) should also increase taxonomic resolution and decrease processing time. When coupled with appropriate net sampling (for the purpose of collecting and verifying the identification of biological samples), the use of ISIIS could improve overall survey design and simultaneously provide detailed, process-oriented information for fisheries scientists and oceanographers.

Phase Behavior and dewetting for polymer blend films studied by in situ AFM and XPS: From thin to ultrathin films

In this work, the film thickness (l(0)) effect on the phase and dewetting behaviors of the blend film of poly(methyl methacrylate)/poly (styrene-ran-acrylonitrile) (PMMA/SAN) has been studied by in situ atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). The thinner film shows the more compatibility of the blend, and the phase separation of the film occurs at l(0) > 5R(g) (radius of gyration). An initially time-independent q*, the characteristic wavenumber of the phase image, which is in good agreement of Cahn's linearized theory for the early stage of spinodal decomposition, has been obtained in real space and discussed in detail. For 5R(g) > l(0) > 3R(g), a "pseudo-dewetting/(phase separation + wetting)" behavior occurs, where the pseudo-wetting is driven by the concentration fluctuation mechanism. For 10 < 3R(g), a "real dewetting/(phase separation + wetting)" behavior occurs.

Development of rRNA and rDNA-targeted probes for fluorescence in situ hybridization to detect Heterosigma akashiwo (Raphidophyceae)

Heterosigma akashiwo (Hada) is a fragile, fish-killing alga. Efforts to understand and prevent blooms due to this harmful species to mitigate the impact on aquaculture require the development of methods for rapid and precise identification and quantification, so that adequate warning of a harmful algal bloom may be given. Here, we report the development and application of rRNA and rDNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH) to aid in the detection and enumeration of H. akashiwo. The designed probes were species specific, showing no cross-reactivity with four common HAB causative species: Prorocentrum micans Ehrenberg, P. minimum (Pavillard) Schiller, Alexandrium tarmarense (Lebour) Balech, and Skeletonema costatum (Greville) Cleve, or with four other microalgae, including Gymnodinium sp. Stein, Platy-monas cordiformis (Karter) Korsch, Skeletonema sp.1 Greville and Skeletonema sp.2. The rRNA-targeted probe hybridized to cytoplasmic rRNA, showing strong green fluorescence throughout the whole cell, while cells labeled by rDNA-targeted probe exhibited exclusively fluorescent nucleus. The detection protocols were optimized and could be completed within an hour. For rRNA and rDNA probes, about a corresponding 80% and 70% of targeted cells could be identified and quantified during the whole growth circle, despite the inapparent variability in the average probe reactivity. The established FISH was proved promising for specific, rapid, precise, and quantitative detection of H. akashiwo. (C) 2008 Elsevier B.V. All rights reserved.

Characterization of eastern oyster (Crassostrea virginica Gmelin) chromosomes by fluorescence in situ hybridization with bacteriophage P1 clones

Chromosome identification is an essential step in genomic research, which so far has not been possible in oysters. We tested bacteriophage P1 clones for chromosomal identification in the eastern oyster Crassostrea virginica, using fluorescence in situ hybridization (FISH). P1 clones were labeled with digoxigenin-11-dUTP using nick translation. Hybridization was detected with fluorescein-isothiocyanate-labeled anti-digoxigenin antibodies and amplified with 2 layers of antibodies. Nine of the 21 P1 clones tested produced clear and consistent FISH signals when Cot-1 DNA was used as a blocking agent against repetitive sequences. Karyotypic analysis and cohybridization positively assigned the 9 P1 clones to 7 chromosomes. The remaining 3 chromosomes can be separated by size and arm ratio. Five of the 9 P1 clones were sequenced at both ends, providing sequence-tagged sites that can be used to integrate linkage and cytogenetic maps. One sequence is part of the bone morphogenetic protein type 1b receptor, a member of the transforming growth factor superfamily, and mapped to the telomeric region of the long arm of chromosome 2. This study shows that large-insert clones such as P1 are useful as chromosome-specific FISH probes and for gene mapping in oysters.

Chromosomal mapping of 5S ribosomal RNA genes in the eastern oyster, Crassostrea virginica gmelin by fluorescence in situ hybridization

Chromosomal location of the 5S ribosomal RNA gene was studied in the eastern oyster, Crassostrea virginica Gmelin. using fluorescence in situ hybridization (FISH). Metaphase chromosomes were obtained from early embryos, and the FISH probe was made by PCR (polymerase chain reaction) amplification of the 5S rRNA gene and labeled by incorporation of digoxigenin-1 1-dUTP during PCR. Hybridization was detected with fluorescein-labeled antidigoxigenin antibodies. Two pairs of FISH signals were observed on metaphase chromosomes. Karyotypic analysis showed that the 5S rRNA gene cluster is interstitially located on short arms of chromosomes 5 and 6. On chromosome 5, the 5S rRNA genes were located immediately next to the centromere, whereas on chromosome 6, they were located approximately half way between the telomere and the centromere. Chromosomes of C. virginica are difficult to identify because of their similarities in size and arm ratio, and the chromosomal location of 5S rRNA genes provides unambiguous identification of chromosomes 5 and 6. Previous studies have mapped the major rRNA gene cluster (18S-5.8S-28S) to chromosome 2. and this study shows that the 5S rRNA gene cluster is not linked to the major rRNA genes and duplicated during evolution.

In situ study of carbon nanotube formation by C2H2 decomposition on an iron-based catalyst

The properties and formation of nanotubes have been extensively studied, but very few deal with the catalytic production mechanism of nanotubes. Two different techniques, thermogravimetric analysis and UV-Raman, have been applied to analyse the carbon deposition by catalysed decomposition of acetylene over an iron-based catalyst. The nature of the produced carbon materials depends on reaction temperature. Also, TEM allows identification of carbon nanotubes, encapsulated particles, and other nanostructures, while UV-Raman confirms its graphitic and graphite-like nature. (C) 2000 Elsevier Science Ltd. All rights reserved.

Hand-held voltammetric analyser for real-time monitoring of heavy metals in situ

This paper presents a novel hand-held instrument capable of real-time in situ detection and identification of heavy metals. The proposed system provides the facilities found in a traditional lab-based instrument in a hand held a design. In contrast to existing commercial systems, it can stand alone without the need of an associated computer. The electrochemical instrument uses anodic stripping voltammetry which is a precise and sensitive analytical method with excellent limits of detection. The sensors comprise disposable screen-printed (solid working) electrodes rather than the more common hanging mercury drop electrodes. The system is reliable, easy to use, safe, avoids expensive and time-consuming procedures and may be used in a variety of situations to help in the fields of environmental assessment and control.

Voltammetric in situ measurements of heavy metals in soil using a portable electrochemical instrument

This paper presents a portable electrochemical instrument capable of detecting and identifying heavy metals in soil, in situ. The instrument has been developed for use in a variety of situations to facilitate contaminated land surveys, avoiding expensive and time-consuming procedures. The system uses differential pulse anodic stripping voltammetry which is a precise and sensitive analytical method with excellent limits of detection. The identification of metals is based on a statistical microprocessor-based method. The instrument is capable of detecting six different toxic metals (lead, cadmium, zinc, nickel, mercury and copper) with good sensitivity

Localization of monoterpenoid indole alkaloid (MIA) biosynthesis by in situ hybridization (ISH)

Monoterpenoid indole alkaloids (MIA) are among the largest and most complex group of nitrogen containing secondary metabolites that are characteristic of the Apocynaceae plant family including the most notable Catharanthus roseus. These compounds have demonstrated activity as successful drugs for treating various cancers, neurological disorders and cardiovascular conditions. Due to the low yields of these compounds and high pharmacological value, their biosynthesis is a major topic of study. Previous work highlighting the leaf epidermis and leaf surface as a highly active area in MIA biosynthesis and MIA accumulation has made the epidermis a major focus of this thesis. This thesis provides an in-depth analysis of the valuable technique of RNA in situ hybridization (ISH) and demonstrates the application of the technique to analyze the location of the biosynthetic steps involved in the production of MIAs. The work presented in this thesis demonstrates that most of the MIAs of Eurasian Vinca minor, African Tabernaemontana e/egans and five Amsonia species, including North American Amsonia hubrichitii and Mediterranean A. orienta/is, accumulate in leaf wax exudates, while the rest of the leaf is almost devoid of alkaloids. Biochemical studies on Vinca minor displayed high tryptophan decarboxylase (TOe) enzyme activity and protein expression in the leaf epidermis compared to whole leaves. ISH studies aimed at localizing TOe and strictosidine synthase suggest the upper and lower epidermis of V. minor and T. e/egans as probable significant production sites for MIAs that will accumulate on the leaf surface, however the results don't eliminate the possibility of the involvement of other cell types. The monoterpenoid precursor to all MIAs, secologanin, is produced through the MEP pathway occurring in two cell types, the IPAP cells (Gl0H) and epidermal cells (LAMT and SLS). The work presented in this thesis, localizes a novel enzymatic step, UDPG-7-deoxyloganetic acid glucosyltransferase (UGT8) to the IPAP cells of Catharanthus longifolius. These results enable the suggestion that all steps from Gl0H up to and including UGT8 occur in the IPAP cells of the leaf, making the IPAP cells the main site for the majority of secologanin biosynthesis. It also makes the IPAP cells a likely cell type to begin searching for the gene of the uncharacterized steps between Gl0H and UGT8. It also narrows the compound to be transported from the IPAP cells to either 7-deoxyloganic acid or loganic acid, which aids in the identification of the transportation mechanism.

Caracterização genética e in situ de Gossypium barbadense na região norte do Brasil

Brazil has been considered one of the diversity centers of Gossypium barbadense species. It is believed that a relatively big erosion genetic process occurs with the species, due to economic, cultural and agricultural problems. A local diagnostic about species situation is the first step for reducing the diversity loss and establishing conservation strategies in situ. This research aimed the identification of the presence of Gossypium populations, characterization, determination of the main risks and collection of the accesses to store in germoplam banks, in Para and Amapa States. Expeditions were conducted in November 2004. An interview was carried out with the plant proprietor for characterizing in situ of G. barbadense species and of the environment where the plants were inserted. On hundred seventy nine plants in 22 municipal districts were collected in Para State and 117 plants in nine municipal districts in Amapa State. The majority of plants belong to G. barbadense species (98% in Amapa and 94% in Para). Plants occur in back yards, beside roads and spontaneously. That ones from back yards were more abundant (97% in Amapa and 95% in Para) and maintained as medicinal plants as the principal reason. Plants in natural environments in both states evaluated were not found, therefore, the creation of reserves and the application of others conventional methods of maintenance in situ are not applicable. The plant proprietors do not use to store or process seeds. Seed storage was reported as a practice by only 1% of the plant proprietors from Para and 11% from Amapa. The most plants collected were from two to three years of age (58% in Amapa and 93% in Para). As conclusions G. barbadense is the species most spread in the two studied states and are found in back yards. In Amapa State the botanical variety barbadense or Quebradinho is predominant, whereas in Para State the predominant variety is brasiliense or Rim-de-boi. Adequate conservation of thestudied species must be carried out in germoplasm collections maintained ex situ

Comparative cytogenetics of cichlid fishes through genomic in-situ hybridization (GISH) with emphasis on Oreochromis niloticus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Isolamento, seleção, identificação e avaliação de microrganismos aeróbios in situ, com habilidade à biodegradação de linamarina

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo de Jatropha gossypifolia e J. multifida (Euphorbiaceae) aplicando métodos analíticos in silico e de desreplicação, visando a detecção e elucidação in situ dos constituintes micromoleculares com atividade acetilcolinesterásicas e antioxidante

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo in vitro para avaliação e validação de medidas lineares na tomografia computadorizada 3D cone beam comparadas às medidas do crânio in situ

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Biochemical and microbiological characteristics of in situ biofilm formed on materials containing fluoride or amorphous calcium phosphate

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)